# Date 2008-01-16 Time 02:20:38 PST -0800 (1200478838.16 s)
#phil __OFF__

Command line arguments: "../792.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2984
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 792

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95137
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927509

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95137
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927509

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1764 [2212/2241]  1992   220   9.9%
  bin  2:  4.1764 -  3.3270 [2116/2139]  1907   209   9.9%
  bin  3:  3.3270 -  2.9099 [2091/2116]  1875   216  10.3%
  bin  4:  2.9099 -  2.6455 [2084/2100]  1883   201   9.6%
  bin  5:  2.6455 -  2.4568 [2052/2091]  1841   211  10.3%
  bin  6:  2.4568 -  2.3125 [2054/2086]  1855   199   9.7%
  bin  7:  2.3125 -  2.1970 [2029/2066]  1823   206  10.2%
  bin  8:  2.1970 -  2.1017 [2036/2078]  1833   203  10.0%
  bin  9:  2.1017 -  2.0210 [2025/2063]  1822   203  10.0%
  bin 10:  2.0210 -  1.9514 [ 890/2077]   799    91  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/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:
        1.48 -     2.17: 18
        2.17 -     2.85: 1106
        2.85 -     3.53: 4443
        3.53 -     4.22: 9340
        4.22 -     4.90: 13633
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.484 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.526 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.848 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28535 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_792/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.16465 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4661   r_free= 0.4708   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.270007                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.3865 0.3785       6.579      6.5797|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.3802 0.3839      6.7542       6.756|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.4281 0.4203      6.6528      6.7235|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.4367 0.4671       6.487      6.4929|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.4919 0.5098      6.3567      6.3608|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.4859 0.5323      6.2517      6.2183|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.5052 0.4466      6.2505      6.1354|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.5232 0.5320      6.1482      6.1948|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.5170 0.5048      6.1218      6.1144|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.5228 0.5178      6.0862      6.1015|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.5179 0.5265      6.0202      6.0218|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.5224 0.5658      5.9435      5.9891|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.5262 0.5126      5.8732      5.8222|
| 14:  2.0001 -  1.9514 0.26    346   35 0.5525 0.6154       5.838      5.8044|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.71  33.59   0.81     0.73      67734.85|
|  2:  4.6586 -  3.7164  1380   144  0.70  34.87   0.89     0.78     101746.34|
|  3:  3.7164 -  3.2521  1358   158  0.59  44.31   0.84     0.72     114170.59|
|  4:  3.2521 -  2.9573  1343   149  0.50  51.67   0.82     0.61     102993.20|
|  5:  2.9573 -  2.7467  1328   148  0.41  58.79   0.74     0.51      85383.38|
|  6:  2.7467 -  2.5857  1335   147  0.41  58.92   0.75     0.48      68427.00|
|  7:  2.5857 -  2.4568  1324   149  0.42  58.10   0.75     0.47      59993.19|
|  8:  2.4568 -  2.3502  1312   143  0.39  60.34   0.72     0.47      55626.80|
|  9:  2.3502 -  2.2601  1315   150  0.37  62.18   0.75     0.45      52781.97|
| 10:  2.2601 -  2.1823  1324   144  0.33  64.91   0.77     0.41      51059.19|
| 11:  2.1823 -  2.1143  1298   141  0.30  67.44   0.77     0.37      47060.79|
| 12:  2.1143 -  2.0540  1311   150  0.26  71.05   0.75     0.33      46025.12|
| 13:  2.0540 -  2.0001  1226   139  0.25  71.49   0.74     0.32      39592.37|
| 14:  2.0001 -  1.9514   346    35  0.27  69.58   0.70     0.34      32645.73|
|alpha:            min =        0.32 max =            0.78 mean =         0.51|
|beta:             min =    32645.73 max =       114170.59 mean =     68409.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.64|
|phase err.(test): min =        0.00 max =           89.76 mean =        57.04|
|-----------------------------------------------------------------------------|

============================== 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 = 13.223020             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.952   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.169585              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.065   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      711 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2670 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3956 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5051 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6670 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7768 |
|-----------------------------------------------------------------------------|
|-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 |       53.410 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.992 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4731   r_free= 0.4767   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4584   r_free= 0.4601   ksol= 0.36   Bsol= 20.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,7.78,9.60,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.269191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.702484             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.233   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.075738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.346   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4584      final r-factor (work) = 0.3808          |
| start r-factor (free) = 0.4601      final r-factor (free) = 0.4113          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.9569 = 10.70 * 0.50 * 6.2691 + 1.00 * 53.4097                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.2018 = 10.70 * 0.50 * 6.1793 + 1.00 * 0.1347                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3808      final r-factor (work) = 0.3344          |
| start r-factor (free) = 0.4113      final r-factor (free) = 0.3911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6617 = 1.08 * 1.00 * 6.1793 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5692 = 1.08 * 1.00 * 6.0931 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.59   12.65    None  None   None       |
|    all(noH): 2823   0      0.00    69.59   12.65    None  None   None       |
|    Sol.    : 438    0      0.00    65.57   26.35    None  None   None       |
|    Mac.    : 2385   0      0.00    69.59   10.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.959: 1112   |   5:    34.794 -  41.753:   86        |
|      1:     6.959 -  13.918:  767   |   6:    41.753 -  48.712:   42        |
|      2:    13.918 -  20.877:  392   |   7:    48.712 -  55.671:   28        |
|      3:    20.877 -  27.835:  246   |   8:    55.671 -  62.629:   10        |
|      4:    27.835 -  34.794:  133   |   9:    62.629 -  69.588:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3344 r_free = 0.3911             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3340 r_free = 0.3910             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3340   r_free= 0.3910   ksol= 0.36   Bsol= 20.00   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,7.78,9.60,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.073592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3310   r_free= 0.3875   ksol= 0.33   Bsol= 39.49   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,4.19,6.52,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.073791                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.109239              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.848   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545782              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.792  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3310      final r-factor (work) = 0.2568          |
