# Date 2008-01-16 Time 00:33:33 PST -0800 (1200472413.64 s)
#phil __OFF__

Command line arguments: "../71.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 619
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 71

-------------------------------------------------------------------------------
  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: (68.4938, 47.1647, 86.39, 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: 3.24, 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: (68.4938, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7734 1.95079
Completeness in resolution range: 0.933966
Completeness with d_max=infinity: 0.931125

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7734
                             d_min =   1.9508

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: (68.4938, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7734 1.95079
Completeness in resolution range: 0.933966
Completeness with d_max=infinity: 0.931125

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7739 -  4.1742 [2201/2229]  1978   223  10.1%
  bin  2:  4.1742 -  3.3256 [2112/2135]  1901   211  10.0%
  bin  3:  3.3256 -  2.9089 [2077/2102]  1872   205   9.9%
  bin  4:  2.9089 -  2.6446 [2079/2095]  1867   212  10.2%
  bin  5:  2.6446 -  2.4560 [2026/2065]  1825   201   9.9%
  bin  6:  2.4560 -  2.3117 [2057/2089]  1852   205  10.0%
  bin  7:  2.3117 -  2.1964 [2033/2070]  1831   202   9.9%
  bin  8:  2.1964 -  2.1010 [2019/2061]  1815   204  10.1%
  bin  9:  2.1010 -  2.0203 [2025/2064]  1832   193   9.5%
  bin 10:  2.0203 -  1.9508 [ 960/2064]   857   103  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.14 -     1.89: 15
        1.89 -     2.64: 92
        2.64 -     3.40: 4413
        3.40 -     4.15: 9471
        4.15 -     4.90: 14689
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.141 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.325 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.488 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.576 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.597 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28675 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_71/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/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 = 68.49375 47.16465 86.39 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 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4622   r_free= 0.4532   ksol= 0.00   Bsol= 0.00   scale= 0.811    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.264225                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7739 -  4.6557 0.99   1432  159 0.3813 0.3771      6.5701      6.5997|
|  2:  4.6557 -  3.7147 0.99   1378  153 0.3630 0.3709      6.7079      6.7408|
|  3:  3.7147 -  3.2508 0.99   1344  150 0.4220 0.4047      6.6315      6.6636|
|  4:  3.2508 -  2.9562 0.99   1339  142 0.4497 0.4268      6.4793      6.4561|
|  5:  2.9562 -  2.7458 0.98   1327  152 0.4864 0.4650      6.3398      6.3708|
|  6:  2.7458 -  2.5848 0.99   1327  148 0.4909 0.5328      6.2758      6.1907|
|  7:  2.5848 -  2.4560 0.99   1296  148 0.4982 0.4719      6.2198       6.158|
|  8:  2.4560 -  2.3495 0.99   1331  141 0.5029 0.4670      6.1667      6.1449|
|  9:  2.3495 -  2.2594 0.99   1315  149 0.5144 0.5224      6.1029      6.1775|
| 10:  2.2594 -  2.1817 0.98   1308  141 0.5054 0.4826      6.0882      6.0515|
| 11:  2.1817 -  2.1136 0.98   1298  148 0.5245 0.5226      6.0387      6.0433|
| 12:  2.1136 -  2.0534 1.00   1301  151 0.5287 0.5043      5.9508      5.9556|
| 13:  2.0534 -  1.9995 0.94   1256  129 0.5248 0.5348      5.8757      5.8491|
| 14:  1.9995 -  1.9508 0.29    378   48 0.5459 0.5025      5.9247      5.6973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7739 -  4.6557  1432   159  0.68  35.68   0.81     0.70      73268.98|
|  2:  4.6557 -  3.7147  1378   153  0.71  34.12   0.91     0.77      97895.49|
|  3:  3.7147 -  3.2508  1344   150  0.64  40.95   0.86     0.74     100187.61|
|  4:  3.2508 -  2.9562  1339   142  0.56  46.94   0.81     0.66      85215.93|
|  5:  2.9562 -  2.7458  1327   152  0.46  54.87   0.75     0.56      74821.38|
|  6:  2.7458 -  2.5848  1327   148  0.43  57.42   0.74     0.50      68068.84|
|  7:  2.5848 -  2.4560  1296   148  0.39  60.44   0.76     0.47      64260.87|
|  8:  2.4560 -  2.3495  1331   141  0.41  59.26   0.75     0.48      54531.03|
|  9:  2.3495 -  2.2594  1315   149  0.42  58.63   0.74     0.51      49300.23|
| 10:  2.2594 -  2.1817  1308   141  0.43  57.75   0.77     0.51      43124.05|
| 11:  2.1817 -  2.1136  1298   148  0.40  60.28   0.75     0.50      43282.12|
| 12:  2.1136 -  2.0534  1301   151  0.35  63.82   0.77     0.46      41774.57|
| 13:  2.0534 -  1.9995  1256   129  0.33  65.34   0.74     0.44      36633.21|
| 14:  1.9995 -  1.9508   378    48  0.39  60.60   0.76     0.41      26172.72|
|alpha:            min =        0.41 max =            0.77 mean =         0.56|
|beta:             min =    26172.72 max =       100187.61 mean =     63625.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.38|
|phase err.(test): min =        0.00 max =           89.97 mean =        53.50|
|-----------------------------------------------------------------------------|

============================== 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 = 10.371594             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.132   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.924034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.897   (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 |  1.013 -  1.402:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.402 -  1.791:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.791 -  2.179:      105 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.179 -  2.568:      531 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.568 -  2.957:     1335 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.957 -  3.345:     2473 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.345 -  3.734:     4011 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.734 -  4.123:     5232 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.123 -  4.511:     6888 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.511 -  4.900:     8097 |
|-----------------------------------------------------------------------------|
|-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 |       53.266 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.013 |       3.149 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    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 = 11.570)------------------------------------------|
|    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 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4690   r_free= 0.4602   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.266502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.4463   ksol= 0.34   Bsol= 10.05   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.02,8.42,8.12,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.254284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.042156             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.005494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.205   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4533      final r-factor (work) = 0.3629          |
| start r-factor (free) = 0.4463      final r-factor (free) = 0.3814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.7407 = 10.04 * 0.50 * 6.2685 + 1.00 * 53.2659                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0503 = 10.04 * 0.50 * 6.1574 + 1.00 * 0.1337                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3629      final r-factor (work) = 0.3075          |
| start r-factor (free) = 0.3814      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2056 = 1.01 * 1.00 * 6.1574 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0857 = 1.01 * 1.00 * 6.0370 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.43   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    78.43   12.48    None  None   None       |
|    Sol.    : 438    0      0.00    78.43   27.18    None  None   None       |
