# Date 2008-01-16 Time 02:04:33 PST -0800 (1200477873.41 s)
#phil __OFF__

Command line arguments: "../688.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21197
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 688

-------------------------------------------------------------------------------
  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: (70.25, 47.3993, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00055
Completeness in resolution range: 0.972255
Completeness with d_max=infinity: 0.969177

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   2.0005

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: (70.25, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00055
Completeness in resolution range: 0.972255
Completeness with d_max=infinity: 0.969177

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2799 [2117/2144]  1904   213  10.1%
  bin  2:  4.2799 -  3.4102 [2028/2044]  1826   202  10.0%
  bin  3:  3.4102 -  2.9829 [2014/2033]  1812   202  10.0%
  bin  4:  2.9829 -  2.7120 [1987/2017]  1789   198  10.0%
  bin  5:  2.7120 -  2.5185 [1970/1989]  1774   196   9.9%
  bin  6:  2.5185 -  2.3707 [1966/1991]  1768   198  10.1%
  bin  7:  2.3707 -  2.2524 [1951/1985]  1760   191   9.8%
  bin  8:  2.2524 -  2.1546 [1947/1977]  1750   197  10.1%
  bin  9:  2.1546 -  2.0719 [1939/1981]  1743   196  10.1%
  bin 10:  2.0719 -  2.0005 [1670/1987]  1504   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2174
        3.04 -     3.66: 4631
        3.66 -     4.28: 8958
        4.28 -     4.90: 12313
  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 "  2.099 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.256 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28080 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_688/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 70.25 47.3993 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4340   r_free= 0.4194   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| 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: 6.227579                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1379  153 0.3590 0.3329      6.5155       6.448|
|  2:  4.7732 -  3.8090 0.99   1310  148 0.3308 0.3610      6.6398      6.7239|
|  3:  3.8090 -  3.3335 0.99   1302  143 0.3772 0.3530       6.577      6.5508|
|  4:  3.3335 -  3.0315 0.99   1293  139 0.4109 0.3655      6.4588      6.3408|
|  5:  3.0315 -  2.8157 0.99   1275  143 0.4563 0.4433      6.3218      6.3475|
|  6:  2.8157 -  2.6506 0.99   1274  144 0.4567 0.5026      6.2386      6.1944|
|  7:  2.6506 -  2.5185 0.99   1272  141 0.4679 0.4553      6.2044      6.1362|
|  8:  2.5185 -  2.4094 0.98   1265  140 0.4852 0.4205       6.162      6.0989|
|  9:  2.4094 -  2.3170 0.98   1251  142 0.4876 0.5059      6.0914      6.1102|
| 10:  2.3170 -  2.2373 0.99   1264  137 0.5060 0.4570      6.1187      6.0363|
| 11:  2.2373 -  2.1675 0.99   1255  143 0.4913 0.4408      6.0111      6.0229|
| 12:  2.1675 -  2.1058 0.97   1244  134 0.5025 0.4700      5.9705      6.0152|
| 13:  2.1058 -  2.0505 0.99   1266  140 0.4913 0.5211      5.8822      5.8521|
| 14:  2.0505 -  2.0005 0.78    980  112 0.5085 0.4656       5.844      5.7445|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7732  1379   153  0.74  30.70   0.81     0.76      57204.97|
|  2:  4.7732 -  3.8090  1310   148  0.78  28.50   0.91     0.81      73624.52|
|  3:  3.8090 -  3.3335  1302   143  0.71  34.16   0.86     0.78      75503.47|
|  4:  3.3335 -  3.0315  1293   139  0.66  38.73   0.83     0.71      65132.70|
|  5:  3.0315 -  2.8157  1275   143  0.57  46.46   0.77     0.63      58351.30|
|  6:  2.8157 -  2.6506  1274   144  0.55  48.44   0.75     0.59      54018.06|
|  7:  2.6506 -  2.5185  1272   141  0.52  50.78   0.76     0.57      50493.37|
|  8:  2.5185 -  2.4094  1265   140  0.52  50.96   0.77     0.58      45661.97|
|  9:  2.4094 -  2.3170  1251   142  0.52  50.47   0.73     0.59      40538.12|
| 10:  2.3170 -  2.2373  1264   137  0.53  50.00   0.75     0.60      37516.43|
| 11:  2.2373 -  2.1675  1255   143  0.49  52.65   0.76     0.58      35515.37|
| 12:  2.1675 -  2.1058  1244   134  0.45  56.14   0.77     0.54      35345.94|
| 13:  2.1058 -  2.0505  1266   140  0.43  57.52   0.75     0.50      31498.29|
| 14:  2.0505 -  2.0005   980   112  0.45  56.64   0.73     0.48      25662.73|
|alpha:            min =        0.48 max =            0.81 mean =         0.63|
|beta:             min =    25662.73 max =        75503.47 mean =     49617.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.22|
|phase err.(test): min =        0.00 max =           89.74 mean =        46.38|
|-----------------------------------------------------------------------------|

============================== 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 = 7.596735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.652434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.226   (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:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2615 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3873 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5032 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6545 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7680 |
|-----------------------------------------------------------------------------|
|-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 |       54.068 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.656 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    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 = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4422   r_free= 0.4217   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.234627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4271   r_free= 0.4068   ksol= 0.33   Bsol= 20.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,9.73,8.62,0.00,0.00,0.00); trace/3= 8.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.222350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.179270              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.771   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.624875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.535   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4271      final r-factor (work) = 0.3135          |
| start r-factor (free) = 0.4068      final r-factor (free) = 0.3339          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.4784 = 7.18 * 0.50 * 6.2430 + 1.00 * 54.0685                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8632 = 7.18 * 0.50 * 6.0575 + 1.00 * 0.1189                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3135      final r-factor (work) = 0.2497          |
| start r-factor (free) = 0.3339      final r-factor (free) = 0.2825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7999 = 0.62 * 1.00 * 6.0575 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6839 = 0.62 * 1.00 * 5.8761 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.67   10.55    None  None   None       |
|    all(noH): 2823   0      0.00    75.67   10.55    None  None   None       |
|    Sol.    : 438    0      0.00    75.67   27.02    None  None   None       |
|    Mac.    : 2385   0      0.00    57.32   7.52     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 -   7.567: 1559   |   5:    37.834 -  45.400:   74        |
|      1:     7.567 -  15.134:  652   |   6:    45.400 -  52.967:   35        |
|      2:    15.134 -  22.700:  234   |   7:    52.967 -  60.534:   10        |
|      3:    22.700 -  30.267:  151   |   8:    60.534 -  68.101:    1        |