| start r-factor (free) = 0.3875      final r-factor (free) = 0.3171          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7363 = 6.11 * 0.50 * 6.0897 + 1.00 * 0.1347                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3107 = 6.11 * 0.50 * 5.9698 + 1.00 * 0.0753                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2568      final r-factor (work) = 0.2375          |
| start r-factor (free) = 0.3171      final r-factor (free) = 0.2979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2730 = 0.55 * 1.00 * 5.9698 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2092 = 0.55 * 1.00 * 5.8328 + 1.00 * 0.0258                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.50   13.20    None  None   None       |
|    all(noH): 2823   0      0.00    71.50   13.20    None  None   None       |
|    Sol.    : 438    0      0.65    69.19   31.57    None  None   None       |
|    Mac.    : 2385   0      0.00    71.50   9.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.150: 1177   |   5:    35.751 -  42.901:  106        |
|      1:     7.150 -  14.300:  784   |   6:    42.901 -  50.051:   71        |
|      2:    14.300 -  21.451:  324   |   7:    50.051 -  57.201:   33        |
|      3:    21.451 -  28.601:  183   |   8:    57.201 -  64.352:   11        |
|      4:    28.601 -  35.751:  128   |   9:    64.352 -  71.502:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2375 r_free = 0.2979             target_work(ml) = 5.805         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2373 r_free = 0.2980             target_work(ml) = 5.804         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2373   r_free= 0.2980   ksol= 0.33   Bsol= 39.49   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,4.19,6.52,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.804099                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2359   r_free= 0.2956   ksol= 0.31   Bsol= 40.46   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.91,4.07,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.802756                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.948982              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.102  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2359      final r-factor (work) = 0.1671          |
| start r-factor (free) = 0.2956      final r-factor (free) = 0.2231          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3484 = 6.95 * 0.50 * 5.8348 + 1.00 * 0.0753                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7844 = 6.95 * 0.50 * 5.6717 + 1.00 * 0.0782                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.2231      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1419 = 0.90 * 1.00 * 5.6717 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9294 = 0.90 * 1.00 * 5.4398 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.16   13.72    None  None   None       |
|    all(noH): 2823   0      0.00    85.16   13.72    None  None   None       |
|    Sol.    : 438    0      3.31    78.22   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    85.16   9.30     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 -   8.516: 1476   |   5:    42.581 -  51.097:   88        |
|      1:     8.516 -  17.033:  715   |   6:    51.097 -  59.614:   69        |
|      2:    17.033 -  25.549:  190   |   7:    59.614 -  68.130:   33        |
|      3:    25.549 -  34.065:  106   |   8:    68.130 -  76.646:   12        |
|      4:    34.065 -  42.581:  131   |   9:    76.646 -  85.162:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.2012             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1462 r_free = 0.2010             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.2010   ksol= 0.31   Bsol= 40.46   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.91,4.07,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.382639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1456   r_free= 0.1996   ksol= 0.32   Bsol= 40.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.89,2.34,0.00,0.00,0.00); trace/3= 1.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.380321                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.645292              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.153  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.474753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.380  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1456      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1996      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2848 = 2.65 * 0.50 * 5.4486 + 1.00 * 0.0783                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1156 = 2.65 * 0.50 * 5.3342 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1288      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5445 = 0.47 * 1.00 * 5.3342 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5087 = 0.47 * 1.00 * 5.2606 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.67   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    91.67   13.58    None  None   None       |
|    Sol.    : 438    0      2.95    80.00   37.61    None  None   None       |
|    Mac.    : 2385   0      0.00    91.67   9.16     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 -   9.167: 1620   |   5:    45.836 -  55.003:   86        |
|      1:     9.167 -  18.334:  637   |   6:    55.003 -  64.170:   43        |
|      2:    18.334 -  27.502:  156   |   7:    64.170 -  73.338:   25        |
|      3:    27.502 -  36.669:  118   |   8:    73.338 -  82.505:    8        |
|      4:    36.669 -  45.836:  128   |   9:    82.505 -  91.672:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1726             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1249 r_free = 0.1723             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1723   ksol= 0.32   Bsol= 40.46   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.89,2.34,0.00,0.00,0.00); trace/3= 1.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.241316                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1723   ksol= 0.32   Bsol= 40.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,1.79,1.99,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.241070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.137607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.191  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.841668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.175  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6825 = 2.14 * 0.50 * 5.2601 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6361 = 2.14 * 0.50 * 5.2169 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4020 = 0.84 * 1.00 * 5.2169 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3766 = 0.84 * 1.00 * 5.1858 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.54   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    99.54   13.55    None  None   None       |
|    Sol.    : 438    0      2.24    86.10   37.72    None  None   None       |
|    Mac.    : 2385   0      0.00    99.54   9.11     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 -   9.954: 1739   |   5:    49.769 -  59.723:   62        |
|      1:     9.954 -  19.908:  567   |   6:    59.723 -  69.676:   41        |
|      2:    19.908 -  29.861:  150   |   7:    69.676 -  79.630:   12        |
|      3:    29.861 -  39.815:  112   |   8:    79.630 -  89.584:    6        |