|    Mac.    : 2385   0      0.00    69.57   9.78     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 -   7.843: 1292   |   5:    39.215 -  47.058:   60        |
|      1:     7.843 -  15.686:  753   |   6:    47.058 -  54.901:   33        |
|      2:    15.686 -  23.529:  354   |   7:    54.901 -  62.744:   22        |
|      3:    23.529 -  31.372:  195   |   8:    62.744 -  70.587:   10        |
|      4:    31.372 -  39.215:  102   |   9:    70.587 -  78.430:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3075 r_free = 0.3532             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3072 r_free = 0.3531             target_work(ml) = 6.002         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3072   r_free= 0.3531   ksol= 0.34   Bsol= 10.05   scale= 1.113   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.02,8.42,8.12,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.002015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3029   r_free= 0.3468   ksol= 0.33   Bsol= 35.73   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,4.47,4.90,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.000622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.159662              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.623   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387420              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.991  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3029      final r-factor (work) = 0.2122          |
| start r-factor (free) = 0.3468      final r-factor (free) = 0.2558          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7436 = 7.16 * 0.50 * 6.0366 + 1.00 * 0.1337                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0207 = 7.16 * 0.50 * 5.8489 + 1.00 * 0.0827                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2122      final r-factor (work) = 0.1873          |
| start r-factor (free) = 0.2558      final r-factor (free) = 0.2326          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2879 = 0.39 * 1.00 * 5.8489 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2172 = 0.39 * 1.00 * 5.6213 + 1.00 * 0.0394                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.39   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    78.39   12.58    None  None   None       |
|    Sol.    : 438    0      2.39    78.39   32.71    None  None   None       |
|    Mac.    : 2385   0      0.00    76.20   8.88     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 -   7.839: 1432   |   5:    39.195 -  47.034:   84        |
|      1:     7.839 -  15.678:  724   |   6:    47.034 -  54.873:   56        |
|      2:    15.678 -  23.517:  218   |   7:    54.873 -  62.712:   30        |
|      3:    23.517 -  31.356:  143   |   8:    62.712 -  70.551:   11        |
|      4:    31.356 -  39.195:  123   |   9:    70.551 -  78.390:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1873 r_free = 0.2326             target_work(ml) = 5.570         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1870 r_free = 0.2325             target_work(ml) = 5.570         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1870   r_free= 0.2325   ksol= 0.33   Bsol= 35.73   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,4.47,4.90,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.569972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1835   r_free= 0.2299   ksol= 0.31   Bsol= 34.81   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.91,3.53,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.564407                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.312741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.233  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.778531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.201   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1835      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2299      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5948 = 2.31 * 0.50 * 5.6319 + 1.00 * 0.0822                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3658 = 2.31 * 0.50 * 5.4553 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1801      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3048 = 0.78 * 1.00 * 5.4553 + 1.00 * 0.0577                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1336 = 0.78 * 1.00 * 5.2936 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.99   13.30    None  None   None       |
|    all(noH): 2823   0      0.00    86.99   13.30    None  None   None       |
|    Sol.    : 438    0      2.10    79.97   37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    86.99   8.89     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:     0.000 -   8.699: 1604   |   5:    43.493 -  52.192:   83        |
|      1:     8.699 -  17.397:  618   |   6:    52.192 -  60.890:   64        |
|      2:    17.397 -  26.096:  173   |   7:    60.890 -  69.589:   36        |
|      3:    26.096 -  34.794:  113   |   8:    69.589 -  78.287:    9        |
|      4:    34.794 -  43.493:  119   |   9:    78.287 -  86.986:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1733             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1318 r_free = 0.1733             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1733   ksol= 0.31   Bsol= 34.81   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.91,3.53,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.270619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1731   ksol= 0.32   Bsol= 38.49   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,2.37,3.15,0.00,0.00,0.00); trace/3= 2.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.268826                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.099950              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.944  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.627356              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.852  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1316      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1731      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2675 = 3.10 * 0.50 * 5.2969 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1524 = 3.10 * 0.50 * 5.2133 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2830 = 0.63 * 1.00 * 5.2133 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2549 = 0.63 * 1.00 * 5.1693 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.70   13.04    None  None   None       |
|    all(noH): 2823   0      0.00    89.70   13.04    None  None   None       |
|    Sol.    : 438    0      2.14    76.20   36.70    None  None   None       |
|    Mac.    : 2385   0      0.00    89.70   8.69     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 -   8.970: 1682   |   5:    44.850 -  53.820:   80        |
|      1:     8.970 -  17.940:  578   |   6:    53.820 -  62.790:   56        |
|      2:    17.940 -  26.910:  156   |   7:    62.790 -  71.760:   24        |
|      3:    26.910 -  35.880:  120   |   8:    71.760 -  80.730:   12        |
|      4:    35.880 -  44.850:  112   |   9:    80.730 -  89.700:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1596             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1596             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1596   ksol= 0.32   Bsol= 38.49   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,2.37,3.15,0.00,0.00,0.00); trace/3= 2.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.162271                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1596   ksol= 0.32   Bsol= 38.49   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,2.37,3.25,0.00,0.00,0.00); trace/3= 2.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162313                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.300451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.652  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.379  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0176 = 2.30 * 0.50 * 5.1692 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9971 = 2.30 * 0.50 * 5.1588 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9074 = 0.17 * 1.00 * 5.1588 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9048 = 0.17 * 1.00 * 5.1597 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.86   12.40    None  None   None       |
