# Date 2008-01-16 Time 06:21:38 PST -0800 (1200493298.30 s)
#phil __OFF__

Command line arguments: "../1111.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16249
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1111

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.2261, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95112
Completeness in resolution range: 0.935259
Completeness with d_max=infinity: 0.932543

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9511

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: (71.655, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95112
Completeness in resolution range: 0.935259
Completeness with d_max=infinity: 0.932543

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1767 [2196/2226]  1980   216   9.8%
  bin  2:  4.1767 -  3.3268 [2113/2129]  1899   214  10.1%
  bin  3:  3.3268 -  2.9097 [2089/2108]  1876   213  10.2%
  bin  4:  2.9097 -  2.6452 [2064/2094]  1862   202   9.8%
  bin  5:  2.6452 -  2.4565 [2059/2078]  1858   201   9.8%
  bin  6:  2.4565 -  2.3122 [2045/2070]  1829   216  10.6%
  bin  7:  2.3122 -  2.1968 [2032/2066]  1829   203  10.0%
  bin  8:  2.1968 -  2.1014 [2024/2054]  1829   195   9.6%
  bin  9:  2.1014 -  2.0207 [1977/2063]  1780   197  10.0%
  bin 10:  2.0207 -  1.9511 [ 990/2057]   888   102  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 19
        2.17 -     2.85: 1135
        2.85 -     3.53: 4484
        3.53 -     4.22: 9418
        4.22 -     4.90: 13602
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.482 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.569 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.708 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.807 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28653 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 =====================


==================== 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/noshake/run_1111/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 71.655 46.22605 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4819   r_free= 0.4868   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.284655                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6593 0.99   1424  161 0.3809 0.3901      6.5569      6.5877|
|  2:  4.6593 -  3.7164 0.99   1377  148 0.4196 0.3956      6.8231      6.8195|
|  3:  3.7164 -  3.2520 0.99   1344  148 0.4668 0.4613      6.6825       6.733|
|  4:  3.2520 -  2.9571 0.99   1343  159 0.4680 0.4837      6.5307      6.5069|
|  5:  2.9571 -  2.7465 0.99   1332  141 0.5038 0.4843       6.368      6.3311|
|  6:  2.7465 -  2.5854 0.99   1328  150 0.5247 0.5442      6.2867      6.3085|
|  7:  2.5854 -  2.4565 0.99   1327  139 0.5262 0.5016      6.2505       6.162|
|  8:  2.4565 -  2.3500 0.98   1299  156 0.5195 0.5342      6.1544      6.1891|
|  9:  2.3500 -  2.2598 0.98   1307  147 0.5245 0.4855      6.1444      6.1008|
| 10:  2.2598 -  2.1821 0.99   1292  142 0.5211 0.5647      6.0754      6.1036|
| 11:  2.1821 -  2.1140 0.99   1339  136 0.5282 0.5876      6.0468      6.0678|
| 12:  2.1140 -  2.0538 0.97   1264  151 0.5347 0.5774      5.9472      5.9778|
| 13:  2.0538 -  1.9998 0.87   1154  132 0.5381 0.5575      5.8822      5.8297|
| 14:  1.9998 -  1.9511 0.37    500   49 0.5505 0.4784       5.824      5.8319|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6593  1424   161  0.70  34.46   0.82     0.75      71077.65|
|  2:  4.6593 -  3.7164  1377   148  0.69  36.41   0.90     0.81     112433.39|
|  3:  3.7164 -  3.2520  1344   148  0.56  47.27   0.90     0.75     125607.69|
|  4:  3.2520 -  2.9571  1343   159  0.45  55.82   0.92     0.65     117064.41|
|  5:  2.9571 -  2.7465  1332   141  0.34  63.95   0.87     0.51      92971.30|
|  6:  2.7465 -  2.5854  1328   150  0.32  65.67   0.88     0.47      79000.68|
|  7:  2.5854 -  2.4565  1327   139  0.31  66.83   0.90     0.43      69055.68|
|  8:  2.4565 -  2.3500  1299   156  0.33  65.21   0.89     0.49      61263.56|
|  9:  2.3500 -  2.2598  1307   147  0.31  66.77   0.93     0.47      57926.92|
| 10:  2.2598 -  2.1821  1292   142  0.26  70.56   0.92     0.40      55079.30|
| 11:  2.1821 -  2.1140  1339   136  0.19  75.99   0.95     0.30      54489.48|
| 12:  2.1140 -  2.0538  1264   151  0.17  77.52   0.93     0.27      48360.97|
| 13:  2.0538 -  1.9998  1154   132  0.18  76.72   0.93     0.30      42746.17|
| 14:  1.9998 -  1.9511   500    49  0.19  75.80   0.91     0.31      36433.67|
|alpha:            min =        0.27 max =            0.81 mean =         0.51|
|beta:             min =    36433.67 max =       125607.69 mean =     75470.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.72|
|phase err.(test): min =        0.00 max =           89.76 mean =        61.87|
|-----------------------------------------------------------------------------|

============================== 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 = 12.346266             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.764   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.431857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.241   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.482 -  1.824:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.824 -  2.165:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.165 -  2.507:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.507 -  2.849:     1091 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.849 -  3.191:     1993 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.191 -  3.533:     2491 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.533 -  3.875:     4695 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.216:     4723 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.216 -  4.558:     6163 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7439 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.482 |       0.509 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4819   r_free= 0.4868   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.284655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4746   r_free= 0.4802   ksol= 0.31   Bsol= 13.69   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,-0.02,1.58,-0.00,0.00,0.00); trace/3= 0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.283758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.054059              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.995   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.442305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.890   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4746      final r-factor (work) = 0.3818          |
