# Date 2008-01-16 Time 03:15:35 PST -0800 (1200482135.52 s)
#phil __OFF__

Command line arguments: "../1168.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14129
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1168

-------------------------------------------------------------------------------
  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: (71.655, 47.3993, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (71.655, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97132
Completeness in resolution range: 0.930726
Completeness with d_max=infinity: 0.927949

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1461
                             d_min =   1.9713

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: (71.655, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97132
Completeness in resolution range: 0.930726
Completeness with d_max=infinity: 0.927949

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1465 -  4.2194 [2210/2239]  1991   219   9.9%
  bin  2:  4.2194 -  3.3611 [2111/2134]  1900   211  10.0%
  bin  3:  3.3611 -  2.9397 [2095/2117]  1879   216  10.3%
  bin  4:  2.9397 -  2.6726 [2076/2095]  1881   195   9.4%
  bin  5:  2.6726 -  2.4819 [2068/2097]  1852   216  10.4%
  bin  6:  2.4819 -  2.3361 [2034/2075]  1835   199   9.8%
  bin  7:  2.3361 -  2.2195 [2049/2085]  1842   207  10.1%
  bin  8:  2.2195 -  2.1232 [2013/2051]  1813   200   9.9%
  bin  9:  2.1232 -  2.0416 [2050/2082]  1845   205  10.0%
  bin 10:  2.0416 -  1.9713 [ 883/2072]   792    91  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 19
        2.31 -     2.96: 1640
        2.96 -     3.60: 4523
        3.60 -     4.25: 9124
        4.25 -     4.90: 12846
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.660 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.953 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.980 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.008 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28147 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_1168/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 = 71.655 47.3993 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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4752   r_free= 0.4694   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277038                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7066 0.99   1427  159 0.3899 0.3745      6.5852      6.5471|
|  2:  4.7066 -  3.7545 0.99   1388  150 0.3862 0.4106      6.7685      6.8396|
|  3:  3.7545 -  3.2854 0.99   1350  156 0.4363 0.3945      6.6505      6.6153|
|  4:  3.2854 -  2.9876 0.99   1347  148 0.4584 0.4600       6.505      6.4937|
|  5:  2.9876 -  2.7748 0.99   1325  146 0.5060 0.5296      6.3617      6.3657|
|  6:  2.7748 -  2.6121 0.98   1325  152 0.5045 0.5062      6.2722       6.235|
|  7:  2.6121 -  2.4819 0.99   1341  146 0.5191 0.4337      6.2485      6.1471|
|  8:  2.4819 -  2.3743 0.99   1308  145 0.5255 0.5286      6.1648      6.2071|
|  9:  2.3743 -  2.2832 0.98   1312  146 0.5243 0.5336      6.1263      6.1128|
| 10:  2.2832 -  2.2046 0.98   1315  151 0.5097 0.5298      6.0782      6.0879|
| 11:  2.2046 -  2.1359 0.98   1313  138 0.5126 0.5175       6.028       6.032|
| 12:  2.1359 -  2.0750 0.99   1303  143 0.5344 0.5545      5.9532      5.9931|
| 13:  2.0750 -  2.0205 0.91   1206  144 0.5460 0.5080      5.8824      5.8333|
| 14:  2.0205 -  1.9713 0.27    370   35 0.5501 0.5348      5.8178      5.7808|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7066  1427   159  0.72  32.78   0.80     0.74      66003.90|
|  2:  4.7066 -  3.7545  1388   150  0.71  34.30   0.88     0.77      99187.54|
|  3:  3.7545 -  3.2854  1350   156  0.59  44.22   0.83     0.71     111189.26|
|  4:  3.2854 -  2.9876  1347   148  0.49  52.83   0.80     0.59     104096.40|
|  5:  2.9876 -  2.7748  1325   146  0.39  60.19   0.73     0.48      86115.20|
|  6:  2.7748 -  2.6121  1325   152  0.39  60.79   0.74     0.47      72415.80|
|  7:  2.6121 -  2.4819  1341   146  0.42  58.61   0.73     0.46      60334.04|
|  8:  2.4819 -  2.3743  1308   145  0.40  60.07   0.71     0.47      56424.06|
|  9:  2.3743 -  2.2832  1312   146  0.36  62.87   0.74     0.43      51846.83|
| 10:  2.2832 -  2.2046  1315   151  0.33  65.49   0.74     0.38      52089.23|
| 11:  2.2046 -  2.1359  1313   138  0.28  69.49   0.77     0.33      48852.86|
| 12:  2.1359 -  2.0750  1303   143  0.23  73.08   0.73     0.30      47344.14|
| 13:  2.0750 -  2.0205  1206   144  0.24  72.21   0.71     0.30      40069.38|
| 14:  2.0205 -  1.9713   370    35  0.30  67.84   0.68     0.35      31637.84|
|alpha:            min =        0.30 max =            0.77 mean =         0.50|
|beta:             min =    31637.84 max =       111189.26 mean =     68595.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.29|
|phase err.(test): min =        0.00 max =           90.00 mean =        57.28|
|-----------------------------------------------------------------------------|

============================== 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 = 15.265601             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.869   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.256264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.788   (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:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2611 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3900 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5042 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6511 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7727 |
|-----------------------------------------------------------------------------|
|-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 |       53.950 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.785 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4747   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.278506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4667   r_free= 0.4582   ksol= 0.32   Bsol= 13.62   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.97,8.82,7.86,0.00,0.00,0.00); trace/3= 8.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.275568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.477575             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.067   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.108819              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.123   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4667      final r-factor (work) = 0.3825          |
| start r-factor (free) = 0.4582      final r-factor (free) = 0.4147          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.1031 = 12.48 * 0.50 * 6.2758 + 1.00 * 53.9496                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6934 = 12.48 * 0.50 * 6.1780 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3825      final r-factor (work) = 0.3406          |
| start r-factor (free) = 0.4147      final r-factor (free) = 0.3971          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8646 = 1.11 * 1.00 * 6.1780 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7747 = 1.11 * 1.00 * 6.0962 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.68   12.16    None  None   None       |
|    all(noH): 2823   0      0.00    87.68   12.16    None  None   None       |
|    Sol.    : 438    0      0.00    87.68   26.26    None  None   None       |
|    Mac.    : 2385   0      0.00    76.02   9.57     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 -   8.768: 1466   |   5:    43.838 -  52.605:   41        |
|      1:     8.768 -  17.535:  724   |   6:    52.605 -  61.373:   23        |
|      2:    17.535 -  26.303:  314   |   7:    61.373 -  70.141:   10        |
|      3:    26.303 -  35.070:  148   |   8:    70.141 -  78.908:    5        |
|      4:    35.070 -  43.838:   90   |   9:    78.908 -  87.676:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3406 r_free = 0.3971             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3402 r_free = 0.3980             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3402   r_free= 0.3980   ksol= 0.32   Bsol= 13.62   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.97,8.82,7.86,0.00,0.00,0.00); trace/3= 8.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.074916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3381   r_free= 0.3941   ksol= 0.33   Bsol= 46.40   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.47,5.44,5.30,0.00,0.00,0.00); trace/3= 5.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.075161                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.011149              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.879   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580060              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3381      final r-factor (work) = 0.2417          |