|    all(noH): 2823   0      0.00    85.86   12.40    None  None   None       |
|    Sol.    : 438    0      1.81    73.65   33.81    None  None   None       |
|    Mac.    : 2385   0      0.00    85.86   8.47     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 -   8.586: 1661   |   5:    42.930 -  51.516:   76        |
|      1:     8.586 -  17.172:  606   |   6:    51.516 -  60.103:   38        |
|      2:    17.172 -  25.758:  160   |   7:    60.103 -  68.689:   21        |
|      3:    25.758 -  34.344:  133   |   8:    68.689 -  77.275:    8        |
|      4:    34.344 -  42.930:  117   |   9:    77.275 -  85.861:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1562             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1562             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1562   ksol= 0.32   Bsol= 38.49   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,2.37,3.25,0.00,0.00,0.00); trace/3= 2.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7739 -  4.6557 0.99   1432  159 0.1022 0.1343      5.4144      5.5837|
|  2:  4.6557 -  3.7147 0.99   1378  153 0.0884 0.1146      5.4548      5.6639|
|  3:  3.7147 -  3.2508 0.99   1344  150 0.1075 0.1445      5.4713      5.7941|
|  4:  3.2508 -  2.9562 0.99   1339  142 0.1215 0.1536      5.4366      5.5967|
|  5:  2.9562 -  2.7458 0.98   1327  152 0.1344 0.1566      5.3235      5.4739|
|  6:  2.7458 -  2.5848 0.99   1327  148 0.1227 0.2098      5.2015      5.5217|
|  7:  2.5848 -  2.4560 0.99   1296  148 0.1237 0.1524      5.1576      5.3156|
|  8:  2.4560 -  2.3495 0.99   1331  141 0.1155 0.1683      5.0741      5.3138|
|  9:  2.3495 -  2.2594 0.99   1315  149 0.1215 0.1946      5.0352      5.3587|
| 10:  2.2594 -  2.1817 0.98   1308  141 0.1150 0.1589      4.9538      5.1164|
| 11:  2.1817 -  2.1136 0.98   1298  148 0.1150 0.1694      4.9156       5.219|
| 12:  2.1136 -  2.0534 1.00   1301  151 0.1119 0.1617      4.8364      5.0853|
| 13:  2.0534 -  1.9995 0.94   1256  129 0.1145 0.1754      4.7722      5.0256|
| 14:  1.9995 -  1.9508 0.29    378   48 0.1115 0.1713      4.7443      4.9207|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7739 -  4.6557  1432   159  0.94   9.47   0.98     0.96       7652.93|
|  2:  4.6557 -  3.7147  1378   153  0.95   8.12   1.02     1.01       9212.81|
|  3:  3.7147 -  3.2508  1344   150  0.93  11.43   1.03     1.02      10427.15|
|  4:  3.2508 -  2.9562  1339   142  0.92  13.47   1.01     1.01       9966.11|
|  5:  2.9562 -  2.7458  1327   152  0.90  15.99   0.99     0.96       8210.98|
|  6:  2.7458 -  2.5848  1327   148  0.90  15.94   0.98     0.96       6766.82|
|  7:  2.5848 -  2.4560  1296   148  0.90  15.71   0.99     0.94       6064.25|
|  8:  2.4560 -  2.3495  1331   141  0.91  15.36   1.01     0.99       5488.63|
|  9:  2.3495 -  2.2594  1315   149  0.90  15.80   1.01     0.98       4993.13|
| 10:  2.2594 -  2.1817  1308   141  0.90  15.84   1.01     0.98       4373.08|
| 11:  2.1817 -  2.1136  1298   148  0.90  15.72   1.01     0.98       4133.54|
| 12:  2.1136 -  2.0534  1301   151  0.91  15.11   1.01     1.01       3591.63|
| 13:  2.0534 -  1.9995  1256   129  0.90  15.92   1.01     1.00       3212.42|
| 14:  1.9995 -  1.9508   378    48  0.91  14.70   0.99     0.95       2792.59|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2792.59 max =        10427.15 mean =      6436.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.09|
|phase err.(test): min =        0.00 max =           89.54 mean =        13.65|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1562   ksol= 0.32   Bsol= 40.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.06,0.94,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1562   ksol= 0.32   Bsol= 40.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.06,0.94,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154311                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7739 -  4.6557 0.99   1432  159 0.1023 0.1342       5.416       5.585|
|  2:  4.6557 -  3.7147 0.99   1378  153 0.0883 0.1145      5.4543      5.6631|
|  3:  3.7147 -  3.2508 0.99   1344  150 0.1075 0.1445      5.4709       5.794|
|  4:  3.2508 -  2.9562 0.99   1339  142 0.1215 0.1537      5.4366      5.5969|
|  5:  2.9562 -  2.7458 0.98   1327  152 0.1345 0.1566      5.3236       5.474|
|  6:  2.7458 -  2.5848 0.99   1327  148 0.1227 0.2098      5.2017      5.5219|
|  7:  2.5848 -  2.4560 0.99   1296  148 0.1237 0.1524      5.1578      5.3157|
|  8:  2.4560 -  2.3495 0.99   1331  141 0.1155 0.1683      5.0742       5.314|
|  9:  2.3495 -  2.2594 0.99   1315  149 0.1215 0.1946      5.0353      5.3587|
| 10:  2.2594 -  2.1817 0.98   1308  141 0.1150 0.1589      4.9539      5.1164|
| 11:  2.1817 -  2.1136 0.98   1298  148 0.1150 0.1694      4.9156       5.219|
| 12:  2.1136 -  2.0534 1.00   1301  151 0.1119 0.1617      4.8364      5.0853|
| 13:  2.0534 -  1.9995 0.94   1256  129 0.1145 0.1754      4.7722      5.0257|
| 14:  1.9995 -  1.9508 0.29    378   48 0.1115 0.1713      4.7444      4.9209|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7739 -  4.6557  1432   159  0.94   9.50   0.98     0.96       7696.67|
|  2:  4.6557 -  3.7147  1378   153  0.95   8.13   1.02     1.01       9220.12|
|  3:  3.7147 -  3.2508  1344   150  0.93  11.42   1.03     1.02      10412.78|
|  4:  3.2508 -  2.9562  1339   142  0.92  13.47   1.01     1.01       9967.11|
|  5:  2.9562 -  2.7458  1327   152  0.90  15.99   0.99     0.96       8213.76|
|  6:  2.7458 -  2.5848  1327   148  0.90  15.94   0.98     0.96       6768.89|
|  7:  2.5848 -  2.4560  1296   148  0.90  15.71   0.99     0.94       6066.08|
|  8:  2.4560 -  2.3495  1331   141  0.91  15.37   1.01     0.99       5490.03|
|  9:  2.3495 -  2.2594  1315   149  0.90  15.81   1.01     0.98       4994.15|
| 10:  2.2594 -  2.1817  1308   141  0.90  15.84   1.01     0.98       4373.56|
| 11:  2.1817 -  2.1136  1298   148  0.90  15.72   1.01     0.98       4133.96|
| 12:  2.1136 -  2.0534  1301   151  0.91  15.11   1.01     1.01       3591.94|
| 13:  2.0534 -  1.9995  1256   129  0.90  15.92   1.01     1.00       3212.87|
| 14:  1.9995 -  1.9508   378    48  0.91  14.70   0.99     0.95       2793.31|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2793.31 max =        10412.78 mean =      6439.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.10|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.31    88.17   14.71    None  None   None       |
|    all(noH): 2823   0      2.31    88.17   14.71    None  None   None       |
|    Sol.    : 438    0      4.12    75.96   36.12    None  None   None       |
|    Mac.    : 2385   0      2.31    88.17   10.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.311 -  10.897: 1661   |   5:    45.242 -  53.828:   76        |
|      1:    10.897 -  19.484:  606   |   6:    53.828 -  62.414:   38        |
|      2:    19.484 -  28.070:  160   |   7:    62.414 -  71.000:   21        |
|      3:    28.070 -  36.656:  133   |   8:    71.000 -  79.586:    8        |
|      4:    36.656 -  45.242:  117   |   9:    79.586 -  88.172:    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)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.388 - 4.774
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 311
   mapped sites are within: 0.728 - 4.774

peak=   11.549 closest distance to " CB  VAL A 230 " =    1.466
peak=    6.238 closest distance to " CG  LEU A   5 " =    1.281
peak=    6.004 closest distance to " CB  VAL A 296 " =    1.133
peak=    5.654 closest distance to " CG2 VAL A 296 " =    1.063
peak=    5.329 closest distance to " CB  ARG A 275 " =    0.932
peak=    5.297 closest distance to " NE2 GLN A  11 " =    1.131
peak=    5.133 closest distance to " O   HOH Z 142 " =    1.790
peak=    5.113 closest distance to " CD2 LEU A   5 " =    1.187
peak=    5.066 closest distance to " O   HOH Z 209 " =    2.252
peak=    4.988 closest distance to " O   HOH Z 193 " =    1.820
peak=    4.945 closest distance to " O   HOH Z 272 " =    1.907
peak=    4.913 closest distance to " NH2 ARG A  56 " =    2.139
peak=    4.886 closest distance to " O   HOH Z 126 " =    1.935
peak=    4.876 closest distance to " CG  LEU A 228 " =    1.212
