# Date 2008-01-16 Time 02:22:18 PST -0800 (1200478938.06 s)
#phil __OFF__

Command line arguments: "../807.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24464
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 807

-------------------------------------------------------------------------------
  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, 85.9581, 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: 2.76, per 1000 atoms: 0.98


================================== 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, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99116
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960386

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9912

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, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99116
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960386

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2603 [2127/2154]  1915   212  10.0%
  bin  2:  4.2603 -  3.3943 [2046/2062]  1840   206  10.1%
  bin  3:  3.3943 -  2.9690 [2031/2050]  1826   205  10.1%
  bin  4:  2.9690 -  2.6993 [2007/2037]  1809   198   9.9%
  bin  5:  2.6993 -  2.5068 [1996/2015]  1800   196   9.8%
  bin  6:  2.5068 -  2.3596 [1963/1999]  1768   195   9.9%
  bin  7:  2.3596 -  2.2418 [1978/2011]  1778   200  10.1%
  bin  8:  2.2418 -  2.1445 [1972/2005]  1771   201  10.2%
  bin  9:  2.1445 -  2.0622 [1960/1989]  1769   191   9.7%
  bin 10:  2.0622 -  1.9912 [1509/2011]  1354   155  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/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: 0.12 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: 12
        2.42 -     3.04: 2180
        3.04 -     3.66: 4650
        3.66 -     4.28: 8955
        4.28 -     4.90: 12341
  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 "  1.958 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.207 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.265 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28133 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_807/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/model_refine_001.geo

CPU time processing inputs: 7.73


============================ 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 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4346   r_free= 0.4204   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| 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: 6.227906                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7516 0.99   1380  154 0.3639 0.3386      6.5196      6.4436|
|  2:  4.7516 -  3.7914 0.99   1346  146 0.3282 0.3574      6.6403      6.7031|
|  3:  3.7914 -  3.3180 0.99   1308  150 0.3802 0.3561      6.5786      6.5582|
|  4:  3.3180 -  3.0173 0.99   1293  142 0.4089 0.3704      6.4502      6.3361|
|  5:  3.0173 -  2.8026 0.99   1295  142 0.4545 0.4457      6.3152      6.3398|
|  6:  2.8026 -  2.6383 0.99   1286  144 0.4608 0.5086      6.2356      6.2227|
|  7:  2.6383 -  2.5068 0.99   1282  139 0.4691 0.4363      6.2094       6.138|
|  8:  2.5068 -  2.3981 0.98   1272  148 0.4791 0.4407      6.1556      6.1019|
|  9:  2.3981 -  2.3061 0.98   1280  139 0.4897 0.4772      6.0939      6.1033|
| 10:  2.3061 -  2.2268 0.98   1242  138 0.4912 0.4907      6.0908      6.0892|
| 11:  2.2268 -  2.1574 1.00   1285  143 0.4986 0.4306      6.0176      6.0001|
| 12:  2.1574 -  2.0959 0.97   1242  136 0.5001 0.4977       5.972      6.0191|
| 13:  2.0959 -  2.0408 0.98   1257  145 0.5080 0.5124      5.8788      5.8456|
| 14:  2.0408 -  1.9912 0.67    862   93 0.5071 0.4522      5.8306      5.7481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7516  1380   154  0.74  30.86   0.81     0.76      57759.52|
|  2:  4.7516 -  3.7914  1346   146  0.78  28.51   0.91     0.81      73376.27|
|  3:  3.7914 -  3.3180  1308   150  0.71  34.78   0.86     0.79      76010.04|
|  4:  3.3180 -  3.0173  1293   142  0.65  39.34   0.83     0.71      66687.98|
|  5:  3.0173 -  2.8026  1295   142  0.56  47.30   0.77     0.63      59485.14|
|  6:  2.8026 -  2.6383  1286   144  0.54  48.53   0.77     0.60      53660.40|
|  7:  2.6383 -  2.5068  1282   139  0.53  49.36   0.76     0.59      49505.43|
|  8:  2.5068 -  2.3981  1272   148  0.52  50.43   0.76     0.59      45563.83|
|  9:  2.3981 -  2.3061  1280   139  0.50  51.81   0.74     0.57      41227.06|
| 10:  2.3061 -  2.2268  1242   138  0.50  52.27   0.77     0.56      39020.38|
| 11:  2.2268 -  2.1574  1285   143  0.47  54.78   0.77     0.54      36708.55|
| 12:  2.1574 -  2.0959  1242   136  0.44  57.06   0.77     0.52      36865.30|
| 13:  2.0959 -  2.0408  1257   145  0.41  59.59   0.74     0.48      32503.43|
| 14:  2.0408 -  1.9912   862    93  0.44  57.11   0.74     0.48      26053.90|
|alpha:            min =        0.48 max =            0.81 mean =         0.62|
|beta:             min =    26053.90 max =        76010.04 mean =     50430.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.80|
|phase err.(test): min =        0.00 max =           89.93 mean =        46.73|
|-----------------------------------------------------------------------------|

