# Date 2008-01-16 Time 02:22:19 PST -0800 (1200478939.01 s)
#phil __OFF__

Command line arguments: "../809.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19521
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 809

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0104

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.3009 [2092/2117]  1883   209  10.0%
  bin  2:  4.3009 -  3.4270 [2025/2043]  1823   202  10.0%
  bin  3:  3.4270 -  2.9977 [1983/2002]  1784   199  10.0%
  bin  4:  2.9977 -  2.7254 [1955/1985]  1760   195  10.0%
  bin  5:  2.7254 -  2.5310 [1960/1979]  1764   196  10.0%
  bin  6:  2.5310 -  2.3824 [1950/1975]  1752   198  10.2%
  bin  7:  2.3824 -  2.2635 [1944/1972]  1755   189   9.7%
  bin  8:  2.2635 -  2.1653 [1938/1974]  1741   197  10.2%
  bin  9:  2.1653 -  2.0821 [1905/1947]  1714   191  10.0%
  bin 10:  2.0821 -  2.0104 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2167
        3.04 -     3.66: 4617
        3.66 -     4.28: 8920
        4.28 -     4.90: 12280
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.944 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.337 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27988 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_809/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/model_refine_001.geo

CPU time processing inputs: 9.70


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4362   r_free= 0.4203   ksol= 0.00   Bsol= 0.00   scale= 0.814    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.229520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.3612 0.3331      6.5222      6.4355|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.3306 0.3573      6.6436      6.7334|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.3779 0.3634      6.5864      6.5611|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.4176 0.3597      6.4727      6.3515|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.4545 0.4297      6.3216      6.3163|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.4578 0.4909      6.2431      6.2314|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.4801 0.4594      6.2132      6.1213|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.4794 0.4251       6.162      6.1317|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.4855 0.4930      6.0961      6.1023|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.5028 0.4816       6.116      6.0898|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.4905 0.4575      6.0221      6.0258|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.5044 0.4538      5.9851       5.995|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.4944 0.5299      5.8872      5.9048|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.5092 0.4648      5.8452      5.7358|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7966  1370   153  0.74  30.37   0.81     0.76      56167.57|
|  2:  4.7966 -  3.8277  1303   145  0.78  28.56   0.91     0.81      73990.23|
|  3:  3.8277 -  3.3500  1280   142  0.71  34.23   0.86     0.78      76696.84|
|  4:  3.3500 -  3.0464  1281   140  0.66  39.27   0.83     0.71      66904.83|
|  5:  3.0464 -  2.8296  1257   142  0.57  46.51   0.77     0.63      59210.28|
|  6:  2.8296 -  2.6637  1273   140  0.54  48.71   0.76     0.59      54748.38|
|  7:  2.6637 -  2.5310  1250   139  0.51  50.91   0.74     0.57      51371.78|
|  8:  2.5310 -  2.4213  1255   140  0.51  51.61   0.78     0.57      46896.83|
|  9:  2.4213 -  2.3284  1240   140  0.51  51.26   0.73     0.57      41507.88|
| 10:  2.3284 -  2.2483  1236   137  0.52  50.92   0.74     0.58      38494.05|
| 11:  2.2483 -  2.1783  1254   137  0.48  53.89   0.77     0.55      36567.26|
| 12:  2.1783 -  2.1162  1234   138  0.45  56.26   0.77     0.53      36163.35|
| 13:  2.1162 -  2.0606  1231   134  0.43  57.45   0.75     0.50      31814.77|
| 14:  2.0606 -  2.0104  1166   132  0.47  54.47   0.72     0.51      24875.25|
|alpha:            min =        0.50 max =            0.81 mean =         0.62|
|beta:             min =    24875.25 max =        76696.84 mean =     50035.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.49|
|phase err.(test): min =        0.00 max =           89.89 mean =        46.55|
|-----------------------------------------------------------------------------|

============================== 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 = 7.826858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.336   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.677142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.384   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1482 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2594 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3868 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5007 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6554 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7637 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.197 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.638 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4439   r_free= 0.4225   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.235521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4291   r_free= 0.4068   ksol= 0.30   Bsol= 20.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,9.48,8.40,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.224487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.422964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.937   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.638218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.742   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4291      final r-factor (work) = 0.3159          |
| start r-factor (free) = 0.4068      final r-factor (free) = 0.3389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.3692 = 7.42 * 0.50 * 6.2434 + 1.00 * 54.1971                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6175 = 7.42 * 0.50 * 6.0613 + 1.00 * 0.1210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3159      final r-factor (work) = 0.2535          |
| start r-factor (free) = 0.3389      final r-factor (free) = 0.2872          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8832 = 0.64 * 1.00 * 6.0613 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7706 = 0.64 * 1.00 * 5.8888 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.35   10.58    None  None   None       |
|    all(noH): 2823   0      0.00    87.35   10.58    None  None   None       |
|    Sol.    : 438    0      0.00    87.35   27.59    None  None   None       |
|    Mac.    : 2385   0      0.00    62.02   7.46     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 -   8.735: 1738   |   5:    43.673 -  52.407:   50        |
|      1:     8.735 -  17.469:  564   |   6:    52.407 -  61.142:   17        |
|      2:    17.469 -  26.204:  220   |   7:    61.142 -  69.876:    3        |
|      3:    26.204 -  34.938:  127   |   8:    69.876 -  78.611:    0        |
|      4:    34.938 -  43.673:  103   |   9:    78.611 -  87.346:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2535 r_free = 0.2872             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2526 r_free = 0.2876             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2526   r_free= 0.2876   ksol= 0.30   Bsol= 20.00   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,9.48,8.40,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.823567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2486   r_free= 0.2816   ksol= 0.33   Bsol= 50.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,5.92,5.32,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.823205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.512976              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.733  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2486      final r-factor (work) = 0.1700          |
| start r-factor (free) = 0.2816      final r-factor (free) = 0.2043          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4736 = 3.51 * 0.50 * 5.8940 + 1.00 * 0.1208                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9791 = 3.51 * 0.50 * 5.6429 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1700      final r-factor (work) = 0.1549          |