| start r-factor (free) = 0.4802      final r-factor (free) = 0.4138          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6030 = 9.05 * 0.50 * 6.2778 + 1.00 * 0.1832                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1435 = 9.05 * 0.50 * 6.1920 + 1.00 * 0.1120                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3818      final r-factor (work) = 0.3473          |
| start r-factor (free) = 0.4138      final r-factor (free) = 0.4213          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9369 = 1.44 * 1.00 * 6.1920 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8177 = 1.44 * 1.00 * 6.0992 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.91   19.47    None  None   None       |
|    all(noH): 2823   0      0.00    95.91   19.47    None  None   None       |
|    Sol.    : 438    0      0.00    95.68   36.35    None  None   None       |
|    Mac.    : 2385   0      0.00    95.91   16.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.591:  799   |   5:    47.956 -  57.547:   99        |
|      1:     9.591 -  19.182:  853   |   6:    57.547 -  67.138:   45        |
|      2:    19.182 -  28.773:  557   |   7:    67.138 -  76.729:   15        |
|      3:    28.773 -  38.365:  295   |   8:    76.729 -  86.320:    9        |
|      4:    38.365 -  47.956:  149   |   9:    86.320 -  95.911:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3473 r_free = 0.4213             target_work(ml) = 6.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3468 r_free = 0.4210             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3468   r_free= 0.4210   ksol= 0.31   Bsol= 13.69   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,-0.02,1.58,-0.00,0.00,0.00); trace/3= 0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.101725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3466   r_free= 0.4203   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.63,0.80,-0.00,0.00,0.00); trace/3= 0.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.101977                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.958595              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.774   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.603204              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.670  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3466      final r-factor (work) = 0.2724          |
| start r-factor (free) = 0.4203      final r-factor (free) = 0.3487          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3827 = 7.96 * 0.50 * 6.0992 + 1.00 * 0.1120                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0424 = 7.96 * 0.50 * 6.0194 + 1.00 * 0.0896                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2724      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3487      final r-factor (free) = 0.3277          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6515 = 0.60 * 1.00 * 6.0194 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5647 = 0.60 * 1.00 * 5.8881 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.70   18.51    None  None   None       |
|    all(noH): 2823   0      0.00    94.70   18.51    None  None   None       |
|    Sol.    : 438    0      1.80    94.70   39.32    None  None   None       |
|    Mac.    : 2385   0      0.00    90.14   14.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.470:  852   |   5:    47.349 -  56.819:   98        |
|      1:     9.470 -  18.940: 1025   |   6:    56.819 -  66.289:   48        |
|      2:    18.940 -  28.410:  399   |   7:    66.289 -  75.759:   19        |
|      3:    28.410 -  37.879:  226   |   8:    75.759 -  85.228:    3        |
|      4:    37.879 -  47.349:  148   |   9:    85.228 -  94.698:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2530 r_free = 0.3277             target_work(ml) = 5.863         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2527 r_free = 0.3273             target_work(ml) = 5.862         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2527   r_free= 0.3273   ksol= 0.34   Bsol= 50.00   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.63,0.80,-0.00,0.00,0.00); trace/3= 0.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.862127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2524   r_free= 0.3263   ksol= 0.34   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-1.42,-0.23,-0.00,-0.00,-0.00); trace/3= -0.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.860138                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.203544              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.522   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413051              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2524      final r-factor (work) = 0.1840          |
| start r-factor (free) = 0.3263      final r-factor (free) = 0.2400          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2979 = 7.20 * 0.50 * 5.8883 + 1.00 * 0.0896                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7695 = 7.20 * 0.50 * 5.7466 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1840      final r-factor (work) = 0.1617          |
| start r-factor (free) = 0.2400      final r-factor (free) = 0.2181          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3894 = 0.41 * 1.00 * 5.7466 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3159 = 0.41 * 1.00 * 5.5237 + 1.00 * 0.0344                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.09   17.96    None  None   None       |
|    all(noH): 2823   0      0.00    89.09   17.96    None  None   None       |
|    Sol.    : 438    0      6.21    89.09   42.47    None  None   None       |
|    Mac.    : 2385   0      0.00    88.52   13.45    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 -   8.909:  760   |   5:    44.547 -  53.456:  111        |
|      1:     8.909 -  17.819: 1222   |   6:    53.456 -  62.365:   78        |
|      2:    17.819 -  26.728:  327   |   7:    62.365 -  71.274:   39        |
|      3:    26.728 -  35.637:  139   |   8:    71.274 -  80.184:   13        |