peak=    4.826 closest distance to " CB  GLN A 223 " =    1.509
peak=    4.783 closest distance to " O   HOH Z  85 " =    1.678
peak=    4.711 closest distance to " O   HOH Z 124 " =    1.431
peak=    4.707 closest distance to " O   HOH Z 232 " =    2.284
peak=    4.692 closest distance to " O   HOH Z 346 " =    1.557
peak=    4.640 closest distance to " O   HOH Z  63 " =    2.111
peak=    4.602 closest distance to " C   PRO A 198 " =    1.476
peak=    4.590 closest distance to " O   HOH Z 402 " =    1.414
peak=    4.588 closest distance to " CB  ARG A  79 " =    1.337
peak=    4.581 closest distance to " CG  PRO A 213 " =    1.268
peak=    4.563 closest distance to " CG1 VAL A 296 " =    1.156
peak=    4.488 closest distance to " O   SER A  87 " =    2.146
peak=    4.485 closest distance to " CB  VAL A 230 " =    1.179
peak=    4.470 closest distance to " ND2 ASN A 187 " =    1.543
peak=    4.467 closest distance to " CB  GLN A 183 " =    1.288
peak=    4.449 closest distance to " O   HOH Z 287 " =    1.895
peak=    4.425 closest distance to " CB  SER A  63 " =    1.156
peak=    4.408 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.381 closest distance to " O   HOH Z 423 " =    1.870
peak=    4.358 closest distance to " O   HOH Z 265 " =    2.277
peak=    4.339 closest distance to " O   HOH Z 368 " =    2.089
peak=    4.319 closest distance to " O   HOH Z  61 " =    1.647
peak=    4.308 closest distance to " O   HOH Z 130 " =    2.654
peak=    4.292 closest distance to " CB  GLU A 152 " =    1.173
peak=    4.263 closest distance to " O   HOH Z 403 " =    1.779
peak=    4.200 closest distance to " CB  ALA A   9 " =    1.678
peak=    4.172 closest distance to " CB  SER A  26 " =    1.803
peak=    4.165 closest distance to " O   HOH Z  80 " =    1.703
peak=    4.123 closest distance to " O   HOH Z 327 " =    1.604
peak=    4.113 closest distance to " O   HOH Z  97 " =    1.971
peak=    4.110 closest distance to " O   HOH Z  54 " =    1.608
peak=    4.098 closest distance to " CG  PRO A 198 " =    1.210
peak=    4.091 closest distance to " CD2 TRP A 179 " =    1.364
peak=    4.068 closest distance to " CB  SER A   3 " =    1.240
peak=    4.065 closest distance to " O   HOH Z  43 " =    1.348
peak=    4.065 closest distance to " O   HOH Z 128 " =    2.189
peak=    4.057 closest distance to " O   HOH Z 406 " =    1.302
peak=    4.053 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.047 closest distance to " O   HOH Z 102 " =    1.292
peak=    4.041 closest distance to " O   HOH Z 188 " =    1.283
peak=    4.038 closest distance to " N   ASN A  39 " =    1.223
peak=    4.033 closest distance to " CD2 LEU A 228 " =    1.339
peak=    4.015 closest distance to " O   HOH Z 234 " =    3.476
peak=    4.013 closest distance to " O   HOH Z 345 " =    2.925
peak=    4.005 closest distance to " CB  ARG A 139 " =    1.054
peak=    4.004 closest distance to " O   HOH Z 427 " =    2.811
peak=    3.989 closest distance to " O   HOH Z 322 " =    2.180
peak=    3.986 closest distance to " O   HOH Z 128 " =    1.909
peak=    3.982 closest distance to " O   HOH Z  78 " =    1.654
peak=    3.980 closest distance to " OE1 GLU A   2 " =    2.188
peak=    3.974 closest distance to " O   HOH Z 273 " =    2.828
peak=    3.970 closest distance to " CA  TYR A  30 " =    0.973
peak=    3.967 closest distance to " O   HOH Z 154 " =    1.576
peak=    3.966 closest distance to " CZ  PHE A 218 " =    1.082
peak=    3.966 closest distance to " O   HOH Z 298 " =    1.768
peak=    3.939 closest distance to " O   HOH Z  97 " =    2.298
peak=    3.936 closest distance to " CB  VAL A 265 " =    1.272
peak=    3.930 closest distance to " O   HOH Z 188 " =    2.868
peak=    3.924 closest distance to " O   HOH Z  43 " =    2.254
peak=    3.924 closest distance to " O   HOH Z  59 " =    2.071
peak=    3.914 closest distance to " O   HOH Z 316 " =    3.017
peak=    3.906 closest distance to " CA  ALA A  51 " =    1.007
peak=    3.899 closest distance to " O   HOH Z 130 " =    2.450
peak=    3.899 closest distance to " O   HOH Z 369 " =    2.370
peak=    3.893 closest distance to " O   HOH Z 238 " =    1.060
peak=    3.875 closest distance to " CB  GLU A 277 " =    3.529
peak=    3.869 closest distance to " O   HOH Z 411 " =    3.767
peak=    3.866 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.864 closest distance to " CG2 ILE A  20 " =    1.411
peak=    3.830 closest distance to " CA  VAL A  41 " =    0.772
peak=    3.824 closest distance to " O   HOH Z 248 " =    1.407
peak=    3.822 closest distance to " O   HOH Z  44 " =    1.916
peak=    3.781 closest distance to " CB  ASN A  39 " =    0.822
peak=    3.780 closest distance to " NH2BARG A 145 " =    2.264
peak=    3.777 closest distance to " O   HOH Z 357 " =    1.899
peak=    3.773 closest distance to " O   HOH Z 371 " =    3.150
peak=    3.755 closest distance to " O   HOH Z 404 " =    2.236
peak=    3.744 closest distance to " CB  ALA A 248 " =    1.363
peak=    3.740 closest distance to " O   HOH Z 435 " =    1.868
peak=    3.731 closest distance to " CG2 ILE A 120 " =    1.325
peak=    3.721 closest distance to " O   TRP A 274 " =    1.892
peak=    3.720 closest distance to " O   HOH Z 303 " =    2.119
peak=    3.697 closest distance to " O   HOH Z 421 " =    1.661
peak=    3.666 closest distance to " O   HOH Z 145 " =    2.263
peak=    3.664 closest distance to " N   ALA A   1 " =    2.930
peak=    3.662 closest distance to " NZ  LYS A 117 " =    2.838
peak=    3.658 closest distance to " O   HOH Z 313 " =    1.853
peak=    3.643 closest distance to " N   PHE A 130 " =    1.341
peak=    3.636 closest distance to " CB  ASN A 187 " =    1.009
peak=    3.634 closest distance to " CB  TYR A 169 " =    0.758
peak=    3.628 closest distance to " O   HOH Z  66 " =    2.233
peak=    3.619 closest distance to " CG AARG A 275 " =    1.242
peak=    3.603 closest distance to " CD  ARG A 269 " =    0.981
peak=    3.597 closest distance to " CB  VAL A 202 " =    1.491
peak=    3.597 closest distance to " O   HOH Z 344 " =    2.687
peak=    3.595 closest distance to " O   HOH Z 389 " =    1.729
peak=    3.590 closest distance to " CG  ARG A  66 " =    1.043
peak=    3.588 closest distance to " O   HOH Z 109 " =    1.955
peak=    3.588 closest distance to " CB  TRP A 266 " =    1.065
peak=    3.585 closest distance to " CB  ALA A 295 " =    1.068
peak=    3.575 closest distance to " OG BSER A 212 " =    2.662
peak=    3.563 closest distance to " O   HOH Z  40 " =    1.652
peak=    3.562 closest distance to " CG BARG A 102 " =    1.692
peak=    3.560 closest distance to " CB  TRP A 179 " =    1.188
peak=    3.556 closest distance to " CB  PRO A  54 " =    0.811
peak=    3.554 closest distance to " O   HOH Z 227 " =    1.611
peak=    3.552 closest distance to " O   HOH Z 183 " =    1.849
peak=    3.551 closest distance to " OD1 ASN A  69 " =    2.541
peak=    3.549 closest distance to " CA  ASN A 176 " =    1.037
peak=    3.546 closest distance to " CD  LYS A  76 " =    1.841
peak=    3.546 closest distance to " O   HOH Z 148 " =    3.273
peak=    3.540 closest distance to " O   HOH Z 245 " =    1.483
peak=    3.532 closest distance to " O   HOH Z   3 " =    1.648
peak=    3.528 closest distance to " O   ASP A 124 " =    1.419
peak=    3.528 closest distance to " O   HOH Z 419 " =    1.699
peak=    3.523 closest distance to " CG  MET A 185 " =    1.109
peak=    3.519 closest distance to " O   HOH Z 414 " =    1.428
peak=    3.519 closest distance to " CD  LYS A 166 " =    1.293
peak=    3.517 closest distance to " O   HOH Z  21 " =    1.789
peak=    3.506 closest distance to " O   HOH Z 438 " =    2.420
peak=    3.501 closest distance to " OG  SER A  97 " =    2.576
peak=    3.497 closest distance to " O   HOH Z 203 " =    1.703
peak=    3.491 closest distance to " O   HOH Z 416 " =    2.703
peak=    3.488 closest distance to " O   HOH Z 236 " =    1.581
peak=    3.486 closest distance to " CB  PHE A 204 " =    0.844
peak=    3.485 closest distance to " O   HOH Z 380 " =    1.861
peak=    3.484 closest distance to " OD2 ASP A 298 " =    3.911
peak=    3.481 closest distance to " CA  ALA A  21 " =    1.100
peak=    3.481 closest distance to " CG  GLN A  77 " =    2.381
peak=    3.470 closest distance to " O   HOH Z  15 " =    2.046