| start r-factor (free) = 0.2043      final r-factor (free) = 0.1920          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0053 = 0.35 * 1.00 * 5.6429 + 1.00 * 0.0238                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9787 = 0.35 * 1.00 * 5.4273 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.87   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    81.87   11.08    None  None   None       |
|    Sol.    : 438    0      0.00    81.87   32.18    None  None   None       |
|    Mac.    : 2385   0      0.00    65.81   7.20     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 -   8.188: 1725   |   5:    40.937 -  49.125:  108        |
|      1:     8.188 -  16.375:  545   |   6:    49.125 -  57.312:   44        |
|      2:    16.375 -  24.562:  158   |   7:    57.312 -  65.500:   14        |
|      3:    24.562 -  32.750:  117   |   8:    65.500 -  73.687:    1        |
|      4:    32.750 -  40.937:  110   |   9:    73.687 -  81.875:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1549 r_free = 0.1920             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1547 r_free = 0.1922             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.1922   ksol= 0.33   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,5.92,5.32,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.399699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.1925   ksol= 0.33   Bsol= 54.83   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.28,4.66,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.400180                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.792540              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.662  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.494582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.759   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1542      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9347 = 1.79 * 0.50 * 5.4307 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8259 = 1.79 * 0.50 * 5.3191 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1297      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9681 = 1.49 * 1.00 * 5.3191 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8359 = 1.49 * 1.00 * 5.2228 + 1.00 * 0.0301                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.92   11.87    None  None   None       |
|    all(noH): 2823   0      0.00    83.92   11.87    None  None   None       |
|    Sol.    : 438    0      0.00    76.22   36.18    None  None   None       |
|    Mac.    : 2385   0      0.00    83.92   7.41     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 -   8.392: 1751   |   5:    41.961 -  50.353:   90        |
|      1:     8.392 -  16.784:  507   |   6:    50.353 -  58.745:   72        |
|      2:    16.784 -  25.177:  146   |   7:    58.745 -  67.137:   38        |
|      3:    25.177 -  33.569:  111   |   8:    67.137 -  75.529:   13        |
|      4:    33.569 -  41.961:   91   |   9:    75.529 -  83.922:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1647             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1241 r_free = 0.1647             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1647   ksol= 0.33   Bsol= 54.83   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.28,4.66,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217621                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1653   ksol= 0.33   Bsol= 54.83   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,3.87,4.57,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219463                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.562536              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.991  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.630149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.904   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7512 = 2.56 * 0.50 * 5.2232 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7125 = 2.56 * 0.50 * 5.1823 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2854 = 0.63 * 1.00 * 5.1823 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2811 = 0.63 * 1.00 * 5.1644 + 1.00 * 0.0268                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.40   11.66    None  None   None       |
|    all(noH): 2823   0      0.00    85.40   11.66    None  None   None       |
|    Sol.    : 438    0      0.41    75.66   35.39    None  None   None       |
|    Mac.    : 2385   0      0.00    85.40   7.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.540: 1792   |   5:    42.700 -  51.239:   92        |
|      1:     8.540 -  17.080:  485   |   6:    51.239 -  59.779:   57        |
|      2:    17.080 -  25.620:  151   |   7:    59.779 -  68.319:   30        |
|      3:    25.620 -  34.160:  100   |   8:    68.319 -  76.859:   13        |
|      4:    34.160 -  42.700:  100   |   9:    76.859 -  85.399:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1594             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1592             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1592   ksol= 0.33   Bsol= 54.83   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,3.87,4.57,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.159746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1592   ksol= 0.32   Bsol= 54.13   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.83,4.65,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.159577                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.764865              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.432  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.462824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.417   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2119 = 2.76 * 0.50 * 5.1641 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1957 = 2.76 * 0.50 * 5.1521 + 1.00 * 0.0732                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3991 = 0.46 * 1.00 * 5.1521 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3963 = 0.46 * 1.00 * 5.1490 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.13   11.27    None  None   None       |
|    all(noH): 2823   0      0.00    86.13   11.27    None  None   None       |
|    Sol.    : 438    0      0.67    74.80   33.86    None  None   None       |
|    Mac.    : 2385   0      0.00    86.13   7.13     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 -   8.613: 1809   |   5:    43.064 -  51.676:   85        |
|      1:     8.613 -  17.226:  477   |   6:    51.676 -  60.289:   50        |
|      2:    17.226 -  25.838:  156   |   7:    60.289 -  68.902:   16        |
|      3:    25.838 -  34.451:  112   |   8:    68.902 -  77.515:   10        |
|      4:    34.451 -  43.064:  105   |   9:    77.515 -  86.127:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1577             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1577             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1577   ksol= 0.32   Bsol= 54.13   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.83,4.65,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148485                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.1013 0.1313      5.3991      5.5215|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.0861 0.1112      5.4434      5.6458|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.1034 0.1480      5.4713       5.861|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.1202 0.1471      5.4514      5.5796|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.1302 0.1758      5.3368      5.5343|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.1217 0.1833      5.2255       5.489|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.1263 0.1716       5.174      5.3939|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.1169 0.1723      5.0909      5.3808|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.1176 0.1725      5.0513       5.272|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.1150 0.1863      5.0045      5.2949|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.1146 0.1681      4.9524       5.229|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.1127 0.1744      4.9014      5.2416|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.1138 0.1698      4.8084      5.0712|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.1061 0.1766      4.6723      4.9586|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7966  1370   153  0.94   9.27   0.97     0.95       7452.96|