| start r-factor (free) = 0.3941      final r-factor (free) = 0.3074          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5552 = 8.01 * 0.50 * 6.0927 + 1.00 * 0.1504                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9432 = 8.01 * 0.50 * 5.9556 + 1.00 * 0.0876                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2417      final r-factor (work) = 0.2180          |
| start r-factor (free) = 0.3074      final r-factor (free) = 0.2790          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4697 = 0.58 * 1.00 * 5.9556 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3567 = 0.58 * 1.00 * 5.7665 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.80   12.53    None  None   None       |
|    all(noH): 2823   0      0.00    84.80   12.53    None  None   None       |
|    Sol.    : 438    0      0.00    84.80   32.89    None  None   None       |
|    Mac.    : 2385   0      0.00    73.51   8.79     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 -   8.480: 1510   |   5:    42.399 -  50.879:   89        |
|      1:     8.480 -  16.960:  685   |   6:    50.879 -  59.359:   42        |
|      2:    16.960 -  25.439:  222   |   7:    59.359 -  67.838:   17        |
|      3:    25.439 -  33.919:  145   |   8:    67.838 -  76.318:    4        |
|      4:    33.919 -  42.399:  107   |   9:    76.318 -  84.798:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2180 r_free = 0.2790             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2177 r_free = 0.2785             target_work(ml) = 5.720         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2177   r_free= 0.2785   ksol= 0.33   Bsol= 46.40   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.47,5.44,5.30,0.00,0.00,0.00); trace/3= 5.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.719610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2156   r_free= 0.2746   ksol= 0.32   Bsol= 46.40   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,3.46,3.43,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.718258                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.684260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.533   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.830539              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.289  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2156      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2746      final r-factor (free) = 0.2007          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4920 = 5.68 * 0.50 * 5.7719 + 1.00 * 0.0876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9871 = 5.68 * 0.50 * 5.5983 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2007      final r-factor (free) = 0.1882          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6614 = 0.83 * 1.00 * 5.5983 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4686 = 0.83 * 1.00 * 5.3642 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.02   13.21    None  None   None       |
|    all(noH): 2823   0      0.00    86.02   13.21    None  None   None       |
|    Sol.    : 438    0      0.32    82.82   37.92    None  None   None       |
|    Mac.    : 2385   0      0.00    86.02   8.67     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 -   8.602: 1592   |   5:    43.008 -  51.610:   96        |
|      1:     8.602 -  17.203:  621   |   6:    51.610 -  60.212:   70        |
|      2:    17.203 -  25.805:  187   |   7:    60.212 -  68.813:   35        |
|      3:    25.805 -  34.407:  100   |   8:    68.813 -  77.415:   11        |
|      4:    34.407 -  43.008:  105   |   9:    77.415 -  86.017:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1389 r_free = 0.1882             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1387 r_free = 0.1882             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1387   r_free= 0.1882   ksol= 0.32   Bsol= 46.40   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,3.46,3.43,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.332500                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1884   ksol= 0.33   Bsol= 50.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.61,2.73,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.333795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.674238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.358  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658446              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.865  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1386      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9405 = 3.67 * 0.50 * 5.3696 + 1.00 * 0.0759                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7876 = 3.67 * 0.50 * 5.2851 + 1.00 * 0.0782                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4933 = 0.66 * 1.00 * 5.2851 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4520 = 0.66 * 1.00 * 5.2230 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.19   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    92.19   13.05    None  None   None       |
|    Sol.    : 438    0      1.02    87.11   37.49    None  None   None       |
|    Mac.    : 2385   0      0.00    92.19   8.57     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 -   9.219: 1698   |   5:    46.096 -  55.315:   93        |
|      1:     9.219 -  18.438:  581   |   6:    55.315 -  64.534:   51        |
|      2:    18.438 -  27.657:  156   |   7:    64.534 -  73.753:   20        |
|      3:    27.657 -  36.876:  108   |   8:    73.753 -  82.972:    7        |
|      4:    36.876 -  46.096:  103   |   9:    82.972 -  92.191:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1687             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1686             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1686   ksol= 0.33   Bsol= 50.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.61,2.73,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.215570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1686   ksol= 0.33   Bsol= 50.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.61,2.73,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.215570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.923368              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.831  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.197  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3238 = 3.92 * 0.50 * 5.2228 + 1.00 * 0.0782                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2798 = 3.92 * 0.50 * 5.1970 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6023 = 0.31 * 1.00 * 5.1970 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6027 = 0.31 * 1.00 * 5.1824 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.71   12.51    None  None   None       |
|    all(noH): 2823   0      0.00    93.71   12.51    None  None   None       |
|    Sol.    : 438    0      1.45    83.88   35.16    None  None   None       |
|    Mac.    : 2385   0      0.00    93.71   8.35     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 -   9.371: 1733   |   5:    46.854 -  56.225:   70        |
|      1:     9.371 -  18.742:  577   |   6:    56.225 -  65.595:   34        |
|      2:    18.742 -  28.112:  150   |   7:    65.595 -  74.966:   12        |
|      3:    28.112 -  37.483:  127   |   8:    74.966 -  84.337:    3        |
|      4:    37.483 -  46.854:  112   |   9:    84.337 -  93.708:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1623             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1623             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1623   ksol= 0.33   Bsol= 50.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.61,2.73,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176273                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7066 0.99   1427  159 0.0959 0.1301      5.3584      5.5375|
|  2:  4.7066 -  3.7545 0.99   1388  150 0.0843 0.1087       5.423      5.6466|