============================== 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 = 7.941202              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.105   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.652734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.406   (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:      163 |
| 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:     1493 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2620 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3869 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5077 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6520 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7684 |
|-----------------------------------------------------------------------------|
|-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 |       54.008 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.668 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    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 = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4419   r_free= 0.4272   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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: 6.232517                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4259   r_free= 0.4111   ksol= 0.34   Bsol= 20.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,9.83,7.90,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.222871                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.656421              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.223   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.539   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4259      final r-factor (work) = 0.3160          |
| start r-factor (free) = 0.4111      final r-factor (free) = 0.3421          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.8995 = 7.66 * 0.50 * 6.2408 + 1.00 * 54.0084                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3378 = 7.66 * 0.50 * 6.0647 + 1.00 * 0.1209                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3160      final r-factor (work) = 0.2542          |
| start r-factor (free) = 0.3421      final r-factor (free) = 0.2894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9674 = 0.65 * 1.00 * 6.0647 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8540 = 0.65 * 1.00 * 5.8947 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.40   10.38    None  None   None       |
|    all(noH): 2823   0      0.00    61.40   10.38    None  None   None       |
|    Sol.    : 438    0      0.00    61.40   26.62    None  None   None       |
|    Mac.    : 2385   0      0.00    55.59   7.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.140: 1329   |   5:    30.702 -  36.842:   83        |
|      1:     6.140 -  12.281:  738   |   6:    36.842 -  42.983:   83        |
|      2:    12.281 -  18.421:  262   |   7:    42.983 -  49.123:   36        |
|      3:    18.421 -  24.562:  155   |   8:    49.123 -  55.263:    7        |
|      4:    24.562 -  30.702:  125   |   9:    55.263 -  61.404:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2542 r_free = 0.2894             target_work(ml) = 5.829         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2536 r_free = 0.2892             target_work(ml) = 5.828         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2536   r_free= 0.2892   ksol= 0.34   Bsol= 20.00   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,9.83,7.90,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.827958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2496   r_free= 0.2828   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,5.92,4.99,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.826794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.565938              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.999   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.341711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.854  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2496      final r-factor (work) = 0.1771          |
| start r-factor (free) = 0.2828      final r-factor (free) = 0.2130          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6938 = 2.57 * 0.50 * 5.9026 + 1.00 * 0.1209                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3201 = 2.57 * 0.50 * 5.6581 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1771      final r-factor (work) = 0.1622          |
| start r-factor (free) = 0.2130      final r-factor (free) = 0.2007          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9472 = 0.34 * 1.00 * 5.6581 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8897 = 0.34 * 1.00 * 5.4690 + 1.00 * 0.0209                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.77   11.10    None  None   None       |
|    all(noH): 2823   0      0.00    67.77   11.10    None  None   None       |
|    Sol.    : 438    0      0.82    64.69   31.68    None  None   None       |
|    Mac.    : 2385   0      0.00    67.77   7.32     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.777: 1494   |   5:    33.887 -  40.664:   99        |
|      1:     6.777 -  13.555:  677   |   6:    40.664 -  47.441:   84        |
|      2:    13.555 -  20.332:  187   |   7:    47.441 -  54.218:   52        |
|      3:    20.332 -  27.109:  112   |   8:    54.218 -  60.996:   15        |
|      4:    27.109 -  33.887:   97   |   9:    60.996 -  67.773:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1622 r_free = 0.2007             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1620 r_free = 0.2007             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1620   r_free= 0.2007   ksol= 0.33   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,5.92,4.99,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.443556                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2004   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.15,4.23,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.443848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.064330              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.066   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.633   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.2004      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4478 = 3.06 * 0.50 * 5.4738 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2412 = 3.06 * 0.50 * 5.3340 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6434 = 0.30 * 1.00 * 5.3340 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6327 = 0.30 * 1.00 * 5.2059 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.04   11.28    None  None   None       |
|    all(noH): 2823   0      0.00    71.04   11.28    None  None   None       |
|    Sol.    : 438    0      0.79    66.69   32.94    None  None   None       |
|    Mac.    : 2385   0      0.00    71.04   7.31     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.104: 1585   |   5:    35.518 -  42.621:  103        |
|      1:     7.104 -  14.207:  608   |   6:    42.621 -  49.725:   85        |
|      2:    14.207 -  21.311:  183   |   7:    49.725 -  56.829:   44        |
|      3:    21.311 -  28.414:  101   |   8:    56.829 -  63.932:   15        |
|      4:    28.414 -  35.518:   92   |   9:    63.932 -  71.036:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1608             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1606             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1606   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.15,4.23,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1614   ksol= 0.33   Bsol= 47.41   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.65,4.05,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.194604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.142296              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.500449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.146   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6453 = 2.14 * 0.50 * 5.2062 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6087 = 2.14 * 0.50 * 5.1759 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6017 = 0.50 * 1.00 * 5.1759 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5974 = 0.50 * 1.00 * 5.1619 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.52   11.35    None  None   None       |
|    all(noH): 2823   0      0.00    76.52   11.35    None  None   None       |
|    Sol.    : 438    0      0.92    67.06   33.46    None  None   None       |
|    Mac.    : 2385   0      0.00    76.52   7.28     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.652: 1683   |   5:    38.260 -  45.911:   95        |
|      1:     7.652 -  15.304:  550   |   6:    45.911 -  53.563:   72        |
|      2:    15.304 -  22.956:  158   |   7:    53.563 -  61.215:   26        |
|      3:    22.956 -  30.608:  110   |   8:    61.215 -  68.867:   13        |
|      4:    30.608 -  38.260:  111   |   9:    68.867 -  76.519:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1583             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1584             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1584   ksol= 0.33   Bsol= 47.41   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.65,4.05,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161935                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1584   ksol= 0.32   Bsol= 47.22   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.59,4.10,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161819                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.484412              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.960  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.370764              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.604   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8956 = 1.48 * 0.50 * 5.1618 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8904 = 1.48 * 0.50 * 5.1675 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9301 = 0.37 * 1.00 * 5.1675 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9499 = 0.37 * 1.00 * 5.1693 + 1.00 * 0.0333                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.57   11.29    None  None   None       |
|    all(noH): 2823   0      0.00    77.57   11.29    None  None   None       |
|    Sol.    : 438    0      0.91    66.43   33.20    None  None   None       |
|    Mac.    : 2385   0      0.00    77.57   7.26     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.757: 1708   |   5:    38.784 -  46.540:   93        |
|      1:     7.757 -  15.514:  535   |   6:    46.540 -  54.297:   68        |
|      2:    15.514 -  23.270:  155   |   7:    54.297 -  62.054:   21        |
|      3:    23.270 -  31.027:  111   |   8:    62.054 -  69.811:   14        |
|      4:    31.027 -  38.784:  113   |   9:    69.811 -  77.567:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1590             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1590             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1590   ksol= 0.32   Bsol= 47.22   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.59,4.10,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.169158                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7516 0.99   1380  154 0.1021 0.1303      5.3982      5.5261|
|  2:  4.7516 -  3.7914 0.99   1346  146 0.0888 0.1084      5.4563      5.6304|
|  3:  3.7914 -  3.3180 0.99   1308  150 0.1075 0.1506      5.4853      5.8641|
|  4:  3.3180 -  3.0173 0.99   1293  142 0.1229 0.1538      5.4675       5.606|
|  5:  3.0173 -  2.8026 0.99   1295  142 0.1375 0.1748       5.358      5.5424|
|  6:  2.8026 -  2.6383 0.99   1286  144 0.1267 0.1937      5.2484      5.4918|
|  7:  2.6383 -  2.5068 0.99   1282  139 0.1298 0.1682      5.1981      5.3969|
|  8:  2.5068 -  2.3981 0.98   1272  148 0.1224 0.1785      5.1077      5.3622|
|  9:  2.3981 -  2.3061 0.98   1280  139 0.1214 0.1841      5.0579      5.3416|
| 10:  2.3061 -  2.2268 0.98   1242  138 0.1174 0.1650      4.9968      5.2003|
| 11:  2.2268 -  2.1574 1.00   1285  143 0.1191 0.1775      4.9485       5.277|
| 12:  2.1574 -  2.0959 0.97   1242  136 0.1135 0.1674      4.8975      5.1504|
| 13:  2.0959 -  2.0408 0.98   1257  145 0.1210 0.1847       4.824      5.1233|
| 14:  2.0408 -  1.9912 0.67    862   93 0.1124 0.1744      4.7099      4.9403|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7516  1380   154  0.94   8.98   0.97     0.95       7192.17|
|  2:  4.7516 -  3.7914  1346   146  0.95   7.92   1.01     0.99       8949.81|
|  3:  3.7914 -  3.3180  1308   150  0.93  11.38   1.02     1.01      10550.06|
|  4:  3.3180 -  3.0173  1293   142  0.92  13.64   1.00     0.98      10456.20|
|  5:  3.0173 -  2.8026  1295   142  0.89  16.46   0.99     0.96       8695.84|
|  6:  2.8026 -  2.6383  1286   144  0.90  16.26   0.97     0.94       7475.14|
|  7:  2.6383 -  2.5068  1282   139  0.90  15.83   0.98     0.96       6539.93|
|  8:  2.5068 -  2.3981  1272   148  0.90  15.66   0.99     0.96       5667.89|
|  9:  2.3981 -  2.3061  1280   139  0.91  15.76   1.00     0.97       5212.98|
| 10:  2.3061 -  2.2268  1242   138  0.90  15.81   0.99     0.96       4634.99|
| 11:  2.2268 -  2.1574  1285   143  0.90  16.28   0.99     0.96       4309.85|
| 12:  2.1574 -  2.0959  1242   136  0.92  14.88   0.99     0.98       3996.65|
| 13:  2.0959 -  2.0408  1257   145  0.90  16.60   0.99     0.99       3538.98|
| 14:  2.0408 -  1.9912   862    93  0.91  15.18   0.97     0.93       2697.84|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2697.84 max =        10550.06 mean =      6549.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1590   ksol= 0.32   Bsol= 50.84   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,0.00,0.55,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1590   ksol= 0.32   Bsol= 50.84   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,0.00,0.55,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169170                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7516 0.99   1380  154 0.1021 0.1303      5.3985      5.5265|
|  2:  4.7516 -  3.7914 0.99   1346  146 0.0889 0.1084      5.4565      5.6304|
|  3:  3.7914 -  3.3180 0.99   1308  150 0.1075 0.1506      5.4854      5.8643|
|  4:  3.3180 -  3.0173 0.99   1293  142 0.1229 0.1538      5.4675       5.606|
|  5:  3.0173 -  2.8026 0.99   1295  142 0.1375 0.1748      5.3579      5.5423|
|  6:  2.8026 -  2.6383 0.99   1286  144 0.1267 0.1937      5.2483      5.4914|
|  7:  2.6383 -  2.5068 0.99   1282  139 0.1298 0.1682      5.1981      5.3972|
|  8:  2.5068 -  2.3981 0.98   1272  148 0.1224 0.1785      5.1077      5.3621|
|  9:  2.3981 -  2.3061 0.98   1280  139 0.1214 0.1840      5.0579      5.3416|
| 10:  2.3061 -  2.2268 0.98   1242  138 0.1173 0.1651      4.9968      5.2006|
| 11:  2.2268 -  2.1574 1.00   1285  143 0.1191 0.1775      4.9484      5.2771|
| 12:  2.1574 -  2.0959 0.97   1242  136 0.1135 0.1674      4.8975      5.1505|
| 13:  2.0959 -  2.0408 0.98   1257  145 0.1210 0.1847      4.8239      5.1232|
| 14:  2.0408 -  1.9912 0.67    862   93 0.1124 0.1743      4.7097      4.9398|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7516  1380   154  0.94   8.98   0.97     0.95       7197.68|
|  2:  4.7516 -  3.7914  1346   146  0.95   7.92   1.01     0.99       8953.93|
|  3:  3.7914 -  3.3180  1308   150  0.93  11.38   1.02     1.01      10553.00|
|  4:  3.3180 -  3.0173  1293   142  0.92  13.64   1.00     0.98      10454.97|
|  5:  3.0173 -  2.8026  1295   142  0.89  16.46   0.99     0.96       8692.41|
|  6:  2.8026 -  2.6383  1286   144  0.90  16.25   0.98     0.95       7472.59|
|  7:  2.6383 -  2.5068  1282   139  0.90  15.83   0.99     0.97       6538.87|
|  8:  2.5068 -  2.3981  1272   148  0.90  15.66   0.99     0.96       5668.17|
|  9:  2.3981 -  2.3061  1280   139  0.91  15.76   1.00     0.97       5213.80|
| 10:  2.3061 -  2.2268  1242   138  0.90  15.81   1.00     0.96       4635.73|
| 11:  2.2268 -  2.1574  1285   143  0.90  16.28   0.99     0.96       4310.18|
| 12:  2.1574 -  2.0959  1242   136  0.92  14.88   1.00     0.98       3997.45|
| 13:  2.0959 -  2.0408  1257   145  0.90  16.60   1.00     0.99       3537.78|
| 14:  2.0408 -  1.9912   862    93  0.91  15.16   0.97     0.93       2695.52|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2695.52 max =        10553.00 mean =      6549.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.038)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.62    81.19   14.90    None  None   None       |
|    all(noH): 2823   0      3.62    81.19   14.90    None  None   None       |
|    Sol.    : 438    0      4.52    70.04   36.82    None  None   None       |
|    Mac.    : 2385   0      3.62    81.19   10.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.618 -  11.375: 1708   |   5:    42.402 -  50.159:   93        |
|      1:    11.375 -  19.132:  535   |   6:    50.159 -  57.916:   68        |
|      2:    19.132 -  26.889:  155   |   7:    57.916 -  65.672:   21        |
|      3:    26.889 -  34.645:  111   |   8:    65.672 -  73.429:   14        |
|      4:    34.645 -  42.402:  113   |   9:    73.429 -  81.186:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.318 - 5.821
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 329
   mapped sites are within: 0.710 - 5.821