|      4:    30.267 -  37.834:  106   |   9:    68.101 -  75.667:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2497 r_free = 0.2825             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2489 r_free = 0.2826             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2489   r_free= 0.2826   ksol= 0.33   Bsol= 20.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,9.73,8.62,0.00,0.00,0.00); trace/3= 8.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.810876                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2443   r_free= 0.2780   ksol= 0.33   Bsol= 42.95   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,6.03,5.45,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.810215                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.628173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.273   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330207              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.625  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2443      final r-factor (work) = 0.1569          |
| start r-factor (free) = 0.2780      final r-factor (free) = 0.1927          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6806 = 5.63 * 0.50 * 5.8854 + 1.00 * 0.1186                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8703 = 5.63 * 0.50 * 5.6132 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1569      final r-factor (work) = 0.1398          |
| start r-factor (free) = 0.1927      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8720 = 0.33 * 1.00 * 5.6132 + 1.00 * 0.0185                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8095 = 0.33 * 1.00 * 5.3490 + 1.00 * 0.0432                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.45   11.00    None  None   None       |
|    all(noH): 2823   0      0.00    68.45   11.00    None  None   None       |
|    Sol.    : 438    0      0.00    68.45   31.79    None  None   None       |
|    Mac.    : 2385   0      0.00    65.23   7.18     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 -   6.845: 1562   |   5:    34.224 -  41.068:  103        |
|      1:     6.845 -  13.689:  624   |   6:    41.068 -  47.913:   86        |
|      2:    13.689 -  20.534:  164   |   7:    47.913 -  54.758:   44        |
|      3:    20.534 -  27.379:  122   |   8:    54.758 -  61.602:   16        |
|      4:    27.379 -  34.224:   96   |   9:    61.602 -  68.447:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1398 r_free = 0.1772             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1396 r_free = 0.1772             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1396   r_free= 0.1772   ksol= 0.33   Bsol= 42.95   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,6.03,5.45,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.307845                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1391   r_free= 0.1776   ksol= 0.32   Bsol= 42.95   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,4.26,4.71,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.308043                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.502899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.608  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.788193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.359   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1391      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1776      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0989 = 1.50 * 0.50 * 5.3555 + 1.00 * 0.0745                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0128 = 1.50 * 0.50 * 5.2664 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1266      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1687 = 0.79 * 1.00 * 5.2664 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1254 = 0.79 * 1.00 * 5.2097 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.84   11.63    None  None   None       |
|    all(noH): 2823   0      0.00    79.84   11.63    None  None   None       |
|    Sol.    : 438    0      0.00    70.58   34.90    None  None   None       |
|    Mac.    : 2385   0      0.00    79.84   7.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.984: 1718   |   5:    39.919 -  47.903:   93        |
|      1:     7.984 -  15.968:  525   |   6:    47.903 -  55.887:   70        |
|      2:    15.968 -  23.951:  152   |   7:    55.887 -  63.870:   39        |
|      3:    23.951 -  31.935:  105   |   8:    63.870 -  71.854:   16        |
|      4:    31.935 -  39.919:  102   |   9:    71.854 -  79.838:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1617             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1225 r_free = 0.1616             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1616   ksol= 0.32   Bsol= 42.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,4.26,4.71,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206056                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1616   ksol= 0.33   Bsol= 51.98   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.83,4.55,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.205214                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.524293              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.734  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.914  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0249 = 1.52 * 0.50 * 5.2082 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0086 = 1.52 * 0.50 * 5.1833 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4203 = 0.27 * 1.00 * 5.1833 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4868 = 0.27 * 1.00 * 5.1785 + 1.00 * 0.0857                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.28   11.18    None  None   None       |
|    all(noH): 2823   0      0.00    79.28   11.18    None  None   None       |
|    Sol.    : 438    0      0.27    68.87   33.12    None  None   None       |
|    Mac.    : 2385   0      0.00    79.28   7.15     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 -   7.928: 1739   |   5:    39.641 -  47.570:   87        |
|      1:     7.928 -  15.857:  519   |   6:    47.570 -  55.498:   62        |
|      2:    15.857 -  23.785:  156   |   7:    55.498 -  63.426:   22        |
|      3:    23.785 -  31.713:  110   |   8:    63.426 -  71.355:   14        |
|      4:    31.713 -  39.641:  111   |   9:    71.355 -  79.283:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1583             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1583             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1583   ksol= 0.33   Bsol= 51.98   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.83,4.55,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1583   ksol= 0.33   Bsol= 51.98   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.83,4.55,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176393                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.052062              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.219  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.537654              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.763   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9619 = 3.05 * 0.50 * 5.1793 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9384 = 3.05 * 0.50 * 5.1505 + 1.00 * 0.0786                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.2399 = 3.54 * 1.00 * 5.1505 + 1.00 * 0.0191                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1755 = 3.54 * 1.00 * 5.1337 + 1.00 * 0.0144                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.55   11.51    None  None   None       |
|    all(noH): 2823   0      0.00    86.55   11.51    None  None   None       |
|    Sol.    : 438    0      0.60    76.76   34.77    None  None   None       |
|    Mac.    : 2385   0      0.00    86.55   7.23     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.655: 1806   |   5:    43.274 -  51.929:   86        |
|      1:     8.655 -  17.310:  473   |   6:    51.929 -  60.584:   59        |
|      2:    17.310 -  25.964:  159   |   7:    60.584 -  69.238:   18        |
|      3:    25.964 -  34.619:  100   |   8:    69.238 -  77.893:   12        |