|  3:  3.7545 -  3.2854 0.99   1350  156 0.1050 0.1700      5.4721      5.9119|
|  4:  3.2854 -  2.9876 0.99   1347  148 0.1269 0.1537      5.4835      5.6173|
|  5:  2.9876 -  2.7748 0.99   1325  146 0.1343 0.1830      5.3566      5.5571|
|  6:  2.7748 -  2.6121 0.98   1325  152 0.1293 0.1949      5.2566      5.5081|
|  7:  2.6121 -  2.4819 0.99   1341  146 0.1280 0.1771       5.204      5.4286|
|  8:  2.4819 -  2.3743 0.99   1308  145 0.1164 0.1729      5.0794      5.3146|
|  9:  2.3743 -  2.2832 0.98   1312  146 0.1214 0.1919      5.0567      5.3619|
| 10:  2.2832 -  2.2046 0.98   1315  151 0.1163 0.1733      5.0018      5.2418|
| 11:  2.2046 -  2.1359 0.98   1313  138 0.1164 0.1868       4.961       5.304|
| 12:  2.1359 -  2.0750 0.99   1303  143 0.1154 0.1739      4.9024      5.1174|
| 13:  2.0750 -  2.0205 0.91   1206  144 0.1192 0.1827      4.8035      5.0577|
| 14:  2.0205 -  1.9713 0.27    370   35 0.1072 0.1638       4.647      4.8854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7066  1427   159  0.94   8.61   0.98     0.96       6904.68|
|  2:  4.7066 -  3.7545  1388   150  0.95   8.22   1.01     0.99       8955.56|
|  3:  3.7545 -  3.2854  1350   156  0.93  11.77   1.02     1.02      10801.06|
|  4:  3.2854 -  2.9876  1347   148  0.91  14.96   1.00     0.97      11232.00|
|  5:  2.9876 -  2.7748  1325   146  0.89  17.31   0.99     0.96       9219.28|
|  6:  2.7748 -  2.6121  1325   152  0.89  17.36   0.98     0.96       7908.89|
|  7:  2.6121 -  2.4819  1341   146  0.90  16.18   0.99     0.96       6818.05|
|  8:  2.4819 -  2.3743  1308   145  0.90  16.16   0.98     0.94       5624.97|
|  9:  2.3743 -  2.2832  1312   146  0.89  17.05   1.00     0.96       5390.28|
| 10:  2.2832 -  2.2046  1315   151  0.90  16.20   1.00     0.97       4929.13|
| 11:  2.2046 -  2.1359  1313   138  0.89  17.15   0.99     0.95       4686.86|
| 12:  2.1359 -  2.0750  1303   143  0.90  16.70   1.00     1.00       4331.94|
| 13:  2.0750 -  2.0205  1206   144  0.90  16.69   0.99     0.97       3443.33|
| 14:  2.0205 -  1.9713   370    35  0.90  16.13   0.99     0.96       2579.60|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2579.60 max =        11232.00 mean =      6900.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.89|
|phase err.(test): min =        0.00 max =           87.75 mean =        14.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1633   ksol= 0.32   Bsol= 53.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.07,0.17,-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: 5.179068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1633   ksol= 0.32   Bsol= 53.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.07,0.17,-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: 5.179068                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7066 0.99   1427  159 0.0963 0.1319      5.3697      5.5534|
|  2:  4.7066 -  3.7545 0.99   1388  150 0.0853 0.1126      5.4373      5.6713|
|  3:  3.7545 -  3.2854 0.99   1350  156 0.1051 0.1707      5.4804      5.9124|
|  4:  3.2854 -  2.9876 0.99   1347  148 0.1277 0.1533      5.4863      5.6189|
|  5:  2.9876 -  2.7748 0.99   1325  146 0.1345 0.1838      5.3573      5.5599|
|  6:  2.7748 -  2.6121 0.98   1325  152 0.1294 0.1947      5.2576      5.5078|
|  7:  2.6121 -  2.4819 0.99   1341  146 0.1280 0.1769      5.2033      5.4274|
|  8:  2.4819 -  2.3743 0.99   1308  145 0.1164 0.1727      5.0796      5.3157|
|  9:  2.3743 -  2.2832 0.98   1312  146 0.1211 0.1917      5.0555      5.3607|
| 10:  2.2832 -  2.2046 0.98   1315  151 0.1161 0.1734      5.0012      5.2422|
| 11:  2.2046 -  2.1359 0.98   1313  138 0.1164 0.1864      4.9601      5.3029|
| 12:  2.1359 -  2.0750 0.99   1303  143 0.1153 0.1743      4.9028      5.1186|
| 13:  2.0750 -  2.0205 0.91   1206  144 0.1193 0.1828      4.8034      5.0576|
| 14:  2.0205 -  1.9713 0.27    370   35 0.1071 0.1633      4.6459      4.8833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7066  1427   159  0.94   9.00   0.97     0.95       7230.21|
|  2:  4.7066 -  3.7545  1388   150  0.95   8.52   1.01     0.99       9377.38|
|  3:  3.7545 -  3.2854  1350   156  0.93  11.96   1.02     1.02      11107.25|
|  4:  3.2854 -  2.9876  1347   148  0.91  15.01   1.00     0.97      11283.39|
|  5:  2.9876 -  2.7748  1325   146  0.89  17.31   0.99     0.96       9217.43|
|  6:  2.7748 -  2.6121  1325   152  0.89  17.41   0.98     0.95       7932.23|
|  7:  2.6121 -  2.4819  1341   146  0.90  16.18   0.99     0.96       6822.88|
|  8:  2.4819 -  2.3743  1308   145  0.90  16.17   0.98     0.94       5637.90|
|  9:  2.3743 -  2.2832  1312   146  0.89  17.04   1.00     0.96       5385.58|
| 10:  2.2832 -  2.2046  1315   151  0.90  16.20   0.99     0.96       4926.15|
| 11:  2.2046 -  2.1359  1313   138  0.89  17.13   0.99     0.95       4678.14|
| 12:  2.1359 -  2.0750  1303   143  0.90  16.70   1.00     1.00       4335.27|
| 13:  2.0750 -  2.0205  1206   144  0.90  16.68   0.99     0.97       3440.81|
| 14:  2.0205 -  1.9713   370    35  0.90  16.11   0.98     0.96       2571.35|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2571.35 max =        11283.39 mean =      6988.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.97|
|phase err.(test): min =        0.00 max =           87.71 mean =        14.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.078)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.57    96.27   15.07    None  None   None       |
|    all(noH): 2823   0      2.57    96.27   15.07    None  None   None       |
|    Sol.    : 438    0      4.02    86.45   37.73    None  None   None       |
|    Mac.    : 2385   0      2.57    96.27   10.91    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:     2.566 -  11.937: 1733   |   5:    49.420 -  58.791:   70        |
|      1:    11.937 -  21.308:  577   |   6:    58.791 -  68.161:   34        |
|      2:    21.308 -  30.678:  150   |   7:    68.161 -  77.532:   12        |
|      3:    30.678 -  40.049:  127   |   8:    77.532 -  86.903:    3        |
|      4:    40.049 -  49.420:  112   |   9:    86.903 -  96.274:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.367 - 5.894
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 345
   mapped sites are within: 0.756 - 5.894

peak=   10.136 closest distance to " CG2 VAL A 230 " =    1.450
peak=    7.088 closest distance to " CG2 VAL A 296 " =    1.117
peak=    6.230 closest distance to " CG  LEU A   5 " =    1.215
peak=    6.094 closest distance to " O   HOH Z 111 " =    2.033
peak=    5.348 closest distance to " CB  SER A  63 " =    1.274
peak=    5.192 closest distance to " CG  LEU A 228 " =    1.209
peak=    5.145 closest distance to " CB  GLN A 223 " =    1.461
peak=    5.020 closest distance to " CG  PRO A  54 " =    1.218
peak=    4.987 closest distance to " CD2 LEU A   5 " =    1.216
peak=    4.778 closest distance to " O   HOH Z  37 " =    1.196
peak=    4.717 closest distance to " O   HOH Z 368 " =    2.248
peak=    4.674 closest distance to " CB  GLU A 152 " =    1.172
peak=    4.626 closest distance to " CB  GLN A 183 " =    1.240
peak=    4.619 closest distance to " CB  VAL A 230 " =    1.261
peak=    4.602 closest distance to " CB  VAL A 296 " =    1.132
peak=    4.596 closest distance to " O   HOH Z 126 " =    1.632
peak=    4.573 closest distance to " O   HOH Z 247 " =    1.441
peak=    4.527 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.521 closest distance to " O   HOH Z 272 " =    1.937
peak=    4.440 closest distance to " CB  PRO A  54 " =    0.826
peak=    4.416 closest distance to " O   HOH Z  80 " =    1.788
peak=    4.404 closest distance to " O   HOH Z  63 " =    1.918
peak=    4.403 closest distance to " O   HOH Z 403 " =    1.725
peak=    4.394 closest distance to " NE2 GLN A  11 " =    1.167
peak=    4.382 closest distance to " O   HOH Z 232 " =    2.279
peak=    4.375 closest distance to " CB  SER A   3 " =    1.436
peak=    4.313 closest distance to " O   HOH Z 263 " =    1.653
peak=    4.232 closest distance to " O   HOH Z 112 " =    1.502
peak=    4.229 closest distance to " CB  GLU A 277 " =    3.671
peak=    4.224 closest distance to " OD1 ASN A  69 " =    2.655
peak=    4.209 closest distance to " CB  GLU A 128 " =    1.100
peak=    4.205 closest distance to " CB  ARG A  79 " =    1.506
peak=    4.204 closest distance to " O   HOH Z 236 " =    1.876
peak=    4.170 closest distance to " NH2 ARG A 156 " =    1.250
peak=    4.163 closest distance to " O   SER A  87 " =    2.204