peak=   10.568 closest distance to " CG2 VAL A 230 " =    1.439
peak=    7.758 closest distance to " CG2 VAL A 296 " =    1.154
peak=    6.015 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.976 closest distance to " NH2 ARG A  56 " =    2.270
peak=    5.625 closest distance to " CB  GLN A 223 " =    1.394
peak=    5.471 closest distance to " CG  LEU A 228 " =    1.219
peak=    5.433 closest distance to " CG  PRO A  54 " =    1.337
peak=    5.291 closest distance to " CD2 LEU A   5 " =    1.193
peak=    5.201 closest distance to " CB  PRO A  54 " =    0.978
peak=    5.022 closest distance to " CG  PRO A 198 " =    1.238
peak=    4.934 closest distance to " CB  SER A  63 " =    1.292
peak=    4.878 closest distance to " CG  PRO A 213 " =    1.256
peak=    4.851 closest distance to " CB  ARG A 275 " =    0.893
peak=    4.850 closest distance to " CB  VAL A 296 " =    1.080
peak=    4.847 closest distance to " CB  VAL A 230 " =    1.231
peak=    4.657 closest distance to " O   HOH Z 232 " =    2.331
peak=    4.580 closest distance to " CB  GLU A 128 " =    1.064
peak=    4.566 closest distance to " O   HOH Z 126 " =    1.945
peak=    4.528 closest distance to " CG  PRO A 243 " =    1.153
peak=    4.451 closest distance to " C   PRO A 198 " =    1.520
peak=    4.402 closest distance to " CB  GLN A 183 " =    1.290
peak=    4.348 closest distance to " O   HOH Z 298 " =    1.856
peak=    4.301 closest distance to " CD2 LEU A 228 " =    1.182
peak=    4.287 closest distance to " O   HOH Z 272 " =    1.927
peak=    4.284 closest distance to " CB  ASN A 148 " =    1.311
peak=    4.283 closest distance to " CB  SER A   3 " =    1.260
peak=    4.279 closest distance to " NE2 GLN A  11 " =    1.071
peak=    4.278 closest distance to " O   HOH Z 369 " =    2.081
peak=    4.278 closest distance to " O   SER A  87 " =    2.283
peak=    4.262 closest distance to " O   HOH Z 316 " =    3.068
peak=    4.206 closest distance to " O   HOH Z 236 " =    1.887
peak=    4.200 closest distance to " CA  TYR A  30 " =    0.900
peak=    4.197 closest distance to " OD1 ASN A  69 " =    2.575
peak=    4.145 closest distance to " O   HOH Z  48 " =    1.511
peak=    4.134 closest distance to " O   HOH Z 423 " =    1.775
peak=    4.131 closest distance to " O   HOH Z 368 " =    2.232
peak=    4.124 closest distance to " CB  GLU A 152 " =    1.114
peak=    4.114 closest distance to " CB  ARG A 190 " =    1.632
peak=    4.098 closest distance to " O   HOH Z  43 " =    2.076
peak=    4.072 closest distance to " O   HOH Z 402 " =    1.500
peak=    4.051 closest distance to " O   HOH Z 403 " =    1.746
peak=    4.047 closest distance to " ND2 ASN A 249 " =    1.900
peak=    4.045 closest distance to " O   HOH Z  44 " =    2.288
peak=    4.039 closest distance to " CB  TRP A 266 " =    0.932
peak=    4.032 closest distance to " NH2 ARG A 156 " =    1.154
peak=    4.013 closest distance to " CZ  PHE A 218 " =    1.067
peak=    4.011 closest distance to " O   HOH Z  54 " =    2.375
peak=    4.010 closest distance to " O   HOH Z  48 " =    1.765
peak=    4.008 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.008 closest distance to " O   TRP A 274 " =    1.881
peak=    4.008 closest distance to " CB  TRP A 179 " =    1.409
peak=    4.007 closest distance to " CB  GLU A 277 " =    3.643
peak=    4.006 closest distance to " O   HOH Z 189 " =    2.695
peak=    3.994 closest distance to " O   HOH Z 203 " =    1.811
peak=    3.991 closest distance to " CB BVAL A  41 " =    1.053
peak=    3.973 closest distance to " O   HOH Z 427 " =    3.061
peak=    3.972 closest distance to " CA  ALA A  21 " =    1.201
peak=    3.965 closest distance to " O   HOH Z 234 " =    3.689
peak=    3.965 closest distance to " CG1BVAL A  72 " =    1.725
peak=    3.961 closest distance to " CA  ALA A  51 " =    1.020
peak=    3.936 closest distance to " O   HOH Z 303 " =    2.121
peak=    3.894 closest distance to " CD  LYS A 166 " =    1.332
peak=    3.892 closest distance to " ND2 ASN A 187 " =    1.474
peak=    3.884 closest distance to " N   ASN A  39 " =    1.175
peak=    3.884 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.879 closest distance to " CB  ASN A  39 " =    0.833
peak=    3.874 closest distance to " O   HOH Z 280 " =    2.922
peak=    3.867 closest distance to " O   HOH Z 247 " =    1.440
peak=    3.867 closest distance to " O   HOH Z  97 " =    2.049
peak=    3.865 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.841 closest distance to " CD  ARG A 269 " =    0.991
peak=    3.835 closest distance to " O   HOH Z 263 " =    1.656
peak=    3.829 closest distance to " O   HOH Z 346 " =    1.547
peak=    3.820 closest distance to " O   HOH Z  78 " =    1.667
peak=    3.819 closest distance to " O   HOH Z  63 " =    1.547
peak=    3.809 closest distance to " CA  THR A 264 " =    0.760
peak=    3.809 closest distance to " CB  ASP A 124 " =    0.710
peak=    3.808 closest distance to " CG1 VAL A 153 " =    0.993
peak=    3.806 closest distance to " O   HOH Z 411 " =    3.724
peak=    3.801 closest distance to " O   HOH Z 158 " =    3.101
peak=    3.800 closest distance to " O   HOH Z  61 " =    1.651
peak=    3.797 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.785 closest distance to " CA  THR A 221 " =    0.905
peak=    3.780 closest distance to " O   HOH Z 344 " =    2.943
peak=    3.776 closest distance to " O   HOH Z  48 " =    1.460
peak=    3.774 closest distance to " NZ  LYS A 166 " =    3.102
peak=    3.774 closest distance to " CB  LEU A 143 " =    1.145
peak=    3.772 closest distance to " O   HOH Z 214 " =    2.241
peak=    3.770 closest distance to " O   HOH Z  68 " =    1.999
peak=    3.764 closest distance to " O   HOH Z  97 " =    2.483
peak=    3.762 closest distance to " CZ  PHE A 192 " =    0.969
peak=    3.759 closest distance to " O   HOH Z 383 " =    2.133
peak=    3.754 closest distance to " CE1 TYR A 186 " =    1.274
peak=    3.745 closest distance to " CB  ASN A 187 " =    1.373
peak=    3.745 closest distance to " OD2 ASP A 286 " =    2.877
peak=    3.741 closest distance to " CB  ALA A 291 " =    1.312
peak=    3.737 closest distance to " O   HOH Z  40 " =    1.659
peak=    3.726 closest distance to " O   HOH Z 102 " =    1.304
peak=    3.722 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.720 closest distance to " CG  ARG A  66 " =    2.765
peak=    3.719 closest distance to " CA  LYS A 117 " =    1.271
peak=    3.711 closest distance to " CB  ARG A  79 " =    1.379
peak=    3.706 closest distance to " O   HOH Z  15 " =    2.119
peak=    3.692 closest distance to " CG2 THR A 221 " =    1.031
peak=    3.692 closest distance to " O   HOH Z 142 " =    1.525
peak=    3.686 closest distance to " CG1 VAL A 296 " =    1.224
peak=    3.684 closest distance to " O   HOH Z  21 " =    1.711