|  2:  4.7966 -  3.8277  1303   145  0.95   8.02   1.00     0.99       9133.79|
|  3:  3.8277 -  3.3500  1280   142  0.94  10.86   1.02     1.01      10309.95|
|  4:  3.3500 -  3.0464  1281   140  0.92  13.20   1.00     0.98      10078.24|
|  5:  3.0464 -  2.8296  1257   142  0.90  15.77   0.99     0.96       8445.39|
|  6:  2.8296 -  2.6637  1273   140  0.90  15.87   0.98     0.95       7257.89|
|  7:  2.6637 -  2.5310  1250   139  0.90  15.71   0.98     0.95       6277.97|
|  8:  2.5310 -  2.4213  1255   140  0.91  14.86   0.99     0.96       5475.89|
|  9:  2.4213 -  2.3284  1240   140  0.91  15.76   1.00     0.97       5232.02|
| 10:  2.3284 -  2.2483  1236   137  0.90  15.93   1.00     0.95       4672.08|
| 11:  2.2483 -  2.1783  1254   137  0.90  16.31   0.99     0.95       4505.09|
| 12:  2.1783 -  2.1162  1234   138  0.91  15.31   1.00     0.99       4083.18|
| 13:  2.1162 -  2.0606  1231   134  0.91  15.65   0.99     0.98       3428.63|
| 14:  2.0606 -  2.0104  1166   132  0.91  14.77   0.97     0.93       2554.93|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2554.93 max =        10309.95 mean =      6406.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1577   ksol= 0.32   Bsol= 54.28   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.12,0.77,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148552                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1577   ksol= 0.32   Bsol= 54.28   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.12,0.77,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148552                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.1011 0.1313      5.3973      5.5202|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.0859 0.1109      5.4413      5.6426|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.1033 0.1481      5.4703      5.8614|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.1203 0.1474      5.4522      5.5803|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.1303 0.1761      5.3383      5.5357|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.1218 0.1834      5.2267      5.4898|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.1264 0.1718      5.1748      5.3948|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.1170 0.1722      5.0914      5.3811|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.1177 0.1724      5.0514      5.2719|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.1150 0.1864      5.0047      5.2956|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.1146 0.1682      4.9528      5.2294|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.1127 0.1745      4.9015      5.2417|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.1138 0.1699      4.8085      5.0715|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.1061 0.1765      4.6724      4.9582|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7966  1370   153  0.94   9.26   0.97     0.95       7432.12|
|  2:  4.7966 -  3.8277  1303   145  0.95   7.99   1.01     0.99       9100.99|
|  3:  3.8277 -  3.3500  1280   142  0.94  10.84   1.02     1.01      10284.97|
|  4:  3.3500 -  3.0464  1281   140  0.92  13.22   1.00     0.98      10096.68|
|  5:  3.0464 -  2.8296  1257   142  0.90  15.79   0.99     0.96       8468.33|
|  6:  2.8296 -  2.6637  1273   140  0.90  15.90   0.98     0.95       7277.25|
|  7:  2.6637 -  2.5310  1250   139  0.90  15.72   0.98     0.96       6288.09|
|  8:  2.5310 -  2.4213  1255   140  0.91  14.87   0.99     0.96       5479.85|
|  9:  2.4213 -  2.3284  1240   140  0.91  15.77   1.00     0.97       5234.19|
| 10:  2.3284 -  2.2483  1236   137  0.90  15.93   1.00     0.95       4674.84|
| 11:  2.2483 -  2.1783  1254   137  0.90  16.32   0.99     0.96       4508.84|
| 12:  2.1783 -  2.1162  1234   138  0.91  15.32   1.00     0.99       4086.03|
| 13:  2.1162 -  2.0606  1231   134  0.91  15.66   0.99     0.98       3429.44|
| 14:  2.0606 -  2.0104  1166   132  0.91  14.77   0.97     0.93       2554.35|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2554.35 max =        10284.97 mean =      6406.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.03|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.94    90.07   15.22    None  None   None       |
|    all(noH): 2823   0      3.94    90.07   15.22    None  None   None       |
|    Sol.    : 438    0      4.61    78.74   37.81    None  None   None       |
|    Mac.    : 2385   0      3.94    90.07   11.07    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:     3.944 -  12.556: 1809   |   5:    47.007 -  55.620:   85        |
|      1:    12.556 -  21.169:  477   |   6:    55.620 -  64.233:   50        |
|      2:    21.169 -  29.782:  156   |   7:    64.233 -  72.845:   16        |
|      3:    29.782 -  38.394:  112   |   8:    72.845 -  81.458:   10        |
|      4:    38.394 -  47.007:  105   |   9:    81.458 -  90.071:    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)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.287 - 4.834
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 322
   mapped sites are within: 0.716 - 4.834

peak=   10.337 closest distance to " CG2 VAL A 230 " =    1.412
peak=    6.389 closest distance to " CG  LEU A   5 " =    1.230
peak=    6.262 closest distance to " CG2 VAL A 296 " =    1.076
peak=    6.084 closest distance to " NH2 ARG A  56 " =    2.318
peak=    5.614 closest distance to " CG  LEU A 228 " =    1.202
peak=    5.609 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.459 closest distance to " CB  VAL A 296 " =    1.068
peak=    5.321 closest distance to " CG  PRO A  54 " =    1.281
peak=    4.917 closest distance to " CB  VAL A 230 " =    1.243
peak=    4.874 closest distance to " CB  SER A  63 " =    1.261
peak=    4.811 closest distance to " CB  PRO A  54 " =    0.912
peak=    4.808 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.762 closest distance to " CD2 LEU A   5 " =    1.148
peak=    4.606 closest distance to " CB  ARG A 275 " =    0.903
peak=    4.604 closest distance to " O   HOH Z 232 " =    2.326
peak=    4.589 closest distance to " NE2 GLN A  11 " =    1.111
peak=    4.521 closest distance to " CZ  PHE A 218 " =    1.102
peak=    4.407 closest distance to " CB  GLU A 152 " =    1.180
peak=    4.401 closest distance to " C   PRO A 198 " =    1.506
peak=    4.323 closest distance to " O   HOH Z 369 " =    2.200
peak=    4.321 closest distance to " O   HOH Z 265 " =    2.293
peak=    4.315 closest distance to " O   HOH Z 423 " =    1.831
peak=    4.286 closest distance to " CB  ARG A 190 " =    1.611
peak=    4.279 closest distance to " CG  PRO A 243 " =    1.134
peak=    4.267 closest distance to " CB  GLU A 277 " =    3.653
peak=    4.251 closest distance to " O   SER A  87 " =    2.274
peak=    4.239 closest distance to " CB  ARG A  79 " =    1.436
peak=    4.230 closest distance to " CG  PRO A 213 " =    1.185
peak=    4.222 closest distance to " O   HOH Z 298 " =    1.826
peak=    4.214 closest distance to " O   HOH Z 346 " =    1.558
peak=    4.211 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.207 closest distance to " O   HOH Z 272 " =    1.915
peak=    4.196 closest distance to " OD1 ASN A  69 " =    2.594
peak=    4.186 closest distance to " O   HOH Z 236 " =    1.898
peak=    4.169 closest distance to " O   HOH Z 126 " =    1.838
peak=    4.161 closest distance to " O   HOH Z 368 " =    2.306
peak=    4.118 closest distance to " CB  ASP A 140 " =    0.976
peak=    4.117 closest distance to " ND2 ASN A 187 " =    1.525