peak=    3.468 closest distance to " O   HOH Z 426 " =    1.461
peak=    3.461 closest distance to " CD  ARG A 159 " =    0.728
peak=    3.460 closest distance to " CB  SER A 141 " =    1.099
peak=    3.458 closest distance to " O   HOH Z 251 " =    1.509
peak=    3.452 closest distance to " O   HOH Z 388 " =    2.072
peak=    3.449 closest distance to " CA  ARG A  36 " =    1.019
peak=    3.449 closest distance to " O   HOH Z 422 " =    2.510
peak=    3.448 closest distance to " O   HOH Z  94 " =    2.062
peak=    3.434 closest distance to " CG1 ILE A  33 " =    1.303
peak=    3.434 closest distance to " OG  SER A 276 " =    1.332
peak=    3.428 closest distance to " CE1 HIS A 108 " =    1.219
peak=    3.426 closest distance to " O   HOH Z 261 " =    1.932
peak=    3.425 closest distance to " CG2AVAL A 121 " =    2.130
peak=    3.422 closest distance to " CB  THR A  31 " =    1.588
peak=    3.419 closest distance to " OG BSER A 164 " =    2.133
peak=    3.418 closest distance to " O   HOH Z 345 " =    1.559
peak=    3.416 closest distance to " CZ2 TRP A 150 " =    1.119
peak=    3.416 closest distance to " CG1 ILE A  49 " =    1.480
peak=    3.414 closest distance to " O   HOH Z 118 " =    1.073
peak=    3.414 closest distance to " O   HOH Z 126 " =    1.449
peak=    3.414 closest distance to " CB  ASN A 110 " =    1.056
peak=    3.413 closest distance to " O   HOH Z 392 " =    2.811
peak=    3.412 closest distance to " CD2 LEU A 297 " =    0.912
peak=    3.412 closest distance to " CD2 HIS A  81 " =    1.063
peak=    3.411 closest distance to " O   HOH Z 367 " =    3.491
peak=    3.408 closest distance to " NH1 ARG A 138 " =    1.294
peak=    3.405 closest distance to " O   HOH Z 173 " =    2.297
peak=    3.405 closest distance to " O   HOH Z  47 " =    1.887
peak=    3.405 closest distance to " O   HOH Z 425 " =    1.928
peak=    3.402 closest distance to " O   HOH Z 253 " =    1.458
peak=    3.401 closest distance to " CA  ASN A 215 " =    1.015
peak=    3.400 closest distance to " CA  ASP A 162 " =    1.009
peak=    3.395 closest distance to " O   HOH Z 246 " =    1.297
peak=    3.393 closest distance to " O   HOH Z 365 " =    2.777
peak=    3.391 closest distance to " CB  GLU A 128 " =    0.934
peak=    3.389 closest distance to " O   HOH Z 216 " =    2.662
peak=    3.386 closest distance to " O   HOH Z 337 " =    3.419
peak=    3.378 closest distance to " O   HOH Z   9 " =    2.104
peak=    3.377 closest distance to " O   HOH Z 118 " =    1.488
peak=    3.372 closest distance to " CB BVAL A  41 " =    1.078
peak=    3.369 closest distance to " CG2 VAL A 257 " =    0.852
peak=    3.368 closest distance to " O   HOH Z 209 " =    2.327
peak=    3.361 closest distance to " O   HOH Z 193 " =    1.928
peak=    3.357 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.355 closest distance to " O   GLY A  91 " =    1.477
peak=    3.355 closest distance to " O   HOH Z 361 " =    3.069
peak=    3.354 closest distance to " CB  THR A  52 " =    1.141
peak=    3.350 closest distance to " O   HOH Z 417 " =    3.457
peak=    3.345 closest distance to " O   HOH Z 180 " =    2.189
peak=    3.344 closest distance to " CA  SER A  32 " =    1.656
peak=    3.343 closest distance to " CG2 THR A 294 " =    1.630
peak=    3.343 closest distance to " O   HOH Z 261 " =    1.821
peak=    3.342 closest distance to " N   SER A 135 " =    1.370
peak=    3.340 closest distance to " O   HOH Z 257 " =    2.147
peak=    3.340 closest distance to " O   HOH Z 408 " =    1.564
peak=    3.337 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.332 closest distance to " CG1BVAL A  72 " =    1.594
peak=    3.331 closest distance to " CD  LYS A 119 " =    1.986
peak=    3.329 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.329 closest distance to " CG2 THR A 221 " =    1.256
peak=    3.326 closest distance to " CB  ASN A 142 " =    1.102
peak=    3.318 closest distance to " CG  LYS A 119 " =    1.152
peak=    3.316 closest distance to " O   HOH Z  99 " =    1.765
peak=    3.314 closest distance to " O   HOH Z 147 " =    1.770
peak=    3.313 closest distance to " CB  GLU A  46 " =    1.083
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.499
peak=    3.311 closest distance to " NE2 GLN A  77 " =    3.142
peak=    3.310 closest distance to " CB  SER A  62 " =    1.322
peak=    3.310 closest distance to " CB  ALA A   1 " =    1.189
peak=    3.310 closest distance to " ND2 ASN A 110 " =    1.526
peak=    3.310 closest distance to " O   HOH Z 293 " =    1.702
peak=    3.308 closest distance to " CB  HIS A 108 " =    0.874
peak=    3.308 closest distance to " O   HOH Z  48 " =    1.674
peak=    3.304 closest distance to " O   HOH Z 254 " =    1.503
peak=    3.303 closest distance to " CA  ARG A 195 " =    1.165
peak=    3.301 closest distance to " CB  TRP A 150 " =    1.437
peak=    3.301 closest distance to " O   HOH Z 350 " =    1.928
peak=    3.300 closest distance to " OD2 ASP A 286 " =    2.712
peak=    3.298 closest distance to " O  BHOH Z 338 " =    2.459
peak=    3.298 closest distance to " OD1 ASP A 286 " =    1.702
peak=    3.293 closest distance to " O   HOH Z 214 " =    2.663
peak=    3.293 closest distance to " O   HOH Z 109 " =    1.326
peak=    3.291 closest distance to " CA  PHE A  59 " =    0.872
peak=    3.287 closest distance to " O   HOH Z 352 " =    1.255
peak=    3.286 closest distance to " C   ALA A 299 " =    0.829
peak=    3.285 closest distance to " O   HOH Z 134 " =    1.361
peak=    3.284 closest distance to " O   HOH Z 130 " =    1.152
peak=    3.282 closest distance to " CA  ALA A 291 " =    0.829
peak=    3.281 closest distance to " CB  GLN A 278 " =    0.773
peak=    3.278 closest distance to " OG ASER A  99 " =    1.584
peak=    3.278 closest distance to " CA  GLY A 133 " =    3.566
peak=    3.272 closest distance to " CB  ARG A 190 " =    1.761
peak=    3.269 closest distance to " O   HOH Z 359 " =    1.405
peak=    3.266 closest distance to " O   HOH Z 234 " =    1.909
peak=    3.262 closest distance to " O   HOH Z  47 " =    1.750
peak=    3.260 closest distance to " CG  LEU A 167 " =    1.208
peak=    3.259 closest distance to " O   HOH Z 244 " =    1.643
peak=    3.254 closest distance to " O   HOH Z 425 " =    1.392
peak=    3.253 closest distance to " CA  ALA A 158 " =    1.305
peak=    3.253 closest distance to " CB  PRO A  90 " =    1.114
peak=    3.251 closest distance to " CZ3 TRP A  85 " =    0.978
peak=    3.250 closest distance to " CA  ASP A 140 " =    1.177
peak=    3.249 closest distance to " CG  LYS A  76 " =    1.017
peak=    3.249 closest distance to " O   HOH Z 344 " =    1.814
peak=    3.248 closest distance to " O   HOH Z  35 " =    2.318
peak=    3.244 closest distance to " CB  LYS A 290 " =    1.050
peak=    3.242 closest distance to " O   HOH Z 164 " =    2.093
peak=    3.240 closest distance to " O   HOH Z 116 " =    2.542
peak=    3.239 closest distance to " CB  ALA A 114 " =    1.189
peak=    3.239 closest distance to " O   HOH Z 227 " =    2.122
peak=    3.238 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.231 closest distance to " O   HOH Z 423 " =    3.207
peak=    3.227 closest distance to " CB  ARG A 156 " =    1.151
peak=    3.225 closest distance to " CB  ARG A 219 " =    1.281
peak=    3.219 closest distance to " O   HOH Z 433 " =    2.057
peak=    3.219 closest distance to " CE BMET A  47 " =    1.007
peak=    3.217 closest distance to " N   ARG A 156 " =    1.348
peak=    3.214 closest distance to " O   HOH Z  11 " =    2.440
peak=    3.214 closest distance to " O   HOH Z  95 " =    1.129
peak=    3.213 closest distance to " O   HOH Z 368 " =    3.564
peak=    3.212 closest distance to " O   HOH Z 406 " =    1.611
peak=    3.208 closest distance to " CA  PHE A 283 " =    1.025
peak=    3.208 closest distance to " O   HOH Z 329 " =    3.830
peak=    3.204 closest distance to " O   HOH Z  50 " =    2.136
peak=    3.190 closest distance to " OH  TYR A 116 " =    1.153
peak=    3.188 closest distance to " CB  ILE A 120 " =    1.298
peak=    3.181 closest distance to " O   SER A 164 " =    1.107
peak=    3.180 closest distance to " N   ASP A 162 " =    1.182
peak=    3.174 closest distance to " O   HOH Z   1 " =    1.796
peak=    3.173 closest distance to " CB  PRO A 198 " =    0.905