peak=    3.682 closest distance to " CB  ASN A 142 " =    1.116
peak=    3.678 closest distance to " O   HOH Z 426 " =    1.532
peak=    3.674 closest distance to " CE1 HIS A 108 " =    1.157
peak=    3.670 closest distance to " O   HOH Z  80 " =    1.773
peak=    3.669 closest distance to " O   HOH Z 126 " =    1.653
peak=    3.664 closest distance to " O   HOH Z 371 " =    3.232
peak=    3.658 closest distance to " O   MET A 105 " =    1.866
peak=    3.649 closest distance to " CG1 ILE A  33 " =    1.329
peak=    3.647 closest distance to " CA  VAL A  41 " =    0.808
peak=    3.639 closest distance to " CA  ASP A 191 " =    0.829
peak=    3.638 closest distance to " O   HOH Z 128 " =    2.274
peak=    3.625 closest distance to " O   HOH Z  88 " =    3.093
peak=    3.618 closest distance to " CD1 LEU A  96 " =    0.714
peak=    3.606 closest distance to " O   ASP A 124 " =    1.154
peak=    3.593 closest distance to " O   HOH Z  20 " =    1.578
peak=    3.592 closest distance to " CB  PRO A 198 " =    1.017
peak=    3.587 closest distance to " O   HOH Z 245 " =    1.389
peak=    3.586 closest distance to " O   HOH Z 273 " =    2.768
peak=    3.585 closest distance to " CG1 ILE A  49 " =    1.512
peak=    3.583 closest distance to " CA  ASP A 140 " =    1.211
peak=    3.574 closest distance to " CB  ASP A 140 " =    0.875
peak=    3.573 closest distance to " CA  ILE A 106 " =    0.789
peak=    3.566 closest distance to " CB  ARG A 139 " =    0.878
peak=    3.560 closest distance to " CB  LEU A 228 " =    1.308
peak=    3.558 closest distance to " CD  ARG A 159 " =    0.777
peak=    3.547 closest distance to " O   HOH Z 134 " =    1.476
peak=    3.546 closest distance to " O   HOH Z 172 " =    3.818
peak=    3.541 closest distance to " O   HOH Z 133 " =    1.658
peak=    3.539 closest distance to " CG  MET A 185 " =    1.138
peak=    3.525 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.525 closest distance to " O   HOH Z 193 " =    2.082
peak=    3.519 closest distance to " N   VAL A 126 " =    1.455
peak=    3.516 closest distance to " O   HOH Z 248 " =    1.707
peak=    3.516 closest distance to " O   HOH Z 227 " =    1.566
peak=    3.513 closest distance to " O   HOH Z 422 " =    2.697
peak=    3.513 closest distance to " CA  SER A  87 " =    1.058
peak=    3.504 closest distance to " CD BLYS A 290 " =    1.032
peak=    3.486 closest distance to " CB  ALA A   9 " =    1.607
peak=    3.485 closest distance to " O   HOH Z 417 " =    2.977
peak=    3.481 closest distance to " O   HOH Z 128 " =    2.060
peak=    3.481 closest distance to " CB  THR A 157 " =    1.209
peak=    3.481 closest distance to " CG BARG A 102 " =    1.847
peak=    3.477 closest distance to " O   HOH Z 329 " =    3.827
peak=    3.476 closest distance to " O   HOH Z 197 " =    2.797
peak=    3.474 closest distance to " CA  ARG A  36 " =    1.095
peak=    3.471 closest distance to " CB  TRP A 150 " =    1.427
peak=    3.469 closest distance to " O   HOH Z 425 " =    1.339
peak=    3.467 closest distance to " CA  ASN A 215 " =    1.249
peak=    3.465 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.465 closest distance to " O   HOH Z 135 " =    1.875
peak=    3.464 closest distance to " CB  SER A 212 " =    1.266
peak=    3.461 closest distance to " N   ARG A 190 " =    1.044
peak=    3.454 closest distance to " CA  LEU A 282 " =    1.055
peak=    3.454 closest distance to " O   HOH Z 261 " =    2.176
peak=    3.452 closest distance to " O   HOH Z 133 " =    2.378
peak=    3.449 closest distance to " CA  ALA A 295 " =    1.063
peak=    3.443 closest distance to " CB  SER A  28 " =    1.102
peak=    3.443 closest distance to " NH1AARG A 145 " =    1.126
peak=    3.437 closest distance to " CB  THR A  31 " =    1.568
peak=    3.433 closest distance to " O   HOH Z 368 " =    3.613
peak=    3.432 closest distance to " OG1 THR A 294 " =    2.325
peak=    3.430 closest distance to " O   HOH Z 437 " =    2.067
peak=    3.430 closest distance to " CB  GLN A 278 " =    0.875
peak=    3.421 closest distance to " CD2 LEU A 297 " =    0.817
peak=    3.411 closest distance to " O   HOH Z 313 " =    1.825
peak=    3.405 closest distance to " OG BSER A 164 " =    2.216
peak=    3.402 closest distance to " O   HOH Z 295 " =    1.482
peak=    3.400 closest distance to " N   SER A 135 " =    1.452
peak=    3.398 closest distance to " CB  MET A  47 " =    1.070
peak=    3.395 closest distance to " O   HOH Z 250 " =    1.396
peak=    3.392 closest distance to " O   HOH Z 238 " =    2.290
peak=    3.391 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.390 closest distance to " O   GLN A 278 " =    1.286
peak=    3.385 closest distance to " NZ  LYS A 117 " =    3.254
peak=    3.385 closest distance to " CD1 ILE A 106 " =    1.011
peak=    3.383 closest distance to " OG  SER A 276 " =    1.252
peak=    3.378 closest distance to " O   HOH Z 417 " =    2.216
peak=    3.363 closest distance to " O   HOH Z 327 " =    2.445
peak=    3.363 closest distance to " CB  ALA A 248 " =    1.064
peak=    3.361 closest distance to " CB  SER A  26 " =    1.696
peak=    3.357 closest distance to " OG  SER A  22 " =    2.782
peak=    3.357 closest distance to " O   HOH Z 345 " =    3.236
peak=    3.355 closest distance to " O   HOH Z 407 " =    2.537
peak=    3.352 closest distance to " O   HOH Z   4 " =    1.850
peak=    3.351 closest distance to " O   HOH Z 112 " =    1.616
peak=    3.351 closest distance to " CE  LYS A  76 " =    0.903
peak=    3.351 closest distance to " O   HOH Z 420 " =    2.000
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.597
peak=    3.347 closest distance to " O   HOH Z 155 " =    3.168
peak=    3.346 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.345 closest distance to " CG  MET A 185 " =    1.091
peak=    3.338 closest distance to " CG2 VAL A 257 " =    0.923
peak=    3.335 closest distance to " O   ALA A 165 " =    1.425
peak=    3.335 closest distance to " O   HOH Z 132 " =    2.729
peak=    3.334 closest distance to " CG2 THR A 220 " =    0.892
peak=    3.333 closest distance to " O   HOH Z 353 " =    2.714
peak=    3.330 closest distance to " O   HOH Z  54 " =    1.570
peak=    3.330 closest distance to " O   HOH Z 435 " =    1.973
peak=    3.327 closest distance to " CA  MET A  40 " =    1.125
peak=    3.324 closest distance to " C   TYR A 214 " =    1.540
peak=    3.321 closest distance to " CA  ALA A 154 " =    0.962
peak=    3.318 closest distance to " O   HOH Z 180 " =    2.118
peak=    3.317 closest distance to " CZ3 TRP A  85 " =    0.988
peak=    3.316 closest distance to " CB  MET A  40 " =    0.786
peak=    3.316 closest distance to " CD  ARG A  66 " =    2.647
peak=    3.315 closest distance to " O   HOH Z 404 " =    2.322
peak=    3.314 closest distance to " O   HOH Z 421 " =    1.764
peak=    3.311 closest distance to " O   HOH Z 130 " =    2.214