peak=    4.117 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.106 closest distance to " O   HOH Z 303 " =    2.168
peak=    4.104 closest distance to " O   HOH Z  43 " =    2.034
peak=    4.083 closest distance to " O   HOH Z 316 " =    3.098
peak=    4.078 closest distance to " O   HOH Z 389 " =    1.970
peak=    4.070 closest distance to " O   HOH Z 189 " =    2.857
peak=    4.068 closest distance to " O   HOH Z 427 " =    3.045
peak=    4.063 closest distance to " O   HOH Z 142 " =    1.573
peak=    4.061 closest distance to " O   HOH Z  78 " =    1.632
peak=    4.050 closest distance to " O   HOH Z  61 " =    1.641
peak=    4.031 closest distance to " O   HOH Z  80 " =    1.695
peak=    4.018 closest distance to " O   HOH Z 280 " =    2.979
peak=    4.000 closest distance to " O   HOH Z 403 " =    1.692
peak=    3.997 closest distance to " O   HOH Z 234 " =    3.649
peak=    3.994 closest distance to " O   HOH Z 402 " =    1.494
peak=    3.991 closest distance to " O   HOH Z 158 " =    3.130
peak=    3.990 closest distance to " NH2 ARG A 156 " =    1.124
peak=    3.973 closest distance to " CB  VAL A 265 " =    1.320
peak=    3.967 closest distance to " OG BSER A 164 " =    2.268
peak=    3.957 closest distance to " O   HOH Z  44 " =    2.198
peak=    3.951 closest distance to " CB  TRP A 266 " =    0.960
peak=    3.935 closest distance to " CB  ASN A 148 " =    1.391
peak=    3.931 closest distance to " O   HOH Z  63 " =    1.939
peak=    3.929 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.902 closest distance to " CG1 VAL A 153 " =    0.999
peak=    3.892 closest distance to " CB  GLU A 128 " =    1.081
peak=    3.888 closest distance to " CD  LYS A 166 " =    1.286
peak=    3.861 closest distance to " O   HOH Z 248 " =    1.630
peak=    3.856 closest distance to " O   HOH Z  15 " =    2.107
peak=    3.836 closest distance to " CA  ALA A  51 " =    0.950
peak=    3.811 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.811 closest distance to " CB  ALA A   9 " =    1.635
peak=    3.798 closest distance to " O   HOH Z 126 " =    1.608
peak=    3.787 closest distance to " CB  SER A   3 " =    1.247
peak=    3.783 closest distance to " O   HOH Z 411 " =    3.719
peak=    3.767 closest distance to " O   HOH Z 193 " =    1.882
peak=    3.765 closest distance to " CB  LEU A 143 " =    1.193
peak=    3.740 closest distance to " O   HOH Z  97 " =    2.017
peak=    3.730 closest distance to " CG1BVAL A  72 " =    1.743
peak=    3.725 closest distance to " CB  TRP A 179 " =    1.467
peak=    3.724 closest distance to " CB  ASN A 187 " =    1.251
peak=    3.722 closest distance to " O   HOH Z  48 " =    1.707
peak=    3.717 closest distance to " CD1 LEU A 300 " =    1.254
peak=    3.705 closest distance to " CD2 LEU A 228 " =    1.142
peak=    3.701 closest distance to " CD  ARG A 269 " =    0.948
peak=    3.700 closest distance to " O   HOH Z 214 " =    2.311
peak=    3.690 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.689 closest distance to " O   HOH Z 197 " =    2.919
peak=    3.689 closest distance to " O   HOH Z 371 " =    3.115
peak=    3.689 closest distance to " O   HOH Z 426 " =    1.506
peak=    3.688 closest distance to " CG2 THR A 221 " =    1.158
peak=    3.685 closest distance to " N   ASN A  39 " =    1.247
peak=    3.683 closest distance to " O   HOH Z 422 " =    2.725
peak=    3.677 closest distance to " O   HOH Z 172 " =    3.853
peak=    3.670 closest distance to " O   HOH Z 203 " =    1.827
peak=    3.662 closest distance to " O   HOH Z 193 " =    1.683
peak=    3.659 closest distance to " O   HOH Z 261 " =    1.870
peak=    3.659 closest distance to " O   HOH Z  40 " =    1.629
peak=    3.656 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.650 closest distance to " O   HOH Z 285 " =    2.890
peak=    3.644 closest distance to " CA  ALA A  21 " =    1.186
peak=    3.632 closest distance to " O   HOH Z  19 " =    2.009
peak=    3.625 closest distance to " CB  ASN A 142 " =    1.095
peak=    3.618 closest distance to " O   HOH Z 313 " =    1.797
peak=    3.618 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.613 closest distance to " O   HOH Z 383 " =    2.120
peak=    3.604 closest distance to " O   MET A 105 " =    1.865
peak=    3.604 closest distance to " O   HOH Z 102 " =    1.329
peak=    3.600 closest distance to " O   HOH Z 130 " =    2.275
peak=    3.597 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.592 closest distance to " CG1 ILE A  49 " =    1.535
peak=    3.591 closest distance to " O   HOH Z 112 " =    1.681
peak=    3.588 closest distance to " O   HOH Z 147 " =    1.811
peak=    3.581 closest distance to " CB  MET A  40 " =    0.793
peak=    3.578 closest distance to " O   HOH Z 145 " =    2.222
peak=    3.576 closest distance to " O   HOH Z 193 " =    2.152
peak=    3.573 closest distance to " CB  THR A 157 " =    1.191
peak=    3.570 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.567 closest distance to " CD ALYS A 290 " =    1.037
peak=    3.562 closest distance to " CA  ALA A 158 " =    1.220
peak=    3.559 closest distance to " NH1AARG A 145 " =    1.221
peak=    3.558 closest distance to " CG  MET A 185 " =    1.151
peak=    3.551 closest distance to " CG  ARG A  66 " =    2.739
peak=    3.549 closest distance to " CB BVAL A  41 " =    1.111
peak=    3.548 closest distance to " CG BARG A 275 " =    1.294
peak=    3.543 closest distance to " O   ASP A 124 " =    1.225
peak=    3.533 closest distance to " CA  THR A 264 " =    0.785
peak=    3.531 closest distance to " O   HOH Z 245 " =    1.374
peak=    3.526 closest distance to " CA  ASP A 191 " =    0.819
peak=    3.522 closest distance to " CB  ALA A 291 " =    1.371
peak=    3.521 closest distance to " O   HOH Z 227 " =    1.708
peak=    3.515 closest distance to " CD2 TRP A 179 " =    1.374
peak=    3.512 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.510 closest distance to " O   HOH Z 273 " =    2.826
peak=    3.508 closest distance to " CA  VAL A  41 " =    0.794
peak=    3.506 closest distance to " O   HOH Z 134 " =    1.415
peak=    3.498 closest distance to " NE2 GLN A  77 " =    3.301
peak=    3.496 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.496 closest distance to " CA  GLY A 267 " =    0.716
peak=    3.494 closest distance to " OD2 ASP A 286 " =    2.906
peak=    3.492 closest distance to " O   TRP A 274 " =    1.889
peak=    3.489 closest distance to " O   HOH Z 250 " =    1.405
peak=    3.478 closest distance to " CG2 VAL A 257 " =    0.848
peak=    3.475 closest distance to " CD  ARG A 159 " =    0.754
peak=    3.475 closest distance to " CA  ASN A 215 " =    1.212
peak=    3.474 closest distance to " CG2 ILE A  20 " =    1.432
peak=    3.472 closest distance to " O   HOH Z 171 " =    3.855
peak=    3.468 closest distance to " O   HOH Z 133 " =    2.349
peak=    3.464 closest distance to " CG1 ILE A  33 " =    1.289
peak=    3.464 closest distance to " CB  ALA A 248 " =    1.475
peak=    3.462 closest distance to " O   HOH Z  20 " =    1.506
peak=    3.460 closest distance to " OG1 THR A 294 " =    2.396
peak=    3.457 closest distance to " O   HOH Z 425 " =    2.001
peak=    3.454 closest distance to " CB  THR A  31 " =    1.612
peak=    3.451 closest distance to " CA  LYS A 117 " =    1.281
peak=    3.451 closest distance to " OD1 ASN A 217 " =    1.620
peak=    3.446 closest distance to " CG1 ILE A 151 " =    1.058
peak=    3.442 closest distance to " CG1 VAL A 296 " =    1.161
peak=    3.442 closest distance to " CB  ALA A 242 " =    0.862
peak=    3.438 closest distance to " O   HOH Z 425 " =    1.344
peak=    3.438 closest distance to " CA  LEU A 282 " =    1.115
peak=    3.437 closest distance to " ND1 HIS A  81 " =    1.677
peak=    3.435 closest distance to " CB  ILE A 120 " =    1.314
peak=    3.430 closest distance to " CB  SER A 273 " =    0.869
peak=    3.428 closest distance to " O   HOH Z 406 " =    1.531
peak=    3.422 closest distance to " O   GLN A 278 " =    1.516
peak=    3.421 closest distance to " O   HOH Z 435 " =    2.017
peak=    3.420 closest distance to " CA  THR A 221 " =    0.905
peak=    3.417 closest distance to " O   HOH Z  88 " =    3.150