peak=    4.145 closest distance to " O   HOH Z 298 " =    1.716
peak=    4.141 closest distance to " CG2 THR A 221 " =    0.990
peak=    4.139 closest distance to " O   HOH Z 303 " =    2.131
peak=    4.123 closest distance to " CD2 LEU A 228 " =    1.207
peak=    4.123 closest distance to " CB  ASN A 148 " =    1.351
peak=    4.120 closest distance to " CG1BVAL A  72 " =    1.647
peak=    4.118 closest distance to " CB  VAL A 265 " =    1.287
peak=    4.114 closest distance to " O   HOH Z 184 " =    1.461
peak=    4.110 closest distance to " O   HOH Z 369 " =    2.040
peak=    4.109 closest distance to " CB  TYR A 169 " =    0.857
peak=    4.104 closest distance to " O   HOH Z  63 " =    1.352
peak=    4.096 closest distance to " O   HOH Z  15 " =    2.045
peak=    4.096 closest distance to " O   HOH Z  97 " =    1.908
peak=    4.091 closest distance to " O   HOH Z 371 " =    3.347
peak=    4.089 closest distance to " CD  ARG A  66 " =    2.666
peak=    4.085 closest distance to " O   HOH Z 183 " =    1.440
peak=    4.083 closest distance to " O   HOH Z 163 " =    1.648
peak=    4.075 closest distance to " O   HOH Z 135 " =    1.933
peak=    4.068 closest distance to " O   HOH Z 316 " =    2.984
peak=    4.044 closest distance to " O   HOH Z  78 " =    1.987
peak=    4.043 closest distance to " O   HOH Z 102 " =    1.302
peak=    4.042 closest distance to " O   HOH Z  48 " =    1.693
peak=    4.028 closest distance to " O   HOH Z 234 " =    3.775
peak=    4.021 closest distance to " O   HOH Z 193 " =    1.956
peak=    4.018 closest distance to " O   HOH Z  54 " =    2.396
peak=    4.018 closest distance to " CD1 LEU A 300 " =    1.220
peak=    4.014 closest distance to " O   HOH Z  68 " =    1.821
peak=    4.008 closest distance to " CB  LEU A 143 " =    1.161
peak=    4.004 closest distance to " OD2 ASP A 286 " =    2.929
peak=    4.001 closest distance to " O   HOH Z  88 " =    3.272
peak=    3.996 closest distance to " O   HOH Z 423 " =    1.830
peak=    3.983 closest distance to " O   HOH Z 124 " =    1.403
peak=    3.979 closest distance to " O   HOH Z 280 " =    3.079
peak=    3.967 closest distance to " O   HOH Z 386 " =    2.217
peak=    3.940 closest distance to " CG  PRO A 243 " =    1.168
peak=    3.938 closest distance to " CA  TYR A  30 " =    0.950
peak=    3.896 closest distance to " CA  LYS A 117 " =    1.279
peak=    3.891 closest distance to " O   HOH Z 295 " =    1.537
peak=    3.883 closest distance to " C   PRO A 198 " =    1.529
peak=    3.864 closest distance to " CA  ALA A  21 " =    1.232
peak=    3.841 closest distance to " CG  ARG A 138 " =    1.134
peak=    3.840 closest distance to " CA  ALA A  51 " =    1.055
peak=    3.830 closest distance to " O   HOH Z 411 " =    3.622
peak=    3.830 closest distance to " O   HOH Z 427 " =    3.109
peak=    3.826 closest distance to " CD  ARG A 159 " =    0.834
peak=    3.823 closest distance to " CB  VAL A 202 " =    1.526
peak=    3.821 closest distance to " CA  THR A 221 " =    0.872
peak=    3.819 closest distance to " CB  TRP A 266 " =    0.931
peak=    3.803 closest distance to " CD1 LEU A   5 " =    1.366
peak=    3.791 closest distance to " O   HOH Z 313 " =    1.896
peak=    3.787 closest distance to " OG BSER A 164 " =    2.098
peak=    3.786 closest distance to " O   HOH Z 118 " =    1.706
peak=    3.784 closest distance to " O   HOH Z 245 " =    1.400
peak=    3.778 closest distance to " O   HOH Z 145 " =    1.874
peak=    3.768 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.765 closest distance to " O   HOH Z 116 " =    1.806
peak=    3.764 closest distance to " O   HOH Z 345 " =    3.443
peak=    3.762 closest distance to " CD ALYS A 290 " =    1.054
peak=    3.758 closest distance to " O   HOH Z 108 " =    2.258
peak=    3.749 closest distance to " OD1 ASN A 217 " =    1.628
peak=    3.747 closest distance to " OE1 GLN A  11 " =    1.809
peak=    3.744 closest distance to " CA  MET A  40 " =    1.113
peak=    3.736 closest distance to " CG  PRO A 280 " =    0.795
peak=    3.728 closest distance to " CG  PRO A 198 " =    1.439
peak=    3.728 closest distance to " O   HOH Z 126 " =    1.737
peak=    3.720 closest distance to " NZ  LYS A 117 " =    3.351
peak=    3.718 closest distance to " O   HOH Z  54 " =    1.525
peak=    3.715 closest distance to " O   HOH Z 426 " =    1.447
peak=    3.714 closest distance to " ND2 ASN A 187 " =    1.540
peak=    3.706 closest distance to " N   ASN A  39 " =    1.314
peak=    3.704 closest distance to " O   HOH Z 281 " =    4.251
peak=    3.703 closest distance to " O   HOH Z 214 " =    2.006
peak=    3.703 closest distance to " CB  TRP A 179 " =    1.424
peak=    3.695 closest distance to " NH1 ARG A  56 " =    1.091
peak=    3.690 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.689 closest distance to " O   HOH Z 180 " =    2.141
peak=    3.676 closest distance to " O   HOH Z  20 " =    2.280
peak=    3.672 closest distance to " CA  GLY A 267 " =    0.894
peak=    3.670 closest distance to " ND2 ASN A 249 " =    1.946
peak=    3.663 closest distance to " O   MET A 105 " =    1.861
peak=    3.662 closest distance to " O   HOH Z 425 " =    1.388
peak=    3.658 closest distance to " O   ALA A 158 " =    1.395
peak=    3.652 closest distance to " O   TRP A 274 " =    1.851
peak=    3.647 closest distance to " CB  ARG A 275 " =    0.847
peak=    3.644 closest distance to " NH2 ARG A  79 " =    1.369
peak=    3.641 closest distance to " CG BARG A 275 " =    1.529
peak=    3.639 closest distance to " CB  SER A 216 " =    0.756
peak=    3.638 closest distance to " OD1 ASP A 231 " =    1.887
peak=    3.635 closest distance to " CB  ARG A 190 " =    1.688
peak=    3.633 closest distance to " O   HOH Z 132 " =    2.701
peak=    3.625 closest distance to " O   HOH Z  43 " =    2.103
peak=    3.624 closest distance to " CD2 LEU A 255 " =    1.447
peak=    3.623 closest distance to " CA  ASP A 191 " =    0.789
peak=    3.619 closest distance to " O   HOH Z 244 " =    1.700
peak=    3.612 closest distance to " NH2BARG A 145 " =    2.063
peak=    3.611 closest distance to " O   HOH Z  21 " =    1.693
peak=    3.605 closest distance to " CA  LEU A 282 " =    1.078
peak=    3.599 closest distance to " O   HOH Z 383 " =    2.112
peak=    3.595 closest distance to " O   HOH Z  44 " =    2.266
peak=    3.593 closest distance to " C   SER A  32 " =    1.022
peak=    3.592 closest distance to " CB  ALA A   9 " =    1.599
peak=    3.586 closest distance to " O   HOH Z 133 " =    2.373
peak=    3.584 closest distance to " CG1 VAL A 153 " =    1.002
peak=    3.574 closest distance to " O   HOH Z 346 " =    1.538
peak=    3.570 closest distance to " O   HOH Z 128 " =    2.079
peak=    3.566 closest distance to " CB  ASP A 140 " =    0.826
peak=    3.566 closest distance to " CG2 VAL A 296 " =    1.710
peak=    3.566 closest distance to " O   HOH Z 394 " =    1.840
peak=    3.563 closest distance to " CB  LEU A 228 " =    1.251
peak=    3.554 closest distance to " O   HOH Z 271 " =    2.443
peak=    3.553 closest distance to " O   HOH Z 344 " =    2.907
peak=    3.550 closest distance to " O   HOH Z 329 " =    3.868
peak=    3.534 closest distance to " CB  ALA A 248 " =    1.035
peak=    3.534 closest distance to " O   HOH Z 189 " =    2.650
peak=    3.530 closest distance to " CD  ARG A 195 " =    0.975
peak=    3.523 closest distance to " O   HOH Z 108 " =    1.263
peak=    3.514 closest distance to " O   HOH Z  58 " =    1.528
peak=    3.514 closest distance to " CG2 VAL A 174 " =    1.330
peak=    3.511 closest distance to " OG  SER A  22 " =    2.872
peak=    3.510 closest distance to " O   HOH Z 437 " =    2.224
peak=    3.507 closest distance to " CA  ASP A 140 " =    1.257
peak=    3.507 closest distance to " CG BARG A 102 " =    1.911
peak=    3.506 closest distance to " O   HOH Z 422 " =    2.689
peak=    3.502 closest distance to " NE2 GLN A  58 " =    5.894
peak=    3.499 closest distance to " O   HOH Z 197 " =    2.088
peak=    3.499 closest distance to " O   HOH Z 286 " =    2.259
peak=    3.492 closest distance to " O   HOH Z 128 " =    1.766
peak=    3.492 closest distance to " CD2 HIS A  81 " =    1.166
peak=    3.492 closest distance to " CA  ASN A  74 " =    1.118
peak=    3.491 closest distance to " CB  ASN A 187 " =    0.977
peak=    3.490 closest distance to " O   HOH Z 368 " =    3.629
peak=    3.489 closest distance to " ND1 HIS A  81 " =    1.604
peak=    3.487 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.485 closest distance to " CA  ALA A 158 " =    1.150