peak=    3.311 closest distance to " C   ALA A 299 " =    0.956
peak=    3.310 closest distance to " CG2 ILE A  20 " =    1.450
peak=    3.309 closest distance to " CD2 TRP A 179 " =    1.362
peak=    3.308 closest distance to " OD1 ASP A 231 " =    1.910
peak=    3.307 closest distance to " O   ALA A 158 " =    1.337
peak=    3.305 closest distance to " O   HOH Z 403 " =    1.350
peak=    3.301 closest distance to " O   HOH Z  66 " =    2.239
peak=    3.301 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.300 closest distance to " CB  PRO A 243 " =    1.359
peak=    3.298 closest distance to " O   HOH Z 261 " =    1.911
peak=    3.295 closest distance to " CG AARG A 275 " =    1.222
peak=    3.293 closest distance to " CB  SER A 216 " =    0.761
peak=    3.291 closest distance to " CG  GLN A  88 " =    1.009
peak=    3.291 closest distance to " O   HOH Z 171 " =    3.819
peak=    3.290 closest distance to " O   HOH Z 291 " =    1.568
peak=    3.289 closest distance to " CG2 ILE A 120 " =    1.132
peak=    3.288 closest distance to " O   HOH Z 365 " =    3.036
peak=    3.284 closest distance to " CG  LEU A 167 " =    1.133
peak=    3.282 closest distance to " CB  ALA A 295 " =    1.224
peak=    3.281 closest distance to " OG1 THR A 294 " =    1.746
peak=    3.277 closest distance to " ND1 HIS A  81 " =    1.681
peak=    3.277 closest distance to " CB  GLN A  89 " =    1.117
peak=    3.276 closest distance to " CA  ALA A 158 " =    1.186
peak=    3.273 closest distance to " O   HOH Z 145 " =    2.646
peak=    3.273 closest distance to " NZ  LYS A  48 " =    1.345
peak=    3.272 closest distance to " O   HOH Z 313 " =    1.732
peak=    3.268 closest distance to " O   HOH Z 163 " =    1.480
peak=    3.267 closest distance to " CG1 ILE A 151 " =    1.092
peak=    3.267 closest distance to " NH1BARG A 190 " =    1.897
peak=    3.267 closest distance to " CA  ASP A 162 " =    1.068
peak=    3.262 closest distance to " O   HOH Z  63 " =    2.438
peak=    3.262 closest distance to " O   HOH Z 216 " =    2.731
peak=    3.249 closest distance to " OG BSER A 212 " =    2.603
peak=    3.247 closest distance to " CD1 LEU A   5 " =    1.399
peak=    3.244 closest distance to " CB  GLN A  88 " =    1.215
peak=    3.241 closest distance to " N   GLY A  98 " =    1.102
peak=    3.229 closest distance to " CB  GLN A 103 " =    0.909
peak=    3.228 closest distance to " CD2 LEU A 255 " =    1.501
peak=    3.227 closest distance to " O   HOH Z  59 " =    2.341
peak=    3.224 closest distance to " O   HOH Z 425 " =    2.023
peak=    3.222 closest distance to " CB  ILE A 120 " =    1.333
peak=    3.220 closest distance to " NZ  LYS A  76 " =    1.480
peak=    3.219 closest distance to " C   SER A  32 " =    1.011
peak=    3.217 closest distance to " OD1 ASN A 217 " =    1.686
peak=    3.217 closest distance to " O   HOH Z 419 " =    1.677
peak=    3.209 closest distance to " O   HOH Z 290 " =    1.125
peak=    3.206 closest distance to " O   HOH Z  10 " =    1.751
peak=    3.206 closest distance to " O   HOH Z 201 " =    3.109
peak=    3.202 closest distance to " CB  SER A 273 " =    0.844
peak=    3.201 closest distance to " CB  ALA A 114 " =    1.228
peak=    3.197 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.197 closest distance to " CB  ASN A 215 " =    1.166
peak=    3.197 closest distance to " O   HOH Z 302 " =    1.947
peak=    3.195 closest distance to " O   HOH Z 336 " =    1.698
peak=    3.194 closest distance to " CG2 VAL A 202 " =    1.144
peak=    3.194 closest distance to " CG1 VAL A 174 " =    1.141
peak=    3.192 closest distance to " O   HOH Z 357 " =    2.037
peak=    3.191 closest distance to " CD1 ILE A  33 " =    1.600
peak=    3.190 closest distance to " O   HOH Z 327 " =    1.726
peak=    3.189 closest distance to " O   ALA A   1 " =    1.524
peak=    3.188 closest distance to " O   HOH Z  19 " =    1.960
peak=    3.184 closest distance to " CA  ASN A 176 " =    1.067
peak=    3.182 closest distance to " CG  GLN A  58 " =    2.815
peak=    3.179 closest distance to " CG2 VAL A 197 " =    1.100
peak=    3.179 closest distance to " CB  TYR A 247 " =    0.984
peak=    3.172 closest distance to " CB  GLN A 205 " =    1.105
peak=    3.169 closest distance to " CZ  PHE A  38 " =    1.217
peak=    3.166 closest distance to " O   HOH Z  85 " =    1.416
peak=    3.161 closest distance to " CA  GLN A 194 " =    1.225
peak=    3.160 closest distance to " O   HOH Z 427 " =    3.121
peak=    3.158 closest distance to " CD  LYS A 119 " =    1.895
peak=    3.158 closest distance to " CG  LEU A 281 " =    1.122
peak=    3.156 closest distance to " OH  TYR A  30 " =    1.163
peak=    3.156 closest distance to " OD2 ASP A 200 " =    1.376
peak=    3.155 closest distance to " CG  GLN A  77 " =    2.197
peak=    3.150 closest distance to " CB  ALA A 242 " =    0.827
peak=    3.144 closest distance to " CB  LEU A  83 " =    0.751
peak=    3.143 closest distance to " CA  VAL A 126 " =    0.883
peak=    3.142 closest distance to " O   HOH Z 271 " =    2.386
peak=    3.140 closest distance to " CE2 TYR A  30 " =    0.765
peak=    3.139 closest distance to " CA  ALA A  84 " =    1.423
peak=    3.136 closest distance to " O   HOH Z 281 " =    4.790
peak=    3.131 closest distance to " O   ASN A  74 " =    2.085
peak=    3.129 closest distance to " CD1 LEU A 222 " =    0.819
peak=    3.127 closest distance to " O   HOH Z 423 " =    3.116
peak=    3.127 closest distance to " O   GLY A  91 " =    1.253
peak=    3.122 closest distance to " ND2 ASN A 110 " =    1.613
peak=    3.112 closest distance to " O   THR A 220 " =    1.239
peak=    3.110 closest distance to " O   HOH Z 109 " =    2.684
peak=    3.105 closest distance to " CA  ALA A 160 " =    0.885
peak=    3.104 closest distance to " OG BSER A 134 " =    2.864
peak=    3.104 closest distance to " O   THR A  31 " =    1.550
peak=    3.100 closest distance to " O   HOH Z 296 " =    1.630
peak=    3.096 closest distance to " O   HOH Z 124 " =    1.275
peak=    3.092 closest distance to " O   HOH Z 367 " =    3.471
peak=    3.079 closest distance to " CG2 ILE A 263 " =    0.900
peak=    3.075 closest distance to " O   HOH Z 305 " =    3.654
peak=    3.071 closest distance to " O   HOH Z  68 " =    1.542
peak=    3.065 closest distance to " N   ARG A 156 " =    1.425
peak=    3.062 closest distance to " OH  TYR A 214 " =    1.159
peak=    3.060 closest distance to " O   HOH Z 380 " =    1.979
peak=    3.060 closest distance to " OG  SER A 206 " =    1.229
peak=    3.059 closest distance to " O   HOH Z 420 " =    5.821
peak=    3.054 closest distance to " O   HOH Z 173 " =    2.424
peak=    3.046 closest distance to " O   HOH Z  90 " =    3.301
peak=    3.044 closest distance to " CD1 ILE A 199 " =    0.816
peak=    3.029 closest distance to " O   HOH Z 430 " =    3.976