|      4:    39.815 -  49.769:  131   |   9:    89.584 -  99.538:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1625             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1625             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1625   ksol= 0.32   Bsol= 40.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,1.79,1.99,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185370                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.0983 0.1259      5.3745      5.5357|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.0875 0.1107      5.4375      5.6399|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.1087 0.1613      5.4842      5.8702|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.1271 0.1488      5.4751      5.5998|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.1353 0.1808      5.3511      5.5298|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.1313 0.1967      5.2664      5.5356|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.1297 0.1814      5.2217      5.4375|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.1211 0.1710      5.0974      5.3159|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.1199 0.1952      5.0531      5.3251|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.1153 0.1802      5.0074      5.2787|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.1191 0.1843      4.9683      5.3129|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.1183 0.1803      4.9148      5.1285|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.1199 0.1851      4.8098      5.0442|
| 14:  2.0001 -  1.9514 0.26    346   35 0.1148 0.1745      4.7001      4.9789|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.94   8.68   0.98     0.96       6917.52|
|  2:  4.6586 -  3.7164  1380   144  0.95   7.90   1.02     1.00       8718.51|
|  3:  3.7164 -  3.2521  1358   158  0.93  11.71   1.03     1.03      10675.09|
|  4:  3.2521 -  2.9573  1343   149  0.92  14.31   1.01     1.00      10720.41|
|  5:  2.9573 -  2.7467  1328   148  0.89  16.97   0.99     0.96       8907.83|
|  6:  2.7467 -  2.5857  1335   147  0.89  17.32   0.99     0.96       8072.09|
|  7:  2.5857 -  2.4568  1324   149  0.89  16.82   0.99     0.95       7104.83|
|  8:  2.4568 -  2.3502  1312   143  0.90  16.78   0.99     0.96       5885.66|
|  9:  2.3502 -  2.2601  1315   150  0.90  16.77   1.00     0.98       5417.88|
| 10:  2.2601 -  2.1823  1324   144  0.90  16.16   1.00     0.97       4981.63|
| 11:  2.1823 -  2.1143  1298   141  0.89  17.34   0.99     0.95       4747.58|
| 12:  2.1143 -  2.0540  1311   150  0.90  16.43   1.00     1.00       4313.59|
| 13:  2.0540 -  2.0001  1226   139  0.89  17.12   1.00     0.98       3539.69|
| 14:  2.0001 -  1.9514   346    35  0.88  17.40   0.99     0.96       2886.61|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2886.61 max =        10720.41 mean =      6887.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.34 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1630   ksol= 0.32   Bsol= 43.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,0.08,0.21,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187224                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1630   ksol= 0.32   Bsol= 43.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,0.08,0.21,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187224                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.0964 0.1291      5.3705      5.5471|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.0897 0.1128      5.4544      5.6621|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.1091 0.1617       5.493      5.8713|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.1279 0.1488       5.481      5.6028|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.1354 0.1797      5.3521      5.5273|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.1313 0.1966       5.266      5.5352|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.1299 0.1818      5.2227      5.4412|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.1210 0.1710      5.0982      5.3193|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.1197 0.1953      5.0528      5.3251|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.1151 0.1794      5.0055       5.275|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.1189 0.1842      4.9666      5.3122|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.1180 0.1806      4.9137      5.1298|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.1199 0.1842      4.8093      5.0406|
| 14:  2.0001 -  1.9514 0.26    346   35 0.1147 0.1747       4.698      4.9832|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.94   8.93   0.98     0.96       7118.43|
|  2:  4.6586 -  3.7164  1380   144  0.95   8.15   1.02     1.00       9025.12|
|  3:  3.7164 -  3.2521  1358   158  0.93  11.92   1.03     1.03      10995.37|
|  4:  3.2521 -  2.9573  1343   149  0.91  14.42   1.02     1.00      10815.20|
|  5:  2.9573 -  2.7467  1328   148  0.89  16.97   0.99     0.96       8908.88|
|  6:  2.7467 -  2.5857  1335   147  0.89  17.34   0.99     0.97       8071.19|
|  7:  2.5857 -  2.4568  1324   149  0.89  16.82   0.99     0.95       7114.55|
|  8:  2.4568 -  2.3502  1312   143  0.90  16.83   0.99     0.96       5913.92|
|  9:  2.3502 -  2.2601  1315   150  0.89  16.79   1.01     0.99       5428.59|
| 10:  2.2601 -  2.1823  1324   144  0.90  16.15   1.01     0.97       4967.88|
| 11:  2.1823 -  2.1143  1298   141  0.89  17.29   1.00     0.96       4733.93|
| 12:  2.1143 -  2.0540  1311   150  0.90  16.40   1.01     1.00       4305.97|
| 13:  2.0540 -  2.0001  1226   139  0.89  17.11   1.00     0.98       3534.65|
| 14:  2.0001 -  1.9514   346    35  0.88  17.38   0.99     0.97       2875.00|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2875.00 max =        10995.37 mean =      6960.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.97|
|phase err.(test): min =        0.00 max =           87.31 mean =        14.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    101.32  15.33    None  None   None       |
|    all(noH): 2823   0      1.79    101.32  15.33    None  None   None       |
|    Sol.    : 438    0      4.02    87.89   39.50    None  None   None       |
|    Mac.    : 2385   0      1.79    101.32  10.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.785 -  11.739: 1739   |   5:    51.554 -  61.508:   62        |
|      1:    11.739 -  21.693:  567   |   6:    61.508 -  71.461:   41        |
|      2:    21.693 -  31.646:  150   |   7:    71.461 -  81.415:   12        |
|      3:    31.646 -  41.600:  112   |   8:    81.415 -  91.369:    6        |
|      4:    41.600 -  51.554:  131   |   9:    91.369 - 101.323:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.405 - 5.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 347
   mapped sites are within: 0.758 - 5.819

peak=   10.201 closest distance to " CB  VAL A 230 " =    1.429
peak=    8.140 closest distance to " CG2 VAL A 296 " =    1.203
peak=    6.637 closest distance to " NH2 ARG A  56 " =    2.258
peak=    6.354 closest distance to " O   HOH Z 279 " =    1.249
peak=    5.948 closest distance to " O   HOH Z  37 " =    1.240
peak=    5.909 closest distance to " CG  LEU A   5 " =    1.242
peak=    5.560 closest distance to " O   HOH Z 278 " =    1.285
peak=    5.472 closest distance to " O   HOH Z 132 " =    1.941
peak=    5.427 closest distance to " CD2 LEU A   5 " =    1.190
peak=    5.316 closest distance to " O   HOH Z 277 " =    1.152
peak=    5.167 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.155 closest distance to " O   HOH Z 202 " =    1.384
peak=    5.104 closest distance to " O   HOH Z 124 " =    1.491
peak=    5.063 closest distance to " O   HOH Z 247 " =    1.316
peak=    5.031 closest distance to " CG  PRO A 213 " =    1.231
peak=    4.995 closest distance to " O   HOH Z 142 " =    1.718
peak=    4.879 closest distance to " O   HOH Z  44 " =    2.537
peak=    4.860 closest distance to " CG  PRO A  54 " =    1.210
peak=    4.795 closest distance to " CB  SER A  63 " =    1.315
peak=    4.783 closest distance to " CB  GLN A 183 " =    1.313
peak=    4.744 closest distance to " CG  PRO A 198 " =    1.270
peak=    4.731 closest distance to " O   HOH Z  97 " =    1.872
peak=    4.727 closest distance to " O   HOH Z 263 " =    1.518
peak=    4.716 closest distance to " CD1AILE A 234 " =    1.014
peak=    4.711 closest distance to " CG  LEU A 228 " =    1.238
peak=    4.688 closest distance to " O   HOH Z  48 " =    1.683
peak=    4.684 closest distance to " NE2 GLN A  11 " =    1.121
peak=    4.621 closest distance to " CB  VAL A 230 " =    1.214
peak=    4.613 closest distance to " O   HOH Z 411 " =    3.767
peak=    4.581 closest distance to " O   HOH Z 199 " =    1.090
peak=    4.560 closest distance to " CB  SER A   3 " =    1.397
peak=    4.557 closest distance to " O   HOH Z 193 " =    1.771
peak=    4.554 closest distance to " CB  ASN A 148 " =    1.387
peak=    4.546 closest distance to " CB  PRO A  54 " =    0.853
peak=    4.512 closest distance to " O   HOH Z 427 " =    2.884
peak=    4.497 closest distance to " O   HOH Z 260 " =    1.221