peak=    3.416 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.411 closest distance to " O   HOH Z 180 " =    2.143
peak=    3.407 closest distance to " CB  GLN A  89 " =    1.135
peak=    3.407 closest distance to " O   HOH Z 294 " =    1.563
peak=    3.404 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.394 closest distance to " O   HOH Z  68 " =    2.121
peak=    3.392 closest distance to " O   HOH Z 251 " =    1.474
peak=    3.391 closest distance to " CE1 TYR A 186 " =    1.295
peak=    3.390 closest distance to " O   HOH Z  97 " =    2.501
peak=    3.380 closest distance to " CA  ASP A 162 " =    1.001
peak=    3.378 closest distance to " O   HOH Z 126 " =    1.779
peak=    3.376 closest distance to " CB  TRP A 150 " =    1.415
peak=    3.372 closest distance to " O   HOH Z 327 " =    2.529
peak=    3.371 closest distance to " N   SER A 135 " =    1.482
peak=    3.369 closest distance to " O   HOH Z 345 " =    3.215
peak=    3.367 closest distance to " CG  GLN A  58 " =    2.879
peak=    3.366 closest distance to " O   ALA A 158 " =    1.339
peak=    3.364 closest distance to " CE1 HIS A 108 " =    1.132
peak=    3.364 closest distance to " O   HOH Z 437 " =    1.893
peak=    3.354 closest distance to " O   HOH Z 128 " =    2.360
peak=    3.354 closest distance to " O   HOH Z 133 " =    1.579
peak=    3.353 closest distance to " O   HOH Z 403 " =    1.396
peak=    3.352 closest distance to " O   HOH Z 187 " =    2.354
peak=    3.351 closest distance to " CZ3 TRP A  85 " =    0.981
peak=    3.349 closest distance to " CB  ALA A 100 " =    1.243
peak=    3.349 closest distance to " N   VAL A 126 " =    1.426
peak=    3.344 closest distance to " CA  VAL A 125 " =    1.197
peak=    3.341 closest distance to " CG  MET A 185 " =    1.056
peak=    3.341 closest distance to " O   HOH Z 234 " =    1.791
peak=    3.338 closest distance to " O   HOH Z 271 " =    2.738
peak=    3.337 closest distance to " O   HOH Z 421 " =    1.799
peak=    3.329 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.329 closest distance to " NH2 ARG A  79 " =    1.294
peak=    3.328 closest distance to " OG  SER A  22 " =    2.791
peak=    3.327 closest distance to " O   HOH Z 305 " =    3.716
peak=    3.323 closest distance to " O   HOH Z 148 " =    3.208
peak=    3.321 closest distance to " CA  SER A  87 " =    1.049
peak=    3.319 closest distance to " CB  HIS A 108 " =    0.748
peak=    3.319 closest distance to " O   HOH Z 313 " =    1.682
peak=    3.317 closest distance to " O  BHOH Z 338 " =    2.443
peak=    3.316 closest distance to " CB  LEU A 228 " =    1.231
peak=    3.311 closest distance to " NZ  LYS A  48 " =    1.300
peak=    3.301 closest distance to " O   HOH Z 327 " =    1.767
peak=    3.301 closest distance to " CB  SER A  26 " =    1.789
peak=    3.300 closest distance to " CA  ARG A  36 " =    1.103
peak=    3.292 closest distance to " O   HOH Z 128 " =    2.154
peak=    3.292 closest distance to " OG  SER A 245 " =    1.619
peak=    3.290 closest distance to " O   HOH Z 247 " =    1.352
peak=    3.288 closest distance to " O   HOH Z 174 " =    2.474
peak=    3.286 closest distance to " CB  ALA A 248 " =    1.076
peak=    3.284 closest distance to " O   HOH Z  89 " =    1.694
peak=    3.283 closest distance to " O   HOH Z 365 " =    2.980
peak=    3.280 closest distance to " O   HOH Z 240 " =    2.369
peak=    3.279 closest distance to " CB  ALA A 295 " =    1.353
peak=    3.277 closest distance to " CB  THR A  52 " =    1.003
peak=    3.273 closest distance to " O   HOH Z 163 " =    1.594
peak=    3.273 closest distance to " CB  LYS A 117 " =    1.207
peak=    3.270 closest distance to " CZ  PHE A  38 " =    1.159
peak=    3.269 closest distance to " CZ  PHE A 192 " =    0.943
peak=    3.267 closest distance to " O   HOH Z 291 " =    1.549
peak=    3.267 closest distance to " CD1 LEU A   5 " =    1.353
peak=    3.265 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.263 closest distance to " CA  ILE A 106 " =    0.743
peak=    3.262 closest distance to " CB  GLN A 278 " =    0.851
peak=    3.257 closest distance to " CA  ALA A 295 " =    1.071
peak=    3.256 closest distance to " O   HOH Z 295 " =    1.501
peak=    3.254 closest distance to " O   HOH Z 420 " =    2.000
peak=    3.254 closest distance to " CA  ALA A 233 " =    1.484
peak=    3.244 closest distance to " CB  ALA A   1 " =    4.834
peak=    3.243 closest distance to " CB  THR A  82 " =    1.454
peak=    3.242 closest distance to " CB  GLN A 205 " =    1.175
peak=    3.242 closest distance to " CA  TYR A 116 " =    1.413
peak=    3.231 closest distance to " O   HOH Z  90 " =    3.316
peak=    3.231 closest distance to " CB  ASN A 224 " =    1.011
peak=    3.226 closest distance to " N   ARG A 190 " =    1.057
peak=    3.226 closest distance to " OE1 GLN A  11 " =    1.818
peak=    3.223 closest distance to " CB  MET A  47 " =    1.082
peak=    3.223 closest distance to " CA  GLY A 211 " =    1.316
peak=    3.219 closest distance to " CA  ASP A 140 " =    1.272
peak=    3.218 closest distance to " CA  MET A 105 " =    0.954
peak=    3.216 closest distance to " CE2 TYR A  30 " =    0.749
peak=    3.215 closest distance to " O   HOH Z 325 " =    2.235
peak=    3.215 closest distance to " CB  SER A 212 " =    1.230
peak=    3.214 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.210 closest distance to " CB  ASN A 110 " =    1.132
peak=    3.209 closest distance to " O   HOH Z 261 " =    1.655
peak=    3.205 closest distance to " O   HOH Z 146 " =    2.385
peak=    3.204 closest distance to " OG BSER A 134 " =    2.840
peak=    3.200 closest distance to " O   ALA A 165 " =    1.417
peak=    3.199 closest distance to " O   HOH Z 417 " =    3.187
peak=    3.199 closest distance to " O   HOH Z 407 " =    2.505
peak=    3.196 closest distance to " O   HOH Z  59 " =    2.297
peak=    3.195 closest distance to " NZ  LYS A  76 " =    1.445
peak=    3.194 closest distance to " CG  LEU A 281 " =    1.105
peak=    3.194 closest distance to " CD1 ILE A  33 " =    1.673
peak=    3.190 closest distance to " O   HOH Z 290 " =    1.063
peak=    3.189 closest distance to " CB  SER A 216 " =    0.793
peak=    3.187 closest distance to " CA  ASN A 176 " =    1.211
peak=    3.186 closest distance to " O   HOH Z 359 " =    1.364
peak=    3.186 closest distance to " O   HOH Z 313 " =    2.147
peak=    3.185 closest distance to " O   HOH Z 166 " =    3.568
peak=    3.184 closest distance to " ND2 ASN A 110 " =    1.556
peak=    3.183 closest distance to " CB  GLN A 103 " =    0.955
peak=    3.183 closest distance to " CB  ALA A  34 " =    0.766
peak=    3.179 closest distance to " CB  PHE A 204 " =    0.858
peak=    3.178 closest distance to " O   GLN A  88 " =    1.677
peak=    3.175 closest distance to " CG1 VAL A 174 " =    1.078
peak=    3.174 closest distance to " O   HOH Z 344 " =    3.047
peak=    3.170 closest distance to " CD1 LEU A 228 " =    1.841
peak=    3.165 closest distance to " C   ALA A 299 " =    0.941
peak=    3.162 closest distance to " C   TYR A 214 " =    1.478
peak=    3.158 closest distance to " CD1 ILE A 106 " =    1.012
peak=    3.153 closest distance to " O   HOH Z 380 " =    1.879
peak=    3.150 closest distance to " O   HOH Z 201 " =    3.030
peak=    3.148 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.148 closest distance to " O   HOH Z 329 " =    3.948
peak=    3.142 closest distance to " CG ALYS A 290 " =    1.109
peak=    3.138 closest distance to " O   HOH Z  10 " =    1.732
peak=    3.137 closest distance to " CG BARG A 102 " =    1.809
peak=    3.136 closest distance to " CG2 VAL A 197 " =    1.068
peak=    3.135 closest distance to " CA  VAL A 126 " =    0.923
peak=    3.134 closest distance to " CA  ALA A 160 " =    0.910
peak=    3.128 closest distance to " O   HOH Z 302 " =    1.952
peak=    3.125 closest distance to " CB  TYR A 116 " =    0.917
peak=    3.122 closest distance to " CB  LEU A  96 " =    1.273
peak=    3.121 closest distance to " CB  LEU A 261 " =    0.933
peak=    3.119 closest distance to " O   HOH Z 353 " =    2.729
peak=    3.116 closest distance to " O   HOH Z 185 " =    1.844
peak=    3.115 closest distance to " CB  ASN A 215 " =    1.217
peak=    3.111 closest distance to " CA  ALA A 248 " =    1.280