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.764 - 5.498
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.764 - 5.498

peak=   -5.604 closest distance to " CG2 VAL A 230 " =    0.770
peak=   -4.501 closest distance to " CD  ARG A 156 " =    2.032
peak=   -4.372 closest distance to " O   HOH Z 266 " =    4.927
peak=   -4.322 closest distance to " O   HOH Z 290 " =    1.072
peak=   -4.167 closest distance to " SG  CYS A 254 " =    3.292
peak=   -4.159 closest distance to " O   HOH Z 196 " =    2.261
peak=   -4.147 closest distance to " CB  ALA A 161 " =    2.576
peak=   -4.079 closest distance to " CE2 TYR A  30 " =    2.772
peak=   -4.077 closest distance to " CD  GLN A  58 " =    1.073
peak=   -4.069 closest distance to " CG  ASP A 231 " =    0.816
peak=   -4.045 closest distance to " CB  PRO A 243 " =    2.678
peak=   -4.015 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.999 closest distance to " O   HOH Z 351 " =    1.535
peak=   -3.946 closest distance to " CG2BVAL A  41 " =    2.687
peak=   -3.914 closest distance to " OE1 GLN A 223 " =    2.072
peak=   -3.899 closest distance to " O   HOH Z 166 " =    1.836
peak=   -3.892 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.839 closest distance to " NH2AARG A 275 " =    5.112
peak=   -3.830 closest distance to " OG  SER A  97 " =    2.281
peak=   -3.826 closest distance to " CZ3 TRP A 179 " =    1.239
peak=   -3.814 closest distance to " OXT GLY A 302 " =    2.901
peak=   -3.812 closest distance to " CD2 LEU A 300 " =    2.664
peak=   -3.771 closest distance to " O   HOH Z  37 " =    1.901
peak=   -3.764 closest distance to " O   HOH Z 231 " =    1.983
peak=   -3.751 closest distance to " N   ALA A 226 " =    2.098
peak=   -3.720 closest distance to " CD2 LEU A 237 " =    2.722
peak=   -3.718 closest distance to " NH2 ARG A  66 " =    1.679
peak=   -3.699 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.699 closest distance to " ND2 ASN A  45 " =    1.101
peak=   -3.692 closest distance to " O   SER A 271 " =    2.152
peak=   -3.690 closest distance to " CE3 TRP A 150 " =    2.068
peak=   -3.690 closest distance to " O   HOH Z  52 " =    1.633
peak=   -3.687 closest distance to " O   HOH Z  11 " =    1.900
peak=   -3.680 closest distance to " O   HOH Z 394 " =    1.590
peak=   -3.679 closest distance to " O   HOH Z 114 " =    3.239
peak=   -3.665 closest distance to " O   HOH Z 222 " =    1.463
peak=   -3.664 closest distance to " CB  PHE A 192 " =    1.962
peak=   -3.655 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -3.644 closest distance to " C   ALA A 158 " =    1.281
peak=   -3.614 closest distance to " CD1 LEU A 101 " =    2.494
peak=   -3.607 closest distance to " CG2 VAL A 296 " =    1.379
peak=   -3.606 closest distance to " NE2 GLN A  88 " =    2.037
peak=   -3.605 closest distance to " CG1 VAL A 265 " =    2.408
peak=   -3.605 closest distance to " O   VAL A  67 " =    2.640
peak=   -3.596 closest distance to " O   HOH Z 185 " =    2.396
peak=   -3.594 closest distance to " O   HOH Z  10 " =    1.578
peak=   -3.591 closest distance to " CG1 VAL A 296 " =    1.301
peak=   -3.591 closest distance to " O   HOH Z  13 " =    1.414
peak=   -3.589 closest distance to " OG ASER A 134 " =    1.352
peak=   -3.580 closest distance to " CD  ARG A  14 " =    2.967
peak=   -3.578 closest distance to " NH2 ARG A 159 " =    2.287
peak=   -3.578 closest distance to " ND2 ASN A 187 " =    1.709
peak=   -3.577 closest distance to " OG BSER A 134 " =    1.175
peak=   -3.571 closest distance to " O   HOH Z 292 " =    4.414
peak=   -3.558 closest distance to " CG  ARG A 269 " =    2.350
peak=   -3.557 closest distance to " CG  GLU A 277 " =    1.096
peak=   -3.551 closest distance to " O   HOH Z  19 " =    2.128
peak=   -3.542 closest distance to " CB  ALA A 248 " =    2.039
peak=   -3.538 closest distance to " N   GLN A  58 " =    1.868
peak=   -3.524 closest distance to " CD  ARG A 139 " =    1.650
peak=   -3.517 closest distance to " N   THR A 235 " =    1.275
peak=   -3.512 closest distance to " CB  PRO A 163 " =    2.629
peak=   -3.509 closest distance to " O   HOH Z 389 " =    1.803
peak=   -3.504 closest distance to " NE2 GLN A 103 " =    1.785
peak=   -3.502 closest distance to " CD2 LEU A 167 " =    1.738
peak=   -3.502 closest distance to " CD1 LEU A 228 " =    2.304
peak=   -3.496 closest distance to " O   HOH Z 283 " =    2.017
peak=   -3.484 closest distance to " ND2 ASN A  45 " =    1.576
peak=   -3.480 closest distance to " CG  TRP A 266 " =    1.887
peak=   -3.479 closest distance to " CE BMET A  47 " =    2.019
peak=   -3.470 closest distance to " CG  GLU A  53 " =    1.493
peak=   -3.465 closest distance to " O   HOH Z 166 " =    1.636
peak=   -3.463 closest distance to " CD  LYS A 289 " =    2.528
peak=   -3.458 closest distance to " C   ASP A 231 " =    2.578
peak=   -3.451 closest distance to " CD1 LEU A  25 " =    2.454
peak=   -3.447 closest distance to " O   HOH Z  60 " =    2.041
peak=   -3.445 closest distance to " O   HOH Z  43 " =    1.675
peak=   -3.443 closest distance to " O   HOH Z 165 " =    1.928
peak=   -3.438 closest distance to " CG  LEU A 101 " =    2.456
peak=   -3.431 closest distance to " CD1 PHE A  59 " =    1.914
peak=   -3.431 closest distance to " NH2 ARG A  79 " =    1.966
peak=   -3.427 closest distance to " O   HOH Z  17 " =    1.414
peak=   -3.427 closest distance to " CB  ALA A 291 " =    2.228
peak=   -3.422 closest distance to " CE2 PHE A 218 " =    2.683
peak=   -3.413 closest distance to " C   SER A 206 " =    1.516
peak=   -3.409 closest distance to " C   MET A 188 " =    1.504
peak=   -3.406 closest distance to " O   HOH Z 353 " =    2.128
peak=   -3.398 closest distance to " CG  ASP A  50 " =    2.359
peak=   -3.393 closest distance to " OD1 ASN A 148 " =    1.458
peak=   -3.393 closest distance to " O   HOH Z 426 " =    1.702
peak=   -3.392 closest distance to " O   HOH Z 311 " =    3.735
peak=   -3.391 closest distance to " C   ASN A 285 " =    2.442
peak=   -3.389 closest distance to " N   THR A 157 " =    1.510
peak=   -3.388 closest distance to " CD1 LEU A 101 " =    2.641
peak=   -3.387 closest distance to " OG  SER A  62 " =    1.671
peak=   -3.383 closest distance to " O   HOH Z  63 " =    1.063
peak=   -3.383 closest distance to " CE  MET A 105 " =    2.146
peak=   -3.382 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.376 closest distance to " CB  ALA A  10 " =    2.274
peak=   -3.373 closest distance to " N   MET A 105 " =    2.662