peak=    4.423 closest distance to " CD2 LEU A 228 " =    1.220
peak=    4.410 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.405 closest distance to " O   HOH Z  59 " =    2.196
peak=    4.386 closest distance to " O   HOH Z 368 " =    2.168
peak=    4.383 closest distance to " O   HOH Z 316 " =    2.367
peak=    4.344 closest distance to " O   SER A  87 " =    2.239
peak=    4.282 closest distance to " O   HOH Z 192 " =    1.298
peak=    4.267 closest distance to " O   HOH Z 423 " =    1.884
peak=    4.246 closest distance to " CB  TYR A 169 " =    0.997
peak=    4.245 closest distance to " CG1BVAL A  72 " =    1.514
peak=    4.242 closest distance to " O   HOH Z 134 " =    1.506
peak=    4.236 closest distance to " C   PRO A 198 " =    1.509
peak=    4.211 closest distance to " O   HOH Z 346 " =    1.543
peak=    4.183 closest distance to " O   HOH Z 128 " =    2.023
peak=    4.172 closest distance to " O   HOH Z 389 " =    1.825
peak=    4.166 closest distance to " O   ASP A 132 " =    3.809
peak=    4.143 closest distance to " O   HOH Z 316 " =    0.927
peak=    4.141 closest distance to " O   HOH Z 334 " =    2.952
peak=    4.135 closest distance to " CB  VAL A 296 " =    1.043
peak=    4.123 closest distance to " O   HOH Z 214 " =    2.232
peak=    4.116 closest distance to " OD1 ASN A  69 " =    2.557
peak=    4.108 closest distance to " O   HOH Z 108 " =    1.492
peak=    4.086 closest distance to " O   HOH Z  92 " =    0.950
peak=    4.082 closest distance to " O   HOH Z 371 " =    3.275
peak=    4.064 closest distance to " OD2 ASP A 286 " =    2.770
peak=    4.063 closest distance to " NH2BARG A 102 " =    0.918
peak=    4.055 closest distance to " CB  TRP A 179 " =    1.288
peak=    4.049 closest distance to " CG  ARG A  66 " =    2.739
peak=    4.046 closest distance to " O   HOH Z 276 " =    1.357
peak=    4.035 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.034 closest distance to " O   HOH Z 272 " =    1.859
peak=    4.027 closest distance to " O   HOH Z  20 " =    1.829
peak=    4.026 closest distance to " O   HOH Z 126 " =    1.918
peak=    4.024 closest distance to " O   HOH Z 118 " =    1.579
peak=    4.018 closest distance to " O   HOH Z 133 " =    1.616
peak=    4.017 closest distance to " CB  LEU A 228 " =    1.397
peak=    4.005 closest distance to " O   HOH Z 189 " =    2.346
peak=    4.003 closest distance to " CB  GLU A 152 " =    1.134
peak=    3.993 closest distance to " O   HOH Z  93 " =    2.646
peak=    3.992 closest distance to " O   HOH Z 298 " =    1.963
peak=    3.989 closest distance to " O   HOH Z 136 " =    1.293
peak=    3.972 closest distance to " O   HOH Z 232 " =    2.112
peak=    3.962 closest distance to " CB  GLU A 277 " =    3.587
peak=    3.957 closest distance to " O   HOH Z  15 " =    2.217
peak=    3.952 closest distance to " O   HOH Z 295 " =    1.559
peak=    3.938 closest distance to " O   HOH Z 236 " =    1.928
peak=    3.938 closest distance to " O   HOH Z 116 " =    1.710
peak=    3.924 closest distance to " O   HOH Z  88 " =    3.274
peak=    3.924 closest distance to " CA  ALA A  21 " =    1.235
peak=    3.923 closest distance to " NZ  LYS A 117 " =    3.179
peak=    3.915 closest distance to " CA  TYR A  30 " =    1.002
peak=    3.902 closest distance to " O   HOH Z 217 " =    1.530
peak=    3.890 closest distance to " CB  GLU A 128 " =    1.205
peak=    3.886 closest distance to " O   HOH Z 155 " =    1.634
peak=    3.883 closest distance to " O   HOH Z  61 " =    1.511
peak=    3.883 closest distance to " CG2 THR A 221 " =    1.031
peak=    3.875 closest distance to " CD  LYS A 119 " =    1.341
peak=    3.854 closest distance to " O   HOH Z 344 " =    2.782
peak=    3.846 closest distance to " O   HOH Z   4 " =    1.619
peak=    3.835 closest distance to " O   HOH Z  80 " =    1.817
peak=    3.828 closest distance to " NE2 GLN A  58 " =    5.819
peak=    3.824 closest distance to " CB  VAL A 265 " =    1.238
peak=    3.820 closest distance to " O   HOH Z  55 " =    2.364
peak=    3.813 closest distance to " O   HOH Z 426 " =    1.467
peak=    3.799 closest distance to " CB  VAL A 202 " =    1.681
peak=    3.776 closest distance to " O   HOH Z 345 " =    3.102
peak=    3.763 closest distance to " CA  THR A 221 " =    0.887
peak=    3.761 closest distance to " O   HOH Z 374 " =    3.038
peak=    3.761 closest distance to " O   HOH Z 112 " =    1.467
peak=    3.755 closest distance to " CB  PRO A 198 " =    1.013
peak=    3.753 closest distance to " NH1 ARG A  14 " =    1.043
peak=    3.748 closest distance to " CG  PRO A 243 " =    1.224
peak=    3.747 closest distance to " CD  ARG A 269 " =    1.016
peak=    3.741 closest distance to " O   HOH Z 215 " =    1.554
peak=    3.738 closest distance to " CD2 LEU A 255 " =    1.218
peak=    3.735 closest distance to " O   HOH Z  48 " =    1.636
peak=    3.734 closest distance to " O   MET A 105 " =    1.785
peak=    3.732 closest distance to " O   HOH Z  78 " =    1.708
peak=    3.728 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.722 closest distance to " O   HOH Z 369 " =    1.945
peak=    3.714 closest distance to " O   HOH Z  40 " =    1.435
peak=    3.708 closest distance to " O   HOH Z  68 " =    1.786
peak=    3.701 closest distance to " CA  ALA A 295 " =    1.047
peak=    3.699 closest distance to " CA  ASP A 191 " =    0.899
peak=    3.699 closest distance to " O   HOH Z 203 " =    1.611
peak=    3.699 closest distance to " O   HOH Z 126 " =    1.568
peak=    3.697 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.692 closest distance to " CA  VAL A  41 " =    0.887
peak=    3.690 closest distance to " O   TRP A 274 " =    1.896
peak=    3.667 closest distance to " O   HOH Z 236 " =    1.665
peak=    3.665 closest distance to " O   ALA A 158 " =    1.285
peak=    3.662 closest distance to " OE1 GLU A   2 " =    2.099
peak=    3.642 closest distance to " CB  GLN A  88 " =    1.225
peak=    3.639 closest distance to " CG2 VAL A 257 " =    0.786
peak=    3.634 closest distance to " CG2 VAL A 174 " =    1.293
peak=    3.632 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.625 closest distance to " O   HOH Z 359 " =    2.108
peak=    3.621 closest distance to " CZ AARG A 102 " =    1.895
peak=    3.614 closest distance to " O   HOH Z  30 " =    1.288
peak=    3.613 closest distance to " O   HOH Z  54 " =    1.577
peak=    3.612 closest distance to " NH2 ARG A 156 " =    1.170
peak=    3.589 closest distance to " O   HOH Z 326 " =    1.426
peak=    3.587 closest distance to " O   HOH Z 394 " =    1.593
peak=    3.586 closest distance to " CG  GLN A  58 " =    2.643
peak=    3.583 closest distance to " O   HOH Z 403 " =    1.672
peak=    3.583 closest distance to " O   HOH Z 245 " =    1.385
peak=    3.582 closest distance to " O   HOH Z 331 " =    1.363
peak=    3.582 closest distance to " CG AARG A 275 " =    1.117
peak=    3.571 closest distance to " O   THR A  31 " =    1.553
peak=    3.571 closest distance to " OD1 ASN A 217 " =    1.732
peak=    3.569 closest distance to " O   HOH Z  21 " =    1.880
peak=    3.567 closest distance to " O   HOH Z 423 " =    3.293
peak=    3.565 closest distance to " O   HOH Z   3 " =    1.550
peak=    3.564 closest distance to " CD1 LEU A 300 " =    1.116
peak=    3.562 closest distance to " O   HOH Z 120 " =    1.014
peak=    3.560 closest distance to " O   HOH Z  63 " =    2.203
peak=    3.559 closest distance to " OG  SER A  22 " =    2.825
peak=    3.556 closest distance to " O   HOH Z 419 " =    1.631
peak=    3.550 closest distance to " O   HOH Z  43 " =    2.254
peak=    3.548 closest distance to " O   HOH Z 271 " =    1.951
peak=    3.546 closest distance to " CA  LEU A 282 " =    1.068
peak=    3.544 closest distance to " CA  VAL A 126 " =    1.069
peak=    3.537 closest distance to " CA  ASN A  74 " =    1.278
peak=    3.537 closest distance to " CB  LEU A 255 " =    0.767
peak=    3.533 closest distance to " O   HOH Z  66 " =    2.100
peak=    3.531 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.531 closest distance to " O   HOH Z 108 " =    1.826
peak=    3.529 closest distance to " O   HOH Z 334 " =    1.500
peak=    3.529 closest distance to " O   HOH Z 171 " =    2.606
peak=    3.522 closest distance to " CA  GLY A 211 " =    1.219
peak=    3.521 closest distance to " O   HOH Z 207 " =    2.107
peak=    3.520 closest distance to " NE2 GLN A  58 " =    4.128