peak=    3.171 closest distance to " O   HOH Z 249 " =    0.968
peak=    3.164 closest distance to " OG1 THR A 221 " =    1.306
peak=    3.164 closest distance to " N   ARG A 190 " =    0.983
peak=    3.163 closest distance to " O   HOH Z 299 " =    4.141
peak=    3.159 closest distance to " NH2 ARG A  79 " =    1.252
peak=    3.155 closest distance to " CG  GLU A 277 " =    2.162
peak=    3.153 closest distance to " CG AARG A 190 " =    1.106
peak=    3.152 closest distance to " CA  SER A 146 " =    1.972
peak=    3.152 closest distance to " O   HOH Z 233 " =    1.741
peak=    3.148 closest distance to " O   HOH Z  71 " =    2.065
peak=    3.147 closest distance to " O   HOH Z  83 " =    1.545
peak=    3.142 closest distance to " O   HOH Z 383 " =    1.924
peak=    3.141 closest distance to " CG  MET A 185 " =    0.936
peak=    3.140 closest distance to " O   HOH Z 222 " =    2.305
peak=    3.131 closest distance to " O   HOH Z 213 " =    1.635
peak=    3.109 closest distance to " O   HOH Z 251 " =    1.721
peak=    3.109 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.108 closest distance to " CG2 VAL A 197 " =    0.875
peak=    3.107 closest distance to " O   HOH Z  63 " =    2.270
peak=    3.100 closest distance to " O   HOH Z 299 " =    2.340
peak=    3.088 closest distance to " O   ALA A   1 " =    1.769
peak=    3.086 closest distance to " NH1AARG A 145 " =    1.182
peak=    3.084 closest distance to " NH1BARG A 190 " =    1.901
peak=    3.081 closest distance to " CA  LEU A 282 " =    1.287
peak=    3.080 closest distance to " O   HOH Z 132 " =    2.398
peak=    3.077 closest distance to " OE2 GLU A  53 " =    2.041
peak=    3.076 closest distance to " CB  ASN A 215 " =    1.106
peak=    3.073 closest distance to " OG BSER A 258 " =    3.323
peak=    3.059 closest distance to " NZ  LYS A  76 " =    1.716
peak=    3.054 closest distance to " O   HOH Z 298 " =    4.774
peak=    3.047 closest distance to " CB  ALA A  71 " =    1.282
peak=    3.022 closest distance to " O   HOH Z  28 " =    1.722

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.491 - 5.861
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 198
   mapped sites are within: 0.775 - 5.861

peak=   -4.688 closest distance to " CG  GLN A  58 " =    1.142
peak=   -4.544 closest distance to " O   VAL A  67 " =    2.525
peak=   -4.534 closest distance to " C   HIS A 108 " =    1.201
peak=   -4.533 closest distance to " CD  ARG A  14 " =    3.179
peak=   -4.458 closest distance to " OXT GLY A 302 " =    2.792
peak=   -4.425 closest distance to " CD1 LEU A 101 " =    2.440
peak=   -4.388 closest distance to " O   HOH Z 290 " =    0.971
peak=   -4.384 closest distance to " CD  ARG A 156 " =    2.044
peak=   -4.220 closest distance to " O   PRO A 163 " =    2.145
peak=   -4.192 closest distance to " NE2 GLN A  88 " =    1.018
peak=   -4.183 closest distance to " OG BSER A 134 " =    1.283
peak=   -4.077 closest distance to " O   HOH Z 351 " =    1.456
peak=   -4.072 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -4.040 closest distance to " O   HOH Z 166 " =    1.877
peak=   -4.029 closest distance to " O   HOH Z 266 " =    4.987
peak=   -3.980 closest distance to " CB  ALA A 248 " =    2.353
peak=   -3.954 closest distance to " CG  GLN A 223 " =    2.005
peak=   -3.904 closest distance to " N   ALA A 248 " =    1.823
peak=   -3.893 closest distance to " CB  ALA A 161 " =    2.402
peak=   -3.882 closest distance to " O   HOH Z 423 " =    2.178
peak=   -3.876 closest distance to " O   HOH Z 114 " =    3.218
peak=   -3.835 closest distance to " CG1 VAL A 112 " =    2.664
peak=   -3.832 closest distance to " CG  ASP A 231 " =    0.805
peak=   -3.811 closest distance to " CD2 PHE A 192 " =    2.121
peak=   -3.795 closest distance to " O   ASN A  45 " =    1.835
peak=   -3.789 closest distance to " ND2 ASN A 187 " =    1.646
peak=   -3.754 closest distance to " CE  MET A 105 " =    2.265
peak=   -3.752 closest distance to " O   GLY A  80 " =    2.399
peak=   -3.749 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.734 closest distance to " CD1 LEU A 255 " =    2.688
peak=   -3.724 closest distance to " NH2AARG A 275 " =    4.668
peak=   -3.720 closest distance to " O   HOH Z 387 " =    2.646
peak=   -3.708 closest distance to " CB  ALA A 291 " =    2.225
peak=   -3.694 closest distance to " CA  VAL A  67 " =    2.832
peak=   -3.693 closest distance to " CA  GLY A 241 " =    2.418
peak=   -3.689 closest distance to " O   PRO A 198 " =    1.159
peak=   -3.686 closest distance to " CD2 TYR A 293 " =    1.977
peak=   -3.676 closest distance to " O   HOH Z 394 " =    1.655
peak=   -3.668 closest distance to " O   HOH Z 174 " =    4.021
peak=   -3.667 closest distance to " CB  PRO A 163 " =    2.598
peak=   -3.649 closest distance to " N   PHE A  59 " =    2.266
peak=   -3.643 closest distance to " CG2 VAL A 296 " =    1.444
peak=   -3.632 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.630 closest distance to " O   PHE A 218 " =    1.694
peak=   -3.625 closest distance to " CB  ASP A 132 " =    2.314
peak=   -3.622 closest distance to " CB  SER A 210 " =    1.293
peak=   -3.621 closest distance to " C   ASP A 231 " =    2.478
peak=   -3.608 closest distance to " O   GLY A 196 " =    1.161
peak=   -3.601 closest distance to " CB  ALA A 248 " =    2.021
peak=   -3.598 closest distance to " CB  ASP A 132 " =    2.230
peak=   -3.593 closest distance to " OD2 ASP A 191 " =    1.387
peak=   -3.561 closest distance to " N   ALA A 226 " =    1.918
peak=   -3.560 closest distance to " CZ  ARG A  66 " =    1.049
peak=   -3.559 closest distance to " C   GLN A 205 " =    1.826
peak=   -3.556 closest distance to " O   ASN A 187 " =    1.550
peak=   -3.555 closest distance to " O   HOH Z  11 " =    1.887
peak=   -3.545 closest distance to " O   HOH Z 211 " =    1.648
peak=   -3.543 closest distance to " O   HOH Z 407 " =    2.773
peak=   -3.538 closest distance to " O   HOH Z 103 " =    1.803
peak=   -3.536 closest distance to " CG1 VAL A 296 " =    1.099
peak=   -3.519 closest distance to " ND2 ASN A  39 " =    1.081
peak=   -3.513 closest distance to " CB  VAL A 296 " =    0.941
peak=   -3.507 closest distance to " NE2 GLN A  88 " =    1.818
peak=   -3.504 closest distance to " O   ALA A   8 " =    1.888
peak=   -3.504 closest distance to " OD1 ASN A 301 " =    2.039
peak=   -3.504 closest distance to " O   HOH Z 109 " =    5.861
peak=   -3.492 closest distance to " C   MET A 188 " =    1.433
peak=   -3.489 closest distance to " CD  ARG A 139 " =    1.634
peak=   -3.485 closest distance to " CG2 THR A 178 " =    2.271
peak=   -3.479 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.472 closest distance to " O   HOH Z 166 " =    1.623
peak=   -3.463 closest distance to " O   HOH Z  13 " =    1.788
peak=   -3.462 closest distance to " CZ3 TRP A 179 " =    1.329
peak=   -3.461 closest distance to " N   SER A 276 " =    1.321
peak=   -3.460 closest distance to " OG  SER A   3 " =    1.455
peak=   -3.454 closest distance to " C   THR A 279 " =    1.203
peak=   -3.445 closest distance to " CG  LEU A   5 " =    0.848
peak=   -3.440 closest distance to " O   HOH Z 203 " =    1.784
peak=   -3.429 closest distance to " O   HOH Z 193 " =    1.707
peak=   -3.424 closest distance to " C   ILE A 239 " =    2.098
peak=   -3.418 closest distance to " CA  GLY A 133 " =    1.914
peak=   -3.413 closest distance to " CD2 LEU A 237 " =    2.704
peak=   -3.410 closest distance to " O   HOH Z  17 " =    1.212
peak=   -3.407 closest distance to " O   SER A 210 " =    1.935
peak=   -3.405 closest distance to " OG ASER A 134 " =    1.437
peak=   -3.402 closest distance to " CB  ASN A  39 " =    2.249
peak=   -3.399 closest distance to " O   HOH Z 154 " =    1.593
peak=   -3.384 closest distance to " O   HOH Z 191 " =    5.389
peak=   -3.380 closest distance to " CZ  TYR A 169 " =    1.845
peak=   -3.378 closest distance to " NH2 ARG A  79 " =    2.024
peak=   -3.377 closest distance to " O   HOH Z  63 " =    1.184
peak=   -3.375 closest distance to " CG  LEU A 228 " =    0.889
peak=   -3.372 closest distance to " O   HOH Z 131 " =    4.011
peak=   -3.368 closest distance to " O   HOH Z 426 " =    1.847
peak=   -3.362 closest distance to " O   HOH Z 196 " =    2.113
peak=   -3.354 closest distance to " C   ILE A 234 " =    1.263