peak=   -3.370 closest distance to " O   HOH Z 407 " =    3.113
peak=   -3.368 closest distance to " OG  SER A 206 " =    1.676
peak=   -3.366 closest distance to " CG1 VAL A 112 " =    2.752
peak=   -3.362 closest distance to " O   HOH Z 252 " =    4.009
peak=   -3.357 closest distance to " N   ALA A  43 " =    2.589
peak=   -3.356 closest distance to " NE2 GLN A  88 " =    0.965
peak=   -3.356 closest distance to " O   HOH Z 128 " =    2.515
peak=   -3.354 closest distance to " N   SER A 212 " =    1.885
peak=   -3.353 closest distance to " O   HOH Z 234 " =    4.229
peak=   -3.353 closest distance to " O   GLY A 196 " =    1.085
peak=   -3.350 closest distance to " OD1 ASN A 187 " =    1.702
peak=   -3.350 closest distance to " C   THR A 279 " =    1.212
peak=   -3.347 closest distance to " CB  ALA A  43 " =    2.520
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.575
peak=   -3.333 closest distance to " O   HOH Z 423 " =    2.171
peak=   -3.331 closest distance to " O   PRO A 198 " =    1.207
peak=   -3.330 closest distance to " O   HOH Z 241 " =    1.223
peak=   -3.328 closest distance to " O   GLY A 203 " =    2.352
peak=   -3.328 closest distance to " CG2 VAL A 112 " =    2.565
peak=   -3.327 closest distance to " CA  GLY A 241 " =    3.067
peak=   -3.326 closest distance to " CD2 TYR A 293 " =    2.081
peak=   -3.323 closest distance to " CD1 PHE A  59 " =    2.335
peak=   -3.318 closest distance to " O   HOH Z  47 " =    1.548
peak=   -3.315 closest distance to " O   HOH Z  38 " =    1.573
peak=   -3.315 closest distance to " O   ALA A   7 " =    1.558
peak=   -3.313 closest distance to " OG BSER A 134 " =    1.866
peak=   -3.311 closest distance to " CD  GLN A 223 " =    0.764
peak=   -3.307 closest distance to " O   HOH Z 211 " =    1.645
peak=   -3.305 closest distance to " NH1 ARG A 195 " =    2.577
peak=   -3.304 closest distance to " CB  ASP A 171 " =    2.335
peak=   -3.293 closest distance to " CG1 VAL A 296 " =    1.292
peak=   -3.283 closest distance to " CB  ASN A  39 " =    2.192
peak=   -3.278 closest distance to " NE1 TRP A 266 " =    2.371
peak=   -3.272 closest distance to " O   SER A  95 " =    1.684
peak=   -3.265 closest distance to " CA  GLY A 133 " =    2.353
peak=   -3.263 closest distance to " O   VAL A 125 " =    2.319
peak=   -3.245 closest distance to " N   SER A   3 " =    2.071
peak=   -3.245 closest distance to " O   HOH Z  44 " =    2.152
peak=   -3.243 closest distance to " O   GLY A 211 " =    1.445
peak=   -3.238 closest distance to " O   HOH Z 275 " =    1.500
peak=   -3.236 closest distance to " OG  SER A  87 " =    1.511
peak=   -3.235 closest distance to " O   HOH Z 123 " =    2.405
peak=   -3.233 closest distance to " C   ASN A 187 " =    1.956
peak=   -3.226 closest distance to " O   HOH Z 368 " =    1.728
peak=   -3.226 closest distance to " CG  PHE A 283 " =    2.782
peak=   -3.225 closest distance to " O   HOH Z 136 " =    2.153
peak=   -3.216 closest distance to " O   ALA A 161 " =    1.670
peak=   -3.212 closest distance to " CG1 VAL A 112 " =    2.900
peak=   -3.209 closest distance to " CA  ASN A 127 " =    1.061
peak=   -3.208 closest distance to " CA  GLY A 203 " =    2.400
peak=   -3.208 closest distance to " O   HOH Z 350 " =    1.847
peak=   -3.205 closest distance to " O   HOH Z 102 " =    1.690
peak=   -3.203 closest distance to " CB  TYR A  15 " =    2.219
peak=   -3.197 closest distance to " O   HOH Z 262 " =    2.799
peak=   -3.196 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.195 closest distance to " O   HOH Z 435 " =    2.712
peak=   -3.194 closest distance to " O   HOH Z 231 " =    1.775
peak=   -3.193 closest distance to " OE1 GLN A  88 " =    1.073
peak=   -3.193 closest distance to " O   HOH Z 295 " =    1.514
peak=   -3.189 closest distance to " O   VAL A 197 " =    1.330
peak=   -3.185 closest distance to " CB  ASN A  69 " =    1.164
peak=   -3.184 closest distance to " CB  PRO A 280 " =    2.157
peak=   -3.184 closest distance to " C   ASP A 270 " =    1.187
peak=   -3.183 closest distance to " O   HOH Z 372 " =    2.340
peak=   -3.181 closest distance to " CD  PRO A 213 " =    2.100
peak=   -3.178 closest distance to " CG  MET A 105 " =    0.910
peak=   -3.177 closest distance to " CG1 VAL A 197 " =    2.270
peak=   -3.176 closest distance to " N   VAL A 230 " =    1.065
peak=   -3.164 closest distance to " CD  ARG A 195 " =    5.090
peak=   -3.162 closest distance to " O   HOH Z 377 " =    1.575
peak=   -3.160 closest distance to " O   LEU A 167 " =    1.489
peak=   -3.160 closest distance to " C   LEU A 222 " =    0.871
peak=   -3.159 closest distance to " O   HOH Z 150 " =    1.846
peak=   -3.159 closest distance to " ND2 ASN A  69 " =    1.770
peak=   -3.155 closest distance to " CB  ASP A 132 " =    2.320
peak=   -3.154 closest distance to " O   HOH Z 193 " =    1.983
peak=   -3.146 closest distance to " O   HOH Z 191 " =    5.498
peak=   -3.141 closest distance to " NE2 GLN A 194 " =    1.824
peak=   -3.139 closest distance to " CG  LEU A 228 " =    0.992
peak=   -3.128 closest distance to " O   HOH Z 431 " =    1.863
peak=   -3.127 closest distance to " CB  GLN A  11 " =    1.680
peak=   -3.124 closest distance to " ND2 ASN A  60 " =    1.435
peak=   -3.118 closest distance to " CD  PRO A 243 " =    2.037
peak=   -3.114 closest distance to " OG  SER A  26 " =    1.309
peak=   -3.112 closest distance to " O   GLY A  17 " =    1.334
peak=   -3.112 closest distance to " OD1 ASN A  39 " =    1.200
peak=   -3.110 closest distance to " CD  ARG A 259 " =    2.492
peak=   -3.109 closest distance to " O   HOH Z 177 " =    1.690
peak=   -3.104 closest distance to " CA  VAL A 197 " =    1.020
peak=   -3.099 closest distance to " CZ2 TRP A  92 " =    2.741
peak=   -3.098 closest distance to " O   HOH Z 175 " =    4.376
peak=   -3.091 closest distance to " OD1 ASP A 191 " =    1.365
peak=   -3.084 closest distance to " NH2 ARG A  79 " =    1.607
peak=   -3.083 closest distance to " O   HOH Z 149 " =    2.088
peak=   -3.076 closest distance to " O   HOH Z 313 " =    1.153
peak=   -3.074 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.072 closest distance to " O   HOH Z 111 " =    2.234
peak=   -3.053 closest distance to " CG  GLU A   2 " =    1.771
peak=   -3.049 closest distance to " O   HOH Z 113 " =    2.101
peak=   -3.028 closest distance to " CA  TYR A  68 " =    2.941
peak=   -3.012 closest distance to " O   HOH Z 298 " =    2.663