peak=    3.517 closest distance to " O   HOH Z 143 " =    1.154
peak=    3.514 closest distance to " O   HOH Z  44 " =    1.763
peak=    3.514 closest distance to " CA  LYS A 117 " =    1.243
peak=    3.511 closest distance to " OE1 GLN A  11 " =    1.754
peak=    3.511 closest distance to " OD1 ASP A 231 " =    1.846
peak=    3.509 closest distance to " CA  LEU A 101 " =    1.604
peak=    3.509 closest distance to " CB  SER A 273 " =    0.852
peak=    3.508 closest distance to " O   HOH Z 284 " =    1.406
peak=    3.503 closest distance to " O   HOH Z 193 " =    2.066
peak=    3.496 closest distance to " CB  ARG A  79 " =    1.350
peak=    3.495 closest distance to " CD BLYS A 290 " =    1.075
peak=    3.495 closest distance to " O   HOH Z 407 " =    3.751
peak=    3.483 closest distance to " O   HOH Z 374 " =    2.432
peak=    3.483 closest distance to " CA  ALA A 248 " =    1.153
peak=    3.481 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.478 closest distance to " O   HOH Z 373 " =    1.578
peak=    3.477 closest distance to " O   HOH Z 197 " =    2.600
peak=    3.472 closest distance to " O   HOH Z 102 " =    1.208
peak=    3.470 closest distance to " CG  MET A 188 " =    1.365
peak=    3.464 closest distance to " CB BVAL A  41 " =    1.180
peak=    3.457 closest distance to " CB  ALA A   9 " =    1.558
peak=    3.456 closest distance to " CB  TRP A 266 " =    1.028
peak=    3.451 closest distance to " O   HOH Z 213 " =    1.886
peak=    3.450 closest distance to " O   HOH Z  49 " =    1.951
peak=    3.448 closest distance to " CB  ARG A 139 " =    0.851
peak=    3.447 closest distance to " NZ  LYS A  76 " =    1.276
peak=    3.444 closest distance to " O   HOH Z 366 " =    2.915
peak=    3.443 closest distance to " CD  LYS A 166 " =    1.485
peak=    3.441 closest distance to " O   HOH Z 403 " =    1.410
peak=    3.439 closest distance to " NH2BARG A 145 " =    2.227
peak=    3.436 closest distance to " O   HOH Z 183 " =    1.243
peak=    3.433 closest distance to " CA  MET A  40 " =    1.044
peak=    3.431 closest distance to " O   HOH Z 322 " =    2.089
peak=    3.430 closest distance to " O   HOH Z  30 " =    1.926
peak=    3.429 closest distance to " O   HOH Z 273 " =    2.569
peak=    3.426 closest distance to " O   HOH Z  49 " =    2.461
peak=    3.424 closest distance to " O   HOH Z 151 " =    1.637
peak=    3.414 closest distance to " CG  LEU A 167 " =    1.137
peak=    3.410 closest distance to " CA  ALA A  51 " =    1.065
peak=    3.410 closest distance to " C   LYS A 290 " =    1.294
peak=    3.405 closest distance to " O   HOH Z  63 " =    1.153
peak=    3.405 closest distance to " CA  ALA A 160 " =    0.758
peak=    3.404 closest distance to " O   HOH Z 283 " =    2.004
peak=    3.394 closest distance to " C   ALA A 299 " =    0.950
peak=    3.392 closest distance to " CA  ASP A 140 " =    1.150
peak=    3.388 closest distance to " CB  ALA A 291 " =    1.356
peak=    3.386 closest distance to " O   HOH Z 344 " =    1.581
peak=    3.386 closest distance to " O   HOH Z 152 " =    1.613
peak=    3.378 closest distance to " CB  MET A  47 " =    1.463
peak=    3.378 closest distance to " O   HOH Z  19 " =    1.993
peak=    3.376 closest distance to " O   HOH Z 197 " =    2.077
peak=    3.375 closest distance to " O   HOH Z 352 " =    1.267
peak=    3.370 closest distance to " O   HOH Z 114 " =    1.263
peak=    3.370 closest distance to " O   HOH Z 426 " =    3.044
peak=    3.368 closest distance to " CD1 ILE A  33 " =    1.635
peak=    3.364 closest distance to " O   HOH Z 422 " =    2.606
peak=    3.364 closest distance to " O   HOH Z 193 " =    1.452
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.222
peak=    3.358 closest distance to " O   HOH Z 261 " =    1.679
peak=    3.355 closest distance to " CG1 ILE A  33 " =    1.297
peak=    3.354 closest distance to " OG BSER A 164 " =    2.171
peak=    3.350 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.349 closest distance to " O   HOH Z 407 " =    2.577
peak=    3.347 closest distance to " CB  ALA A 248 " =    1.000
peak=    3.336 closest distance to " O   HOH Z 123 " =    1.007
peak=    3.334 closest distance to " O   HOH Z 357 " =    2.021
peak=    3.333 closest distance to " CA  ALA A 233 " =    1.470
peak=    3.333 closest distance to " O   HOH Z  11 " =    1.252
peak=    3.333 closest distance to " O   HOH Z 189 " =    2.965
peak=    3.328 closest distance to " CB  TYR A  30 " =    1.509
peak=    3.327 closest distance to " OG1 THR A 294 " =    2.340
peak=    3.326 closest distance to " O   HOH Z 215 " =    1.439
peak=    3.323 closest distance to " CZ  PHE A 192 " =    1.092
peak=    3.322 closest distance to " CA  ASN A 176 " =    1.176
peak=    3.322 closest distance to " O   HOH Z 184 " =    1.999
peak=    3.322 closest distance to " O   SER A  26 " =    1.612
peak=    3.321 closest distance to " O   GLN A 278 " =    1.253
peak=    3.320 closest distance to " O   HOH Z 383 " =    2.105
peak=    3.319 closest distance to " O   HOH Z  71 " =    1.197
peak=    3.319 closest distance to " O   HOH Z 281 " =    4.355
peak=    3.318 closest distance to " O   ASN A 217 " =    1.285
peak=    3.316 closest distance to " CB  SER A  62 " =    1.212
peak=    3.315 closest distance to " O   HOH Z  85 " =    1.237
peak=    3.313 closest distance to " CG2 ILE A 120 " =    1.295
peak=    3.313 closest distance to " O   HOH Z 155 " =    2.637
peak=    3.312 closest distance to " O   HOH Z 191 " =    1.524
peak=    3.311 closest distance to " CB  GLN A  89 " =    1.084
peak=    3.308 closest distance to " CD2 TYR A 186 " =    1.018
peak=    3.308 closest distance to " O   HOH Z  48 " =    2.218
peak=    3.305 closest distance to " CA  GLN A 194 " =    1.170
peak=    3.296 closest distance to " O   HOH Z 133 " =    2.048
peak=    3.294 closest distance to " CB  ASN A 148 " =    1.907
peak=    3.294 closest distance to " O   HOH Z  63 " =    1.428
peak=    3.288 closest distance to " O   HOH Z  96 " =    2.275
peak=    3.282 closest distance to " O   HOH Z 355 " =    1.810
peak=    3.280 closest distance to " O   HOH Z 367 " =    3.584
peak=    3.279 closest distance to " O   HOH Z 402 " =    1.405
peak=    3.275 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.273 closest distance to " O   HOH Z 345 " =    1.735
peak=    3.272 closest distance to " O   HOH Z  50 " =    1.827
peak=    3.270 closest distance to " C   SER A  32 " =    1.117
peak=    3.266 closest distance to " CG  MET A  93 " =    1.068
peak=    3.266 closest distance to " O   HOH Z  50 " =    1.393
peak=    3.265 closest distance to " CD2 LEU A 282 " =    1.886
peak=    3.249 closest distance to " NH2 ARG A  79 " =    1.342
peak=    3.247 closest distance to " CA  ASN A 215 " =    1.245
peak=    3.245 closest distance to " CB  SER A 141 " =    1.085
peak=    3.240 closest distance to " CB  THR A  31 " =    1.656
peak=    3.226 closest distance to " NH2BARG A 190 " =    1.809
peak=    3.226 closest distance to " O   HOH Z  66 " =    2.273
peak=    3.224 closest distance to " O   HOH Z 261 " =    1.546
peak=    3.223 closest distance to " C   ALA A   1 " =    1.646
peak=    3.223 closest distance to " O   HOH Z 126 " =    1.885
peak=    3.221 closest distance to " CB  ARG A 102 " =    0.822
peak=    3.220 closest distance to " O   HOH Z  10 " =    1.879
peak=    3.218 closest distance to " O   HOH Z 270 " =    1.764
peak=    3.215 closest distance to " CZ2 TRP A 179 " =    1.681
peak=    3.215 closest distance to " O   ALA A 165 " =    1.331
peak=    3.211 closest distance to " CE  MET A  93 " =    1.442
peak=    3.208 closest distance to " O   HOH Z 420 " =    2.001
peak=    3.207 closest distance to " O   HOH Z 133 " =    3.542
peak=    3.205 closest distance to " ND2 ASN A 187 " =    1.671
peak=    3.201 closest distance to " N   GLY A  57 " =    1.435
peak=    3.201 closest distance to " CG  MET A 185 " =    1.226
peak=    3.193 closest distance to " O   HOH Z 329 " =    3.331
peak=    3.191 closest distance to " CA  TYR A 116 " =    1.593
peak=    3.191 closest distance to " CB  ALA A 100 " =    1.286
peak=    3.189 closest distance to " O   HOH Z 280 " =    2.280
peak=    3.188 closest distance to " CD1 LEU A  96 " =    0.876
peak=    3.188 closest distance to " O   HOH Z 280 " =    1.509
peak=    3.187 closest distance to " CD2 HIS A  81 " =    1.147
peak=    3.182 closest distance to " OD1 ASP A 286 " =    1.627