peak=    3.483 closest distance to " O   HOH Z 419 " =    1.682
peak=    3.480 closest distance to " CB  SER A 141 " =    1.010
peak=    3.479 closest distance to " O   HOH Z  40 " =    1.498
peak=    3.473 closest distance to " O   HOH Z 374 " =    2.734
peak=    3.473 closest distance to " CG2 THR A 220 " =    0.911
peak=    3.472 closest distance to " CB  PRO A  54 " =    1.279
peak=    3.472 closest distance to " OD2 ASP A 298 " =    4.031
peak=    3.470 closest distance to " CZ  PHE A 192 " =    0.991
peak=    3.466 closest distance to " ND1 HIS A  86 " =    1.639
peak=    3.466 closest distance to " NZ  LYS A 166 " =    3.120
peak=    3.463 closest distance to " CA  ALA A 160 " =    0.890
peak=    3.460 closest distance to " CG AARG A 275 " =    1.201
peak=    3.459 closest distance to " O   HOH Z  61 " =    1.648
peak=    3.455 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.450 closest distance to " O   HOH Z 134 " =    1.484
peak=    3.449 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.446 closest distance to " O   HOH Z 261 " =    2.003
peak=    3.446 closest distance to " CB  ARG A 139 " =    0.877
peak=    3.446 closest distance to " O   ALA A   1 " =    1.573
peak=    3.438 closest distance to " CB  ILE A 120 " =    1.486
peak=    3.438 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.433 closest distance to " CA  ASP A 162 " =    1.183
peak=    3.428 closest distance to " O   HOH Z 227 " =    1.911
peak=    3.423 closest distance to " O   HOH Z 387 " =    2.859
peak=    3.423 closest distance to " CZ  PHE A 218 " =    1.026
peak=    3.422 closest distance to " O   HOH Z 260 " =    1.149
peak=    3.420 closest distance to " CA  TYR A 116 " =    1.472
peak=    3.419 closest distance to " CA  ALA A 295 " =    1.061
peak=    3.412 closest distance to " O   HOH Z 147 " =    1.716
peak=    3.408 closest distance to " O   HOH Z 420 " =    2.376
peak=    3.400 closest distance to " CG2 THR A  42 " =    0.867
peak=    3.394 closest distance to " O   HOH Z  30 " =    1.220
peak=    3.393 closest distance to " O   HOH Z  93 " =    2.737
peak=    3.389 closest distance to " O   HOH Z 327 " =    2.329
peak=    3.388 closest distance to " O   HOH Z  53 " =    2.494
peak=    3.387 closest distance to " O   HOH Z 395 " =    1.362
peak=    3.386 closest distance to " O   HOH Z 213 " =    1.648
peak=    3.385 closest distance to " CB  MET A  47 " =    1.066
peak=    3.378 closest distance to " O   HOH Z 171 " =    3.845
peak=    3.374 closest distance to " NH1AARG A 145 " =    1.051
peak=    3.372 closest distance to " CB  ALA A 291 " =    1.370
peak=    3.371 closest distance to " CA  ALA A 154 " =    1.209
peak=    3.369 closest distance to " CB  ALA A 100 " =    1.321
peak=    3.368 closest distance to " O   HOH Z 410 " =    1.435
peak=    3.366 closest distance to " O   HOH Z 215 " =    1.646
peak=    3.361 closest distance to " O   ASP A 124 " =    1.161
peak=    3.360 closest distance to " O   HOH Z   4 " =    1.927
peak=    3.360 closest distance to " NH2 ARG A 219 " =    1.833
peak=    3.358 closest distance to " O   HOH Z 175 " =    3.540
peak=    3.356 closest distance to " O   HOH Z 407 " =    2.542
peak=    3.353 closest distance to " O   GLN A 278 " =    1.185
peak=    3.351 closest distance to " O   HOH Z 128 " =    2.248
peak=    3.348 closest distance to " CD1 ILE A  33 " =    1.566
peak=    3.340 closest distance to " O   HOH Z  49 " =    2.551
peak=    3.339 closest distance to " CB  TRP A 150 " =    1.472
peak=    3.337 closest distance to " CA  ASN A 215 " =    1.196
peak=    3.336 closest distance to " O   ALA A 165 " =    1.343
peak=    3.336 closest distance to " CB  LYS A 117 " =    1.135
peak=    3.334 closest distance to " CG1 ILE A  49 " =    1.568
peak=    3.333 closest distance to " O   HOH Z 156 " =    2.766
peak=    3.332 closest distance to " O   HOH Z 203 " =    1.796
peak=    3.328 closest distance to " CD1 TRP A 266 " =    1.179
peak=    3.323 closest distance to " O   HOH Z 130 " =    2.225
peak=    3.321 closest distance to " O   HOH Z 355 " =    1.818
peak=    3.315 closest distance to " O   ASN A 217 " =    1.309
peak=    3.314 closest distance to " O   THR A  31 " =    1.540
peak=    3.314 closest distance to " O   HOH Z 420 " =    5.665
peak=    3.313 closest distance to " O   HOH Z 139 " =    3.226
peak=    3.311 closest distance to " CD  LYS A 119 " =    1.891
peak=    3.308 closest distance to " O   HOH Z  11 " =    1.232
peak=    3.308 closest distance to " O   HOH Z   9 " =    1.661
peak=    3.301 closest distance to " CA  GLY A  75 " =    1.259
peak=    3.301 closest distance to " O   HOH Z 409 " =    3.407
peak=    3.294 closest distance to " CB  ASN A 142 " =    0.994
peak=    3.291 closest distance to " O   HOH Z  85 " =    2.149
peak=    3.289 closest distance to " CB  THR A  31 " =    1.599
peak=    3.287 closest distance to " O   HOH Z 298 " =    2.497
peak=    3.287 closest distance to " O   HOH Z 197 " =    2.518
peak=    3.282 closest distance to " N   PHE A 130 " =    1.317
peak=    3.279 closest distance to " CA  THR A 264 " =    0.800
peak=    3.276 closest distance to " O   HOH Z  44 " =    2.905
peak=    3.275 closest distance to " O   HOH Z 278 " =    1.224
peak=    3.272 closest distance to " C   ALA A 299 " =    0.957
peak=    3.270 closest distance to " CG2BVAL A  41 " =    1.205
peak=    3.270 closest distance to " OG  SER A 245 " =    1.599
peak=    3.263 closest distance to " CB  THR A  82 " =    1.386
peak=    3.259 closest distance to " O   HOH Z  50 " =    2.069
peak=    3.258 closest distance to " O   HOH Z  85 " =    1.450
peak=    3.257 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.253 closest distance to " O   HOH Z  57 " =    1.374
peak=    3.252 closest distance to " CB  MET A  40 " =    0.802
peak=    3.251 closest distance to " O   ALA A 291 " =    1.512
peak=    3.251 closest distance to " CB  ASN A 148 " =    1.982
peak=    3.250 closest distance to " O   HOH Z 227 " =    2.106
peak=    3.249 closest distance to " O   HOH Z 134 " =    2.446
peak=    3.244 closest distance to " O   HOH Z 301 " =    1.958
peak=    3.243 closest distance to " O   HOH Z 137 " =    1.756
peak=    3.241 closest distance to " O   HOH Z 388 " =    1.997
peak=    3.240 closest distance to " O   HOH Z  22 " =    2.951
peak=    3.240 closest distance to " O   HOH Z  90 " =    3.174
peak=    3.239 closest distance to " O   HOH Z 174 " =    2.418
peak=    3.239 closest distance to " CG1 VAL A 202 " =    1.947
peak=    3.236 closest distance to " CG  MET A 185 " =    1.248
peak=    3.235 closest distance to " CB  TYR A 116 " =    1.056
peak=    3.232 closest distance to " O   HOH Z 328 " =    1.658
peak=    3.231 closest distance to " O   HOH Z  66 " =    2.257
peak=    3.225 closest distance to " O   HOH Z  46 " =    1.487
peak=    3.225 closest distance to " O   HOH Z 158 " =    3.013
peak=    3.224 closest distance to " CD  LYS A 166 " =    1.313
peak=    3.221 closest distance to " O   HOH Z 186 " =    2.085
peak=    3.218 closest distance to " OG BSER A 134 " =    3.028
peak=    3.217 closest distance to " O   HOH Z 193 " =    1.625
peak=    3.213 closest distance to " CA  ARG A  36 " =    1.190
peak=    3.213 closest distance to " N   SER A 135 " =    1.498
peak=    3.211 closest distance to " CB  ALA A 295 " =    1.296
peak=    3.208 closest distance to " CB  ALA A 248 " =    1.342
peak=    3.206 closest distance to " CB  ALA A  71 " =    1.311
peak=    3.204 closest distance to " O   HOH Z 114 " =    1.354
peak=    3.200 closest distance to " O   HOH Z 406 " =    1.561
peak=    3.200 closest distance to " CA  VAL A 126 " =    0.957
peak=    3.199 closest distance to " O   HOH Z 303 " =    1.776
peak=    3.198 closest distance to " CA  VAL A  41 " =    0.899
peak=    3.197 closest distance to " N   ASN A 127 " =    1.174
peak=    3.197 closest distance to " O   HOH Z  47 " =    1.356
peak=    3.193 closest distance to " O   HOH Z 272 " =    2.661
peak=    3.191 closest distance to " CG  MET A 188 " =    0.920
peak=    3.189 closest distance to " O   HOH Z  59 " =    2.350
peak=    3.183 closest distance to " O   HOH Z 411 " =    1.830
peak=    3.181 closest distance to " O   GLN A  58 " =    1.759
peak=    3.167 closest distance to " O   HOH Z 423 " =    3.241
peak=    3.166 closest distance to " O   HOH Z 273 " =    2.646
peak=    3.164 closest distance to " CB  ILE A 199 " =    0.986
peak=    3.163 closest distance to " CB  ALA A  34 " =    0.780