|      4:    34.619 -  43.274:  107   |   9:    77.893 -  86.548:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1099 r_free = 0.1572             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1572             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1572   ksol= 0.33   Bsol= 51.98   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.83,4.55,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.141091                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1379  153 0.0998 0.1285      5.3906      5.5127|
|  2:  4.7732 -  3.8090 0.99   1310  148 0.0835 0.1091       5.422      5.6214|
|  3:  3.8090 -  3.3335 0.99   1302  143 0.1030 0.1458      5.4601      5.8401|
|  4:  3.3335 -  3.0315 0.99   1293  139 0.1170 0.1496      5.4314       5.587|
|  5:  3.0315 -  2.8157 0.99   1275  143 0.1290 0.1670      5.3211      5.5221|
|  6:  2.8157 -  2.6506 0.99   1274  144 0.1199 0.1880      5.2117      5.4862|
|  7:  2.6506 -  2.5185 0.99   1272  141 0.1232 0.1649      5.1632      5.3515|
|  8:  2.5185 -  2.4094 0.98   1265  140 0.1162 0.1811      5.0952      5.4024|
|  9:  2.4094 -  2.3170 0.98   1251  142 0.1171 0.1882      5.0449      5.3189|
| 10:  2.3170 -  2.2373 0.99   1264  137 0.1115 0.1729      4.9944      5.2295|
| 11:  2.2373 -  2.1675 0.99   1255  143 0.1113 0.1779      4.9403      5.2665|
| 12:  2.1675 -  2.1058 0.97   1244  134 0.1107 0.1661      4.8814      5.1999|
| 13:  2.1058 -  2.0505 0.99   1266  140 0.1097 0.1695       4.791      5.0524|
| 14:  2.0505 -  2.0005 0.78    980  112 0.1009 0.1770      4.6633      4.9656|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7732  1379   153  0.94   9.35   0.97     0.95       7378.01|
|  2:  4.7732 -  3.8090  1310   148  0.95   7.80   1.01     0.99       8855.73|
|  3:  3.8090 -  3.3335  1302   143  0.94  10.87   1.02     1.02      10088.87|
|  4:  3.3335 -  3.0315  1293   139  0.93  12.94   1.00     0.99       9798.79|
|  5:  3.0315 -  2.8157  1275   143  0.90  15.74   0.99     0.97       8331.80|
|  6:  2.8157 -  2.6506  1274   144  0.90  15.86   0.98     0.94       7053.47|
|  7:  2.6506 -  2.5185  1272   141  0.91  15.58   0.98     0.96       6261.56|
|  8:  2.5185 -  2.4094  1265   140  0.91  15.30   0.98     0.96       5678.23|
|  9:  2.4094 -  2.3170  1251   142  0.90  16.10   1.00     0.96       5254.52|
| 10:  2.3170 -  2.2373  1264   137  0.90  16.30   0.99     0.95       4824.96|
| 11:  2.2373 -  2.1675  1255   143  0.90  16.26   0.99     0.95       4475.83|
| 12:  2.1675 -  2.1058  1244   134  0.91  15.48   1.00     0.98       4039.83|
| 13:  2.1058 -  2.0505  1266   140  0.91  15.65   0.99     0.97       3390.01|
| 14:  2.0505 -  2.0005   980   112  0.91  14.71   0.96     0.92       2583.45|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2583.45 max =        10088.87 mean =      6379.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.07|
|phase err.(test): min =        0.00 max =           88.68 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1572   ksol= 0.32   Bsol= 54.86   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.04,0.79,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.140856                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1572   ksol= 0.32   Bsol= 54.86   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.04,0.79,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.140856                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1379  153 0.0997 0.1285      5.3882       5.511|
|  2:  4.7732 -  3.8090 0.99   1310  148 0.0836 0.1092      5.4222       5.622|
|  3:  3.8090 -  3.3335 0.99   1302  143 0.1030 0.1459      5.4606      5.8408|
|  4:  3.3335 -  3.0315 0.99   1293  139 0.1170 0.1496      5.4315      5.5872|
|  5:  3.0315 -  2.8157 0.99   1275  143 0.1290 0.1671       5.321      5.5219|
|  6:  2.8157 -  2.6506 0.99   1274  144 0.1199 0.1878      5.2114      5.4853|
|  7:  2.6506 -  2.5185 0.99   1272  141 0.1233 0.1651      5.1632      5.3521|
|  8:  2.5185 -  2.4094 0.98   1265  140 0.1163 0.1811      5.0955      5.4027|
|  9:  2.4094 -  2.3170 0.98   1251  142 0.1171 0.1881      5.0449      5.3188|
| 10:  2.3170 -  2.2373 0.99   1264  137 0.1115 0.1731      4.9943        5.23|
| 11:  2.2373 -  2.1675 0.99   1255  143 0.1113 0.1778        4.94      5.2662|
| 12:  2.1675 -  2.1058 0.97   1244  134 0.1107 0.1661      4.8813      5.1993|
| 13:  2.1058 -  2.0505 0.99   1266  140 0.1097 0.1694      4.7906      5.0525|
| 14:  2.0505 -  2.0005 0.78    980  112 0.1010 0.1768      4.6627      4.9647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7732  1379   153  0.94   9.32   0.97     0.95       7337.98|
|  2:  4.7732 -  3.8090  1310   148  0.95   7.80   1.01     0.99       8847.29|
|  3:  3.8090 -  3.3335  1302   143  0.94  10.88   1.02     1.02      10104.35|
|  4:  3.3335 -  3.0315  1293   139  0.93  12.94   1.00     0.99       9800.53|
|  5:  3.0315 -  2.8157  1275   143  0.90  15.73   1.00     0.97       8327.02|
|  6:  2.8157 -  2.6506  1274   144  0.90  15.86   0.98     0.95       7050.14|
|  7:  2.6506 -  2.5185  1272   141  0.91  15.58   0.99     0.96       6262.23|
|  8:  2.5185 -  2.4094  1265   140  0.91  15.30   0.99     0.96       5681.03|
|  9:  2.4094 -  2.3170  1251   142  0.90  16.10   1.00     0.96       5257.25|
| 10:  2.3170 -  2.2373  1264   137  0.90  16.30   1.00     0.96       4824.60|
| 11:  2.2373 -  2.1675  1255   143  0.90  16.25   0.99     0.96       4474.95|
| 12:  2.1675 -  2.1058  1244   134  0.91  15.47   1.01     0.99       4038.66|
| 13:  2.1058 -  2.0505  1266   140  0.91  15.64   1.00     0.98       3386.05|
| 14:  2.0505 -  2.0005   980   112  0.91  14.68   0.97     0.93       2577.45|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2577.45 max =        10104.35 mean =      6376.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.07|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.081)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.91    90.46   15.42    None  None   None       |
|    all(noH): 2823   0      3.91    90.46   15.42    None  None   None       |
|    Sol.    : 438    0      4.52    80.67   38.68    None  None   None       |
|    Mac.    : 2385   0      3.91    90.46   11.15    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:     3.911 -  12.566: 1806   |   5:    47.185 -  55.840:   86        |
|      1:    12.566 -  21.221:  473   |   6:    55.840 -  64.495:   59        |
|      2:    21.221 -  29.876:  159   |   7:    64.495 -  73.150:   18        |
|      3:    29.876 -  38.530:  100   |   8:    73.150 -  81.804:   12        |
|      4:    38.530 -  47.185:  107   |   9:    81.804 -  90.459:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.251 - 5.812
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 306
   mapped sites are within: 0.745 - 5.812

peak=   10.312 closest distance to " CG2 VAL A 230 " =    1.336
peak=    6.145 closest distance to " NH2 ARG A  56 " =    2.284
peak=    6.073 closest distance to " CG  LEU A   5 " =    1.153
peak=    5.946 closest distance to " CB  VAL A 296 " =    1.132
peak=    5.943 closest distance to " CG  LEU A 228 " =    1.168
peak=    5.291 closest distance to " CB  VAL A 230 " =    1.196
peak=    5.203 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.174 closest distance to " CG  PRO A  54 " =    1.233
peak=    5.058 closest distance to " NE2 GLN A  11 " =    1.083
peak=    4.950 closest distance to " CB  GLN A 183 " =    1.319
peak=    4.889 closest distance to " CD2 LEU A   5 " =    1.123
peak=    4.763 closest distance to " CB  SER A  63 " =    1.271
peak=    4.718 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.613 closest distance to " CG2 VAL A 296 " =    0.990
peak=    4.580 closest distance to " O   HOH Z 232 " =    2.393
peak=    4.545 closest distance to " O   HOH Z 142 " =    1.595
peak=    4.484 closest distance to " O   HOH Z 126 " =    1.932
peak=    4.473 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.421 closest distance to " CB  PRO A  54 " =    0.862
peak=    4.390 closest distance to " O   HOH Z 272 " =    1.925
peak=    4.333 closest distance to " O   SER A  87 " =    2.284
peak=    4.319 closest distance to " CB  ARG A 190 " =    1.634
peak=    4.312 closest distance to " O   HOH Z  43 " =    2.013
peak=    4.293 closest distance to " CB  ARG A  79 " =    1.487
peak=    4.277 closest distance to " O   HOH Z  44 " =    2.263