|      4:    35.637 -  44.547:  128   |   9:    80.184 -  89.093:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1617 r_free = 0.2181             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1616 r_free = 0.2176             target_work(ml) = 5.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1616   r_free= 0.2176   ksol= 0.34   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-1.42,-0.23,-0.00,-0.00,-0.00); trace/3= -0.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.469204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2166   ksol= 0.33   Bsol= 48.99   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-2.53,-1.62,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.466871                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.424410              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.435  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.069264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.722   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.2166      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7771 = 2.42 * 0.50 * 5.5316 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6106 = 2.42 * 0.50 * 5.4093 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1862      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7959 = 1.07 * 1.00 * 5.4093 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6816 = 1.07 * 1.00 * 5.3033 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.15   18.23    None  None   None       |
|    all(noH): 2823   0      0.00    98.15   18.23    None  None   None       |
|    Sol.    : 438    0      6.60    93.00   45.23    None  None   None       |
|    Mac.    : 2385   0      0.00    98.15   13.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.815:  990   |   5:    49.076 -  58.891:  103        |
|      1:     9.815 -  19.630: 1127   |   6:    58.891 -  68.706:   64        |
|      2:    19.630 -  29.446:  252   |   7:    68.706 -  78.521:   37        |
|      3:    29.446 -  39.261:  120   |   8:    78.521 -  88.337:   15        |
|      4:    39.261 -  49.076:  106   |   9:    88.337 -  98.152:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1323 r_free = 0.1807             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1323 r_free = 0.1805             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1805   ksol= 0.33   Bsol= 48.99   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-2.53,-1.62,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.287541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1807   ksol= 0.32   Bsol= 50.04   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.75,-1.90,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.287200                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.374435              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.521  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.529  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3496 = 2.37 * 0.50 * 5.3033 + 1.00 * 0.0535                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2902 = 2.37 * 0.50 * 5.2496 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0219 = 0.38 * 1.00 * 5.2496 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0052 = 0.38 * 1.00 * 5.2097 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.89    101.45  17.70    None  None   None       |
|    all(noH): 2823   0      0.89    101.45  17.70    None  None   None       |
|    Sol.    : 438    0      6.29    98.62   43.03    None  None   None       |
|    Mac.    : 2385   0      0.89    101.45  13.05    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:     0.893 -  10.948: 1238   |   5:    51.169 -  61.225:   85        |
|      1:    10.948 -  21.004:  972   |   6:    61.225 -  71.280:   39        |
|      2:    21.004 -  31.059:  207   |   7:    71.280 -  81.335:   29        |
|      3:    31.059 -  41.114:  123   |   8:    81.335 -  91.391:   10        |
|      4:    41.114 -  51.169:  115   |   9:    91.391 - 101.446:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1189 r_free = 0.1655             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1652             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1652   ksol= 0.32   Bsol= 50.04   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.75,-1.90,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193343                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6593 0.99   1424  161 0.0992 0.1384      5.3949      5.6096|
|  2:  4.6593 -  3.7164 0.99   1377  148 0.0887 0.1150      5.4727      5.6828|
|  3:  3.7164 -  3.2520 0.99   1344  148 0.1152 0.1655      5.5217      5.8903|
|  4:  3.2520 -  2.9571 0.99   1343  159 0.1333 0.1653      5.5146      5.6435|
|  5:  2.9571 -  2.7465 0.99   1332  141 0.1393 0.1818      5.3526      5.5457|
|  6:  2.7465 -  2.5854 0.99   1328  150 0.1302 0.1728      5.2413      5.4368|
|  7:  2.5854 -  2.4565 0.99   1327  139 0.1320 0.1945      5.1962      5.4273|
|  8:  2.4565 -  2.3500 0.98   1299  156 0.1251 0.1713      5.0929      5.3349|
|  9:  2.3500 -  2.2598 0.98   1307  147 0.1207 0.1909      5.0601      5.3696|
| 10:  2.2598 -  2.1821 0.99   1292  142 0.1162 0.1801      4.9795      5.2534|
| 11:  2.1821 -  2.1140 0.99   1339  136 0.1226 0.1866      4.9914      5.3268|
| 12:  2.1140 -  2.0538 0.97   1264  151 0.1193 0.1803      4.9165      5.1227|
| 13:  2.0538 -  1.9998 0.87   1154  132 0.1273 0.1915       4.852      5.1078|
| 14:  1.9998 -  1.9511 0.37    500   49 0.1199 0.1478      4.7352      4.9463|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6593  1424   161  0.94   9.63   0.97     0.95       7558.34|
|  2:  4.6593 -  3.7164  1377   148  0.95   8.47   1.02     1.02       9784.53|
|  3:  3.7164 -  3.2520  1344   148  0.93  12.20   1.04     1.03      11104.51|
|  4:  3.2520 -  2.9571  1343   159  0.90  15.49   1.01     0.99      11583.78|
|  5:  2.9571 -  2.7465  1332   141  0.90  16.29   1.00     0.98       8570.18|
|  6:  2.7465 -  2.5854  1328   150  0.89  16.62   0.99     0.97       7400.19|
|  7:  2.5854 -  2.4565  1327   139  0.90  16.26   0.99     0.97       6567.70|
|  8:  2.4565 -  2.3500  1299   156  0.90  15.84   0.99     0.96       5565.03|
|  9:  2.3500 -  2.2598  1307   147  0.90  16.46   1.01     0.97       5271.13|
| 10:  2.2598 -  2.1821  1292   142  0.90  16.01   1.00     0.97       4647.02|
| 11:  2.1821 -  2.1140  1339   136  0.88  17.83   0.99     0.95       4857.99|
| 12:  2.1140 -  2.0538  1264   151  0.90  16.96   1.00     1.00       4432.14|
| 13:  2.0538 -  1.9998  1154   132  0.89  17.39   1.00     0.98       3762.51|
| 14:  1.9998 -  1.9511   500    49  0.90  16.49   0.99     0.96       2908.66|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2908.66 max =        11583.78 mean =      6959.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.81 mean =        14.99|
|phase err.(test): min =        0.00 max =           88.90 mean =        14.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1652   ksol= 0.32   Bsol= 50.01   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.66,-1.90,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193357                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1652   ksol= 0.32   Bsol= 50.01   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.66,-1.90,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193357                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6593 0.99   1424  161 0.0992 0.1384      5.3948      5.6096|