peak=    3.160 closest distance to " N   ARG A 190 " =    1.090
peak=    3.159 closest distance to " CB  ASN A 127 " =    0.949
peak=    3.158 closest distance to " NH1BARG A 145 " =    1.303
peak=    3.139 closest distance to " O   HOH Z 425 " =    2.133
peak=    3.138 closest distance to " O   PRO A 213 " =    1.556
peak=    3.137 closest distance to " CA  GLY A 196 " =    0.761
peak=    3.137 closest distance to " O   HOH Z 133 " =    1.711
peak=    3.137 closest distance to " CD1 ILE A 106 " =    1.027
peak=    3.130 closest distance to " O   HOH Z 173 " =    1.532
peak=    3.129 closest distance to " NE2 GLN A  58 " =    4.221
peak=    3.129 closest distance to " CG1 VAL A 296 " =    1.142
peak=    3.127 closest distance to " O   GLY A  91 " =    1.125
peak=    3.125 closest distance to " O   HOH Z 173 " =    2.210
peak=    3.120 closest distance to " O   HOH Z 427 " =    3.152
peak=    3.118 closest distance to " CA  ILE A 106 " =    0.839
peak=    3.117 closest distance to " O   HOH Z 155 " =    3.025
peak=    3.114 closest distance to " CD  ARG A 219 " =    1.061
peak=    3.112 closest distance to " CG  GLN A  55 " =    2.157
peak=    3.111 closest distance to " CE2 TYR A 186 " =    0.928
peak=    3.111 closest distance to " O   GLU A   2 " =    1.818
peak=    3.110 closest distance to " O   HOH Z 302 " =    1.840
peak=    3.107 closest distance to " CG2 VAL A 197 " =    1.063
peak=    3.101 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.100 closest distance to " NZ  LYS A  76 " =    1.314
peak=    3.100 closest distance to " CB  ALA A 104 " =    0.779
peak=    3.099 closest distance to " CD1 LEU A 101 " =    1.161
peak=    3.095 closest distance to " CB  ALA A 242 " =    0.878
peak=    3.094 closest distance to " CB  LEU A 255 " =    1.360
peak=    3.093 closest distance to " OG BSER A 212 " =    2.318
peak=    3.083 closest distance to " O   HOH Z 345 " =    1.672
peak=    3.077 closest distance to " O   HOH Z 280 " =    1.674
peak=    3.074 closest distance to " O   HOH Z 417 " =    3.159
peak=    3.073 closest distance to " OE1 GLU A   2 " =    2.200
peak=    3.072 closest distance to " CB  ALA A 256 " =    1.332
peak=    3.069 closest distance to " O   HOH Z 291 " =    1.644
peak=    3.067 closest distance to " O   HOH Z  10 " =    1.889
peak=    3.050 closest distance to " CB  LEU A 255 " =    0.836
peak=    3.041 closest distance to " O   HOH Z  98 " =    1.893
peak=    3.027 closest distance to " CB  SER A 212 " =    1.227
peak=    3.025 closest distance to " O   HOH Z 391 " =    3.000

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.658 - 5.211
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 196
   mapped sites are within: 0.751 - 5.211

peak=   -5.492 closest distance to " CG2 VAL A 230 " =    0.878
peak=   -4.280 closest distance to " O   HOH Z 266 " =    4.461
peak=   -4.228 closest distance to " CD  ARG A 156 " =    1.993
peak=   -4.202 closest distance to " O   HOH Z  19 " =    2.242
peak=   -4.202 closest distance to " CD2 LEU A 300 " =    2.919
peak=   -4.198 closest distance to " O   ILE A 109 " =    2.694
peak=   -4.166 closest distance to " CG  LEU A 101 " =    2.578
peak=   -4.126 closest distance to " CD2 LEU A 237 " =    2.688
peak=   -4.051 closest distance to " CD1 LEU A 228 " =    2.432
peak=   -4.034 closest distance to " OG ASER A 134 " =    1.397
peak=   -4.029 closest distance to " O   HOH Z  52 " =    1.679
peak=   -4.012 closest distance to " OG  SER A  26 " =    1.348
peak=   -3.999 closest distance to " O   HOH Z  17 " =    1.435
peak=   -3.997 closest distance to " O   HOH Z 166 " =    1.807
peak=   -3.935 closest distance to " O   HOH Z  38 " =    1.404
peak=   -3.932 closest distance to " CD  LYS A 289 " =    2.442
peak=   -3.924 closest distance to " O   HOH Z 241 " =    1.126
peak=   -3.897 closest distance to " CD  GLN A  88 " =    2.266
peak=   -3.890 closest distance to " OG BSER A 134 " =    1.814
peak=   -3.889 closest distance to " CD1 PHE A  59 " =    1.916
peak=   -3.889 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -3.884 closest distance to " O   HOH Z 231 " =    2.069
peak=   -3.879 closest distance to " C   ALA A 158 " =    1.257
peak=   -3.876 closest distance to " O   HOH Z 290 " =    1.111
peak=   -3.869 closest distance to " O   HOH Z 377 " =    1.124
peak=   -3.862 closest distance to " O   HOH Z 184 " =    1.382
peak=   -3.861 closest distance to " O   HOH Z  13 " =    1.370
peak=   -3.850 closest distance to " CG2 VAL A 112 " =    2.575
peak=   -3.845 closest distance to " O   PRO A 163 " =    2.082
peak=   -3.819 closest distance to " N   ALA A  43 " =    2.681
peak=   -3.808 closest distance to " O   HOH Z 407 " =    3.486
peak=   -3.801 closest distance to " OXT GLY A 302 " =    2.933
peak=   -3.788 closest distance to " O   HOH Z 353 " =    2.346
peak=   -3.776 closest distance to " O   HOH Z  71 " =    1.176
peak=   -3.770 closest distance to " CG  GLN A 223 " =    2.230
peak=   -3.764 closest distance to " OG  SER A  87 " =    1.572
peak=   -3.758 closest distance to " CZ3 TRP A 179 " =    1.195
peak=   -3.751 closest distance to " CG2 THR A   4 " =    1.941
peak=   -3.746 closest distance to " O   HOH Z 283 " =    1.950
peak=   -3.731 closest distance to " O   HOH Z  11 " =    1.781
peak=   -3.722 closest distance to " O   HOH Z 151 " =    1.567
peak=   -3.708 closest distance to " O   HOH Z 377 " =    1.727
peak=   -3.700 closest distance to " CG1 VAL A 296 " =    1.498
peak=   -3.698 closest distance to " NH2AARG A 275 " =    5.211
peak=   -3.692 closest distance to " N   ALA A 226 " =    2.073
peak=   -3.685 closest distance to " O   HOH Z 196 " =    2.209
peak=   -3.676 closest distance to " N   GLN A  58 " =    1.726
peak=   -3.674 closest distance to " O   HOH Z 275 " =    1.516
peak=   -3.670 closest distance to " CD2 LEU A 167 " =    1.716
peak=   -3.667 closest distance to " O   HOH Z  43 " =    1.570
peak=   -3.667 closest distance to " CB  PRO A 163 " =    2.779
peak=   -3.665 closest distance to " O   HOH Z 234 " =    4.417
peak=   -3.656 closest distance to " NH2 ARG A  66 " =    1.822
peak=   -3.641 closest distance to " CG  GLU A  53 " =    1.606
peak=   -3.632 closest distance to " OG  SER A  97 " =    2.252
peak=   -3.625 closest distance to " O   HOH Z 103 " =    1.908
peak=   -3.620 closest distance to " O   HOH Z 292 " =    4.570
peak=   -3.618 closest distance to " O   HOH Z  63 " =    0.751
peak=   -3.610 closest distance to " CG  ASP A 231 " =    0.873
peak=   -3.608 closest distance to " O   HOH Z  92 " =    1.333
peak=   -3.604 closest distance to " O   HOH Z 389 " =    1.894
peak=   -3.600 closest distance to " O   HOH Z  10 " =    1.575
peak=   -3.591 closest distance to " O   VAL A 125 " =    2.190
peak=   -3.589 closest distance to " CG2BVAL A  41 " =    2.686
peak=   -3.584 closest distance to " OD1 ASN A 148 " =    1.628
peak=   -3.581 closest distance to " CB  CYS A 254 " =    2.338
peak=   -3.581 closest distance to " CG  TRP A 266 " =    1.693
peak=   -3.568 closest distance to " CB  ALA A 248 " =    1.944
peak=   -3.567 closest distance to " O   HOH Z 252 " =    3.956
peak=   -3.548 closest distance to " CG1 VAL A 197 " =    2.313
peak=   -3.538 closest distance to " SG  CYS A 254 " =    3.196
peak=   -3.536 closest distance to " OE2 GLU A   2 " =    1.674
peak=   -3.534 closest distance to " O   HOH Z 198 " =    2.382
peak=   -3.526 closest distance to " CG2 VAL A 296 " =    1.402
peak=   -3.526 closest distance to " CD1 TYR A 247 " =    2.333
peak=   -3.525 closest distance to " O   HOH Z 350 " =    1.705
peak=   -3.524 closest distance to " OD2 ASP A  50 " =    2.289
peak=   -3.517 closest distance to " CB  PRO A 243 " =    2.644
peak=   -3.510 closest distance to " CD2 TYR A 293 " =    2.110
peak=   -3.506 closest distance to " O   GLY A 211 " =    1.557
peak=   -3.490 closest distance to " NE2 GLN A 103 " =    1.648
peak=   -3.489 closest distance to " CA  GLY A 203 " =    2.268
peak=   -3.483 closest distance to " SG ACYS A 201 " =    2.176
peak=   -3.477 closest distance to " O   SER A 271 " =    2.217
peak=   -3.473 closest distance to " CG  PRO A 163 " =    2.482
peak=   -3.467 closest distance to " O   HOH Z 426 " =    1.783
peak=   -3.454 closest distance to " ND2 ASN A 187 " =    1.728
peak=   -3.441 closest distance to " C   ASN A 187 " =    1.798
peak=   -3.440 closest distance to " CD1 LEU A 101 " =    2.965
peak=   -3.439 closest distance to " CB  ASN A  39 " =    2.002
peak=   -3.436 closest distance to " C   HIS A 108 " =    1.179