peak=    3.110 closest distance to " O   HOH Z 430 " =    3.977
peak=    3.108 closest distance to " CA  ALA A 154 " =    0.963
peak=    3.104 closest distance to " O   HOH Z  85 " =    2.172
peak=    3.103 closest distance to " O   HOH Z 141 " =    1.564
peak=    3.102 closest distance to " ND1 HIS A  86 " =    1.655
peak=    3.088 closest distance to " N   ASP A 162 " =    1.319
peak=    3.085 closest distance to " CZ3 TRP A 266 " =    1.105
peak=    3.083 closest distance to " NE2 HIS A 207 " =    1.306
peak=    3.080 closest distance to " O   HOH Z 162 " =    1.965
peak=    3.078 closest distance to " O   HOH Z 256 " =    2.440
peak=    3.052 closest distance to " CD  LYS A  76 " =    1.922
peak=    3.052 closest distance to " CG  ASN A 252 " =    1.262
peak=    3.049 closest distance to " O   HOH Z  49 " =    2.840
peak=    3.043 closest distance to " O   HOH Z 139 " =    4.672
peak=    3.018 closest distance to " O   SER A 164 " =    1.155

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.585
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.780 - 5.585

peak=   -5.605 closest distance to " CG2 VAL A 230 " =    0.784
peak=   -4.514 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.506 closest distance to " CG2BVAL A  41 " =    2.649
peak=   -4.370 closest distance to " SG  CYS A 254 " =    3.417
peak=   -4.308 closest distance to " CB  PRO A 243 " =    2.684
peak=   -4.289 closest distance to " O   HOH Z 196 " =    2.148
peak=   -4.289 closest distance to " CD  GLN A  58 " =    1.053
peak=   -4.209 closest distance to " O   HOH Z 266 " =    5.182
peak=   -4.095 closest distance to " C   HIS A 108 " =    1.162
peak=   -4.020 closest distance to " N   ALA A  43 " =    2.599
peak=   -4.019 closest distance to " OG  SER A  97 " =    2.331
peak=   -3.991 closest distance to " O   ILE A 109 " =    2.650
peak=   -3.980 closest distance to " O   HOH Z 351 " =    1.567
peak=   -3.973 closest distance to " OG BSER A 134 " =    1.224
peak=   -3.967 closest distance to " O   HOH Z 114 " =    3.168
peak=   -3.947 closest distance to " O   HOH Z  37 " =    1.928
peak=   -3.945 closest distance to " O   HOH Z 290 " =    1.183
peak=   -3.943 closest distance to " OE1 GLN A 223 " =    2.172
peak=   -3.928 closest distance to " O   HOH Z  52 " =    1.591
peak=   -3.913 closest distance to " CD1 LEU A 101 " =    2.460
peak=   -3.911 closest distance to " O   HOH Z 166 " =    1.844
peak=   -3.903 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.897 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -3.879 closest distance to " O   HOH Z 231 " =    2.155
peak=   -3.867 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.857 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.847 closest distance to " OXT GLY A 302 " =    2.886
peak=   -3.847 closest distance to " CG1 VAL A 250 " =    2.773
peak=   -3.839 closest distance to " O   PRO A 163 " =    2.184
peak=   -3.829 closest distance to " CG  ASP A 231 " =    0.802
peak=   -3.788 closest distance to " O   VAL A  67 " =    2.813
peak=   -3.774 closest distance to " O   HOH Z 394 " =    1.528
peak=   -3.759 closest distance to " CB  PHE A 192 " =    1.997
peak=   -3.716 closest distance to " NH2AARG A 275 " =    5.142
peak=   -3.715 closest distance to " OD1 ASN A 148 " =    1.500
peak=   -3.706 closest distance to " O   HOH Z 292 " =    4.606
peak=   -3.671 closest distance to " CE2 PHE A 218 " =    2.556
peak=   -3.659 closest distance to " O   HOH Z 185 " =    2.435
peak=   -3.651 closest distance to " O   HOH Z 166 " =    1.657
peak=   -3.644 closest distance to " C   ALA A 158 " =    1.300
peak=   -3.643 closest distance to " CG1 VAL A 112 " =    2.646
peak=   -3.641 closest distance to " ND2 ASN A  45 " =    1.092
peak=   -3.636 closest distance to " O   HOH Z  73 " =    2.212
peak=   -3.624 closest distance to " O   HOH Z 435 " =    2.706
peak=   -3.614 closest distance to " CG1 VAL A 112 " =    2.770
peak=   -3.591 closest distance to " O   VAL A 189 " =    2.633
peak=   -3.588 closest distance to " O   HOH Z  44 " =    2.207
peak=   -3.579 closest distance to " NE2 GLN A  88 " =    1.960
peak=   -3.565 closest distance to " O   HOH Z  11 " =    1.886
peak=   -3.565 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.563 closest distance to " CG2 VAL A 296 " =    1.134
peak=   -3.560 closest distance to " O   HOH Z 377 " =    2.108
peak=   -3.559 closest distance to " ND2 ASN A 187 " =    1.687
peak=   -3.557 closest distance to " CD1 LEU A 101 " =    2.632
peak=   -3.547 closest distance to " O   HOH Z 389 " =    1.968
peak=   -3.542 closest distance to " N   ALA A 226 " =    2.112
peak=   -3.536 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.534 closest distance to " O   HOH Z 407 " =    3.096
peak=   -3.534 closest distance to " O   HOH Z  10 " =    1.524
peak=   -3.532 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.526 closest distance to " O   HOH Z 222 " =    1.523
peak=   -3.515 closest distance to " CG  ARG A 269 " =    2.501
peak=   -3.512 closest distance to " O   HOH Z 234 " =    4.259
peak=   -3.501 closest distance to " C   ILE A 234 " =    1.305
peak=   -3.490 closest distance to " O   SER A 271 " =    2.095
peak=   -3.478 closest distance to " CE3 TRP A 150 " =    2.214
peak=   -3.474 closest distance to " O   HOH Z  13 " =    1.584
peak=   -3.469 closest distance to " CE  MET A 105 " =    2.106
peak=   -3.464 closest distance to " CD2 TYR A 293 " =    2.074
peak=   -3.460 closest distance to " CB  ALA A 114 " =    2.459
peak=   -3.459 closest distance to " O   HOH Z 165 " =    1.890
peak=   -3.457 closest distance to " CG  TRP A 266 " =    1.862
peak=   -3.457 closest distance to " CD2 LEU A 300 " =    2.683
peak=   -3.457 closest distance to " C   LEU A 143 " =    1.067
peak=   -3.449 closest distance to " NE2 GLN A 103 " =    1.780
peak=   -3.449 closest distance to " O   HOH Z  60 " =    2.186
peak=   -3.448 closest distance to " CD2 LEU A 167 " =    1.791
peak=   -3.436 closest distance to " CE BMET A  47 " =    2.016
peak=   -3.431 closest distance to " NE2 GLN A 194 " =    1.863
peak=   -3.423 closest distance to " CB  ALA A 291 " =    2.216
peak=   -3.420 closest distance to " CB  ALA A 291 " =    2.270
peak=   -3.420 closest distance to " CB  PRO A 163 " =    2.617
peak=   -3.420 closest distance to " O   HOH Z 136 " =    2.314
peak=   -3.420 closest distance to " O   HOH Z  17 " =    1.439
peak=   -3.418 closest distance to " O   SER A 210 " =    1.891
peak=   -3.414 closest distance to " O   HOH Z 353 " =    2.157
peak=   -3.413 closest distance to " ND2 ASN A  45 " =    1.645
peak=   -3.413 closest distance to " CG  GLU A 277 " =    1.129
peak=   -3.412 closest distance to " CD1 LEU A  25 " =    2.469
peak=   -3.410 closest distance to " CB  ALA A 248 " =    2.072
peak=   -3.396 closest distance to " O   HOH Z 311 " =    3.738
peak=   -3.394 closest distance to " CB  ASP A 171 " =    2.329
peak=   -3.394 closest distance to " CB  ALA A  43 " =    2.555
peak=   -3.393 closest distance to " N   ASP A 171 " =    2.311
peak=   -3.392 closest distance to " O   HOH Z 241 " =    1.302
peak=   -3.389 closest distance to " OG  SER A  62 " =    1.694
peak=   -3.386 closest distance to " O   HOH Z 128 " =    2.648
peak=   -3.375 closest distance to " N   MET A 105 " =    2.687
peak=   -3.371 closest distance to " O   HOH Z  38 " =    1.584
peak=   -3.371 closest distance to " NE2 GLN A  88 " =    0.987
peak=   -3.370 closest distance to " CA  GLY A 241 " =    2.348
peak=   -3.369 closest distance to " CA  GLY A 203 " =    2.382
peak=   -3.368 closest distance to " C   MET A 188 " =    1.414
peak=   -3.368 closest distance to " O   HOH Z  19 " =    2.281
peak=   -3.361 closest distance to " O   HOH Z 113 " =    2.441
peak=   -3.359 closest distance to " CG2 ILE A 263 " =    2.392
peak=   -3.358 closest distance to " CG1 VAL A 296 " =    1.412
peak=   -3.355 closest distance to " CD1 LEU A 228 " =    2.288
peak=   -3.354 closest distance to " CG  LEU A 101 " =    2.431
peak=   -3.352 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.350 closest distance to " O   HOH Z 211 " =    1.600