peak=    4.266 closest distance to " O   HOH Z  63 " =    1.959
peak=    4.255 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.243 closest distance to " O   HOH Z 423 " =    1.828
peak=    4.235 closest distance to " O   HOH Z 303 " =    2.105
peak=    4.229 closest distance to " CZ  PHE A 218 " =    1.144
peak=    4.227 closest distance to " O   HOH Z 368 " =    2.362
peak=    4.227 closest distance to " O   HOH Z  61 " =    1.651
peak=    4.219 closest distance to " C   PRO A 198 " =    1.500
peak=    4.209 closest distance to " O   HOH Z 369 " =    2.282
peak=    4.193 closest distance to " O   HOH Z 193 " =    1.788
peak=    4.191 closest distance to " O   HOH Z 298 " =    1.878
peak=    4.190 closest distance to " O   HOH Z 427 " =    2.971
peak=    4.147 closest distance to " O   HOH Z 236 " =    1.945
peak=    4.138 closest distance to " O   HOH Z 316 " =    3.108
peak=    4.137 closest distance to " O   HOH Z 248 " =    1.598
peak=    4.115 closest distance to " O   HOH Z 346 " =    1.578
peak=    4.114 closest distance to " O   HOH Z 403 " =    1.669
peak=    4.110 closest distance to " O   HOH Z  15 " =    2.152
peak=    4.101 closest distance to " OD1 ASN A  69 " =    2.573
peak=    4.096 closest distance to " O   HOH Z 234 " =    3.637
peak=    4.095 closest distance to " O   HOH Z 280 " =    2.866
peak=    4.062 closest distance to " CB  ASN A 148 " =    1.396
peak=    4.042 closest distance to " O   HOH Z 158 " =    3.149
peak=    4.036 closest distance to " CG  PRO A 213 " =    1.177
peak=    4.019 closest distance to " OG BSER A 164 " =    2.265
peak=    4.016 closest distance to " O   HOH Z 189 " =    2.704
peak=    4.004 closest distance to " CB  TRP A 266 " =    0.981
peak=    4.003 closest distance to " CB  GLU A 277 " =    3.629
peak=    3.983 closest distance to " CB  ASP A 140 " =    1.031
peak=    3.972 closest distance to " O   HOH Z  59 " =    2.272
peak=    3.969 closest distance to " O   HOH Z 203 " =    1.741
peak=    3.960 closest distance to " O   HOH Z  78 " =    1.659
peak=    3.957 closest distance to " O   HOH Z 402 " =    1.441
peak=    3.913 closest distance to " CB  GLU A 128 " =    1.078
peak=    3.907 closest distance to " O   HOH Z 214 " =    2.274
peak=    3.902 closest distance to " O   HOH Z  40 " =    1.788
peak=    3.885 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.875 closest distance to " CB  VAL A 202 " =    1.513
peak=    3.857 closest distance to " CG1 VAL A 296 " =    1.178
peak=    3.856 closest distance to " O   HOH Z  97 " =    2.017
peak=    3.839 closest distance to " ND2 ASN A 187 " =    1.454
peak=    3.818 closest distance to " O   HOH Z 411 " =    3.852
peak=    3.817 closest distance to " CG1BVAL A  72 " =    1.766
peak=    3.817 closest distance to " ND2 ASN A 249 " =    1.920
peak=    3.816 closest distance to " O   HOH Z  80 " =    1.739
peak=    3.811 closest distance to " O   HOH Z 265 " =    2.226
peak=    3.808 closest distance to " O   HOH Z 147 " =    1.797
peak=    3.807 closest distance to " O   HOH Z 197 " =    2.882
peak=    3.804 closest distance to " O   HOH Z 422 " =    2.666
peak=    3.793 closest distance to " O   HOH Z  66 " =    2.231
peak=    3.783 closest distance to " O   HOH Z 365 " =    2.906
peak=    3.767 closest distance to " CB  TRP A 179 " =    1.430
peak=    3.762 closest distance to " CG  PRO A 243 " =    1.140
peak=    3.761 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.727 closest distance to " CB  SER A   3 " =    1.229
peak=    3.721 closest distance to " O   HOH Z 285 " =    2.884
peak=    3.718 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.699 closest distance to " O   HOH Z 180 " =    2.170
peak=    3.697 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.694 closest distance to " CB  VAL A 265 " =    1.322
peak=    3.692 closest distance to " O   HOH Z  19 " =    1.886
peak=    3.691 closest distance to " CD2 TRP A 179 " =    1.363
peak=    3.687 closest distance to " CD2 LEU A 228 " =    1.165
peak=    3.682 closest distance to " O   HOH Z  48 " =    1.627
peak=    3.675 closest distance to " CG1 ILE A  49 " =    1.528
peak=    3.672 closest distance to " O   HOH Z  97 " =    2.452
peak=    3.666 closest distance to " O   HOH Z 261 " =    1.850
peak=    3.664 closest distance to " O   HOH Z 193 " =    2.124
peak=    3.662 closest distance to " CA  THR A 264 " =    0.745
peak=    3.660 closest distance to " O   HOH Z 250 " =    1.334
peak=    3.659 closest distance to " OG1 THR A 294 " =    2.402
peak=    3.654 closest distance to " O   HOH Z 108 " =    2.624
peak=    3.654 closest distance to " O   ALA A 165 " =    1.461
peak=    3.644 closest distance to " O   HOH Z 313 " =    1.761
peak=    3.634 closest distance to " CG  PRO A 198 " =    1.182
peak=    3.632 closest distance to " NH2 ARG A 156 " =    1.120
peak=    3.628 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.626 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.623 closest distance to " CE1 TYR A 186 " =    1.290
peak=    3.621 closest distance to " O   HOH Z 261 " =    1.787
peak=    3.617 closest distance to " CD BLYS A 290 " =    0.993
peak=    3.615 closest distance to " O   HOH Z 371 " =    3.209
peak=    3.605 closest distance to " O   HOH Z 126 " =    1.609
peak=    3.595 closest distance to " O   HOH Z 417 " =    3.102
peak=    3.594 closest distance to " CB  ARG A 139 " =    0.936
peak=    3.593 closest distance to " CB  THR A  31 " =    1.625
peak=    3.591 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.587 closest distance to " N   ASN A  39 " =    1.330
peak=    3.587 closest distance to " CG1 ILE A  33 " =    1.199
peak=    3.577 closest distance to " O   HOH Z 299 " =    4.369
peak=    3.572 closest distance to " CB  SER A  26 " =    1.777
peak=    3.570 closest distance to " CA  ALA A 158 " =    1.285
peak=    3.567 closest distance to " NE2 GLN A  77 " =    3.308
peak=    3.565 closest distance to " CB  GLU A  46 " =    1.042
peak=    3.562 closest distance to " CB BVAL A  41 " =    1.071
peak=    3.560 closest distance to " CB  ASN A 142 " =    1.140
peak=    3.557 closest distance to " CA  LYS A 117 " =    1.288
peak=    3.551 closest distance to " CG  ARG A  66 " =    2.632
peak=    3.551 closest distance to " CA  ASN A 215 " =    1.178
peak=    3.547 closest distance to " O   HOH Z 273 " =    2.915
peak=    3.547 closest distance to " CA  VAL A 125 " =    1.272
peak=    3.537 closest distance to " CG2 THR A 221 " =    1.220
peak=    3.535 closest distance to " CG1 VAL A 153 " =    0.983
peak=    3.534 closest distance to " O   HOH Z 437 " =    1.804
peak=    3.533 closest distance to " CA  ARG A  36 " =    1.044
peak=    3.531 closest distance to " O   HOH Z  54 " =    1.536
peak=    3.527 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.525 closest distance to " CA  ALA A 291 " =    0.871
peak=    3.521 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.516 closest distance to " CB  THR A  52 " =    0.941
peak=    3.512 closest distance to " C   ILE A 106 " =    1.884
peak=    3.510 closest distance to " CA  TYR A 116 " =    1.418
peak=    3.497 closest distance to " N   VAL A 126 " =    1.461
peak=    3.494 closest distance to " O   HOH Z 426 " =    1.566
peak=    3.493 closest distance to " O   HOH Z 407 " =    2.477
peak=    3.488 closest distance to " CG  MET A 185 " =    1.089
peak=    3.488 closest distance to " N   ASP A 162 " =    1.301
peak=    3.488 closest distance to " CA  VAL A  41 " =    0.802
peak=    3.488 closest distance to " O   HOH Z 102 " =    1.284
peak=    3.483 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.481 closest distance to " O   TRP A 274 " =    1.860
peak=    3.480 closest distance to " CB  ALA A   9 " =    1.617
peak=    3.480 closest distance to " CB  ASN A 148 " =    1.949
peak=    3.478 closest distance to " CG  MET A 185 " =    1.215
peak=    3.476 closest distance to " CB  ASN A 110 " =    1.142
peak=    3.475 closest distance to " O   HOH Z 128 " =    2.278
peak=    3.474 closest distance to " CD  ARG A 269 " =    0.976
peak=    3.472 closest distance to " OD2 ASP A 298 " =    3.862