|  2:  4.6593 -  3.7164 0.99   1377  148 0.0887 0.1150      5.4726      5.6828|
|  3:  3.7164 -  3.2520 0.99   1344  148 0.1152 0.1655      5.5215      5.8902|
|  4:  3.2520 -  2.9571 0.99   1343  159 0.1333 0.1653      5.5146      5.6435|
|  5:  2.9571 -  2.7465 0.99   1332  141 0.1393 0.1819      5.3527      5.5458|
|  6:  2.7465 -  2.5854 0.99   1328  150 0.1302 0.1728      5.2414      5.4373|
|  7:  2.5854 -  2.4565 0.99   1327  139 0.1320 0.1945      5.1963      5.4271|
|  8:  2.4565 -  2.3500 0.98   1299  156 0.1251 0.1713       5.093       5.335|
|  9:  2.3500 -  2.2598 0.98   1307  147 0.1207 0.1909      5.0602      5.3697|
| 10:  2.2598 -  2.1821 0.99   1292  142 0.1161 0.1801      4.9795      5.2529|
| 11:  2.1821 -  2.1140 0.99   1339  136 0.1226 0.1865      4.9912      5.3267|
| 12:  2.1140 -  2.0538 0.97   1264  151 0.1192 0.1805      4.9164       5.123|
| 13:  2.0538 -  1.9998 0.87   1154  132 0.1273 0.1913      4.8521      5.1074|
| 14:  1.9998 -  1.9511 0.37    500   49 0.1199 0.1482      4.7358      4.9483|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6593  1424   161  0.94   9.63   0.98     0.95       7559.19|
|  2:  4.6593 -  3.7164  1377   148  0.95   8.47   1.02     1.02       9783.89|
|  3:  3.7164 -  3.2520  1344   148  0.93  12.20   1.04     1.03      11101.03|
|  4:  3.2520 -  2.9571  1343   159  0.90  15.49   1.01     0.99      11583.16|
|  5:  2.9571 -  2.7465  1332   141  0.90  16.29   1.00     0.98       8574.19|
|  6:  2.7465 -  2.5854  1328   150  0.89  16.63   1.00     0.97       7403.36|
|  7:  2.5854 -  2.4565  1327   139  0.90  16.26   0.99     0.97       6571.51|
|  8:  2.4565 -  2.3500  1299   156  0.90  15.84   0.99     0.97       5566.96|
|  9:  2.3500 -  2.2598  1307   147  0.90  16.46   1.01     0.97       5270.43|
| 10:  2.2598 -  2.1821  1292   142  0.90  16.01   1.00     0.97       4645.30|
| 11:  2.1821 -  2.1140  1339   136  0.88  17.82   0.99     0.95       4853.80|
| 12:  2.1140 -  2.0538  1264   151  0.90  16.96   1.00     1.00       4430.09|
| 13:  2.0538 -  1.9998  1154   132  0.89  17.39   1.00     0.98       3763.87|
| 14:  1.9998 -  1.9511   500    49  0.90  16.50   0.99     0.96       2914.15|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2914.15 max =        11583.16 mean =      6960.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.81 mean =        14.99|
|phase err.(test): min =        0.00 max =           88.90 mean =        14.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.643)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    101.42  17.67    None  None   None       |
|    all(noH): 2823   0      0.86    101.42  17.67    None  None   None       |
|    Sol.    : 438    0      6.26    98.59   43.00    None  None   None       |
|    Mac.    : 2385   0      0.86    101.42  13.02    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:     0.862 -  10.918: 1238   |   5:    51.139 -  61.194:   85        |
|      1:    10.918 -  20.973:  972   |   6:    61.194 -  71.250:   39        |
|      2:    20.973 -  31.028:  207   |   7:    71.250 -  81.305:   29        |
|      3:    31.028 -  41.084:  123   |   8:    81.305 -  91.360:   10        |
|      4:    41.084 -  51.139:  115   |   9:    91.360 - 101.416:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.755 - 5.955
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 326
   mapped sites are within: 0.755 - 5.955

peak=    7.090 closest distance to " O   HOH Z 103 " =    1.091
peak=    6.452 closest distance to " O   HOH Z 278 " =    1.417
peak=    6.065 closest distance to " NE2 GLN A  11 " =    1.267
peak=    5.871 closest distance to " O   HOH Z 214 " =    1.672
peak=    5.815 closest distance to " O   HOH Z   7 " =    1.570
peak=    5.589 closest distance to " NH2BARG A 102 " =    1.086
peak=    5.548 closest distance to " O   HOH Z 134 " =    1.753
peak=    5.484 closest distance to " CB  GLN A 223 " =    1.510
peak=    5.339 closest distance to " CG  PRO A  54 " =    1.275
peak=    5.232 closest distance to " O   HOH Z 144 " =    1.762
peak=    5.209 closest distance to " O   HOH Z 260 " =    1.586
peak=    5.185 closest distance to " NH2 ARG A  56 " =    2.001
peak=    5.078 closest distance to " O   HOH Z  49 " =    1.355
peak=    4.908 closest distance to " O   HOH Z 126 " =    1.667
peak=    4.855 closest distance to " CB  SER A  63 " =    1.319
peak=    4.788 closest distance to " O   HOH Z 126 " =    2.045
peak=    4.744 closest distance to " CG  PRO A 198 " =    1.390
peak=    4.684 closest distance to " CB  ASN A 148 " =    1.420
peak=    4.678 closest distance to " O   HOH Z  97 " =    1.277
peak=    4.672 closest distance to " O   HOH Z 183 " =    1.559
peak=    4.642 closest distance to " O   HOH Z 423 " =    1.828
peak=    4.616 closest distance to " O   HOH Z 117 " =    1.330
peak=    4.610 closest distance to " O   HOH Z 202 " =    1.559
peak=    4.598 closest distance to " O   HOH Z 182 " =    1.467
peak=    4.584 closest distance to " O   HOH Z 427 " =    2.522
peak=    4.573 closest distance to " O   HOH Z  68 " =    1.768
peak=    4.559 closest distance to " O   HOH Z 124 " =    1.471
peak=    4.540 closest distance to " O   HOH Z 425 " =    1.572
peak=    4.527 closest distance to " O   HOH Z 221 " =    1.795
peak=    4.508 closest distance to " O   HOH Z 186 " =    1.427
peak=    4.479 closest distance to " O   HOH Z 298 " =    2.009
peak=    4.412 closest distance to " O   HOH Z  48 " =    1.753
peak=    4.404 closest distance to " CG  PRO A  90 " =    1.153
peak=    4.392 closest distance to " O   HOH Z 403 " =    1.505
peak=    4.326 closest distance to " CB  GLU A 152 " =    1.349
peak=    4.322 closest distance to " O   HOH Z 287 " =    2.180
peak=    4.295 closest distance to " O   HOH Z  78 " =    2.172
peak=    4.292 closest distance to " CB  GLN A 183 " =    1.137
peak=    4.267 closest distance to " CB  PRO A  54 " =    0.888
peak=    4.265 closest distance to " O   HOH Z 132 " =    2.032
peak=    4.265 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.264 closest distance to " O   PRO A 198 " =    1.553
peak=    4.250 closest distance to " O   HOH Z 316 " =    3.051
peak=    4.240 closest distance to " O   SER A  87 " =    2.245
peak=    4.175 closest distance to " OD1 ASN A  69 " =    2.540
peak=    4.138 closest distance to " O   HOH Z 227 " =    1.747
peak=    4.129 closest distance to " O   HOH Z 135 " =    1.653