================= 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    :  0.4346 0.4204   6.227906e+00   6.204425e+00
   1_bss:  0.4259 0.4111   6.222871e+00   6.191142e+00
   1_xyz:  0.3160 0.3421   6.011037e+00   6.064658e+00
   1_adp:  0.2542 0.2894   5.828980e+00   5.936742e+00
   1_occ:  0.2536 0.2892   5.827958e+00   5.936881e+00
   2_bss:  0.2496 0.2828   5.826794e+00   5.930521e+00
   2_xyz:  0.1771 0.2130   5.516979e+00   5.679677e+00
   2_adp:  0.1622 0.2007   5.443676e+00   5.619678e+00
   2_occ:  0.1620 0.2007   5.443556e+00   5.620170e+00
   3_bss:  0.1612 0.2004   5.443848e+00   5.620134e+00
   3_xyz:  0.1258 0.1651   5.224690e+00   5.441068e+00
   3_adp:  0.1208 0.1608   5.193369e+00   5.417206e+00
   3_occ:  0.1206 0.1606   5.192490e+00   5.416511e+00
   4_bss:  0.1209 0.1614   5.194604e+00   5.417868e+00
   4_xyz:  0.1154 0.1586   5.168140e+00   5.402647e+00
   4_adp:  0.1140 0.1583   5.161784e+00   5.400643e+00
   4_occ:  0.1140 0.1584   5.161935e+00   5.401050e+00
   5_bss:  0.1140 0.1584   5.161819e+00   5.401036e+00
   5_xyz:  0.1155 0.1590   5.169278e+00   5.404705e+00
   5_adp:  0.1156 0.1590   5.169707e+00   5.404968e+00
   5_occ:  0.1155 0.1590   5.169158e+00   5.404736e+00
   5_bss:  0.1155 0.1590   5.169170e+00   5.404758e+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:  0.339  20.001   7.319   9.831   7.896   0.000   0.000   0.000
   1_xyz:  0.339  20.001   7.319   9.831   7.896   0.000   0.000   0.000
   1_adp:  0.339  20.001   7.319   9.831   7.896   0.000   0.000   0.000
   1_occ:  0.339  20.001   7.319   9.831   7.896   0.000   0.000   0.000
   2_bss:  0.334  50.001   3.992   5.923   4.992   0.000   0.000   0.000
   2_xyz:  0.334  50.001   3.992   5.923   4.992   0.000   0.000   0.000
   2_adp:  0.334  50.001   3.992   5.923   4.992   0.000   0.000   0.000
   2_occ:  0.334  50.001   3.992   5.923   4.992   0.000   0.000   0.000
   3_bss:  0.334  50.001   3.055   4.150   4.227   0.000   0.000   0.000
   3_xyz:  0.334  50.001   3.055   4.150   4.227   0.000   0.000   0.000
   3_adp:  0.334  50.001   3.055   4.150   4.227   0.000   0.000   0.000
   3_occ:  0.334  50.001   3.055   4.150   4.227   0.000   0.000   0.000
   4_bss:  0.325  47.409   2.924   3.648   4.045   0.000   0.000   0.000
   4_xyz:  0.325  47.409   2.924   3.648   4.045   0.000   0.000   0.000
   4_adp:  0.325  47.409   2.924   3.648   4.045   0.000   0.000   0.000
   4_occ:  0.325  47.409   2.924   3.648   4.045   0.000   0.000   0.000
   5_bss:  0.322  47.219   2.999   3.591   4.097   0.000   0.000   0.000
   5_xyz:  0.322  47.219   2.999   3.591   4.097   0.000   0.000   0.000
   5_adp:  0.322  47.219   2.999   3.591   4.097   0.000   0.000   0.000
   5_occ:  0.322  47.219   2.999   3.591   4.097   0.000   0.000   0.000
   5_bss:  0.322  50.837  -0.549   0.000   0.549   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.792 0.5619  0.6232    50430.525
   1_bss:  46.621 0.5619  0.8000    48348.968
   1_xyz:  37.001 0.6769  0.9389    31954.485
   1_adp:  29.173 0.7678  1.0334    21910.139
   1_occ:  29.199 0.7674  1.0325    21916.548
   2_bss:  28.880 0.7708  0.9186    21523.413
   2_xyz:  20.836 0.8534  0.9873    11709.614
   2_adp:  19.238 0.8692  1.0002    10354.412
   2_occ:  19.245 0.8691  0.9999    10365.113
   3_bss:  19.227 0.8694  0.9592    10390.632
   3_xyz:  15.122 0.9055  0.9799     6976.636
   3_adp:  14.544 0.9106  0.9818     6707.727
   3_occ:  14.533 0.9107  0.9817     6699.885
   4_bss:  14.584 0.9103  0.9718     6752.785
   4_xyz:  14.213 0.9136  0.9713     6535.736
   4_adp:  14.160 0.9141  0.9681     6513.660
   4_occ:  14.165 0.9141  0.9679     6521.770
   5_bss:  14.164 0.9141  0.9688     6522.518
   5_xyz:  14.206 0.9138  0.9689     6552.342
   5_adp:  14.205 0.9138  0.9671     6548.671
   5_occ:  14.201 0.9138  0.9670     6549.237
   5_bss:  14.200 0.9138  0.9689     6549.609
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4008e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4008e+01
   1_xyz:   1.556  0.012  0.103 17.776  0.006  4.112   1.2087e-01
   1_adp:   1.556  0.012  0.103 17.776  0.006  4.112   1.2087e-01
   1_occ:   1.556  0.012  0.103 17.776  0.006  4.112   1.2087e-01
   2_bss:   1.556  0.012  0.103 17.776  0.006  4.112   1.2087e-01
   2_xyz:   0.971  0.007  0.071 15.894  0.004  4.126   6.0941e-02
   2_adp:   0.971  0.007  0.071 15.894  0.004  4.126   6.0941e-02
   2_occ:   0.971  0.007  0.071 15.894  0.004  4.126   6.0941e-02
   3_bss:   0.971  0.007  0.071 15.894  0.004  4.126   6.0941e-02
   3_xyz:   1.067  0.008  0.084 15.670  0.004  4.114   6.8670e-02
   3_adp:   1.067  0.008  0.084 15.670  0.004  4.114   6.8670e-02
   3_occ:   1.067  0.008  0.084 15.670  0.004  4.114   6.8670e-02
   4_bss:   1.067  0.008  0.084 15.670  0.004  4.114   6.8670e-02
   4_xyz:   1.023  0.008  0.084 15.586  0.004  4.116   6.4523e-02
   4_adp:   1.023  0.008  0.084 15.586  0.004  4.116   6.4523e-02
   4_occ:   1.023  0.008  0.084 15.586  0.004  4.116   6.4523e-02
   5_bss:   1.023  0.008  0.084 15.586  0.004  4.116   6.4523e-02
   5_xyz:   0.931  0.006  0.075 15.212  0.003  4.116   5.5057e-02
   5_adp:   0.931  0.006  0.075 15.212  0.003  4.116   5.5057e-02
   5_occ:   0.931  0.006  0.075 15.212  0.003  4.116   5.5057e-02
   5_bss:   0.931  0.006  0.075 15.212  0.003  4.116   5.5057e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0028e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0028e+00
   1_xyz:  13.537  0.145  0.464 88.529  0.044  2.304   9.2216e-02
   1_adp:  13.537  0.145  0.464 88.529  0.044  2.304   9.2216e-02
   1_occ:  13.537  0.145  0.464 88.529  0.044  2.304   9.2216e-02
   2_bss:  13.537  0.145  0.464 88.529  0.044  2.304   9.2216e-02
   2_xyz:   6.464  0.046  0.218 86.879  0.027  2.303   9.4017e-02
   2_adp:   6.464  0.046  0.218 86.879  0.027  2.303   9.4017e-02
   2_occ:   6.464  0.046  0.218 86.879  0.027  2.303   9.4017e-02
   3_bss:   6.464  0.046  0.218 86.879  0.027  2.303   9.4017e-02
   3_xyz:   6.957  0.052  0.572 82.707  0.043  2.340   6.1875e-02
   3_adp:   6.957  0.052  0.572 82.707  0.043  2.340   6.1875e-02
   3_occ:   6.957  0.052  0.572 82.707  0.043  2.340   6.1875e-02
   4_bss:   6.957  0.052  0.572 82.707  0.043  2.340   6.1875e-02
   4_xyz:   7.239  0.043  0.576 83.012  0.039  2.357   5.0345e-02
   4_adp:   7.239  0.043  0.576 83.012  0.039  2.357   5.0345e-02
   4_occ:   7.239  0.043  0.576 83.012  0.039  2.357   5.0345e-02
   5_bss:   7.239  0.043  0.576 83.012  0.039  2.357   5.0345e-02
   5_xyz:   6.780  0.042  0.459 82.245  0.038  2.402   3.2104e-02
   5_adp:   6.780  0.042  0.459 82.245  0.038  2.402   3.2104e-02
   5_occ:   6.780  0.042  0.459 82.245  0.038  2.402   3.2104e-02
   5_bss:   6.780  0.042  0.459 82.245  0.038  2.402   3.2104e-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:  61.40   0.00  10.38  55.59   0.00   7.40  61.40   0.00  26.62
   1_occ:  61.40   0.00  10.38  55.59   0.00   7.40  61.40   0.00  26.62
   2_bss:  61.40   0.00  10.38  55.59   0.00   7.40  61.40   0.00  26.62
   2_xyz:  61.40   0.00  10.38  55.59   0.00   7.40  61.40   0.00  26.62
   2_adp:  67.77   0.00  11.10  67.77   0.00   7.32  64.69   0.82  31.68
   2_occ:  67.77   0.00  11.10  67.77   0.00   7.32  64.69   0.82  31.68
   3_bss:  67.77   0.00  11.10  67.77   0.00   7.32  64.69   0.82  31.68
   3_xyz:  67.77   0.00  11.10  67.77   0.00   7.32  64.69   0.82  31.68
   3_adp:  71.04   0.00  11.28  71.04   0.00   7.31  66.69   0.79  32.94
   3_occ:  71.04   0.00  11.28  71.04   0.00   7.31  66.69   0.79  32.94
   4_bss:  71.04   0.00  11.28  71.04   0.00   7.31  66.69   0.79  32.94
   4_xyz:  71.04   0.00  11.28  71.04   0.00   7.31  66.69   0.79  32.94
   4_adp:  76.52   0.00  11.35  76.52   0.00   7.28  67.06   0.92  33.46
   4_occ:  76.52   0.00  11.35  76.52   0.00   7.28  67.06   0.92  33.46
   5_bss:  76.52   0.00  11.35  76.52   0.00   7.28  67.06   0.92  33.46
   5_xyz:  76.52   0.00  11.35  76.52   0.00   7.28  67.06   0.92  33.46
   5_adp:  77.57   0.00  11.29  77.57   0.00   7.26  66.43   0.91  33.20
   5_occ:  77.57   0.00  11.29  77.57   0.00   7.26  66.43   0.91  33.20
   5_bss:  81.19   3.62  14.90  81.19   3.62  10.88  70.04   4.52  36.82
------------------------------------------------------------------------
 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:    1.185    0.024    0.407
   1_adp:    1.185    0.024    0.407
   1_occ:    1.185    0.024    0.407
   2_bss:    1.185    0.024    0.407
   2_xyz:    1.568    0.015    0.514
   2_adp:    1.568    0.015    0.514
   2_occ:    1.568    0.015    0.514
   3_bss:    1.568    0.015    0.514
   3_xyz:    1.513    0.041    0.555
   3_adp:    1.513    0.041    0.555
   3_occ:    1.513    0.041    0.555
   4_bss:    1.513    0.041    0.555
   4_xyz:    1.572    0.041    0.572
   4_adp:    1.572    0.041    0.572
   4_occ:    1.572    0.041    0.572
   5_bss:    1.572    0.041    0.572
   5_xyz:    1.677    0.030    0.578
   5_adp:    1.677    0.030    0.578
   5_occ:    1.677    0.030    0.578
   5_bss:    1.677    0.030    0.578
------------------------------------------------------------------------

CPU time actual refinement: 281.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/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_807/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_807/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 281.73 
  Macro-tasks:
    bulk solvent and scale       = 35.34  
    individual site refinement   = 123.18 
    weights calculation          = 26.34  
    collect and process          = 5.40   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 190.35 
  Micro-tasks:
    mask                            = 1.48   
    f_calc                          = 85.25  
    alpha_beta                      = 6.85   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 97.30  
    fmodel                         = 6.00   
    r_factors                      = 0.22   
    phase_errors                   = 8.97   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 207.25 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.848 micro seconds
Total CPU time: 4.89 minutes
from_scatterers_fft:    672 calls, 84.92 s
gradients_fft:          617 calls, 84.61 s

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

# Date 2008-01-16 Time 02:27:10 PST -0800 (1200479230.74 s)
Start R-work = 0.4346, R-free = 0.4204 (no bulk solvent and anisotropic scale)
Final R-work = 0.1322, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.4259, R-free = 0.4111
Final R-work = 0.1155, R-free = 0.1590