peak=    3.468 closest distance to " CB  TRP A 150 " =    1.374
peak=    3.467 closest distance to " CE  LYS A  76 " =    0.846
peak=    3.464 closest distance to " CB  GLN A  89 " =    1.231
peak=    3.460 closest distance to " O   GLN A 278 " =    1.236
peak=    3.457 closest distance to " CB  SER A 212 " =    1.089
peak=    3.456 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.452 closest distance to " O   HOH Z 383 " =    1.992
peak=    3.449 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.448 closest distance to " O   HOH Z 133 " =    2.357
peak=    3.433 closest distance to " CG  GLN A  58 " =    2.872
peak=    3.428 closest distance to " CG2 ILE A  20 " =    1.340
peak=    3.427 closest distance to " O  BHOH Z 338 " =    2.364
peak=    3.422 closest distance to " CG  GLN A  77 " =    2.230
peak=    3.420 closest distance to " O   HOH Z 134 " =    1.326
peak=    3.419 closest distance to " O   HOH Z 112 " =    1.676
peak=    3.417 closest distance to " O   HOH Z 261 " =    2.308
peak=    3.408 closest distance to " O   HOH Z 305 " =    3.664
peak=    3.406 closest distance to " O   HOH Z 344 " =    3.057
peak=    3.400 closest distance to " O   ASP A 124 " =    1.204
peak=    3.397 closest distance to " NH2 ARG A  79 " =    1.315
peak=    3.395 closest distance to " CB  THR A 157 " =    1.156
peak=    3.393 closest distance to " O   HOH Z 251 " =    1.467
peak=    3.388 closest distance to " O   HOH Z 425 " =    2.035
peak=    3.387 closest distance to " O   HOH Z 327 " =    1.771
peak=    3.385 closest distance to " CA  PHE A 283 " =    1.265
peak=    3.383 closest distance to " CB  GLN A  88 " =    1.189
peak=    3.378 closest distance to " OE1 GLN A  11 " =    1.825
peak=    3.374 closest distance to " CB  GLN A 205 " =    1.105
peak=    3.371 closest distance to " CA  ASP A 162 " =    1.061
peak=    3.367 closest distance to " O   HOH Z  88 " =    3.125
peak=    3.365 closest distance to " ND1 HIS A  81 " =    1.677
peak=    3.361 closest distance to " CB  MET A  47 " =    1.087
peak=    3.359 closest distance to " CG2 VAL A 257 " =    0.807
peak=    3.358 closest distance to " NZ  LYS A  48 " =    1.346
peak=    3.356 closest distance to " O   HOH Z 325 " =    2.186
peak=    3.355 closest distance to " CB  ALA A 100 " =    1.225
peak=    3.355 closest distance to " CB  ALA A 291 " =    1.381
peak=    3.351 closest distance to " CA  ASP A 191 " =    1.119
peak=    3.346 closest distance to " CA  ALA A 295 " =    1.081
peak=    3.343 closest distance to " NH2AARG A 275 " =    3.557
peak=    3.343 closest distance to " CZ3 TRP A  85 " =    0.937
peak=    3.342 closest distance to " O   HOH Z 291 " =    1.570
peak=    3.342 closest distance to " O   ASN A  74 " =    1.562
peak=    3.341 closest distance to " CB  ALA A 248 " =    1.034
peak=    3.324 closest distance to " O   HOH Z 359 " =    1.393
peak=    3.324 closest distance to " O   HOH Z 425 " =    1.281
peak=    3.321 closest distance to " OD1 ASN A 217 " =    1.691
peak=    3.320 closest distance to " CB  HIS A 108 " =    0.783
peak=    3.318 closest distance to " CB  THR A  82 " =    1.387
peak=    3.317 closest distance to " CD1 LEU A   5 " =    1.339
peak=    3.316 closest distance to " CB  ALA A 295 " =    1.205
peak=    3.312 closest distance to " O   HOH Z 148 " =    3.245
peak=    3.310 closest distance to " OD2 ASP A 286 " =    2.855
peak=    3.296 closest distance to " O   HOH Z 166 " =    3.640
peak=    3.293 closest distance to " O   ALA A 158 " =    1.343
peak=    3.293 closest distance to " CB  LEU A 228 " =    1.265
peak=    3.292 closest distance to " O   HOH Z 353 " =    2.729
peak=    3.291 closest distance to " O   HOH Z 345 " =    3.146
peak=    3.289 closest distance to " CG  LEU A 167 " =    1.181
peak=    3.286 closest distance to " O   HOH Z  21 " =    1.738
peak=    3.278 closest distance to " CG  GLN A 205 " =    0.912
peak=    3.277 closest distance to " NZ  LYS A 117 " =    3.295
peak=    3.276 closest distance to " OG  SER A  22 " =    2.767
peak=    3.275 closest distance to " CA  THR A 221 " =    0.922
peak=    3.264 closest distance to " O   HOH Z 171 " =    3.851
peak=    3.264 closest distance to " CA  LEU A 282 " =    1.086
peak=    3.262 closest distance to " CD1 LEU A 228 " =    1.843
peak=    3.256 closest distance to " O   HOH Z 403 " =    1.395
peak=    3.255 closest distance to " O   HOH Z 406 " =    1.520
peak=    3.255 closest distance to " O   HOH Z  35 " =    2.488
peak=    3.254 closest distance to " O   HOH Z 189 " =    2.735
peak=    3.253 closest distance to " CB  MET A  40 " =    0.812
peak=    3.253 closest distance to " O   HOH Z 133 " =    1.545
peak=    3.252 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.250 closest distance to " OE1 GLU A   2 " =    2.010
peak=    3.249 closest distance to " O   HOH Z 329 " =    4.030
peak=    3.246 closest distance to " CZ  PHE A  38 " =    1.267
peak=    3.245 closest distance to " O   HOH Z 171 " =    2.360
peak=    3.244 closest distance to " O   HOH Z 368 " =    3.651
peak=    3.232 closest distance to " CA  ALA A 160 " =    0.862
peak=    3.229 closest distance to " CA  SER A 146 " =    1.727
peak=    3.226 closest distance to " O   HOH Z  85 " =    1.372
peak=    3.226 closest distance to " CB  ASN A 187 " =    1.072
peak=    3.225 closest distance to " O   HOH Z 421 " =    1.739
peak=    3.222 closest distance to " CA  LYS A 181 " =    1.080
peak=    3.219 closest distance to " O   HOH Z 435 " =    1.958
peak=    3.218 closest distance to " O   HOH Z  66 " =    2.257
peak=    3.214 closest distance to " OD1 ASP A 231 " =    1.904
peak=    3.213 closest distance to " O   HOH Z 256 " =    2.398
peak=    3.212 closest distance to " O   HOH Z 420 " =    5.812
peak=    3.210 closest distance to " O   HOH Z 240 " =    2.315
peak=    3.209 closest distance to " CA  ALA A 248 " =    1.287
peak=    3.206 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.202 closest distance to " O   HOH Z 417 " =    2.366
peak=    3.200 closest distance to " O   HOH Z 438 " =    3.001
peak=    3.195 closest distance to " CB  SER A 273 " =    0.819
peak=    3.194 closest distance to " CE1 HIS A 108 " =    1.131
peak=    3.191 closest distance to " O   HOH Z  10 " =    1.718
peak=    3.188 closest distance to " ND2 ASN A 110 " =    1.564
peak=    3.187 closest distance to " O   HOH Z 420 " =    2.040
peak=    3.184 closest distance to " N   SER A 135 " =    1.454
peak=    3.183 closest distance to " CA  ASP A 140 " =    1.161
peak=    3.182 closest distance to " CA  ASN A 176 " =    1.177
peak=    3.181 closest distance to " CB  LEU A   5 " =    1.296
peak=    3.180 closest distance to " CG  GLN A  88 " =    1.040
peak=    3.174 closest distance to " CA  ILE A 106 " =    0.759
peak=    3.170 closest distance to " CG BARG A 275 " =    1.289
peak=    3.169 closest distance to " CA  GLY A 211 " =    1.341
peak=    3.169 closest distance to " CD2 TYR A 186 " =    1.030
peak=    3.166 closest distance to " CB  MET A 113 " =    1.877
peak=    3.164 closest distance to " CD1 ILE A  33 " =    1.674
peak=    3.158 closest distance to " O   HOH Z 391 " =    2.944
peak=    3.157 closest distance to " O   HOH Z  88 " =    2.525
peak=    3.155 closest distance to " NE2 HIS A 207 " =    1.349
peak=    3.155 closest distance to " O   HOH Z 419 " =    1.592
peak=    3.154 closest distance to " CD  ARG A  79 " =    2.004
peak=    3.154 closest distance to " O   HOH Z  90 " =    3.335
peak=    3.151 closest distance to " CD  LYS A 119 " =    1.903
peak=    3.149 closest distance to " O   HOH Z 367 " =    2.238
peak=    3.147 closest distance to " O   HOH Z 295 " =    1.510
peak=    3.139 closest distance to " CA  ALA A  84 " =    1.377
peak=    3.138 closest distance to " CA  VAL A 126 " =    0.960
peak=    3.137 closest distance to " O   HOH Z 380 " =    1.888
peak=    3.128 closest distance to " CA  MET A 105 " =    1.001
peak=    3.125 closest distance to " O   HOH Z 357 " =    1.972
peak=    3.119 closest distance to " O   HOH Z  48 " =    1.425
peak=    3.118 closest distance to " CB  ASN A 224 " =    1.000