peak=   -3.349 closest distance to " CA  GLY A  23 " =    1.782
peak=   -3.346 closest distance to " O   HOH Z 210 " =    0.848
peak=   -3.345 closest distance to " O   HOH Z 389 " =    1.906
peak=   -3.343 closest distance to " OG  SER A  97 " =    2.292
peak=   -3.342 closest distance to " CG  GLU A 152 " =    0.881
peak=   -3.341 closest distance to " O   HOH Z 421 " =    3.552
peak=   -3.339 closest distance to " ND2 ASN A  69 " =    1.767
peak=   -3.336 closest distance to " N   THR A  52 " =    1.703
peak=   -3.327 closest distance to " N   THR A 157 " =    1.525
peak=   -3.320 closest distance to " O   HOH Z  11 " =    1.880
peak=   -3.320 closest distance to " CE BMET A  47 " =    1.570
peak=   -3.316 closest distance to " O   HOH Z 102 " =    1.757
peak=   -3.309 closest distance to " O   HOH Z 313 " =    1.809
peak=   -3.306 closest distance to " CG  GLU A   2 " =    1.918
peak=   -3.305 closest distance to " OXT GLY A 302 " =    3.475
peak=   -3.303 closest distance to " O   LEU A 167 " =    1.534
peak=   -3.294 closest distance to " CA  ASP A 298 " =    1.093
peak=   -3.293 closest distance to " O   ALA A  51 " =    1.284
peak=   -3.292 closest distance to " O  BHOH Z 338 " =    1.248
peak=   -3.290 closest distance to " C   SER A 206 " =    1.623
peak=   -3.289 closest distance to " O   PRO A 198 " =    1.193
peak=   -3.285 closest distance to " O   HOH Z 165 " =    1.923
peak=   -3.280 closest distance to " CG  MET A 105 " =    0.851
peak=   -3.270 closest distance to " CZ  TYR A 172 " =    1.804
peak=   -3.267 closest distance to " O   ILE A 106 " =    1.867
peak=   -3.257 closest distance to " O   HOH Z 185 " =    2.483
peak=   -3.255 closest distance to " ND2 ASN A 173 " =    1.260
peak=   -3.250 closest distance to " O   ALA A 161 " =    1.749
peak=   -3.250 closest distance to " CG  GLU A  53 " =    1.642
peak=   -3.238 closest distance to " CG  TRP A 266 " =    1.915
peak=   -3.238 closest distance to " CG  PHE A 283 " =    2.737
peak=   -3.237 closest distance to " C   ALA A 158 " =    1.267
peak=   -3.231 closest distance to " CD1 PHE A 130 " =    2.229
peak=   -3.229 closest distance to " CE1 TYR A 247 " =    2.524
peak=   -3.224 closest distance to " O   HOH Z 197 " =    5.040
peak=   -3.221 closest distance to " O   HOH Z 250 " =    1.308
peak=   -3.221 closest distance to " O   SER A  95 " =    1.471
peak=   -3.219 closest distance to " O   HOH Z 427 " =    1.403
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    2.260
peak=   -3.213 closest distance to " O   HOH Z 193 " =    2.184
peak=   -3.210 closest distance to " CB  ALA A  43 " =    2.337
peak=   -3.209 closest distance to " O   HOH Z 116 " =    1.257
peak=   -3.206 closest distance to " CD2 LEU A 300 " =    2.875
peak=   -3.204 closest distance to " CD1 ILE A 199 " =    2.337
peak=   -3.204 closest distance to " OG BSER A 134 " =    1.752
peak=   -3.203 closest distance to " CB  ASN A  69 " =    1.111
peak=   -3.202 closest distance to " C   ASN A 285 " =    2.107
peak=   -3.200 closest distance to " O   HOH Z 348 " =    2.314
peak=   -3.198 closest distance to " OD2 ASP A  50 " =    1.360
peak=   -3.198 closest distance to " O   HOH Z 372 " =    2.281
peak=   -3.197 closest distance to " O   HOH Z 256 " =    1.300
peak=   -3.194 closest distance to " O   GLY A  80 " =    2.614
peak=   -3.190 closest distance to " O   GLY A  75 " =    1.554
peak=   -3.185 closest distance to " N   PRO A 163 " =    1.471
peak=   -3.179 closest distance to " N   THR A 220 " =    2.207
peak=   -3.178 closest distance to " O   HOH Z 249 " =    0.974
peak=   -3.177 closest distance to " CD  GLN A  11 " =    0.813
peak=   -3.177 closest distance to " O   HOH Z 295 " =    1.507
peak=   -3.173 closest distance to " O   HOH Z 111 " =    4.784
peak=   -3.173 closest distance to " NH1 ARG A 195 " =    2.515
peak=   -3.172 closest distance to " CA  GLY A 133 " =    2.252
peak=   -3.171 closest distance to " N   ALA A  43 " =    2.746
peak=   -3.169 closest distance to " O   HOH Z 139 " =    5.009
peak=   -3.165 closest distance to " CE1 TYR A 169 " =    2.309
peak=   -3.159 closest distance to " CD2 LEU A 237 " =    2.761
peak=   -3.153 closest distance to " CG  GLU A 277 " =    1.217
peak=   -3.142 closest distance to " O   HOH Z 139 " =    3.371
peak=   -3.140 closest distance to " ND2 ASN A  60 " =    1.376
peak=   -3.139 closest distance to " C   VAL A 265 " =    0.775
peak=   -3.137 closest distance to " O   HOH Z 339 " =    1.667
peak=   -3.137 closest distance to " O   MET A  40 " =    2.804
peak=   -3.131 closest distance to " OE1 GLN A 183 " =    1.490
peak=   -3.130 closest distance to " O   SER A   3 " =    1.013
peak=   -3.128 closest distance to " O   HOH Z  52 " =    1.629
peak=   -3.124 closest distance to " CE  LYS A 166 " =    3.034
peak=   -3.124 closest distance to " O   HOH Z 377 " =    1.201
peak=   -3.121 closest distance to " O   HOH Z 285 " =    3.674
peak=   -3.119 closest distance to " CD1 LEU A 228 " =    2.152
peak=   -3.118 closest distance to " O   VAL A 174 " =    2.163
peak=   -3.114 closest distance to " CZ  PHE A  38 " =    2.079
peak=   -3.108 closest distance to " CA  VAL A 296 " =    0.958
peak=   -3.108 closest distance to " O   HOH Z 174 " =    2.269
peak=   -3.107 closest distance to " CZ  ARG A 259 " =    0.807
peak=   -3.107 closest distance to " CE BMET A  47 " =    1.269
peak=   -3.106 closest distance to " O   HOH Z 422 " =    1.542
peak=   -3.105 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.099 closest distance to " N   HIS A 115 " =    2.191
peak=   -3.081 closest distance to " CG  PHE A 225 " =    1.257
peak=   -3.077 closest distance to " CB  ALA A  64 " =    2.503
peak=   -3.069 closest distance to " CB  TYR A 172 " =    2.374
peak=   -3.068 closest distance to " NE2 GLN A  88 " =    1.263
peak=   -3.066 closest distance to " O   SER A 276 " =    1.760
peak=   -3.064 closest distance to " O   ALA A 227 " =    1.427
peak=   -3.062 closest distance to " CG  ARG A 269 " =    2.128
peak=   -3.058 closest distance to " O   HOH Z 113 " =    1.861
peak=   -3.054 closest distance to " CG2 VAL A 189 " =    1.972
peak=   -3.012 closest distance to " CG  PRO A 163 " =    2.642

================= 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    :  0.4622 0.4532   6.264225e+00   6.255654e+00
   1_bss:  0.4533 0.4463   6.254284e+00   6.248352e+00
   1_xyz:  0.3629 0.3814   6.116898e+00   6.162958e+00
   1_adp:  0.3075 0.3532   6.002974e+00   6.104218e+00
   1_occ:  0.3072 0.3531   6.002015e+00   6.104500e+00
   2_bss:  0.3029 0.3468   6.000622e+00   6.101454e+00
   2_xyz:  0.2122 0.2558   5.683943e+00   5.848665e+00
   2_adp:  0.1873 0.2326   5.570414e+00   5.749831e+00
   2_occ:  0.1870 0.2325   5.569972e+00   5.750560e+00
   3_bss:  0.1835 0.2299   5.564407e+00   5.745189e+00
   3_xyz:  0.1419 0.1801   5.331151e+00   5.525653e+00
   3_adp:  0.1320 0.1733   5.271150e+00   5.479998e+00
   3_occ:  0.1318 0.1733   5.270619e+00   5.479822e+00
   4_bss:  0.1316 0.1731   5.268826e+00   5.476791e+00
   4_xyz:  0.1157 0.1612   5.178295e+00   5.414844e+00
   4_adp:  0.1130 0.1596   5.162720e+00   5.402337e+00
   4_occ:  0.1130 0.1596   5.162271e+00   5.401910e+00
   5_bss:  0.1130 0.1596   5.162313e+00   5.401943e+00
   5_xyz:  0.1119 0.1578   5.152546e+00   5.392159e+00
   5_adp:  0.1134 0.1562   5.154526e+00   5.384515e+00
   5_occ:  0.1134 0.1562   5.154187e+00   5.384417e+00
   5_bss:  0.1134 0.1562   5.154311e+00   5.384526e+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:  0.344  10.050   9.015   8.416   8.125   0.000   0.000   0.000
   1_xyz:  0.344  10.050   9.015   8.416   8.125   0.000   0.000   0.000
   1_adp:  0.344  10.050   9.015   8.416   8.125   0.000   0.000   0.000
   1_occ:  0.344  10.050   9.015   8.416   8.125   0.000   0.000   0.000
   2_bss:  0.326  35.730   5.142   4.467   4.896   0.000   0.000   0.000
   2_xyz:  0.326  35.730   5.142   4.467   4.896   0.000   0.000   0.000
   2_adp:  0.326  35.730   5.142   4.467   4.896   0.000   0.000   0.000
   2_occ:  0.326  35.730   5.142   4.467   4.896   0.000   0.000   0.000
   3_bss:  0.312  34.811   2.115   2.912   3.533   0.000   0.000   0.000
   3_xyz:  0.312  34.811   2.115   2.912   3.533   0.000   0.000   0.000
   3_adp:  0.312  34.811   2.115   2.912   3.533   0.000   0.000   0.000