peak=   -3.436 closest distance to " NE2 GLN A  88 " =    0.897
peak=   -3.432 closest distance to " O   HOH Z 211 " =    1.524
peak=   -3.427 closest distance to " N   ALA A 248 " =    2.277
peak=   -3.426 closest distance to " O   HOH Z 231 " =    1.187
peak=   -3.422 closest distance to " CG  MET A 105 " =    0.916
peak=   -3.418 closest distance to " OD1 ASP A 191 " =    1.626
peak=   -3.412 closest distance to " CG  ARG A 269 " =    2.296
peak=   -3.398 closest distance to " CD  GLN A  88 " =    0.788
peak=   -3.396 closest distance to " O   HOH Z 292 " =    3.017
peak=   -3.395 closest distance to " CG1 VAL A 112 " =    2.576
peak=   -3.384 closest distance to " O   HOH Z 394 " =    1.607
peak=   -3.383 closest distance to " C   GLN A 240 " =    2.283
peak=   -3.379 closest distance to " C   ASN A 142 " =    1.293
peak=   -3.379 closest distance to " O   HOH Z 351 " =    1.508
peak=   -3.379 closest distance to " CD  ARG A 259 " =    2.575
peak=   -3.377 closest distance to " O   GLY A 196 " =    1.245
peak=   -3.372 closest distance to " CZ  TYR A 172 " =    1.676
peak=   -3.370 closest distance to " O   HOH Z  92 " =    1.373
peak=   -3.350 closest distance to " CE  MET A 105 " =    2.048
peak=   -3.347 closest distance to " O   VAL A  67 " =    2.676
peak=   -3.346 closest distance to " CG2 ILE A 263 " =    2.415
peak=   -3.341 closest distance to " O   HOH Z 147 " =    2.016
peak=   -3.340 closest distance to " CG  ARG A  66 " =    2.370
peak=   -3.340 closest distance to " CE1 TYR A 169 " =    2.584
peak=   -3.337 closest distance to " O   HOH Z 435 " =    2.563
peak=   -3.335 closest distance to " CE3 TRP A  70 " =    1.746
peak=   -3.334 closest distance to " N   SER A 276 " =    1.413
peak=   -3.323 closest distance to " CD  ARG A 139 " =    1.630
peak=   -3.322 closest distance to " O   HOH Z 118 " =    2.856
peak=   -3.318 closest distance to " CA  ASP A 298 " =    1.098
peak=   -3.313 closest distance to " CA  GLY A 241 " =    2.291
peak=   -3.312 closest distance to " CA  GLY A  98 " =    2.078
peak=   -3.308 closest distance to " CA  ASN A 127 " =    1.097
peak=   -3.307 closest distance to " O   SER A 210 " =    2.009
peak=   -3.307 closest distance to " C   LEU A 143 " =    1.239
peak=   -3.297 closest distance to " CA  GLY A 241 " =    3.056
peak=   -3.297 closest distance to " O   HOH Z 128 " =    2.512
peak=   -3.296 closest distance to " O   HOH Z 128 " =    4.172
peak=   -3.296 closest distance to " CB  TYR A  15 " =    2.295
peak=   -3.291 closest distance to " CB  GLN A  55 " =    1.506
peak=   -3.289 closest distance to " O   GLY A  80 " =    2.551
peak=   -3.279 closest distance to " O   HOH Z 177 " =    1.599
peak=   -3.277 closest distance to " CB  ALA A  43 " =    2.475
peak=   -3.276 closest distance to " O   HOH Z 117 " =    4.387
peak=   -3.275 closest distance to " O   HOH Z 165 " =    2.072
peak=   -3.275 closest distance to " N   SER A   3 " =    2.228
peak=   -3.272 closest distance to " CD  ARG A 195 " =    5.045
peak=   -3.270 closest distance to " O   HOH Z  22 " =    2.467
peak=   -3.265 closest distance to " O   HOH Z  98 " =    1.550
peak=   -3.264 closest distance to " O   HOH Z 222 " =    1.410
peak=   -3.260 closest distance to " CG  LEU A  83 " =    2.010
peak=   -3.256 closest distance to " ND2 ASN A  60 " =    1.493
peak=   -3.252 closest distance to " O   HOH Z 409 " =    4.758
peak=   -3.252 closest distance to " CG1 VAL A 296 " =    1.402
peak=   -3.251 closest distance to " CD1 LEU A 297 " =    1.973
peak=   -3.243 closest distance to " O   HOH Z 311 " =    3.791
peak=   -3.240 closest distance to " N   PHE A  59 " =    2.155
peak=   -3.238 closest distance to " O   HOH Z 396 " =    1.794
peak=   -3.237 closest distance to " O   ASN A 301 " =    1.404
peak=   -3.237 closest distance to " OG1 THR A 279 " =    1.374
peak=   -3.230 closest distance to " O   HOH Z  60 " =    2.123
peak=   -3.228 closest distance to " O   HOH Z  55 " =    2.632
peak=   -3.226 closest distance to " OG BSER A 134 " =    1.313
peak=   -3.225 closest distance to " O   HOH Z 385 " =    3.881
peak=   -3.225 closest distance to " O   HOH Z 132 " =    1.247
peak=   -3.216 closest distance to " CA  GLY A 133 " =    2.290
peak=   -3.208 closest distance to " O   HOH Z 266 " =    4.699
peak=   -3.205 closest distance to " OD2 ASP A 171 " =    2.166
peak=   -3.204 closest distance to " NH1 ARG A 195 " =    2.244
peak=   -3.203 closest distance to " O   HOH Z 185 " =    2.415
peak=   -3.198 closest distance to " CB  TRP A  85 " =    2.492
peak=   -3.194 closest distance to " N   THR A 157 " =    1.623
peak=   -3.192 closest distance to " N   GLY A  23 " =    2.178
peak=   -3.190 closest distance to " CB  ARG A  79 " =    2.517
peak=   -3.189 closest distance to " O   HOH Z 243 " =    1.529
peak=   -3.189 closest distance to " CB  ILE A 239 " =    2.093
peak=   -3.186 closest distance to " CD1 LEU A   5 " =    2.539
peak=   -3.184 closest distance to " O   HOH Z 313 " =    1.103
peak=   -3.182 closest distance to " CG1 VAL A 112 " =    2.826
peak=   -3.180 closest distance to " CG  LYS A 193 " =    2.610
peak=   -3.176 closest distance to " O   HOH Z 265 " =    1.945
peak=   -3.174 closest distance to " ND2 ASN A 249 " =    2.223
peak=   -3.172 closest distance to " CZ  TYR A 169 " =    1.778
peak=   -3.169 closest distance to " O   VAL A 174 " =    2.144
peak=   -3.152 closest distance to " O   HOH Z 236 " =    1.223
peak=   -3.143 closest distance to " CB  SER A 258 " =    2.009
peak=   -3.142 closest distance to " NE  ARG A 259 " =    1.109
peak=   -3.136 closest distance to " CB  ALA A 248 " =    2.480
peak=   -3.136 closest distance to " CG  GLU A 277 " =    1.103
peak=   -3.136 closest distance to " OD2 ASP A 171 " =    1.895
peak=   -3.134 closest distance to " ND2 ASN A  60 " =    1.722
peak=   -3.129 closest distance to " CB  PHE A 192 " =    1.858
peak=   -3.129 closest distance to " O   HOH Z 323 " =    1.366
peak=   -3.124 closest distance to " O   HOH Z  70 " =    2.221
peak=   -3.122 closest distance to " NH1AARG A 102 " =    1.559
peak=   -3.122 closest distance to " CG  LEU A 228 " =    0.948
peak=   -3.117 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.107 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.102 closest distance to " CB  ALA A 227 " =    2.337
peak=   -3.101 closest distance to " O   HOH Z 285 " =    1.276
peak=   -3.098 closest distance to " O   GLY A 203 " =    2.520
peak=   -3.095 closest distance to " O   HOH Z 423 " =    2.303
peak=   -3.065 closest distance to " CB  ALA A 291 " =    2.341

================= 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    :  0.4752 0.4694   6.277038e+00   6.267525e+00
   1_bss:  0.4667 0.4582   6.275568e+00   6.263197e+00
   1_xyz:  0.3825 0.4147   6.150423e+00   6.203155e+00
   1_adp:  0.3406 0.3971   6.075325e+00   6.174532e+00
   1_occ:  0.3402 0.3980   6.074916e+00   6.175319e+00
   2_bss:  0.3381 0.3941   6.075161e+00   6.173491e+00
   2_xyz:  0.2417 0.3074   5.811159e+00   5.986146e+00
   2_adp:  0.2180 0.2790   5.720713e+00   5.907637e+00
   2_occ:  0.2177 0.2785   5.719610e+00   5.906720e+00
   3_bss:  0.2156 0.2746   5.718258e+00   5.903402e+00
   3_xyz:  0.1543 0.2007   5.409822e+00   5.625785e+00
   3_adp:  0.1389 0.1882   5.332796e+00   5.563059e+00
   3_occ:  0.1387 0.1882   5.332500e+00   5.563145e+00
   4_bss:  0.1386 0.1884   5.333795e+00   5.563933e+00
   4_xyz:  0.1221 0.1715   5.231861e+00   5.475827e+00
   4_adp:  0.1190 0.1687   5.215578e+00   5.462199e+00
   4_occ:  0.1189 0.1686   5.215570e+00   5.462357e+00
   5_bss:  0.1189 0.1686   5.215570e+00   5.462357e+00
   5_xyz:  0.1131 0.1640   5.181083e+00   5.435999e+00
   5_adp:  0.1133 0.1623   5.176230e+00   5.426150e+00
   5_occ:  0.1133 0.1623   5.176273e+00   5.426361e+00
   5_bss:  0.1136 0.1633   5.179068e+00   5.429762e+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:  0.318  13.622   8.971   8.823   7.864   0.000   0.000   0.000
   1_xyz:  0.318  13.622   8.971   8.823   7.864   0.000   0.000   0.000
   1_adp:  0.318  13.622   8.971   8.823   7.864   0.000   0.000   0.000
   1_occ:  0.318  13.622   8.971   8.823   7.864   0.000   0.000   0.000
   2_bss:  0.327  46.402   5.470   5.436   5.300   0.000   0.000   0.000
   2_xyz:  0.327  46.402   5.470   5.436   5.300   0.000   0.000   0.000
   2_adp:  0.327  46.402   5.470   5.436   5.300   0.000   0.000   0.000
   2_occ:  0.327  46.402   5.470   5.436   5.300   0.000   0.000   0.000