peak=    4.127 closest distance to " O   HOH Z  61 " =    1.777
peak=    4.125 closest distance to " O   HOH Z 261 " =    2.010
peak=    4.124 closest distance to " O   HOH Z 232 " =    2.236
peak=    4.119 closest distance to " O   HOH Z 368 " =    1.977
peak=    4.096 closest distance to " O   HOH Z 193 " =    1.810
peak=    4.096 closest distance to " O   HOH Z 371 " =    2.267
peak=    4.082 closest distance to " CG  LEU A 167 " =    1.187
peak=    4.080 closest distance to " O   HOH Z 132 " =    1.141
peak=    4.073 closest distance to " CB  TRP A 179 " =    1.430
peak=    4.067 closest distance to " CB  LEU A 228 " =    1.108
peak=    4.051 closest distance to " O   HOH Z 211 " =    1.330
peak=    4.036 closest distance to " O   HOH Z   3 " =    2.026
peak=    4.018 closest distance to " O   HOH Z 108 " =    1.936
peak=    4.004 closest distance to " CG2 THR A 221 " =    1.179
peak=    4.000 closest distance to " O   HOH Z  10 " =    1.845
peak=    3.989 closest distance to " O   HOH Z 272 " =    1.889
peak=    3.966 closest distance to " CB  SER A   3 " =    1.493
peak=    3.961 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.957 closest distance to " O   HOH Z  21 " =    1.651
peak=    3.953 closest distance to " O   HOH Z  78 " =    1.643
peak=    3.951 closest distance to " O   HOH Z 411 " =    3.431
peak=    3.947 closest distance to " NE AARG A 275 " =    1.503
peak=    3.927 closest distance to " O   HOH Z  11 " =    1.257
peak=    3.927 closest distance to " CD BLYS A 290 " =    1.078
peak=    3.911 closest distance to " CB  TYR A 169 " =    0.883
peak=    3.910 closest distance to " O   HOH Z 409 " =    2.129
peak=    3.909 closest distance to " CB  GLU A 128 " =    1.032
peak=    3.905 closest distance to " O   HOH Z 247 " =    1.282
peak=    3.902 closest distance to " CB  VAL A 265 " =    1.231
peak=    3.898 closest distance to " ND2 ASN A 187 " =    1.530
peak=    3.897 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.896 closest distance to " O   HOH Z 263 " =    2.473
peak=    3.888 closest distance to " CA  GLU A 152 " =    1.246
peak=    3.886 closest distance to " O   HOH Z 313 " =    1.802
peak=    3.876 closest distance to " O   HOH Z 344 " =    1.213
peak=    3.866 closest distance to " O   HOH Z 437 " =    2.266
peak=    3.865 closest distance to " O   HOH Z  59 " =    1.627
peak=    3.858 closest distance to " CB  ARG A 139 " =    1.067
peak=    3.854 closest distance to " O   HOH Z 171 " =    2.800
peak=    3.850 closest distance to " O   HOH Z 133 " =    1.651
peak=    3.836 closest distance to " O   HOH Z  97 " =    1.544
peak=    3.820 closest distance to " O   HOH Z  63 " =    1.411
peak=    3.818 closest distance to " O   HOH Z 389 " =    1.924
peak=    3.795 closest distance to " O   HOH Z 371 " =    2.001
peak=    3.788 closest distance to " O   HOH Z 133 " =    2.255
peak=    3.778 closest distance to " CB  ALA A 291 " =    3.445
peak=    3.767 closest distance to " O   HOH Z 352 " =    1.861
peak=    3.736 closest distance to " CB  SER A 216 " =    1.038
peak=    3.731 closest distance to " O   HOH Z 155 " =    1.875
peak=    3.719 closest distance to " O   HOH Z   2 " =    1.898
peak=    3.718 closest distance to " O   GLY A  57 " =    2.498
peak=    3.716 closest distance to " N   PHE A 130 " =    1.318
peak=    3.715 closest distance to " O   HOH Z 281 " =    4.399
peak=    3.705 closest distance to " O   HOH Z  73 " =    1.654
peak=    3.702 closest distance to " NZ  LYS A 117 " =    1.218
peak=    3.694 closest distance to " O   HOH Z 271 " =    2.249
peak=    3.678 closest distance to " CB  LEU A 300 " =    1.007
peak=    3.673 closest distance to " NH1AARG A 145 " =    0.997
peak=    3.672 closest distance to " CG2 VAL A 257 " =    0.851
peak=    3.671 closest distance to " CA  TYR A 186 " =    1.524
peak=    3.667 closest distance to " O   HOH Z 234 " =    3.756
peak=    3.667 closest distance to " CD  LYS A 166 " =    1.409
peak=    3.666 closest distance to " OD2 ASP A 286 " =    2.807
peak=    3.665 closest distance to " CG1 ILE A  33 " =    1.190
peak=    3.661 closest distance to " O   HOH Z   6 " =    2.012
peak=    3.660 closest distance to " O   HOH Z  15 " =    2.298
peak=    3.643 closest distance to " ND2 ASN A  60 " =    3.081
peak=    3.640 closest distance to " CA  ALA A  21 " =    1.196
peak=    3.637 closest distance to " O   HOH Z 217 " =    2.965
peak=    3.634 closest distance to " O   HOH Z 116 " =    1.735
peak=    3.632 closest distance to " O   HOH Z  63 " =    2.453
peak=    3.630 closest distance to " CD1 ILE A  33 " =    1.560
peak=    3.626 closest distance to " O   TYR A 116 " =    1.431
peak=    3.611 closest distance to " O   HOH Z 344 " =    3.252
peak=    3.610 closest distance to " OD1BASN A 224 " =    2.102
peak=    3.607 closest distance to " O   HOH Z 373 " =    1.602
peak=    3.602 closest distance to " O   HOH Z  44 " =    1.727
peak=    3.602 closest distance to " O   HOH Z 195 " =    1.523
peak=    3.596 closest distance to " CA  GLY A 267 " =    1.299
peak=    3.595 closest distance to " OG  SER A  62 " =    3.013
peak=    3.585 closest distance to " O   ALA A 233 " =    1.751
peak=    3.584 closest distance to " CA  LYS A  48 " =    1.439
peak=    3.583 closest distance to " OD1 ASN A 217 " =    1.594
peak=    3.577 closest distance to " O   HOH Z 148 " =    1.679
peak=    3.574 closest distance to " O   HOH Z 128 " =    1.409
peak=    3.568 closest distance to " O   HOH Z 180 " =    2.034
peak=    3.565 closest distance to " CA  THR A 264 " =    0.782
peak=    3.563 closest distance to " N   ARG A 156 " =    1.327
peak=    3.550 closest distance to " CG  GLN A  77 " =    2.246
peak=    3.546 closest distance to " O   HOH Z  88 " =    3.334
peak=    3.542 closest distance to " O   HOH Z 207 " =    1.830
peak=    3.541 closest distance to " O   HOH Z  97 " =    1.835
peak=    3.540 closest distance to " CA  MET A  40 " =    1.104
peak=    3.539 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.536 closest distance to " O   HOH Z 394 " =    1.532
peak=    3.534 closest distance to " CD2 TRP A 179 " =    2.128
peak=    3.532 closest distance to " O   HOH Z 374 " =    2.798
peak=    3.530 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.530 closest distance to " O   SER A  26 " =    1.545
peak=    3.523 closest distance to " CD BARG A 102 " =    1.251
peak=    3.521 closest distance to " O   HOH Z 207 " =    1.901
peak=    3.520 closest distance to " ND1 HIS A  86 " =    1.816
peak=    3.515 closest distance to " O   MET A 105 " =    1.714
peak=    3.503 closest distance to " CA  SER A  87 " =    0.961
peak=    3.495 closest distance to " CD1 LEU A 300 " =    1.232