peak=    3.182 closest distance to " O   HOH Z 175 " =    3.468
peak=    3.182 closest distance to " CA  PHE A 283 " =    1.317
peak=    3.179 closest distance to " O   ALA A   1 " =    1.498
peak=    3.177 closest distance to " O   HOH Z 141 " =    1.508
peak=    3.177 closest distance to " CA  TYR A 186 " =    1.349
peak=    3.171 closest distance to " CB  ARG A 190 " =    1.710
peak=    3.162 closest distance to " NH1 ARG A  56 " =    1.053
peak=    3.159 closest distance to " O   HOH Z 359 " =    3.705
peak=    3.158 closest distance to " CB  ASN A 142 " =    1.103
peak=    3.156 closest distance to " O   THR A 220 " =    1.355
peak=    3.154 closest distance to " O   HOH Z   9 " =    1.625
peak=    3.154 closest distance to " CB  ALA A 161 " =    0.924
peak=    3.154 closest distance to " O   HOH Z 209 " =    2.305
peak=    3.152 closest distance to " CB  LYS A 193 " =    1.184
peak=    3.151 closest distance to " O   HOH Z 334 " =    1.360
peak=    3.146 closest distance to " O   HOH Z 290 " =    1.106
peak=    3.143 closest distance to " N   ARG A 156 " =    1.354
peak=    3.141 closest distance to " O   HOH Z 111 " =    3.731
peak=    3.141 closest distance to " CA  ARG A  36 " =    1.071
peak=    3.138 closest distance to " O   HOH Z 411 " =    1.822
peak=    3.129 closest distance to " CA  THR A 264 " =    0.768
peak=    3.129 closest distance to " O   HOH Z 279 " =    2.141
peak=    3.126 closest distance to " OG  SER A 206 " =    1.235
peak=    3.122 closest distance to " CG2 ILE A  20 " =    1.527
peak=    3.117 closest distance to " CB  LEU A 143 " =    1.128
peak=    3.117 closest distance to " O   HOH Z 148 " =    3.019
peak=    3.116 closest distance to " OD2 ASP A 298 " =    4.013
peak=    3.116 closest distance to " CA  ALA A 158 " =    1.104
peak=    3.110 closest distance to " CD1 ILE A 199 " =    0.968
peak=    3.109 closest distance to " O   HOH Z 267 " =    2.229
peak=    3.104 closest distance to " O   HOH Z 364 " =    2.324
peak=    3.104 closest distance to " CB  ASN A  39 " =    0.783
peak=    3.103 closest distance to " N   ASN A  39 " =    1.268
peak=    3.103 closest distance to " O   HOH Z 327 " =    2.048
peak=    3.101 closest distance to " CD1 TRP A 266 " =    1.162
peak=    3.099 closest distance to " O   HOH Z 163 " =    1.330
peak=    3.092 closest distance to " O   HOH Z 291 " =    1.625
peak=    3.084 closest distance to " O   HOH Z 381 " =    1.518
peak=    3.066 closest distance to " CA  ARG A 195 " =    1.172
peak=    3.054 closest distance to " CA  ALA A 154 " =    1.239
peak=    3.043 closest distance to " O   HOH Z  85 " =    1.953
peak=    3.038 closest distance to " O   HOH Z 380 " =    2.093
peak=    3.024 closest distance to " O   HOH Z 211 " =    2.218

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.740 - 5.314
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 185
   mapped sites are within: 0.740 - 5.314

peak=   -4.999 closest distance to " CG2 VAL A 230 " =    0.854
peak=   -4.412 closest distance to " O   ILE A 109 " =    2.606
peak=   -4.338 closest distance to " O   HOH Z 198 " =    2.492
peak=   -4.325 closest distance to " OG ASER A 134 " =    1.204
peak=   -4.312 closest distance to " O   HOH Z  92 " =    1.278
peak=   -4.286 closest distance to " O   HOH Z 266 " =    4.249
peak=   -4.255 closest distance to " O   HOH Z  13 " =    1.132
peak=   -4.212 closest distance to " O   HOH Z 274 " =    2.661
peak=   -4.137 closest distance to " CA  SER A 164 " =    2.068
peak=   -4.111 closest distance to " OG1 THR A   4 " =    1.869
peak=   -4.070 closest distance to " O   HOH Z  11 " =    1.693
peak=   -4.020 closest distance to " N   SER A 276 " =    1.311
peak=   -4.020 closest distance to " CD  ARG A 139 " =    1.680
peak=   -3.997 closest distance to " CD  ARG A 156 " =    2.052
peak=   -3.920 closest distance to " C   ALA A 158 " =    1.148
peak=   -3.920 closest distance to " SG  CYS A 254 " =    3.169
peak=   -3.906 closest distance to " O   HOH Z  43 " =    1.644
peak=   -3.888 closest distance to " C   ASN A 187 " =    1.835
peak=   -3.888 closest distance to " O   HOH Z 377 " =    1.711
peak=   -3.867 closest distance to " OE2 GLU A   2 " =    1.840
peak=   -3.865 closest distance to " O   HOH Z 290 " =    1.024
peak=   -3.842 closest distance to " N   GLN A  58 " =    1.778
peak=   -3.839 closest distance to " O   HOH Z 231 " =    1.599
peak=   -3.835 closest distance to " CG  LYS A 193 " =    2.364
peak=   -3.835 closest distance to " CD2 LEU A 237 " =    2.669
peak=   -3.823 closest distance to " CD1 LEU A 228 " =    2.291
peak=   -3.800 closest distance to " O   HOH Z  19 " =    2.109
peak=   -3.788 closest distance to " O   HOH Z 166 " =    1.480
peak=   -3.787 closest distance to " CB  TYR A  15 " =    2.144
peak=   -3.786 closest distance to " CD  LYS A 289 " =    2.499
peak=   -3.754 closest distance to " O   HOH Z 166 " =    1.806
peak=   -3.740 closest distance to " O   HOH Z 423 " =    2.253
peak=   -3.739 closest distance to " O   HOH Z 350 " =    2.023
peak=   -3.720 closest distance to " O   ASN A 187 " =    1.402
peak=   -3.702 closest distance to " CG  ASP A  50 " =    2.282
peak=   -3.697 closest distance to " O   ALA A 161 " =    1.497
peak=   -3.695 closest distance to " O   HOH Z  98 " =    1.650
peak=   -3.690 closest distance to " CD2 LEU A 300 " =    2.844
peak=   -3.688 closest distance to " CG  GLN A 223 " =    2.320
peak=   -3.667 closest distance to " CD1 LEU A 101 " =    2.638
peak=   -3.663 closest distance to " ND2 ASN A  45 " =    1.091
peak=   -3.658 closest distance to " CD  GLN A  88 " =    2.257
peak=   -3.654 closest distance to " CB  SER A 134 " =    1.767
peak=   -3.651 closest distance to " ND2 ASN A  60 " =    1.374
peak=   -3.644 closest distance to " N   ALA A 226 " =    2.079
peak=   -3.644 closest distance to " CB  ALA A  51 " =    1.790
peak=   -3.638 closest distance to " O   HOH Z 234 " =    4.182
peak=   -3.625 closest distance to " O   HOH Z 151 " =    1.384
peak=   -3.625 closest distance to " O   HOH Z 407 " =    3.063
peak=   -3.624 closest distance to " NH2AARG A 275 " =    5.254
peak=   -3.623 closest distance to " NH2 ARG A  66 " =    1.637
peak=   -3.611 closest distance to " NH2 ARG A  79 " =    1.890
peak=   -3.597 closest distance to " CD2 LEU A 167 " =    1.754
peak=   -3.593 closest distance to " O   HOH Z  71 " =    1.085
peak=   -3.587 closest distance to " O   HOH Z 103 " =    1.759
peak=   -3.585 closest distance to " CG  LEU A 228 " =    1.026
peak=   -3.578 closest distance to " OG BSER A 134 " =    1.142
peak=   -3.577 closest distance to " O   HOH Z 266 " =    4.521
peak=   -3.567 closest distance to " N   ALA A 248 " =    1.693
peak=   -3.564 closest distance to " CZ  TYR A 169 " =    1.794
peak=   -3.556 closest distance to " CB  CYS A 254 " =    2.469
peak=   -3.545 closest distance to " O   HOH Z 388 " =    1.886
peak=   -3.534 closest distance to " CG  MET A 105 " =    0.901
peak=   -3.533 closest distance to " O   GLY A 196 " =    1.065
peak=   -3.529 closest distance to " O   VAL A  67 " =    2.734
peak=   -3.528 closest distance to " O   HOH Z  17 " =    1.342
peak=   -3.520 closest distance to " CB  ALA A 248 " =    1.920
peak=   -3.519 closest distance to " CB  PRO A 243 " =    2.655
peak=   -3.506 closest distance to " CA  ASP A 298 " =    1.016
peak=   -3.499 closest distance to " C   HIS A 108 " =    1.148
peak=   -3.495 closest distance to " OG1 THR A  82 " =    1.449
peak=   -3.494 closest distance to " C   ASN A 285 " =    2.502
peak=   -3.491 closest distance to " CE2 TYR A  30 " =    2.757
peak=   -3.490 closest distance to " O   HOH Z 241 " =    1.379
peak=   -3.486 closest distance to " CB  ALA A  43 " =    2.267
peak=   -3.483 closest distance to " O   HOH Z 292 " =    4.378
peak=   -3.482 closest distance to " O   HOH Z 147 " =    2.075
peak=   -3.482 closest distance to " O   ALA A 100 " =    2.488
peak=   -3.472 closest distance to " CA  ASN A 127 " =    1.021
peak=   -3.471 closest distance to " CG  ASP A 231 " =    0.851
peak=   -3.470 closest distance to " CG  GLU A  53 " =    1.484
peak=   -3.466 closest distance to " CG  GLU A 277 " =    1.127
peak=   -3.459 closest distance to " O   HOH Z  52 " =    1.732
peak=   -3.457 closest distance to " CD  GLN A  88 " =    1.094
peak=   -3.454 closest distance to " CD2 TYR A 293 " =    2.115
peak=   -3.453 closest distance to " N   THR A 157 " =    1.579