peak=    3.115 closest distance to " O   HOH Z   1 " =    2.354
peak=    3.112 closest distance to " CD  LYS A  76 " =    1.937
peak=    3.112 closest distance to " O   HOH Z 227 " =    2.011
peak=    3.110 closest distance to " CB  ILE A 120 " =    1.385
peak=    3.105 closest distance to " CB  LYS A 117 " =    1.149
peak=    3.102 closest distance to " CD  ARG A  66 " =    2.723
peak=    3.096 closest distance to " O   HOH Z 302 " =    1.976
peak=    3.095 closest distance to " O   HOH Z 213 " =    2.468
peak=    3.090 closest distance to " O   HOH Z 301 " =    1.926
peak=    3.067 closest distance to " O   HOH Z 213 " =    1.792
peak=    3.066 closest distance to " OE2 GLU A  53 " =    2.060
peak=    3.059 closest distance to " CG  MET A 188 " =    0.888
peak=    3.051 closest distance to " O   HOH Z 298 " =    4.870
peak=    3.027 closest distance to " CB  TYR A 116 " =    0.840
peak=    3.019 closest distance to " O   HOH Z 201 " =    3.131

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.802 - 5.572
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.802 - 5.572

peak=   -5.256 closest distance to " CG2 VAL A 230 " =    0.833
peak=   -4.654 closest distance to " SG  CYS A 254 " =    3.364
peak=   -4.637 closest distance to " CD  ARG A 156 " =    2.021
peak=   -4.500 closest distance to " O   HOH Z 266 " =    5.156
peak=   -4.466 closest distance to " CG2BVAL A  41 " =    2.491
peak=   -4.355 closest distance to " CG  GLN A 223 " =    2.133
peak=   -4.351 closest distance to " O   HOH Z 196 " =    2.084
peak=   -4.265 closest distance to " CD  GLN A  58 " =    1.080
peak=   -4.135 closest distance to " CB  PRO A 243 " =    2.645
peak=   -4.115 closest distance to " C   HIS A 108 " =    1.160
peak=   -4.073 closest distance to " OXT GLY A 302 " =    2.848
peak=   -4.055 closest distance to " OG BSER A 134 " =    1.218
peak=   -4.017 closest distance to " CA  VAL A  67 " =    2.793
peak=   -4.005 closest distance to " CB  ALA A 161 " =    2.530
peak=   -3.966 closest distance to " CG1 VAL A 250 " =    2.762
peak=   -3.957 closest distance to " O   HOH Z 231 " =    2.182
peak=   -3.944 closest distance to " NE2 GLN A  88 " =    1.929
peak=   -3.936 closest distance to " CG2BVAL A  41 " =    1.697
peak=   -3.926 closest distance to " O   PRO A 163 " =    2.170
peak=   -3.924 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.862 closest distance to " CG1 VAL A 112 " =    2.719
peak=   -3.856 closest distance to " N   ALA A  43 " =    2.677
peak=   -3.847 closest distance to " CB  PHE A 192 " =    1.934
peak=   -3.846 closest distance to " O   HOH Z 114 " =    3.110
peak=   -3.817 closest distance to " OG  SER A  97 " =    2.301
peak=   -3.795 closest distance to " CE3 TRP A 150 " =    2.220
peak=   -3.769 closest distance to " CZ2 TRP A  92 " =    2.827
peak=   -3.757 closest distance to " ND2 ASN A  45 " =    1.221
peak=   -3.745 closest distance to " ND2 ASN A 187 " =    1.622
peak=   -3.740 closest distance to " O   HOH Z  37 " =    1.841
peak=   -3.705 closest distance to " O   HOH Z 166 " =    1.854
peak=   -3.697 closest distance to " O   HOH Z 283 " =    2.249
peak=   -3.691 closest distance to " CZ3 TRP A 179 " =    1.208
peak=   -3.684 closest distance to " O   HOH Z 351 " =    1.556
peak=   -3.673 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -3.663 closest distance to " CD1 PHE A  59 " =    2.015
peak=   -3.640 closest distance to " CD1 LEU A 101 " =    2.437
peak=   -3.639 closest distance to " CB  ALA A 248 " =    2.117
peak=   -3.631 closest distance to " CB  ASP A 171 " =    2.262
peak=   -3.611 closest distance to " CB  ASP A 132 " =    2.320
peak=   -3.607 closest distance to " CG2 ILE A 263 " =    2.355
peak=   -3.606 closest distance to " CG1 VAL A 296 " =    1.179
peak=   -3.604 closest distance to " N   ALA A 226 " =    2.072
peak=   -3.600 closest distance to " C   ALA A 158 " =    1.229
peak=   -3.600 closest distance to " CB  ALA A 248 " =    2.300
peak=   -3.597 closest distance to " O   HOH Z  13 " =    1.653
peak=   -3.596 closest distance to " O   HOH Z  52 " =    1.546
peak=   -3.591 closest distance to " O   HOH Z 290 " =    1.242
peak=   -3.590 closest distance to " O   HOH Z 426 " =    1.616
peak=   -3.586 closest distance to " O   HOH Z  11 " =    1.909
peak=   -3.573 closest distance to " CE  MET A 105 " =    2.210
peak=   -3.572 closest distance to " OD1 ASN A 148 " =    1.486
peak=   -3.572 closest distance to " O   HOH Z 113 " =    2.283
peak=   -3.567 closest distance to " CD  LYS A 289 " =    2.456
peak=   -3.562 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.561 closest distance to " O   HOH Z  60 " =    1.996
peak=   -3.549 closest distance to " ND2 ASN A  45 " =    1.723
peak=   -3.548 closest distance to " CB  ALA A 291 " =    2.324
peak=   -3.542 closest distance to " CD2 LEU A 167 " =    1.772
peak=   -3.540 closest distance to " O   HOH Z 311 " =    3.769
peak=   -3.536 closest distance to " O   VAL A 189 " =    2.621
peak=   -3.533 closest distance to " O   HOH Z 165 " =    1.880
peak=   -3.532 closest distance to " OG ASER A 134 " =    1.254
peak=   -3.530 closest distance to " CG  ARG A 269 " =    2.367
peak=   -3.526 closest distance to " O   HOH Z  19 " =    2.203
peak=   -3.515 closest distance to " CG  GLU A 277 " =    1.165
peak=   -3.507 closest distance to " CB  PRO A 163 " =    2.540
peak=   -3.503 closest distance to " O   HOH Z  44 " =    2.202
peak=   -3.503 closest distance to " O   HOH Z 389 " =    1.920
peak=   -3.492 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.490 closest distance to " O   HOH Z 185 " =    2.415
peak=   -3.490 closest distance to " O   HOH Z 435 " =    2.746
peak=   -3.488 closest distance to " O   HOH Z 353 " =    2.150
peak=   -3.482 closest distance to " CG  ASP A 231 " =    0.802
peak=   -3.479 closest distance to " C   ILE A 239 " =    2.148
peak=   -3.475 closest distance to " NE2 GLN A 103 " =    1.758
peak=   -3.468 closest distance to " CD2 LEU A 300 " =    2.619
peak=   -3.459 closest distance to " O   HOH Z 102 " =    1.609
peak=   -3.458 closest distance to " CG1 VAL A 112 " =    2.876
peak=   -3.457 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.455 closest distance to " O   HOH Z 166 " =    1.516
peak=   -3.449 closest distance to " N   THR A 235 " =    1.300
peak=   -3.449 closest distance to " C   LEU A 143 " =    1.028
peak=   -3.444 closest distance to " O   HOH Z 211 " =    1.628
peak=   -3.443 closest distance to " CA  GLY A 241 " =    3.088
peak=   -3.433 closest distance to " NH2AARG A 275 " =    5.102
peak=   -3.431 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.424 closest distance to " O   ARG A  24 " =    2.073
peak=   -3.419 closest distance to " O   HOH Z 198 " =    2.336
peak=   -3.419 closest distance to " CA  SER A  62 " =    2.651
peak=   -3.415 closest distance to " O   HOH Z  88 " =    4.537
peak=   -3.415 closest distance to " O   SER A 210 " =    1.910
peak=   -3.408 closest distance to " CG2 VAL A 296 " =    1.257
peak=   -3.407 closest distance to " O   HOH Z  10 " =    1.498
peak=   -3.405 closest distance to " CG  TRP A 266 " =    1.864
peak=   -3.402 closest distance to " O   HOH Z  38 " =    1.652
peak=   -3.401 closest distance to " CE BMET A  47 " =    1.943
peak=   -3.395 closest distance to " CD2 TYR A 293 " =    2.029
peak=   -3.391 closest distance to " OG  SER A  87 " =    1.440
peak=   -3.384 closest distance to " O   HOH Z  43 " =    1.742
peak=   -3.378 closest distance to " CD2 TYR A 247 " =    2.271
peak=   -3.377 closest distance to " NH2 ARG A  79 " =    2.043
peak=   -3.377 closest distance to " O   SER A 271 " =    2.031
peak=   -3.375 closest distance to " CD  ARG A 139 " =    1.652
peak=   -3.373 closest distance to " CD1 ILE A 199 " =    2.440
peak=   -3.372 closest distance to " O   HOH Z 234 " =    4.169
peak=   -3.368 closest distance to " O   HOH Z 407 " =    3.150
peak=   -3.365 closest distance to " C   MET A 188 " =    1.473
peak=   -3.362 closest distance to " CB  ALA A 291 " =    2.194
peak=   -3.356 closest distance to " O   HOH Z 193 " =    1.911
peak=   -3.355 closest distance to " O   HOH Z  17 " =    1.393