peak=    3.489 closest distance to " CG  PRO A 280 " =    0.847
peak=    3.485 closest distance to " O   HOH Z 151 " =    1.619
peak=    3.484 closest distance to " CD  LYS A 119 " =    1.078
peak=    3.482 closest distance to " O   HOH Z 213 " =    1.922
peak=    3.478 closest distance to " O   HOH Z   1 " =    1.831
peak=    3.478 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.477 closest distance to " NE  ARG A  66 " =    3.543
peak=    3.471 closest distance to " O   HOH Z 220 " =    1.351
peak=    3.467 closest distance to " CA  ALA A 299 " =    0.925
peak=    3.462 closest distance to " O   HOH Z 225 " =    1.782
peak=    3.462 closest distance to " O   HOH Z 287 " =    2.132
peak=    3.457 closest distance to " CA  ALA A 158 " =    1.123
peak=    3.457 closest distance to " O   HOH Z 145 " =    1.476
peak=    3.452 closest distance to " O   HOH Z 112 " =    2.631
peak=    3.452 closest distance to " CB  SER A 276 " =    1.091
peak=    3.446 closest distance to " O   HOH Z  58 " =    1.864
peak=    3.443 closest distance to " O   HOH Z 334 " =    2.884
peak=    3.443 closest distance to " CB  ALA A  34 " =    1.180
peak=    3.440 closest distance to " O   HOH Z  59 " =    2.045
peak=    3.440 closest distance to " O   HOH Z 345 " =    3.404
peak=    3.439 closest distance to " CG  PRO A 243 " =    1.123
peak=    3.438 closest distance to " CB  MET A  47 " =    1.064
peak=    3.437 closest distance to " NH1 ARG A  14 " =    1.107
peak=    3.436 closest distance to " N   ASN A  39 " =    1.356
peak=    3.435 closest distance to " O   HOH Z  66 " =    2.058
peak=    3.426 closest distance to " O   HOH Z 334 " =    1.604
peak=    3.421 closest distance to " O   HOH Z 106 " =    2.182
peak=    3.415 closest distance to " CG  GLN A  55 " =    1.950
peak=    3.413 closest distance to " CB  GLU A 236 " =    1.306
peak=    3.408 closest distance to " O   HOH Z 357 " =    1.900
peak=    3.408 closest distance to " CB  ILE A 234 " =    1.004
peak=    3.405 closest distance to " O   ALA A 165 " =    1.288
peak=    3.402 closest distance to " O   HOH Z 244 " =    1.739
peak=    3.399 closest distance to " CD  GLN A  58 " =    5.619
peak=    3.395 closest distance to " O   HOH Z 152 " =    2.544
peak=    3.388 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.387 closest distance to " CB  MET A 105 " =    1.450
peak=    3.384 closest distance to " CA  ILE A 234 " =    1.013
peak=    3.379 closest distance to " O   HOH Z  15 " =    1.833
peak=    3.379 closest distance to " O   HOH Z 250 " =    1.407
peak=    3.377 closest distance to " O   HOH Z 108 " =    1.610
peak=    3.375 closest distance to " O   HOH Z 209 " =    2.558
peak=    3.372 closest distance to " O   HOH Z 139 " =    2.589
peak=    3.372 closest distance to " O   HOH Z 193 " =    2.220
peak=    3.368 closest distance to " O   HOH Z   5 " =    1.384
peak=    3.362 closest distance to " O   HOH Z 156 " =    2.734
peak=    3.358 closest distance to " O   HOH Z 334 " =    1.473
peak=    3.356 closest distance to " O   HOH Z 258 " =    2.212
peak=    3.355 closest distance to " CB  PHE A  16 " =    0.902
peak=    3.351 closest distance to " O   GLY A 302 " =    1.565
peak=    3.350 closest distance to " O   HOH Z 414 " =    1.255
peak=    3.349 closest distance to " O   HOH Z 236 " =    1.632
peak=    3.347 closest distance to " CA  MET A 105 " =    0.906
peak=    3.340 closest distance to " O   HOH Z 277 " =    2.617
peak=    3.337 closest distance to " O   HOH Z  44 " =    3.287
peak=    3.336 closest distance to " CD  ARG A  66 " =    2.205
peak=    3.334 closest distance to " NH2 ARG A 219 " =    1.750
peak=    3.323 closest distance to " OG  SER A  22 " =    2.936
peak=    3.322 closest distance to " C   GLU A 277 " =    1.338
peak=    3.316 closest distance to " O   HOH Z 109 " =    1.274
peak=    3.314 closest distance to " N   GLN A 278 " =    0.918
peak=    3.310 closest distance to " CB  THR A 157 " =    1.007
peak=    3.306 closest distance to " CB  ALA A 291 " =    1.526
peak=    3.305 closest distance to " CA  LEU A 282 " =    1.321
peak=    3.305 closest distance to " O   GLN A 278 " =    1.471
peak=    3.304 closest distance to " CB  ASP A 124 " =    0.845
peak=    3.302 closest distance to " O   HOH Z 194 " =    2.144
peak=    3.301 closest distance to " O   HOH Z 122 " =    1.478
peak=    3.292 closest distance to " CA  ASN A  74 " =    1.168
peak=    3.291 closest distance to " O   HOH Z 153 " =    1.689
peak=    3.289 closest distance to " N   TYR A  15 " =    0.976
peak=    3.286 closest distance to " O   ASN A 209 " =    1.496
peak=    3.286 closest distance to " CB  ASN A 187 " =    0.951
peak=    3.286 closest distance to " O   HOH Z  64 " =    1.809
peak=    3.283 closest distance to " CG  ARG A 159 " =    0.856
peak=    3.281 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.278 closest distance to " O   HOH Z 115 " =    1.827
peak=    3.276 closest distance to " O   HOH Z  40 " =    2.090
peak=    3.274 closest distance to " N   ASN A 127 " =    1.389
peak=    3.274 closest distance to " O   HOH Z 345 " =    1.677
peak=    3.272 closest distance to " CG2 THR A 220 " =    1.087
peak=    3.268 closest distance to " CZ3 TRP A 123 " =    1.251
peak=    3.264 closest distance to " CG  PRO A 213 " =    1.101
peak=    3.261 closest distance to " O   HOH Z 119 " =    1.574
peak=    3.261 closest distance to " CB  ALA A 161 " =    0.952
peak=    3.259 closest distance to " CB  ARG A 102 " =    0.808
peak=    3.259 closest distance to " O   HOH Z 387 " =    3.126
peak=    3.255 closest distance to " CD  ARG A 138 " =    0.781
peak=    3.255 closest distance to " O   HOH Z 419 " =    2.298
peak=    3.253 closest distance to " CD  ARG A 219 " =    1.047
peak=    3.252 closest distance to " O   HOH Z 286 " =    2.438
peak=    3.246 closest distance to " O   HOH Z 234 " =    3.938
peak=    3.245 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.245 closest distance to " O   HOH Z 175 " =    3.580
peak=    3.241 closest distance to " O   HOH Z 346 " =    1.422
peak=    3.240 closest distance to " O   HOH Z 296 " =    1.554
peak=    3.237 closest distance to " CD2 LEU A 255 " =    0.917
peak=    3.235 closest distance to " O   HOH Z 248 " =    1.428
peak=    3.231 closest distance to " CA  ALA A 154 " =    1.009
peak=    3.227 closest distance to " O   HOH Z 158 " =    2.701
peak=    3.223 closest distance to " O   HOH Z 116 " =    2.909
peak=    3.223 closest distance to " O   HOH Z 295 " =    1.541
peak=    3.223 closest distance to " N   GLY A 196 " =    1.078
peak=    3.221 closest distance to " O   HOH Z 189 " =    1.934
peak=    3.221 closest distance to " O   HOH Z 288 " =    2.088