peak=   -3.448 closest distance to " O   PRO A 198 " =    1.356
peak=   -3.445 closest distance to " OD1 ASN A 249 " =    0.987
peak=   -3.442 closest distance to " CD1 PHE A  59 " =    1.836
peak=   -3.423 closest distance to " N   GLY A 133 " =    1.802
peak=   -3.423 closest distance to " O   HOH Z 308 " =    1.742
peak=   -3.421 closest distance to " O   HOH Z 435 " =    2.770
peak=   -3.414 closest distance to " CA  TYR A  68 " =    2.734
peak=   -3.405 closest distance to " O   HOH Z  63 " =    0.740
peak=   -3.397 closest distance to " O   LEU A 228 " =    2.360
peak=   -3.392 closest distance to " CG2 VAL A 112 " =    2.593
peak=   -3.381 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.369 closest distance to " CG  TRP A 266 " =    1.553
peak=   -3.358 closest distance to " CB  ASN A  39 " =    2.187
peak=   -3.353 closest distance to " O   HOH Z 310 " =    1.580
peak=   -3.352 closest distance to " O   SER A 271 " =    1.948
peak=   -3.342 closest distance to " OG  SER A 206 " =    1.802
peak=   -3.340 closest distance to " CG2 VAL A 296 " =    1.492
peak=   -3.335 closest distance to " CA  VAL A 232 " =    2.394
peak=   -3.330 closest distance to " O   HOH Z 283 " =    1.752
peak=   -3.323 closest distance to " O   HOH Z  10 " =    1.525
peak=   -3.321 closest distance to " O   HOH Z 165 " =    2.128
peak=   -3.317 closest distance to " O   SER A 135 " =    1.572
peak=   -3.307 closest distance to " O   HOH Z 385 " =    1.959
peak=   -3.307 closest distance to " O   ALA A   8 " =    1.740
peak=   -3.306 closest distance to " ND2 ASN A  39 " =    1.392
peak=   -3.303 closest distance to " O   HOH Z 352 " =    1.036
peak=   -3.300 closest distance to " O   HOH Z 396 " =    1.534
peak=   -3.296 closest distance to " O   ALA A  51 " =    1.488
peak=   -3.292 closest distance to " CD1 LEU A   5 " =    2.350
peak=   -3.291 closest distance to " ND2 ASN A 249 " =    2.177
peak=   -3.290 closest distance to " C   LEU A 143 " =    1.247
peak=   -3.289 closest distance to " O   HOH Z 339 " =    1.823
peak=   -3.285 closest distance to " CD1 ILE A 263 " =    2.455
peak=   -3.279 closest distance to " CB  GLN A  55 " =    1.496
peak=   -3.279 closest distance to " CE3 TRP A 150 " =    1.943
peak=   -3.276 closest distance to " CE3 TRP A  70 " =    1.629
peak=   -3.276 closest distance to " OD2 ASP A  50 " =    1.419
peak=   -3.274 closest distance to " O   HOH Z  97 " =    1.809
peak=   -3.273 closest distance to " CH2 TRP A 179 " =    1.317
peak=   -3.271 closest distance to " O   HOH Z 411 " =    3.581
peak=   -3.269 closest distance to " O   GLY A 211 " =    1.357
peak=   -3.269 closest distance to " O   GLU A  44 " =    1.746
peak=   -3.259 closest distance to " CG  ASN A  45 " =    1.688
peak=   -3.258 closest distance to " CD2 PHE A  61 " =    1.846
peak=   -3.257 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.252 closest distance to " CD1 TRP A 179 " =    1.132
peak=   -3.247 closest distance to " O   ALA A 160 " =    1.231
peak=   -3.247 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.246 closest distance to " NE2 GLN A  73 " =    1.707
peak=   -3.244 closest distance to " OD2 ASP A 171 " =    1.754
peak=   -3.243 closest distance to " OXT GLY A 302 " =    3.194
peak=   -3.241 closest distance to " O   MET A  40 " =    2.702
peak=   -3.241 closest distance to " CG1 VAL A 296 " =    1.300
peak=   -3.238 closest distance to " O   HOH Z 252 " =    4.161
peak=   -3.238 closest distance to " O   HOH Z 277 " =    1.617
peak=   -3.238 closest distance to " CD1 LEU A  96 " =    2.405
peak=   -3.238 closest distance to " N   ALA A 248 " =    2.158
peak=   -3.236 closest distance to " OE1 GLN A  73 " =    2.336
peak=   -3.236 closest distance to " O   HOH Z  93 " =    1.718
peak=   -3.236 closest distance to " CA  GLY A 203 " =    2.133
peak=   -3.234 closest distance to " NH2 ARG A 159 " =    2.381
peak=   -3.228 closest distance to " O   ASP A 171 " =    2.047
peak=   -3.227 closest distance to " O   HOH Z  60 " =    2.399
peak=   -3.225 closest distance to " CB  SER A 245 " =    2.337
peak=   -3.225 closest distance to " N   GLN A  77 " =    1.539
peak=   -3.222 closest distance to " CG  PHE A 283 " =    2.824
peak=   -3.218 closest distance to " CE  MET A 105 " =    2.067
peak=   -3.206 closest distance to " CG  PRO A 163 " =    2.618
peak=   -3.205 closest distance to " OG  SER A  26 " =    1.148
peak=   -3.204 closest distance to " CB  ALA A 227 " =    2.371
peak=   -3.200 closest distance to " CB  PRO A 163 " =    2.690
peak=   -3.199 closest distance to " CG  GLU A 152 " =    2.426
peak=   -3.197 closest distance to " OD1 ASP A 200 " =    1.249
peak=   -3.196 closest distance to " O   HOH Z 265 " =    1.868
peak=   -3.183 closest distance to " O   HOH Z 191 " =    5.314
peak=   -3.175 closest distance to " N   HIS A 115 " =    2.029
peak=   -3.168 closest distance to " O   HOH Z 430 " =    1.825
peak=   -3.162 closest distance to " C   LEU A 255 " =    1.782
peak=   -3.162 closest distance to " OG  SER A  62 " =    1.473
peak=   -3.159 closest distance to " OD1 ASN A 148 " =    1.704
peak=   -3.150 closest distance to " O   HOH Z 134 " =    2.498
peak=   -3.136 closest distance to " OD1 ASN A 187 " =    1.599
peak=   -3.128 closest distance to " C   ARG A 102 " =    1.421
peak=   -3.127 closest distance to " CD2 LEU A 237 " =    2.663
peak=   -3.122 closest distance to " CG  LEU A 281 " =    1.813
peak=   -3.114 closest distance to " N   GLY A  23 " =    2.015
peak=   -3.112 closest distance to " O   HOH Z 429 " =    1.902
peak=   -3.111 closest distance to " O   HOH Z 341 " =    1.249
peak=   -3.094 closest distance to " NH2 ARG A 156 " =    1.180
peak=   -3.091 closest distance to " CB  ALA A 100 " =    1.871
peak=   -3.087 closest distance to " O   HOH Z  98 " =    1.497
peak=   -3.085 closest distance to " CZ  PHE A  59 " =    1.602
peak=   -3.071 closest distance to " CG2 ILE A  20 " =    2.765
peak=   -3.065 closest distance to " NH1BARG A 190 " =    2.256
peak=   -3.060 closest distance to " CG  PHE A  59 " =    2.199
peak=   -3.043 closest distance to " ND2 ASN A 252 " =    1.690
peak=   -3.035 closest distance to " NH2 ARG A  79 " =    1.743
peak=   -3.000 closest distance to " CB  CYS A 201 " =    2.497

================= 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    :  0.4661 0.4708   6.270007e+00   6.268350e+00
   1_bss:  0.4584 0.4601   6.269191e+00   6.258349e+00
   1_xyz:  0.3808 0.4113   6.153684e+00   6.197470e+00
   1_adp:  0.3344 0.3911   6.073906e+00   6.167297e+00
   1_occ:  0.3340 0.3910   6.073592e+00   6.167475e+00
   2_bss:  0.3310 0.3875   6.073791e+00   6.165685e+00
   2_xyz:  0.2568 0.3171   5.865717e+00   6.016330e+00
   2_adp:  0.2375 0.2979   5.804945e+00   5.970454e+00
   2_occ:  0.2373 0.2980   5.804099e+00   5.970780e+00
   3_bss:  0.2359 0.2956   5.802756e+00   5.968268e+00
   3_xyz:  0.1671 0.2231   5.498264e+00   5.712829e+00
   3_adp:  0.1465 0.2012   5.383404e+00   5.616840e+00
   3_occ:  0.1462 0.2010   5.382639e+00   5.616163e+00
   4_bss:  0.1456 0.1996   5.380321e+00   5.612496e+00
   4_xyz:  0.1288 0.1780   5.270965e+00   5.504180e+00
   4_adp:  0.1251 0.1726   5.242257e+00   5.472867e+00
   4_occ:  0.1249 0.1723   5.241316e+00   5.472180e+00
   5_bss:  0.1249 0.1723   5.241070e+00   5.471985e+00
   5_xyz:  0.1174 0.1631   5.192067e+00   5.426165e+00
   5_adp:  0.1157 0.1625   5.185653e+00   5.424246e+00
   5_occ:  0.1156 0.1625   5.185370e+00   5.424182e+00
   5_bss:  0.1158 0.1630   5.187224e+00   5.426976e+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:  0.360  20.001   6.771   7.779   9.596   0.000   0.000   0.000
   1_xyz:  0.360  20.001   6.771   7.779   9.596   0.000   0.000   0.000
   1_adp:  0.360  20.001   6.771   7.779   9.596   0.000   0.000   0.000
   1_occ:  0.360  20.001   6.771   7.779   9.596   0.000   0.000   0.000
   2_bss:  0.327  39.492   3.344   4.191   6.521   0.000   0.000   0.000
   2_xyz:  0.327  39.492   3.344   4.191   6.521   0.000   0.000   0.000
   2_adp:  0.327  39.492   3.344   4.191   6.521   0.000   0.000   0.000
   2_occ:  0.327  39.492   3.344   4.191   6.521   0.000   0.000   0.000
   3_bss:  0.313  40.461   2.015   2.910   4.069   0.000   0.000   0.000
   3_xyz:  0.313  40.461   2.015   2.910   4.069   0.000   0.000   0.000
   3_adp:  0.313  40.461   2.015   2.910   4.069   0.000   0.000   0.000