peak=   -3.349 closest distance to " CD  LYS A 289 " =    2.463
peak=   -3.347 closest distance to " O   HOH Z 411 " =    1.561
peak=   -3.340 closest distance to " CD  ARG A 139 " =    1.637
peak=   -3.333 closest distance to " O   HOH Z 377 " =    1.624
peak=   -3.326 closest distance to " C   PHE A  59 " =    1.325
peak=   -3.326 closest distance to " C   SER A 206 " =    1.487
peak=   -3.322 closest distance to " CA  GLY A  98 " =    2.002
peak=   -3.322 closest distance to " CZ  TYR A 169 " =    1.749
peak=   -3.322 closest distance to " NH2 ARG A 159 " =    2.337
peak=   -3.311 closest distance to " O   HOH Z 150 " =    1.950
peak=   -3.302 closest distance to " O   LYS A 117 " =    1.731
peak=   -3.302 closest distance to " CB  VAL A 230 " =    1.019
peak=   -3.299 closest distance to " CG1 VAL A 197 " =    2.225
peak=   -3.297 closest distance to " OG ASER A 134 " =    1.367
peak=   -3.295 closest distance to " O   HOH Z 313 " =    1.131
peak=   -3.294 closest distance to " N   THR A 157 " =    1.557
peak=   -3.294 closest distance to " CD1 ILE A 199 " =    2.535
peak=   -3.293 closest distance to " O   HOH Z 177 " =    1.727
peak=   -3.291 closest distance to " O   GLY A 196 " =    1.122
peak=   -3.290 closest distance to " O   HOH Z 193 " =    1.903
peak=   -3.278 closest distance to " O   HOH Z 275 " =    1.477
peak=   -3.273 closest distance to " O   LEU A 167 " =    1.525
peak=   -3.271 closest distance to " CD2 PHE A  61 " =    2.490
peak=   -3.270 closest distance to " N   SER A   3 " =    2.056
peak=   -3.270 closest distance to " N   SER A 276 " =    1.440
peak=   -3.266 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.264 closest distance to " N   GLN A  58 " =    1.578
peak=   -3.263 closest distance to " OG BSER A 134 " =    1.856
peak=   -3.260 closest distance to " CG  GLU A  53 " =    1.667
peak=   -3.257 closest distance to " O   HOH Z 426 " =    1.729
peak=   -3.255 closest distance to " ND2 ASN A  69 " =    1.817
peak=   -3.254 closest distance to " CD  PRO A 213 " =    2.184
peak=   -3.253 closest distance to " CG2 VAL A 189 " =    2.058
peak=   -3.246 closest distance to " N   THR A  18 " =    1.338
peak=   -3.243 closest distance to " O   HOH Z 264 " =    1.762
peak=   -3.242 closest distance to " OD1 ASN A 187 " =    1.621
peak=   -3.239 closest distance to " CB  ALA A  10 " =    2.308
peak=   -3.235 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.235 closest distance to " O   HOH Z  90 " =    1.692
peak=   -3.232 closest distance to " O   SER A 258 " =    1.995
peak=   -3.230 closest distance to " NE2 GLN A 278 " =    1.945
peak=   -3.230 closest distance to " CG  LYS A 166 " =    2.200
peak=   -3.227 closest distance to " O   HOH Z 102 " =    1.607
peak=   -3.226 closest distance to " CA  GLY A 133 " =    2.329
peak=   -3.215 closest distance to " CZ  PHE A  59 " =    1.664
peak=   -3.210 closest distance to " CD1 LEU A   5 " =    2.523
peak=   -3.210 closest distance to " NH2 ARG A  79 " =    1.576
peak=   -3.206 closest distance to " OG  SER A  26 " =    1.330
peak=   -3.206 closest distance to " O   ALA A  10 " =    1.721
peak=   -3.204 closest distance to " O   ILE A 234 " =    1.264
peak=   -3.203 closest distance to " CA  PRO A 243 " =    2.499
peak=   -3.202 closest distance to " CG1 VAL A 112 " =    2.925
peak=   -3.191 closest distance to " OG  SER A 206 " =    1.695
peak=   -3.188 closest distance to " O   HOH Z 423 " =    2.197
peak=   -3.177 closest distance to " O   HOH Z  71 " =    1.464
peak=   -3.176 closest distance to " O   HOH Z 191 " =    5.585
peak=   -3.175 closest distance to " N   ALA A 248 " =    1.803
peak=   -3.173 closest distance to " O   HOH Z 174 " =    2.268
peak=   -3.173 closest distance to " O   HOH Z   6 " =    1.717
peak=   -3.172 closest distance to " C   ASN A 285 " =    2.386
peak=   -3.172 closest distance to " O   HOH Z 232 " =    1.772
peak=   -3.171 closest distance to " O   SER A 276 " =    1.714
peak=   -3.170 closest distance to " CB  ASN A  69 " =    1.249
peak=   -3.169 closest distance to " CD  GLN A 223 " =    0.780
peak=   -3.169 closest distance to " O   VAL A 125 " =    2.304
peak=   -3.167 closest distance to " O   HOH Z 252 " =    3.979
peak=   -3.165 closest distance to " O   HOH Z 350 " =    1.975
peak=   -3.162 closest distance to " O   HOH Z 295 " =    1.590
peak=   -3.147 closest distance to " O   HOH Z 262 " =    2.888
peak=   -3.142 closest distance to " CG  PRO A 163 " =    2.560
peak=   -3.137 closest distance to " O   GLN A 240 " =    2.138
peak=   -3.133 closest distance to " O   HOH Z 175 " =    4.347
peak=   -3.131 closest distance to " O   HOH Z 434 " =    1.712
peak=   -3.131 closest distance to " OD2 ASP A  50 " =    2.337
peak=   -3.131 closest distance to " C   ASN A 187 " =    1.893
peak=   -3.130 closest distance to " CG  MET A 105 " =    0.915
peak=   -3.129 closest distance to " OG1 THR A  82 " =    1.395
peak=   -3.125 closest distance to " O   HOH Z 392 " =    1.804
peak=   -3.118 closest distance to " O   HOH Z 285 " =    1.605
peak=   -3.117 closest distance to " O   HOH Z 133 " =    1.443
peak=   -3.110 closest distance to " C   ASP A 231 " =    2.505
peak=   -3.110 closest distance to " C   ASP A 270 " =    1.291
peak=   -3.108 closest distance to " O   HOH Z 111 " =    2.160
peak=   -3.105 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.096 closest distance to " N   ALA A 248 " =    2.449
peak=   -3.090 closest distance to " NH2 ARG A  66 " =    1.837
peak=   -3.089 closest distance to " O   GLY A  80 " =    2.494
peak=   -3.082 closest distance to " CD  ARG A 195 " =    5.155
peak=   -3.081 closest distance to " O   HOH Z 353 " =    2.105
peak=   -3.071 closest distance to " O   HOH Z 429 " =    2.075
peak=   -3.065 closest distance to " O   HOH Z 139 " =    3.100
peak=   -3.052 closest distance to " O   ASP A 171 " =    1.967
peak=   -3.050 closest distance to " CD2 TYR A 247 " =    2.248
peak=   -3.042 closest distance to " CA  SER A  62 " =    2.465

================= 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    :  0.4362 0.4203   6.229520e+00   6.202302e+00
   1_bss:  0.4291 0.4068   6.224487e+00   6.187416e+00
   1_xyz:  0.3159 0.3389   6.010058e+00   6.052332e+00
   1_adp:  0.2535 0.2872   5.824843e+00   5.928395e+00
   1_occ:  0.2526 0.2876   5.823567e+00   5.929492e+00
   2_bss:  0.2486 0.2816   5.823205e+00   5.924717e+00
   2_xyz:  0.1700 0.2043   5.477745e+00   5.644733e+00
   2_adp:  0.1549 0.1920   5.399949e+00   5.581469e+00
   2_occ:  0.1547 0.1922   5.399699e+00   5.581981e+00
   3_bss:  0.1542 0.1925   5.400180e+00   5.582205e+00
   3_xyz:  0.1297 0.1657   5.244411e+00   5.446520e+00
   3_adp:  0.1242 0.1647   5.217913e+00   5.434945e+00
   3_occ:  0.1241 0.1647   5.217621e+00   5.435072e+00
   4_bss:  0.1244 0.1653   5.219463e+00   5.435781e+00
   4_xyz:  0.1146 0.1607   5.167000e+00   5.409317e+00
   4_adp:  0.1140 0.1594   5.160380e+00   5.402042e+00
   4_occ:  0.1137 0.1592   5.159746e+00   5.401708e+00
   5_bss:  0.1137 0.1592   5.159577e+00   5.401615e+00
   5_xyz:  0.1118 0.1584   5.149182e+00   5.397937e+00
   5_adp:  0.1118 0.1577   5.148537e+00   5.396191e+00
   5_occ:  0.1118 0.1577   5.148485e+00   5.396373e+00
   5_bss:  0.1118 0.1577   5.148552e+00   5.396449e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   7.060   9.483   8.405   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.060   9.483   8.405   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.060   9.483   8.405   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.060   9.483   8.405   0.000   0.000   0.000
   2_bss:  0.327  50.001   3.951   5.922   5.321   0.000   0.000   0.000
   2_xyz:  0.327  50.001   3.951   5.922   5.321   0.000   0.000   0.000
   2_adp:  0.327  50.001   3.951   5.922   5.321   0.000   0.000   0.000
   2_occ:  0.327  50.001   3.951   5.922   5.321   0.000   0.000   0.000
   3_bss:  0.328  54.835   3.184   4.281   4.661   0.000   0.000   0.000
   3_xyz:  0.328  54.835   3.184   4.281   4.661   0.000   0.000   0.000
   3_adp:  0.328  54.835   3.184   4.281   4.661   0.000   0.000   0.000
   3_occ:  0.328  54.835   3.184   4.281   4.661   0.000   0.000   0.000
   4_bss:  0.328  54.835   3.139   3.870   4.567   0.000   0.000   0.000