peak=    3.220 closest distance to " O   HOH Z 410 " =    1.758
peak=    3.216 closest distance to " O   HOH Z  43 " =    1.834
peak=    3.214 closest distance to " O   HOH Z 148 " =    3.461
peak=    3.213 closest distance to " O   HOH Z  98 " =    1.596
peak=    3.208 closest distance to " CG  GLU A   2 " =    1.188
peak=    3.208 closest distance to " O   HOH Z 286 " =    2.375
peak=    3.205 closest distance to " CA  LYS A 117 " =    1.165
peak=    3.204 closest distance to " CG  LYS A  76 " =    1.398
peak=    3.203 closest distance to " O   HOH Z 380 " =    1.584
peak=    3.202 closest distance to " O   HOH Z 216 " =    1.909
peak=    3.202 closest distance to " O   HOH Z  32 " =    2.174
peak=    3.202 closest distance to " CG  GLN A 144 " =    1.081
peak=    3.197 closest distance to " CB  GLN A  88 " =    1.346
peak=    3.192 closest distance to " CB  ARG A 190 " =    1.812
peak=    3.190 closest distance to " CE  LYS A 166 " =    1.893
peak=    3.189 closest distance to " NH2AARG A 190 " =    1.443
peak=    3.186 closest distance to " CA  ASN A 215 " =    1.296
peak=    3.182 closest distance to " O   HOH Z  80 " =    1.575
peak=    3.178 closest distance to " NZ  LYS A  76 " =    1.267
peak=    3.177 closest distance to " NE2 GLN A 278 " =    3.826
peak=    3.174 closest distance to " CB  MET A  40 " =    0.876
peak=    3.170 closest distance to " CA  PHE A 208 " =    0.977
peak=    3.170 closest distance to " O   HOH Z 302 " =    1.698
peak=    3.164 closest distance to " O   HOH Z 329 " =    3.482
peak=    3.161 closest distance to " O   HOH Z 181 " =    1.999
peak=    3.156 closest distance to " CB  PRO A 198 " =    1.004
peak=    3.155 closest distance to " CB  ASN A 285 " =    0.964
peak=    3.154 closest distance to " O   HOH Z  50 " =    1.656
peak=    3.143 closest distance to " O   HOH Z 128 " =    1.992
peak=    3.142 closest distance to " O   HOH Z 359 " =    3.761
peak=    3.140 closest distance to " NE2 GLN A  73 " =    3.501
peak=    3.139 closest distance to " CD2 LEU A 255 " =    1.384
peak=    3.138 closest distance to " O   HOH Z 365 " =    5.955
peak=    3.136 closest distance to " O   HOH Z 423 " =    2.146
peak=    3.136 closest distance to " O   HOH Z 299 " =    4.260
peak=    3.129 closest distance to " CA  ARG A  36 " =    1.243
peak=    3.128 closest distance to " CB  ARG A  79 " =    1.355
peak=    3.128 closest distance to " CA  ALA A 160 " =    0.805
peak=    3.126 closest distance to " CB  ASP A 132 " =    3.946
peak=    3.124 closest distance to " O   HOH Z 112 " =    1.152
peak=    3.124 closest distance to " N   SER A 135 " =    1.337
peak=    3.120 closest distance to " O   HOH Z 260 " =    2.162
peak=    3.116 closest distance to " O   HOH Z 125 " =    2.263
peak=    3.112 closest distance to " CB  TYR A 116 " =    0.912
peak=    3.106 closest distance to " CA  VAL A  41 " =    0.980
peak=    3.103 closest distance to " CG2 THR A 264 " =    0.774
peak=    3.103 closest distance to " N   CYS A 260 " =    0.768
peak=    3.102 closest distance to " O   HOH Z 284 " =    1.566
peak=    3.102 closest distance to " CH2 TRP A  92 " =    2.056
peak=    3.100 closest distance to " OD1 ASP A 238 " =    0.853
peak=    3.096 closest distance to " CB  GLU A 277 " =    3.546
peak=    3.095 closest distance to " O   HOH Z  18 " =    1.941
peak=    3.094 closest distance to " O   HOH Z 371 " =    2.743
peak=    3.093 closest distance to " O   HOH Z 362 " =    2.454
peak=    3.092 closest distance to " CB  LEU A 255 " =    1.131
peak=    3.088 closest distance to " O  BHOH Z 338 " =    2.304
peak=    3.086 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.085 closest distance to " O   HOH Z 281 " =    2.200
peak=    3.083 closest distance to " CB  LEU A 237 " =    0.815
peak=    3.077 closest distance to " O   HOH Z 154 " =    1.993
peak=    3.075 closest distance to " O   HOH Z 269 " =    3.411
peak=    3.065 closest distance to " O   HOH Z  89 " =    1.487
peak=    3.065 closest distance to " CD2 HIS A  81 " =    1.324
peak=    3.051 closest distance to " O   HOH Z 118 " =    1.908
peak=    3.043 closest distance to " O   HOH Z 368 " =    3.525
peak=    3.027 closest distance to " N   SER A  97 " =    0.826
peak=    3.011 closest distance to " O   HOH Z 213 " =    2.705
peak=    3.006 closest distance to " O   HOH Z 383 " =    3.248

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.586 - 5.772
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 199
   mapped sites are within: 0.704 - 5.772

peak=   -5.148 closest distance to " O   HOH Z 377 " =    1.475
peak=   -4.586 closest distance to " O   PRO A 198 " =    1.327
peak=   -4.578 closest distance to " CD  ARG A  14 " =    3.267
peak=   -4.497 closest distance to " CG  MET A 105 " =    0.957
peak=   -4.438 closest distance to " O   HOH Z  98 " =    1.659
peak=   -4.363 closest distance to " O   HOH Z 290 " =    1.003
peak=   -4.275 closest distance to " OE1 GLN A  88 " =    1.021
peak=   -4.259 closest distance to " CD  GLN A  88 " =    0.859
peak=   -4.255 closest distance to " O   HOH Z 198 " =    2.176
peak=   -4.230 closest distance to " O   HOH Z 166 " =    1.085
peak=   -4.225 closest distance to " CB  PRO A 243 " =    2.529
peak=   -4.225 closest distance to " OG ASER A 134 " =    1.208
peak=   -4.149 closest distance to " CB  TYR A  15 " =    2.199
peak=   -4.133 closest distance to " O   HOH Z 231 " =    1.565
peak=   -4.033 closest distance to " O   HOH Z 388 " =    1.825
peak=   -3.999 closest distance to " CB  PRO A  54 " =    2.384
peak=   -3.981 closest distance to " C   ALA A 158 " =    1.343
peak=   -3.966 closest distance to " O   HOH Z 266 " =    4.401
peak=   -3.958 closest distance to " O   HOH Z  92 " =    1.698
peak=   -3.943 closest distance to " C   ASN A 285 " =    2.433
peak=   -3.904 closest distance to " O   HOH Z 205 " =    0.893
peak=   -3.877 closest distance to " O   HOH Z  97 " =    1.495
peak=   -3.839 closest distance to " O   ALA A 161 " =    1.730
peak=   -3.834 closest distance to " O   HOH Z 407 " =    3.378
peak=   -3.804 closest distance to " O   HOH Z 137 " =    1.351
peak=   -3.792 closest distance to " CD  ARG A 156 " =    1.917
peak=   -3.786 closest distance to " O   HOH Z  52 " =    1.472
peak=   -3.786 closest distance to " ND2 ASN A  45 " =    0.926
peak=   -3.776 closest distance to " O   HOH Z  20 " =    2.235
peak=   -3.765 closest distance to " CB  ASP A  27 " =    2.395
peak=   -3.761 closest distance to " N   GLN A  58 " =    1.607
peak=   -3.749 closest distance to " CE  MET A  93 " =    1.354
peak=   -3.747 closest distance to " CB  ALA A  43 " =    2.304
peak=   -3.740 closest distance to " CB  CYS A 201 " =    2.332