peak=   -3.350 closest distance to " CG1 VAL A 230 " =    1.954
peak=   -3.348 closest distance to " CB  ALA A  43 " =    2.536
peak=   -3.346 closest distance to " O   HOH Z   6 " =    1.681
peak=   -3.346 closest distance to " N   SER A 276 " =    1.412
peak=   -3.344 closest distance to " CE2 PHE A 218 " =    2.548
peak=   -3.344 closest distance to " CZ  PHE A  59 " =    1.636
peak=   -3.343 closest distance to " CG2 VAL A 189 " =    2.084
peak=   -3.343 closest distance to " NH2 ARG A  66 " =    1.776
peak=   -3.342 closest distance to " OG BSER A 134 " =    1.871
peak=   -3.326 closest distance to " O   HOH Z 359 " =    3.027
peak=   -3.320 closest distance to " N   ALA A 248 " =    1.783
peak=   -3.315 closest distance to " NE2 GLN A  88 " =    1.119
peak=   -3.312 closest distance to " N   ASP A 171 " =    2.250
peak=   -3.310 closest distance to " O   HOH Z 313 " =    1.173
peak=   -3.306 closest distance to " C   ASN A 187 " =    1.892
peak=   -3.304 closest distance to " NE2 GLN A 194 " =    1.854
peak=   -3.298 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.298 closest distance to " CD1 ILE A 151 " =    2.379
peak=   -3.297 closest distance to " CG1 VAL A 197 " =    2.214
peak=   -3.293 closest distance to " CA  GLY A 133 " =    2.327
peak=   -3.287 closest distance to " N   GLN A  58 " =    1.589
peak=   -3.286 closest distance to " O   ILE A 234 " =    1.244
peak=   -3.282 closest distance to " O   GLY A  75 " =    1.887
peak=   -3.278 closest distance to " OD2 ASP A  50 " =    2.241
peak=   -3.271 closest distance to " C   SER A 206 " =    1.469
peak=   -3.268 closest distance to " CB  ALA A  10 " =    2.245
peak=   -3.260 closest distance to " ND2 ASN A  69 " =    1.849
peak=   -3.259 closest distance to " CG  PHE A 283 " =    2.731
peak=   -3.258 closest distance to " OG  SER A  26 " =    1.324
peak=   -3.254 closest distance to " CB  ASN A  39 " =    2.285
peak=   -3.250 closest distance to " NH2 ARG A 159 " =    2.331
peak=   -3.238 closest distance to " N   THR A 157 " =    1.545
peak=   -3.235 closest distance to " N   ALA A 248 " =    2.419
peak=   -3.235 closest distance to " O   ALA A  10 " =    1.747
peak=   -3.231 closest distance to " O   HOH Z 139 " =    3.099
peak=   -3.230 closest distance to " O   HOH Z 191 " =    5.572
peak=   -3.229 closest distance to " OG  SER A  62 " =    1.702
peak=   -3.223 closest distance to " O   ALA A 161 " =    1.758
peak=   -3.213 closest distance to " NH2 ARG A  79 " =    1.636
peak=   -3.211 closest distance to " CD1 LEU A 228 " =    2.211
peak=   -3.208 closest distance to " CG1 VAL A  67 " =    3.141
peak=   -3.208 closest distance to " O   LYS A 117 " =    1.677
peak=   -3.205 closest distance to " CD1 LEU A  25 " =    2.469
peak=   -3.202 closest distance to " O   GLY A 196 " =    1.125
peak=   -3.198 closest distance to " N   ASN A  60 " =    1.319
peak=   -3.192 closest distance to " CA  GLY A 203 " =    2.409
peak=   -3.190 closest distance to " C   ASP A 270 " =    1.199
peak=   -3.184 closest distance to " CD  ARG A 195 " =    5.187
peak=   -3.184 closest distance to " CD  PRO A 213 " =    2.159
peak=   -3.181 closest distance to " O   HOH Z 123 " =    2.420
peak=   -3.180 closest distance to " O   VAL A 125 " =    2.345
peak=   -3.179 closest distance to " O   HOH Z 177 " =    1.723
peak=   -3.177 closest distance to " N   SER A   3 " =    2.080
peak=   -3.176 closest distance to " O   HOH Z 339 " =    1.826
peak=   -3.174 closest distance to " O   PHE A 218 " =    1.675
peak=   -3.171 closest distance to " O   PRO A 198 " =    1.372
peak=   -3.167 closest distance to " O   LEU A 167 " =    1.512
peak=   -3.167 closest distance to " CG  GLU A  53 " =    1.605
peak=   -3.166 closest distance to " NE2 GLN A 278 " =    1.965
peak=   -3.160 closest distance to " O   HOH Z  47 " =    1.668
peak=   -3.157 closest distance to " O   HOH Z 136 " =    2.292
peak=   -3.157 closest distance to " O   SER A  95 " =    1.710
peak=   -3.156 closest distance to " O   HOH Z 422 " =    1.622
peak=   -3.156 closest distance to " O   MET A  40 " =    2.786
peak=   -3.151 closest distance to " OXT GLY A 302 " =    3.460
peak=   -3.147 closest distance to " CB  GLN A  11 " =    1.869
peak=   -3.147 closest distance to " CD2 PHE A  61 " =    2.525
peak=   -3.145 closest distance to " CB  ASP A 132 " =    2.370
peak=   -3.140 closest distance to " O   HOH Z 409 " =    4.988
peak=   -3.139 closest distance to " N   MET A 105 " =    2.629
peak=   -3.138 closest distance to " O   HOH Z 252 " =    3.984
peak=   -3.128 closest distance to " CB  TRP A  85 " =    2.531
peak=   -3.125 closest distance to " O   ASP A 171 " =    1.950
peak=   -3.124 closest distance to " O   HOH Z 285 " =    1.591
peak=   -3.123 closest distance to " SG ACYS A 201 " =    2.120
peak=   -3.123 closest distance to " O   HOH Z 292 " =    1.899
peak=   -3.120 closest distance to " O   HOH Z 131 " =    4.058
peak=   -3.116 closest distance to " O   HOH Z 251 " =    5.182
peak=   -3.111 closest distance to " NH1 ARG A 195 " =    2.620
peak=   -3.097 closest distance to " O   HOH Z 222 " =    1.546
peak=   -3.090 closest distance to " O   HOH Z  90 " =    1.680
peak=   -3.088 closest distance to " O   ALA A  51 " =    1.391
peak=   -3.078 closest distance to " CB  PHE A 208 " =    2.325
peak=   -3.078 closest distance to " CD  GLN A 223 " =    1.679
peak=   -3.072 closest distance to " O   ASN A 301 " =    1.456
peak=   -3.071 closest distance to " O   HOH Z 244 " =    1.463
peak=   -3.069 closest distance to " CD2 LEU A 237 " =    2.639
peak=   -3.064 closest distance to " O   HOH Z 353 " =    2.095
peak=   -3.050 closest distance to " O   HOH Z 298 " =    2.609
peak=   -3.049 closest distance to " CD1 TYR A 247 " =    2.400
peak=   -3.028 closest distance to " CG  GLU A 152 " =    1.496
peak=   -3.008 closest distance to " CD1 ILE A 239 " =    2.368

================= 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    :  0.4340 0.4194   6.227579e+00   6.198660e+00
   1_bss:  0.4271 0.4068   6.222350e+00   6.184145e+00
   1_xyz:  0.3135 0.3339   6.003338e+00   6.040808e+00
   1_adp:  0.2497 0.2825   5.812160e+00   5.915835e+00
   1_occ:  0.2489 0.2826   5.810876e+00   5.916554e+00
   2_bss:  0.2443 0.2780   5.810215e+00   5.911764e+00
   2_xyz:  0.1569 0.1927   5.408891e+00   5.592323e+00
   2_adp:  0.1398 0.1772   5.308465e+00   5.506387e+00
   2_occ:  0.1396 0.1772   5.307845e+00   5.506363e+00
   3_bss:  0.1391 0.1776   5.308043e+00   5.505194e+00
   3_xyz:  0.1266 0.1629   5.225230e+00   5.427584e+00
   3_adp:  0.1227 0.1617   5.206737e+00   5.419222e+00
   3_occ:  0.1225 0.1616   5.206056e+00   5.419099e+00
   4_bss:  0.1224 0.1616   5.205214e+00   5.418648e+00
   4_xyz:  0.1168 0.1596   5.176197e+00   5.405389e+00
   4_adp:  0.1172 0.1583   5.174533e+00   5.398872e+00
   4_occ:  0.1171 0.1583   5.174514e+00   5.399135e+00
   5_bss:  0.1175 0.1583   5.176393e+00   5.399566e+00
   5_xyz:  0.1112 0.1557   5.139848e+00   5.382820e+00
   5_adp:  0.1099 0.1572   5.141008e+00   5.391697e+00
   5_occ:  0.1099 0.1572   5.141091e+00   5.391944e+00
   5_bss:  0.1099 0.1572   5.140856e+00   5.391815e+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:  0.333  20.000   7.000   9.733   8.618   0.000   0.000   0.000
   1_xyz:  0.333  20.000   7.000   9.733   8.618   0.000   0.000   0.000
   1_adp:  0.333  20.000   7.000   9.733   8.618   0.000   0.000   0.000
   1_occ:  0.333  20.000   7.000   9.733   8.618   0.000   0.000   0.000
   2_bss:  0.327  42.951   3.777   6.025   5.447   0.000   0.000   0.000
   2_xyz:  0.327  42.951   3.777   6.025   5.447   0.000   0.000   0.000
   2_adp:  0.327  42.951   3.777   6.025   5.447   0.000   0.000   0.000
   2_occ:  0.327  42.951   3.777   6.025   5.447   0.000   0.000   0.000
   3_bss:  0.319  42.951   3.076   4.262   4.706   0.000   0.000   0.000
   3_xyz:  0.319  42.951   3.076   4.262   4.706   0.000   0.000   0.000
   3_adp:  0.319  42.951   3.076   4.262   4.706   0.000   0.000   0.000
   3_occ:  0.319  42.951   3.076   4.262   4.706   0.000   0.000   0.000