   3_bss:  0.321  46.403   3.381   3.457   3.429   0.000   0.000   0.000
   3_xyz:  0.321  46.403   3.381   3.457   3.429   0.000   0.000   0.000
   3_adp:  0.321  46.403   3.381   3.457   3.429   0.000   0.000   0.000
   3_occ:  0.321  46.403   3.381   3.457   3.429   0.000   0.000   0.000
   4_bss:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   4_xyz:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   4_adp:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   4_occ:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   5_bss:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   5_xyz:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   5_adp:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   5_occ:  0.329  50.455   2.520   2.607   2.730   0.000   0.000   0.000
   5_bss:  0.323  53.021  -0.098  -0.069   0.167  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.286 0.4281  0.4971    68602.269
   1_bss:  57.950 0.4169  0.6112    66373.679
   1_xyz:  49.414 0.5248  0.7608    51399.516
   1_adp:  45.455 0.5745  0.8573    45661.613
   1_occ:  45.584 0.5728  0.8541    45875.621
   2_bss:  45.322 0.5760  0.7730    45487.095
   2_xyz:  32.395 0.7297  0.9561    25700.406
   2_adp:  28.454 0.7744  0.9973    20818.132
   2_occ:  28.406 0.7749  0.9978    20774.334
   3_bss:  28.263 0.7763  0.9311    20594.096
   3_xyz:  19.495 0.8656  0.9894    10458.844
   3_adp:  17.925 0.8809  0.9931     9229.276
   3_occ:  17.923 0.8809  0.9930     9229.471
   4_bss:  17.941 0.8808  0.9649     9264.294
   4_xyz:  15.936 0.8987  0.9738     7630.532
   4_adp:  15.609 0.9017  0.9719     7445.587
   4_occ:  15.608 0.9017  0.9717     7447.769
   5_bss:  15.608 0.9017  0.9717     7447.769
   5_xyz:  15.067 0.9062  0.9729     7016.290
   5_adp:  14.823 0.9084  0.9706     6895.720
   5_occ:  14.828 0.9084  0.9705     6900.822
   5_bss:  14.904 0.9078  0.9681     6989.390
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3950e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3950e+01
   1_xyz:   1.767  0.014  0.111 18.090  0.007  4.111   1.5038e-01
   1_adp:   1.767  0.014  0.111 18.090  0.007  4.111   1.5038e-01
   1_occ:   1.767  0.014  0.111 18.090  0.007  4.111   1.5038e-01
   2_bss:   1.767  0.014  0.111 18.090  0.007  4.111   1.5038e-01
   2_xyz:   1.192  0.009  0.081 16.371  0.005  4.112   8.7589e-02
   2_adp:   1.192  0.009  0.081 16.371  0.005  4.112   8.7589e-02
   2_occ:   1.192  0.009  0.081 16.371  0.005  4.112   8.7589e-02
   3_bss:   1.192  0.009  0.081 16.371  0.005  4.112   8.7589e-02
   3_xyz:   1.152  0.009  0.084 15.719  0.004  4.133   7.5922e-02
   3_adp:   1.152  0.009  0.084 15.719  0.004  4.133   7.5922e-02
   3_occ:   1.152  0.009  0.084 15.719  0.004  4.133   7.5922e-02
   4_bss:   1.152  0.009  0.084 15.719  0.004  4.133   7.5922e-02
   4_xyz:   1.165  0.009  0.087 15.823  0.004  4.113   7.8234e-02
   4_adp:   1.165  0.009  0.087 15.823  0.004  4.113   7.8234e-02
   4_occ:   1.165  0.009  0.087 15.823  0.004  4.113   7.8234e-02
   5_bss:   1.165  0.009  0.087 15.823  0.004  4.113   7.8234e-02
   5_xyz:   1.193  0.011  0.094 15.624  0.004  4.117   8.4917e-02
   5_adp:   1.193  0.011  0.094 15.624  0.004  4.117   8.4917e-02
   5_occ:   1.193  0.011  0.094 15.624  0.004  4.117   8.4917e-02
   5_bss:   1.193  0.011  0.094 15.624  0.004  4.117   8.4917e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9942e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9942e+00
   1_xyz:  15.711  0.175  0.511 85.473  0.053  2.181   1.0727e-01
   1_adp:  15.711  0.175  0.511 85.473  0.053  2.181   1.0727e-01
   1_occ:  15.711  0.175  0.511 85.473  0.053  2.181   1.0727e-01
   2_bss:  15.711  0.175  0.511 85.473  0.053  2.181   1.0727e-01
   2_xyz:   7.646  0.108  0.296 80.968  0.045  2.173   8.3622e-02
   2_adp:   7.646  0.108  0.296 80.968  0.045  2.173   8.3622e-02
   2_occ:   7.646  0.108  0.296 80.968  0.045  2.173   8.3622e-02
   3_bss:   7.646  0.108  0.296 80.968  0.045  2.173   8.3622e-02
   3_xyz:   7.976  0.065  0.476 86.203  0.033  2.320   6.0225e-02
   3_adp:   7.976  0.065  0.476 86.203  0.033  2.320   6.0225e-02
   3_occ:   7.976  0.065  0.476 86.203  0.033  2.320   6.0225e-02
   4_bss:   7.976  0.065  0.476 86.203  0.033  2.320   6.0225e-02
   4_xyz:   8.604  0.057  0.554 83.346  0.033  2.314   5.2987e-02
   4_adp:   8.604  0.057  0.554 83.346  0.033  2.314   5.2987e-02
   4_occ:   8.604  0.057  0.554 83.346  0.033  2.314   5.2987e-02
   5_bss:   8.604  0.057  0.554 83.346  0.033  2.314   5.2987e-02
   5_xyz:   7.719  0.052  0.669 82.453  0.033  2.276   6.4916e-02
   5_adp:   7.719  0.052  0.669 82.453  0.033  2.276   6.4916e-02
   5_occ:   7.719  0.052  0.669 82.453  0.033  2.276   6.4916e-02
   5_bss:   7.719  0.052  0.669 82.453  0.033  2.276   6.4916e-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:  87.68   0.00  12.16  76.02   0.00   9.57  87.68   0.00  26.26
   1_occ:  87.68   0.00  12.16  76.02   0.00   9.57  87.68   0.00  26.26
   2_bss:  87.68   0.00  12.16  76.02   0.00   9.57  87.68   0.00  26.26
   2_xyz:  87.68   0.00  12.16  76.02   0.00   9.57  87.68   0.00  26.26
   2_adp:  84.80   0.00  12.53  73.51   0.00   8.79  84.80   0.00  32.89
   2_occ:  84.80   0.00  12.53  73.51   0.00   8.79  84.80   0.00  32.89
   3_bss:  84.80   0.00  12.53  73.51   0.00   8.79  84.80   0.00  32.89
   3_xyz:  84.80   0.00  12.53  73.51   0.00   8.79  84.80   0.00  32.89
   3_adp:  86.02   0.00  13.21  86.02   0.00   8.67  82.82   0.32  37.92
   3_occ:  86.02   0.00  13.21  86.02   0.00   8.67  82.82   0.32  37.92
   4_bss:  86.02   0.00  13.21  86.02   0.00   8.67  82.82   0.32  37.92
   4_xyz:  86.02   0.00  13.21  86.02   0.00   8.67  82.82   0.32  37.92
   4_adp:  92.19   0.00  13.05  92.19   0.00   8.57  87.11   1.02  37.49
   4_occ:  92.19   0.00  13.05  92.19   0.00   8.57  87.11   1.02  37.49
   5_bss:  92.19   0.00  13.05  92.19   0.00   8.57  87.11   1.02  37.49
   5_xyz:  92.19   0.00  13.05  92.19   0.00   8.57  87.11   1.02  37.49
   5_adp:  93.71   0.00  12.51  93.71   0.00   8.35  83.88   1.45  35.16
   5_occ:  93.71   0.00  12.51  93.71   0.00   8.35  83.88   1.45  35.16
   5_bss:  96.27   2.57  15.07  96.27   2.57  10.91  86.45   4.02  37.73
------------------------------------------------------------------------
 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:    1.213    0.046    0.419
   1_adp:    1.213    0.046    0.419
   1_occ:    1.213    0.046    0.419
   2_bss:    1.213    0.046    0.419
   2_xyz:    1.592    0.048    0.603
   2_adp:    1.592    0.048    0.603
   2_occ:    1.592    0.048    0.603
   3_bss:    1.592    0.048    0.603
   3_xyz:    1.598    0.037    0.686
   3_adp:    1.598    0.037    0.686
   3_occ:    1.598    0.037    0.686
   4_bss:    1.598    0.037    0.686
   4_xyz:    1.647    0.044    0.717
   4_adp:    1.647    0.044    0.717
   4_occ:    1.647    0.044    0.717
   5_bss:    1.647    0.044    0.717
   5_xyz:    1.709    0.033    0.733
   5_adp:    1.709    0.033    0.733
   5_occ:    1.709    0.033    0.733
   5_bss:    1.709    0.033    0.733
------------------------------------------------------------------------

CPU time actual refinement: 347.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/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_1168/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1168/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.72 
  Macro-tasks:
    bulk solvent and scale       = 40.90  
    individual site refinement   = 145.36 
    weights calculation          = 33.10  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 226.00 
  Micro-tasks:
    mask                            = 2.58   
    f_calc                          = 109.88 
    alpha_beta                      = 8.33   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.11 
    fmodel                         = 7.18   
    r_factors                      = 0.30   
    phase_errors                   = 10.19  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 258.98 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.944 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    619 calls, 109.55 s
gradients_fft:          564 calls, 106.12 s

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

# Date 2008-01-16 Time 03:21:35 PST -0800 (1200482495.93 s)
Start R-work = 0.4752, R-free = 0.4694 (no bulk solvent and anisotropic scale)
Final R-work = 0.1299, R-free = 0.1788 (no bulk solvent and anisotropic scale)

Start R-work = 0.4667, R-free = 0.4582
Final R-work = 0.1136, R-free = 0.1633