   3_occ:  0.312  34.811   2.115   2.912   3.533   0.000   0.000   0.000
   4_bss:  0.316  38.486   1.325   2.366   3.149   0.000   0.000   0.000
   4_xyz:  0.316  38.486   1.325   2.366   3.149   0.000   0.000   0.000
   4_adp:  0.316  38.486   1.325   2.366   3.149   0.000   0.000   0.000
   4_occ:  0.316  38.486   1.325   2.366   3.149   0.000   0.000   0.000
   5_bss:  0.316  38.486   1.315   2.369   3.251   0.000   0.000   0.000
   5_xyz:  0.316  38.486   1.315   2.369   3.251   0.000   0.000   0.000
   5_adp:  0.316  38.486   1.315   2.369   3.251   0.000   0.000   0.000
   5_occ:  0.316  38.486   1.315   2.369   3.251   0.000   0.000   0.000
   5_bss:  0.320  40.798  -0.997   0.057   0.939   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.394 0.4792  0.5589    63619.900
   1_bss:  53.845 0.4715  0.7114    61932.205
   1_xyz:  43.615 0.5982  0.8796    43416.862
   1_adp:  38.129 0.6651  1.0046    35921.119
   1_occ:  38.121 0.6652  1.0035    35906.284
   2_bss:  37.652 0.6708  0.8878    35330.252
   2_xyz:  26.440 0.7952  1.0071    17569.906
   2_adp:  22.867 0.8330  1.0438    13939.688
   2_occ:  22.882 0.8328  1.0432    13956.301
   3_bss:  22.687 0.8347  0.9701    13740.878
   3_xyz:  17.099 0.8887  0.9997     8564.372
   3_adp:  16.100 0.8977  1.0025     7875.721
   3_occ:  16.089 0.8977  1.0026     7869.683
   4_bss:  16.022 0.8982  0.9824     7791.759
   4_xyz:  14.779 0.9086  0.9849     6864.556
   4_adp:  14.483 0.9113  0.9818     6710.379
   4_occ:  14.471 0.9114  0.9818     6701.822
   5_bss:  14.473 0.9113  0.9829     6701.416
   5_xyz:  14.244 0.9132  0.9837     6523.320
   5_adp:  14.053 0.9149  0.9835     6441.787
   5_occ:  14.047 0.9149  0.9834     6435.103
   5_bss:  14.051 0.9149  0.9834     6439.027
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3266e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3266e+01
   1_xyz:   1.617  0.012  0.105 18.209  0.006  4.105   1.3365e-01
   1_adp:   1.617  0.012  0.105 18.209  0.006  4.105   1.3365e-01
   1_occ:   1.617  0.012  0.105 18.209  0.006  4.105   1.3365e-01
   2_bss:   1.617  0.012  0.105 18.209  0.006  4.105   1.3365e-01
   2_xyz:   1.165  0.008  0.083 16.584  0.005  4.122   8.2727e-02
   2_adp:   1.165  0.008  0.083 16.584  0.005  4.122   8.2727e-02
   2_occ:   1.165  0.008  0.083 16.584  0.005  4.122   8.2727e-02
   3_bss:   1.165  0.008  0.083 16.584  0.005  4.122   8.2727e-02
   3_xyz:   0.968  0.006  0.071 15.651  0.004  4.119   5.7416e-02
   3_adp:   0.968  0.006  0.071 15.651  0.004  4.119   5.7416e-02
   3_occ:   0.968  0.006  0.071 15.651  0.004  4.119   5.7416e-02
   4_bss:   0.968  0.006  0.071 15.651  0.004  4.119   5.7416e-02
   4_xyz:   1.112  0.008  0.085 16.006  0.004  4.124   7.1852e-02
   4_adp:   1.112  0.008  0.085 16.006  0.004  4.124   7.1852e-02
   4_occ:   1.112  0.008  0.085 16.006  0.004  4.124   7.1852e-02
   5_bss:   1.112  0.008  0.085 16.006  0.004  4.124   7.1852e-02
   5_xyz:   1.028  0.007  0.080 15.648  0.004  4.116   6.3320e-02
   5_adp:   1.028  0.007  0.080 15.648  0.004  4.116   6.3320e-02
   5_occ:   1.028  0.007  0.080 15.648  0.004  4.116   6.3320e-02
   5_bss:   1.028  0.007  0.080 15.648  0.004  4.116   6.3320e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.013   6.8948e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.013   6.8948e+00
   1_xyz:  14.517  0.156  0.477 84.925  0.034  2.223   9.4214e-02
   1_adp:  14.517  0.156  0.477 84.925  0.034  2.223   9.4214e-02
   1_occ:  14.517  0.156  0.477 84.925  0.034  2.223   9.4214e-02
   2_bss:  14.517  0.156  0.477 84.925  0.034  2.223   9.4214e-02
   2_xyz:   6.769  0.102  0.297 83.373  0.053  2.224   6.9369e-02
   2_adp:   6.769  0.102  0.297 83.373  0.053  2.224   6.9369e-02
   2_occ:   6.769  0.102  0.297 83.373  0.053  2.224   6.9369e-02
   3_bss:   6.769  0.102  0.297 83.373  0.053  2.224   6.9369e-02
   3_xyz:   7.241  0.040  0.316 82.979  0.034  2.301   3.8481e-02
   3_adp:   7.241  0.040  0.316 82.979  0.034  2.301   3.8481e-02
   3_occ:   7.241  0.040  0.316 82.979  0.034  2.301   3.8481e-02
   4_bss:   7.241  0.040  0.316 82.979  0.034  2.301   3.8481e-02
   4_xyz:   7.083  0.051  0.497 82.965  0.035  2.239   6.6027e-02
   4_adp:   7.083  0.051  0.497 82.965  0.035  2.239   6.6027e-02
   4_occ:   7.083  0.051  0.497 82.965  0.035  2.239   6.6027e-02
   5_bss:   7.083  0.051  0.497 82.965  0.035  2.239   6.6027e-02
   5_xyz:   6.753  0.052  0.429 82.028  0.033  2.326   4.2732e-02
   5_adp:   6.753  0.052  0.429 82.028  0.033  2.326   4.2732e-02
   5_occ:   6.753  0.052  0.429 82.028  0.033  2.326   4.2732e-02
   5_bss:   6.753  0.052  0.429 82.028  0.033  2.326   4.2732e-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:  78.43   0.00  12.48  69.57   0.00   9.78  78.43   0.00  27.18
   1_occ:  78.43   0.00  12.48  69.57   0.00   9.78  78.43   0.00  27.18
   2_bss:  78.43   0.00  12.48  69.57   0.00   9.78  78.43   0.00  27.18
   2_xyz:  78.43   0.00  12.48  69.57   0.00   9.78  78.43   0.00  27.18
   2_adp:  78.39   0.00  12.58  76.20   0.00   8.88  78.39   2.39  32.71
   2_occ:  78.39   0.00  12.58  76.20   0.00   8.88  78.39   2.39  32.71
   3_bss:  78.39   0.00  12.58  76.20   0.00   8.88  78.39   2.39  32.71
   3_xyz:  78.39   0.00  12.58  76.20   0.00   8.88  78.39   2.39  32.71
   3_adp:  86.99   0.00  13.30  86.99   0.00   8.89  79.97   2.10  37.32
   3_occ:  86.99   0.00  13.30  86.99   0.00   8.89  79.97   2.10  37.32
   4_bss:  86.99   0.00  13.30  86.99   0.00   8.89  79.97   2.10  37.32
   4_xyz:  86.99   0.00  13.30  86.99   0.00   8.89  79.97   2.10  37.32
   4_adp:  89.70   0.00  13.04  89.70   0.00   8.69  76.20   2.14  36.70
   4_occ:  89.70   0.00  13.04  89.70   0.00   8.69  76.20   2.14  36.70
   5_bss:  89.70   0.00  13.04  89.70   0.00   8.69  76.20   2.14  36.70
   5_xyz:  89.70   0.00  13.04  89.70   0.00   8.69  76.20   2.14  36.70
   5_adp:  85.86   0.00  12.40  85.86   0.00   8.47  73.65   1.81  33.81
   5_occ:  85.86   0.00  12.40  85.86   0.00   8.47  73.65   1.81  33.81
   5_bss:  88.17   2.31  14.71  88.17   2.31  10.78  75.96   4.12  36.12
------------------------------------------------------------------------
 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:    1.224    0.021    0.409
   1_adp:    1.224    0.021    0.409
   1_occ:    1.224    0.021    0.409
   2_bss:    1.224    0.021    0.409
   2_xyz:    1.595    0.037    0.580
   2_adp:    1.595    0.037    0.580
   2_occ:    1.595    0.037    0.580
   3_bss:    1.595    0.037    0.580
   3_xyz:    1.619    0.037    0.617
   3_adp:    1.619    0.037    0.617
   3_occ:    1.619    0.037    0.617
   4_bss:    1.619    0.037    0.617
   4_xyz:    1.751    0.054    0.651
   4_adp:    1.751    0.054    0.651
   4_occ:    1.751    0.054    0.651
   5_bss:    1.751    0.054    0.651
   5_xyz:    1.784    0.046    0.657
   5_adp:    1.784    0.046    0.657
   5_occ:    1.784    0.046    0.657
   5_bss:    1.784    0.046    0.657
------------------------------------------------------------------------

CPU time actual refinement: 332.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/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_71/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_71/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.45 
  Macro-tasks:
    bulk solvent and scale       = 39.32  
    individual site refinement   = 132.97 
    weights calculation          = 32.30  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 211.23 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 104.15 
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.45 
    fmodel                         = 6.99   
    r_factors                      = 0.26   
    phase_errors                   = 10.61  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 246.95 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.758 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    638 calls, 103.91 s
gradients_fft:          584 calls, 100.83 s

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

# Date 2008-01-16 Time 00:39:19 PST -0800 (1200472759.14 s)
Start R-work = 0.4622, R-free = 0.4532 (no bulk solvent and anisotropic scale)
Final R-work = 0.1317, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.4533, R-free = 0.4463
Final R-work = 0.1134, R-free = 0.1562