   3_occ:  0.313  40.461   2.015   2.910   4.069   0.000   0.000   0.000
   4_bss:  0.323  40.461   1.444   1.894   2.339   0.000   0.000   0.000
   4_xyz:  0.323  40.461   1.444   1.894   2.339   0.000   0.000   0.000
   4_adp:  0.323  40.461   1.444   1.894   2.339   0.000   0.000   0.000
   4_occ:  0.323  40.461   1.444   1.894   2.339   0.000   0.000   0.000
   5_bss:  0.323  40.461   1.382   1.788   1.989   0.000   0.000   0.000
   5_xyz:  0.323  40.461   1.382   1.788   1.989   0.000   0.000   0.000
   5_adp:  0.323  40.461   1.382   1.788   1.989   0.000   0.000   0.000
   5_occ:  0.323  40.461   1.382   1.788   1.989   0.000   0.000   0.000
   5_bss:  0.318  43.227  -0.287   0.081   0.206   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.683 0.4362  0.5143    68411.386
   1_bss:  56.831 0.4315  0.6356    65241.696
   1_xyz:  48.356 0.5381  0.7824    49966.532
   1_adp:  44.720 0.5840  0.8871    44910.112
   1_occ:  44.760 0.5835  0.8866    45058.214
   2_bss:  44.456 0.5872  0.7945    44681.347
   2_xyz:  33.951 0.7122  0.9436    27793.802
   2_adp:  31.134 0.7448  0.9823    24318.578
   2_occ:  31.123 0.7449  0.9820    24299.018
   3_bss:  30.915 0.7470  0.9262    24057.003
   3_xyz:  21.912 0.8426  1.0004    12863.184
   3_adp:  19.319 0.8681  1.0112    10550.378
   3_occ:  19.300 0.8683  1.0110    10529.141
   4_bss:  19.193 0.8693  0.9716    10432.007
   4_xyz:  16.711 0.8917  0.9823     8196.537
   4_adp:  15.885 0.8993  0.9836     7675.554
   4_occ:  15.867 0.8995  0.9835     7665.815
   5_bss:  15.862 0.8995  0.9774     7666.952
   5_xyz:  14.944 0.9073  0.9797     6920.819
   5_adp:  14.870 0.9081  0.9767     6885.872
   5_occ:  14.863 0.9081  0.9766     6888.225
   5_bss:  14.927 0.9077  0.9786     6960.877
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3410e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3410e+01
   1_xyz:   1.640  0.013  0.105 18.160  0.007  4.108   1.3471e-01
   1_adp:   1.640  0.013  0.105 18.160  0.007  4.108   1.3471e-01
   1_occ:   1.640  0.013  0.105 18.160  0.007  4.108   1.3471e-01
   2_bss:   1.640  0.013  0.105 18.160  0.007  4.108   1.3471e-01
   2_xyz:   1.093  0.008  0.077 16.187  0.004  4.114   7.5261e-02
   2_adp:   1.093  0.008  0.077 16.187  0.004  4.114   7.5261e-02
   2_occ:   1.093  0.008  0.077 16.187  0.004  4.114   7.5261e-02
   3_bss:   1.093  0.008  0.077 16.187  0.004  4.114   7.5261e-02
   3_xyz:   1.191  0.008  0.087 15.869  0.004  4.128   7.8218e-02
   3_adp:   1.191  0.008  0.087 15.869  0.004  4.128   7.8218e-02
   3_occ:   1.191  0.008  0.087 15.869  0.004  4.128   7.8218e-02
   4_bss:   1.191  0.008  0.087 15.869  0.004  4.128   7.8218e-02
   4_xyz:   1.000  0.006  0.076 15.541  0.003  4.118   6.0400e-02
   4_adp:   1.000  0.006  0.076 15.541  0.003  4.118   6.0400e-02
   4_occ:   1.000  0.006  0.076 15.541  0.003  4.118   6.0400e-02
   5_bss:   1.000  0.006  0.076 15.541  0.003  4.118   6.0400e-02
   5_xyz:   1.013  0.006  0.077 15.288  0.003  4.112   6.0234e-02
   5_adp:   1.013  0.006  0.077 15.288  0.003  4.112   6.0234e-02
   5_occ:   1.013  0.006  0.077 15.288  0.003  4.112   6.0234e-02
   5_bss:   1.013  0.006  0.077 15.288  0.003  4.112   6.0234e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9226e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9226e+00
   1_xyz:  14.143  0.159  0.448 85.961  0.055  2.202   9.4304e-02
   1_adp:  14.143  0.159  0.448 85.961  0.055  2.202   9.4304e-02
   1_occ:  14.143  0.159  0.448 85.961  0.055  2.202   9.4304e-02
   2_bss:  14.143  0.159  0.448 85.961  0.055  2.202   9.4304e-02
   2_xyz:   6.285  0.069  0.271 80.377  0.028  2.185   5.7275e-02
   2_adp:   6.285  0.069  0.271 80.377  0.028  2.185   5.7275e-02
   2_occ:   6.285  0.069  0.271 80.377  0.028  2.185   5.7275e-02
   3_bss:   6.285  0.069  0.271 80.377  0.028  2.185   5.7275e-02
   3_xyz:   8.634  0.052  0.494 82.130  0.033  2.286   6.2635e-02
   3_adp:   8.634  0.052  0.494 82.130  0.033  2.286   6.2635e-02
   3_occ:   8.634  0.052  0.494 82.130  0.033  2.286   6.2635e-02
   4_bss:   8.634  0.052  0.494 82.130  0.033  2.286   6.2635e-02
   4_xyz:   7.064  0.038  0.466 81.371  0.029  2.378   4.3891e-02
   4_adp:   7.064  0.038  0.466 81.371  0.029  2.378   4.3891e-02
   4_occ:   7.064  0.038  0.466 81.371  0.029  2.378   4.3891e-02
   5_bss:   7.064  0.038  0.466 81.371  0.029  2.378   4.3891e-02
   5_xyz:   6.636  0.034  0.509 82.415  0.027  2.358   3.7322e-02
   5_adp:   6.636  0.034  0.509 82.415  0.027  2.358   3.7322e-02
   5_occ:   6.636  0.034  0.509 82.415  0.027  2.358   3.7322e-02
   5_bss:   6.636  0.034  0.509 82.415  0.027  2.358   3.7322e-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:  69.59   0.00  12.65  69.59   0.00  10.14  65.57   0.00  26.35
   1_occ:  69.59   0.00  12.65  69.59   0.00  10.14  65.57   0.00  26.35
   2_bss:  69.59   0.00  12.65  69.59   0.00  10.14  65.57   0.00  26.35
   2_xyz:  69.59   0.00  12.65  69.59   0.00  10.14  65.57   0.00  26.35
   2_adp:  71.50   0.00  13.20  71.50   0.00   9.83  69.19   0.65  31.57
   2_occ:  71.50   0.00  13.20  71.50   0.00   9.83  69.19   0.65  31.57
   3_bss:  71.50   0.00  13.20  71.50   0.00   9.83  69.19   0.65  31.57
   3_xyz:  71.50   0.00  13.20  71.50   0.00   9.83  69.19   0.65  31.57
   3_adp:  85.16   0.00  13.72  85.16   0.00   9.30  78.22   3.31  37.74
   3_occ:  85.16   0.00  13.72  85.16   0.00   9.30  78.22   3.31  37.74
   4_bss:  85.16   0.00  13.72  85.16   0.00   9.30  78.22   3.31  37.74
   4_xyz:  85.16   0.00  13.72  85.16   0.00   9.30  78.22   3.31  37.74
   4_adp:  91.67   0.00  13.58  91.67   0.00   9.16  80.00   2.95  37.61
   4_occ:  91.67   0.00  13.58  91.67   0.00   9.16  80.00   2.95  37.61
   5_bss:  91.67   0.00  13.58  91.67   0.00   9.16  80.00   2.95  37.61
   5_xyz:  91.67   0.00  13.58  91.67   0.00   9.16  80.00   2.95  37.61
   5_adp:  99.54   0.00  13.55  99.54   0.00   9.11  86.10   2.24  37.72
   5_occ:  99.54   0.00  13.55  99.54   0.00   9.11  86.10   2.24  37.72
   5_bss: 101.32   1.79  15.33 101.32   1.79  10.89  87.89   4.02  39.50
------------------------------------------------------------------------
 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:    1.220    0.022    0.407
   1_adp:    1.220    0.022    0.407
   1_occ:    1.220    0.022    0.407
   2_bss:    1.220    0.022    0.407
   2_xyz:    1.731    0.038    0.554
   2_adp:    1.731    0.038    0.554
   2_occ:    1.731    0.038    0.554
   3_bss:    1.731    0.038    0.554
   3_xyz:    1.702    0.055    0.662
   3_adp:    1.702    0.055    0.662
   3_occ:    1.702    0.055    0.662
   4_bss:    1.702    0.055    0.662
   4_xyz:    1.664    0.008    0.684
   4_adp:    1.664    0.008    0.684
   4_occ:    1.664    0.008    0.684
   5_bss:    1.664    0.008    0.684
   5_xyz:    1.719    0.046    0.702
   5_adp:    1.719    0.046    0.702
   5_occ:    1.719    0.046    0.702
   5_bss:    1.719    0.046    0.702
------------------------------------------------------------------------

CPU time actual refinement: 357.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/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_792/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_792/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.45 
  Macro-tasks:
    bulk solvent and scale       = 42.61  
    individual site refinement   = 147.05 
    weights calculation          = 33.46  
    collect and process          = 6.56   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 229.81 
  Micro-tasks:
    mask                            = 2.53   
    f_calc                          = 114.17 
    alpha_beta                      = 8.43   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 122.60 
    fmodel                         = 7.54   
    r_factors                      = 0.20   
    phase_errors                   = 10.55  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 267.49 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.056 micro seconds
Total CPU time: 6.19 minutes
from_scatterers_fft:    637 calls, 113.77 s
gradients_fft:          581 calls, 109.75 s

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

# Date 2008-01-16 Time 02:26:48 PST -0800 (1200479208.62 s)
Start R-work = 0.4661, R-free = 0.4708 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1803 (no bulk solvent and anisotropic scale)

Start R-work = 0.4584, R-free = 0.4601
Final R-work = 0.1158, R-free = 0.1630