   4_xyz:  0.328  54.835   3.139   3.870   4.567   0.000   0.000   0.000
   4_adp:  0.328  54.835   3.139   3.870   4.567   0.000   0.000   0.000
   4_occ:  0.328  54.835   3.139   3.870   4.567   0.000   0.000   0.000
   5_bss:  0.324  54.129   3.252   3.833   4.652   0.000   0.000   0.000
   5_xyz:  0.324  54.129   3.252   3.833   4.652   0.000   0.000   0.000
   5_adp:  0.324  54.129   3.252   3.833   4.652   0.000   0.000   0.000
   5_occ:  0.324  54.129   3.252   3.833   4.652   0.000   0.000   0.000
   5_bss:  0.320  54.280  -0.652  -0.115   0.768  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.493 0.5658  0.6212    50034.022
   1_bss:  45.513 0.5766  0.8115    47489.052
   1_xyz:  36.569 0.6823  0.9321    31178.608
   1_adp:  29.041 0.7691  1.0184    21537.349
   1_occ:  29.068 0.7688  1.0176    21579.805
   2_bss:  28.832 0.7712  0.9085    21259.547
   2_xyz:  19.915 0.8624  0.9852    10827.207
   2_adp:  18.250 0.8785  0.9971     9496.010
   2_occ:  18.259 0.8784  0.9969     9508.945
   3_bss:  18.246 0.8787  0.9607     9536.913
   3_xyz:  15.133 0.9058  0.9746     7061.139
   3_adp:  14.840 0.9084  0.9733     6900.756
   3_occ:  14.841 0.9084  0.9731     6903.125
   4_bss:  14.852 0.9084  0.9667     6929.395
   4_xyz:  14.307 0.9128  0.9690     6594.363
   4_adp:  14.132 0.9143  0.9672     6512.608
   4_occ:  14.132 0.9143  0.9670     6507.684
   5_bss:  14.129 0.9144  0.9690     6506.746
   5_xyz:  14.023 0.9153  0.9692     6430.615
   5_adp:  13.973 0.9157  0.9664     6404.148
   5_occ:  13.975 0.9157  0.9663     6406.045
   5_bss:  13.978 0.9156  0.9674     6406.389
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4197e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4197e+01
   1_xyz:   1.547  0.012  0.103 17.799  0.006  4.127   1.2096e-01
   1_adp:   1.547  0.012  0.103 17.799  0.006  4.127   1.2096e-01
   1_occ:   1.547  0.012  0.103 17.799  0.006  4.127   1.2096e-01
   2_bss:   1.547  0.012  0.103 17.799  0.006  4.127   1.2096e-01
   2_xyz:   1.050  0.008  0.073 16.095  0.004  4.129   6.7348e-02
   2_adp:   1.050  0.008  0.073 16.095  0.004  4.129   6.7348e-02
   2_occ:   1.050  0.008  0.073 16.095  0.004  4.129   6.7348e-02
   3_bss:   1.050  0.008  0.073 16.095  0.004  4.129   6.7348e-02
   3_xyz:   0.969  0.007  0.077 15.606  0.004  4.138   5.8521e-02
   3_adp:   0.969  0.007  0.077 15.606  0.004  4.138   5.8521e-02
   3_occ:   0.969  0.007  0.077 15.606  0.004  4.138   5.8521e-02
   4_bss:   0.969  0.007  0.077 15.606  0.004  4.138   5.8521e-02
   4_xyz:   1.090  0.009  0.090 15.662  0.004  4.129   7.2694e-02
   4_adp:   1.090  0.009  0.090 15.662  0.004  4.129   7.2694e-02
   4_occ:   1.090  0.009  0.090 15.662  0.004  4.129   7.2694e-02
   5_bss:   1.090  0.009  0.090 15.662  0.004  4.129   7.2694e-02
   5_xyz:   1.091  0.010  0.090 15.514  0.004  4.123   7.3232e-02
   5_adp:   1.091  0.010  0.090 15.514  0.004  4.123   7.3232e-02
   5_occ:   1.091  0.010  0.090 15.514  0.004  4.123   7.3232e-02
   5_bss:   1.091  0.010  0.090 15.514  0.004  4.123   7.3232e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0274e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0274e+00
   1_xyz:  13.297  0.142  0.447 89.358  0.038  2.310   9.2438e-02
   1_adp:  13.297  0.142  0.447 89.358  0.038  2.310   9.2438e-02
   1_occ:  13.297  0.142  0.447 89.358  0.038  2.310   9.2438e-02
   2_bss:  13.297  0.142  0.447 89.358  0.038  2.310   9.2438e-02
   2_xyz:   7.261  0.085  0.260 81.507  0.029  2.228   5.7118e-02
   2_adp:   7.261  0.085  0.260 81.507  0.029  2.228   5.7118e-02
   2_occ:   7.261  0.085  0.260 81.507  0.029  2.228   5.7118e-02
   3_bss:   7.261  0.085  0.260 81.507  0.029  2.228   5.7118e-02
   3_xyz:   6.671  0.044  0.472 82.562  0.043  2.366   4.0837e-02
   3_adp:   6.671  0.044  0.472 82.562  0.043  2.366   4.0837e-02
   3_occ:   6.671  0.044  0.472 82.562  0.043  2.366   4.0837e-02
   4_bss:   6.671  0.044  0.472 82.562  0.043  2.366   4.0837e-02
   4_xyz:   7.507  0.046  0.634 83.186  0.042  2.328   5.2643e-02
   4_adp:   7.507  0.046  0.634 83.186  0.042  2.328   5.2643e-02
   4_occ:   7.507  0.046  0.634 83.186  0.042  2.328   5.2643e-02
   5_bss:   7.507  0.046  0.634 83.186  0.042  2.328   5.2643e-02
   5_xyz:   7.549  0.053  0.633 81.507  0.040  2.350   5.1850e-02
   5_adp:   7.549  0.053  0.633 81.507  0.040  2.350   5.1850e-02
   5_occ:   7.549  0.053  0.633 81.507  0.040  2.350   5.1850e-02
   5_bss:   7.549  0.053  0.633 81.507  0.040  2.350   5.1850e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  87.35   0.00  10.58  62.02   0.00   7.46  87.35   0.00  27.59
   1_occ:  87.35   0.00  10.58  62.02   0.00   7.46  87.35   0.00  27.59
   2_bss:  87.35   0.00  10.58  62.02   0.00   7.46  87.35   0.00  27.59
   2_xyz:  87.35   0.00  10.58  62.02   0.00   7.46  87.35   0.00  27.59
   2_adp:  81.87   0.00  11.08  65.81   0.00   7.20  81.87   0.00  32.18
   2_occ:  81.87   0.00  11.08  65.81   0.00   7.20  81.87   0.00  32.18
   3_bss:  81.87   0.00  11.08  65.81   0.00   7.20  81.87   0.00  32.18
   3_xyz:  81.87   0.00  11.08  65.81   0.00   7.20  81.87   0.00  32.18
   3_adp:  83.92   0.00  11.87  83.92   0.00   7.41  76.22   0.00  36.18
   3_occ:  83.92   0.00  11.87  83.92   0.00   7.41  76.22   0.00  36.18
   4_bss:  83.92   0.00  11.87  83.92   0.00   7.41  76.22   0.00  36.18
   4_xyz:  83.92   0.00  11.87  83.92   0.00   7.41  76.22   0.00  36.18
   4_adp:  85.40   0.00  11.66  85.40   0.00   7.30  75.66   0.41  35.39
   4_occ:  85.40   0.00  11.66  85.40   0.00   7.30  75.66   0.41  35.39
   5_bss:  85.40   0.00  11.66  85.40   0.00   7.30  75.66   0.41  35.39
   5_xyz:  85.40   0.00  11.66  85.40   0.00   7.30  75.66   0.41  35.39
   5_adp:  86.13   0.00  11.27  86.13   0.00   7.13  74.80   0.67  33.86
   5_occ:  86.13   0.00  11.27  86.13   0.00   7.13  74.80   0.67  33.86
   5_bss:  90.07   3.94  15.22  90.07   3.94  11.07  78.74   4.61  37.81
------------------------------------------------------------------------
 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:    1.196    0.009    0.405
   1_adp:    1.196    0.009    0.405
   1_occ:    1.196    0.009    0.405
   2_bss:    1.196    0.009    0.405
   2_xyz:    1.550    0.031    0.511
   2_adp:    1.550    0.031    0.511
   2_occ:    1.550    0.031    0.511
   3_bss:    1.550    0.031    0.511
   3_xyz:    1.551    0.005    0.544
   3_adp:    1.551    0.005    0.544
   3_occ:    1.551    0.005    0.544
   4_bss:    1.551    0.005    0.544
   4_xyz:    1.603    0.048    0.568
   4_adp:    1.603    0.048    0.568
   4_occ:    1.603    0.048    0.568
   5_bss:    1.603    0.048    0.568
   5_xyz:    1.653    0.029    0.578
   5_adp:    1.653    0.029    0.578
   5_occ:    1.653    0.029    0.578
   5_bss:    1.653    0.029    0.578
------------------------------------------------------------------------

CPU time actual refinement: 334.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/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_809/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_809/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.20 
  Macro-tasks:
    bulk solvent and scale       = 40.71  
    individual site refinement   = 134.36 
    weights calculation          = 32.47  
    collect and process          = 6.43   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.09 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 103.23 
    alpha_beta                      = 8.14   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 114.39 
    fmodel                         = 7.11   
    r_factors                      = 0.23   
    phase_errors                   = 10.68  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 247.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.681 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    679 calls, 102.88 s
gradients_fft:          624 calls, 100.60 s

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

# Date 2008-01-16 Time 02:28:05 PST -0800 (1200479285.49 s)
Start R-work = 0.4362, R-free = 0.4203 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.4291, R-free = 0.4068
Final R-work = 0.1118, R-free = 0.1577