   4_bss:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   4_xyz:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   4_adp:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   4_occ:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   5_bss:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   5_xyz:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   5_adp:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   5_occ:  0.328  51.984   2.982   3.831   4.552   0.000   0.000   0.000
   5_bss:  0.322  54.864  -0.748  -0.039   0.787  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.233 0.5690  0.6269    49614.308
   1_bss:  45.266 0.5796  0.8236    47022.331
   1_xyz:  35.837 0.6908  0.9518    30121.106
   1_adp:  28.704 0.7726  1.0320    21023.386
   1_occ:  28.725 0.7724  1.0311    21045.457
   2_bss:  28.491 0.7749  0.9167    20721.317
   2_xyz:  18.689 0.8737  0.9979     9609.022
   2_adp:  16.687 0.8921  1.0100     8111.339
   2_occ:  16.682 0.8921  1.0100     8108.317
   3_bss:  16.662 0.8923  0.9716     8119.058
   3_xyz:  14.781 0.9088  0.9773     6822.701
   3_adp:  14.593 0.9105  0.9764     6730.530
   3_occ:  14.589 0.9106  0.9762     6731.578
   4_bss:  14.572 0.9107  0.9689     6729.732
   4_xyz:  14.288 0.9131  0.9696     6564.312
   4_adp:  14.117 0.9146  0.9687     6490.254
   4_occ:  14.122 0.9145  0.9686     6494.692
   5_bss:  14.161 0.9142  0.9681     6512.915
   5_xyz:  13.831 0.9166  0.9705     6289.746
   5_adp:  14.018 0.9152  0.9659     6374.816
   5_occ:  14.022 0.9152  0.9658     6378.977
   5_bss:  14.018 0.9152  0.9702     6375.552
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4068e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4068e+01
   1_xyz:   1.533  0.012  0.103 17.772  0.006  4.126   1.1894e-01
   1_adp:   1.533  0.012  0.103 17.772  0.006  4.126   1.1894e-01
   1_occ:   1.533  0.012  0.103 17.772  0.006  4.126   1.1894e-01
   2_bss:   1.533  0.012  0.103 17.772  0.006  4.126   1.1894e-01
   2_xyz:   1.109  0.009  0.078 16.098  0.004  4.132   7.4190e-02
   2_adp:   1.109  0.009  0.078 16.098  0.004  4.132   7.4190e-02
   2_occ:   1.109  0.009  0.078 16.098  0.004  4.132   7.4190e-02
   3_bss:   1.109  0.009  0.078 16.098  0.004  4.132   7.4190e-02
   3_xyz:   0.931  0.006  0.073 15.566  0.003  4.125   5.5388e-02
   3_adp:   0.931  0.006  0.073 15.566  0.003  4.125   5.5388e-02
   3_occ:   0.931  0.006  0.073 15.566  0.003  4.125   5.5388e-02
   4_bss:   0.931  0.006  0.073 15.566  0.003  4.125   5.5388e-02
   4_xyz:   0.970  0.007  0.078 15.323  0.003  4.124   5.8151e-02
   4_adp:   0.970  0.007  0.078 15.323  0.003  4.124   5.8151e-02
   4_occ:   0.970  0.007  0.078 15.323  0.003  4.124   5.8151e-02
   5_bss:   0.970  0.007  0.078 15.323  0.003  4.124   5.8151e-02
   5_xyz:   1.143  0.010  0.093 15.661  0.004  4.129   7.8564e-02
   5_adp:   1.143  0.010  0.093 15.661  0.004  4.129   7.8564e-02
   5_occ:   1.143  0.010  0.093 15.661  0.004  4.129   7.8564e-02
   5_bss:   1.143  0.010  0.093 15.661  0.004  4.129   7.8564e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0106e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0106e+00
   1_xyz:  13.269  0.139  0.448 87.067  0.037  2.310   9.0676e-02
   1_adp:  13.269  0.139  0.448 87.067  0.037  2.310   9.0676e-02
   1_occ:  13.269  0.139  0.448 87.067  0.037  2.310   9.0676e-02
   2_bss:  13.269  0.139  0.448 87.067  0.037  2.310   9.0676e-02
   2_xyz:   7.168  0.057  0.290 82.025  0.035  2.239   6.1716e-02
   2_adp:   7.168  0.057  0.290 82.025  0.035  2.239   6.1716e-02
   2_occ:   7.168  0.057  0.290 82.025  0.035  2.239   6.1716e-02
   3_bss:   7.168  0.057  0.290 82.025  0.035  2.239   6.1716e-02
   3_xyz:   6.343  0.043  0.347 82.128  0.040  2.375   3.2602e-02
   3_adp:   6.343  0.043  0.347 82.128  0.040  2.375   3.2602e-02
   3_occ:   6.343  0.043  0.347 82.128  0.040  2.375   3.2602e-02
   4_bss:   6.343  0.043  0.347 82.128  0.040  2.375   3.2602e-02
   4_xyz:   6.959  0.045  0.408 82.470  0.038  2.360   3.4741e-02
   4_adp:   6.959  0.045  0.408 82.470  0.038  2.360   3.4741e-02
   4_occ:   6.959  0.045  0.408 82.470  0.038  2.360   3.4741e-02
   5_bss:   6.959  0.045  0.408 82.470  0.038  2.360   3.4741e-02
   5_xyz:   8.013  0.055  0.602 81.925  0.040  2.272   5.6706e-02
   5_adp:   8.013  0.055  0.602 81.925  0.040  2.272   5.6706e-02
   5_occ:   8.013  0.055  0.602 81.925  0.040  2.272   5.6706e-02
   5_bss:   8.013  0.055  0.602 81.925  0.040  2.272   5.6706e-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:  75.67   0.00  10.55  57.32   0.00   7.52  75.67   0.00  27.02
   1_occ:  75.67   0.00  10.55  57.32   0.00   7.52  75.67   0.00  27.02
   2_bss:  75.67   0.00  10.55  57.32   0.00   7.52  75.67   0.00  27.02
   2_xyz:  75.67   0.00  10.55  57.32   0.00   7.52  75.67   0.00  27.02
   2_adp:  68.45   0.00  11.00  65.23   0.00   7.18  68.45   0.00  31.79
   2_occ:  68.45   0.00  11.00  65.23   0.00   7.18  68.45   0.00  31.79
   3_bss:  68.45   0.00  11.00  65.23   0.00   7.18  68.45   0.00  31.79
   3_xyz:  68.45   0.00  11.00  65.23   0.00   7.18  68.45   0.00  31.79
   3_adp:  79.84   0.00  11.63  79.84   0.00   7.35  70.58   0.00  34.90
   3_occ:  79.84   0.00  11.63  79.84   0.00   7.35  70.58   0.00  34.90
   4_bss:  79.84   0.00  11.63  79.84   0.00   7.35  70.58   0.00  34.90
   4_xyz:  79.84   0.00  11.63  79.84   0.00   7.35  70.58   0.00  34.90
   4_adp:  79.28   0.00  11.18  79.28   0.00   7.15  68.87   0.27  33.12
   4_occ:  79.28   0.00  11.18  79.28   0.00   7.15  68.87   0.27  33.12
   5_bss:  79.28   0.00  11.18  79.28   0.00   7.15  68.87   0.27  33.12
   5_xyz:  79.28   0.00  11.18  79.28   0.00   7.15  68.87   0.27  33.12
   5_adp:  86.55   0.00  11.51  86.55   0.00   7.23  76.76   0.60  34.77
   5_occ:  86.55   0.00  11.51  86.55   0.00   7.23  76.76   0.60  34.77
   5_bss:  90.46   3.91  15.42  90.46   3.91  11.15  80.67   4.52  38.68
------------------------------------------------------------------------
 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:    1.198    0.023    0.404
   1_adp:    1.198    0.023    0.404
   1_occ:    1.198    0.023    0.404
   2_bss:    1.198    0.023    0.404
   2_xyz:    1.448    0.029    0.525
   2_adp:    1.448    0.029    0.525
   2_occ:    1.448    0.029    0.525
   3_bss:    1.448    0.029    0.525
   3_xyz:    1.506    0.033    0.543
   3_adp:    1.506    0.033    0.543
   3_occ:    1.506    0.033    0.543
   4_bss:    1.506    0.033    0.543
   4_xyz:    1.650    0.040    0.564
   4_adp:    1.650    0.040    0.564
   4_occ:    1.650    0.040    0.564
   5_bss:    1.650    0.040    0.564
   5_xyz:    1.576    0.054    0.572
   5_adp:    1.576    0.054    0.572
   5_occ:    1.576    0.054    0.572
   5_bss:    1.576    0.054    0.572
------------------------------------------------------------------------

CPU time actual refinement: 314.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/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_688/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_688/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.88 
  Macro-tasks:
    bulk solvent and scale       = 40.96  
    individual site refinement   = 126.89 
    weights calculation          = 31.97  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.39 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 93.80  
    alpha_beta                      = 8.19   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 104.76 
    fmodel                         = 7.10   
    r_factors                      = 0.23   
    phase_errors                   = 11.04  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 228.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.453 micro seconds
Total CPU time: 5.46 minutes
from_scatterers_fft:    630 calls, 93.47 s
gradients_fft:          574 calls, 91.74 s

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

# Date 2008-01-16 Time 02:09:59 PST -0800 (1200478199.39 s)
Start R-work = 0.4340, R-free = 0.4194 (no bulk solvent and anisotropic scale)
Final R-work = 0.1270, R-free = 0.1723 (no bulk solvent and anisotropic scale)

Start R-work = 0.4271, R-free = 0.4068
Final R-work = 0.1099, R-free = 0.1572