peak=   -3.693 closest distance to " CG  LYS A 193 " =    2.357
peak=   -3.684 closest distance to " O   HOH Z 222 " =    0.808
peak=   -3.673 closest distance to " O   HOH Z 124 " =    1.035
peak=   -3.659 closest distance to " CD  GLN A 223 " =    2.393
peak=   -3.650 closest distance to " O   HOH Z 368 " =    2.471
peak=   -3.642 closest distance to " CB  ALA A 227 " =    2.264
peak=   -3.640 closest distance to " O   GLY A 211 " =    1.403
peak=   -3.639 closest distance to " N   HIS A 115 " =    2.088
peak=   -3.639 closest distance to " OG  SER A  97 " =    2.154
peak=   -3.637 closest distance to " O   TRP A  70 " =    1.395
peak=   -3.635 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.633 closest distance to " OG BSER A 134 " =    1.255
peak=   -3.626 closest distance to " OD1 ASP A 191 " =    1.850
peak=   -3.624 closest distance to " O   HOH Z 231 " =    1.266
peak=   -3.621 closest distance to " CD2 LEU A 237 " =    2.308
peak=   -3.619 closest distance to " CD  ARG A 195 " =    5.016
peak=   -3.615 closest distance to " CZ  PHE A  59 " =    1.637
peak=   -3.586 closest distance to " NH1 ARG A  56 " =    2.401
peak=   -3.586 closest distance to " O   HOH Z  71 " =    0.821
peak=   -3.585 closest distance to " O   HOH Z 438 " =    0.971
peak=   -3.577 closest distance to " CA  GLY A 133 " =    1.921
peak=   -3.574 closest distance to " O   HOH Z 274 " =    2.930
peak=   -3.567 closest distance to " OG  SER A 245 " =    1.091
peak=   -3.564 closest distance to " O   HOH Z 351 " =    1.476
peak=   -3.548 closest distance to " O   HOH Z 298 " =    1.264
peak=   -3.546 closest distance to " CG  ASP A 231 " =    0.788
peak=   -3.535 closest distance to " O   HOH Z 350 " =    2.459
peak=   -3.526 closest distance to " O   SER A 135 " =    1.484
peak=   -3.518 closest distance to " O   HOH Z  13 " =    1.277
peak=   -3.516 closest distance to " CB  CYS A 254 " =    2.132
peak=   -3.500 closest distance to " O   HOH Z 185 " =    2.331
peak=   -3.500 closest distance to " O   HOH Z  97 " =    2.360
peak=   -3.495 closest distance to " O   HOH Z 148 " =    2.466
peak=   -3.494 closest distance to " N   GLN A  58 " =    1.520
peak=   -3.490 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.485 closest distance to " O   HOH Z  43 " =    1.552
peak=   -3.482 closest distance to " OG1 THR A   4 " =    1.912
peak=   -3.477 closest distance to " CB  GLN A  55 " =    1.215
peak=   -3.476 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.464 closest distance to " CD2 LEU A 237 " =    2.713
peak=   -3.463 closest distance to " O   HOH Z 207 " =    1.808
peak=   -3.456 closest distance to " CE2 TYR A  30 " =    2.935
peak=   -3.452 closest distance to " N   ALA A   1 " =    3.309
peak=   -3.449 closest distance to " O   HOH Z 275 " =    1.553
peak=   -3.446 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.443 closest distance to " CB  TRP A  85 " =    2.445
peak=   -3.428 closest distance to " O   HOH Z 250 " =    1.478
peak=   -3.428 closest distance to " O   HOH Z 389 " =    1.746
peak=   -3.427 closest distance to " O   ASP A  50 " =    1.407
peak=   -3.403 closest distance to " CD1 LEU A 167 " =    2.108
peak=   -3.397 closest distance to " O   VAL A 197 " =    1.441
peak=   -3.388 closest distance to " O   ALA A   1 " =    1.165
peak=   -3.388 closest distance to " O   HOH Z  60 " =    1.781
peak=   -3.388 closest distance to " O   HOH Z 134 " =    2.017
peak=   -3.387 closest distance to " CB  ALA A 291 " =    2.181
peak=   -3.384 closest distance to " CB  ALA A   7 " =    2.003
peak=   -3.378 closest distance to " CA  GLY A 241 " =    2.195
peak=   -3.374 closest distance to " OG  SER A  87 " =    1.304
peak=   -3.363 closest distance to " OH  TYR A 214 " =    1.161
peak=   -3.360 closest distance to " O   HOH Z 103 " =    0.704
peak=   -3.354 closest distance to " O   HOH Z 435 " =    2.857
peak=   -3.354 closest distance to " O   HOH Z  28 " =    1.931
peak=   -3.349 closest distance to " CB  ASP A 132 " =    2.284
peak=   -3.339 closest distance to " O   GLY A  98 " =    2.103
peak=   -3.335 closest distance to " OD1 ASN A 301 " =    1.930
peak=   -3.331 closest distance to " O   LEU A 143 " =    1.486
peak=   -3.320 closest distance to " N   THR A 157 " =    1.576
peak=   -3.318 closest distance to " N   ALA A   9 " =    1.391
peak=   -3.309 closest distance to " O   HOH Z  37 " =    2.444
peak=   -3.306 closest distance to " NH2AARG A 275 " =    5.517
peak=   -3.295 closest distance to " O   HOH Z 298 " =    2.724
peak=   -3.292 closest distance to " O   ASN A 301 " =    1.451
peak=   -3.292 closest distance to " CD2 LEU A 143 " =    2.535
peak=   -3.288 closest distance to " CE3 TRP A 150 " =    1.945
peak=   -3.287 closest distance to " O   HOH Z 278 " =    1.254
peak=   -3.285 closest distance to " O   HOH Z 417 " =    2.395
peak=   -3.284 closest distance to " O   VAL A 189 " =    2.413
peak=   -3.276 closest distance to " O   HOH Z  98 " =    1.390
peak=   -3.274 closest distance to " OE2 GLU A 152 " =    2.352
peak=   -3.273 closest distance to " O   HOH Z  76 " =    1.204
peak=   -3.273 closest distance to " O   PRO A 163 " =    1.822
peak=   -3.268 closest distance to " CA  SER A 146 " =    2.286
peak=   -3.267 closest distance to " CG  ARG A 269 " =    2.403
peak=   -3.264 closest distance to " CE2 PHE A 218 " =    2.545
peak=   -3.263 closest distance to " OG ASER A 216 " =    1.109
peak=   -3.262 closest distance to " OE1 GLN A  77 " =    1.962
peak=   -3.261 closest distance to " N   GLN A  88 " =    1.723
peak=   -3.260 closest distance to " CG  PRO A 163 " =    2.418
peak=   -3.254 closest distance to " C   LEU A 143 " =    1.531
peak=   -3.253 closest distance to " O   HOH Z 436 " =    1.092
peak=   -3.252 closest distance to " O   HOH Z  90 " =    1.520
peak=   -3.251 closest distance to " N   MET A 188 " =    1.742
peak=   -3.243 closest distance to " O   SER A  62 " =    2.237
peak=   -3.241 closest distance to " N   ARG A  14 " =    1.061
peak=   -3.241 closest distance to " O   GLY A 196 " =    1.185
peak=   -3.238 closest distance to " CG1 ILE A  20 " =    2.432
peak=   -3.229 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.228 closest distance to " O   HOH Z 409 " =    5.772
peak=   -3.224 closest distance to " O   HOH Z 221 " =    1.757
peak=   -3.221 closest distance to " O   HOH Z 310 " =    3.540
peak=   -3.215 closest distance to " CE  LYS A  76 " =    2.750
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    1.638
peak=   -3.214 closest distance to " OD1 ASP A 200 " =    1.277
peak=   -3.209 closest distance to " O   HOH Z 193 " =    1.785
peak=   -3.209 closest distance to " O   HOH Z  44 " =    2.024
peak=   -3.208 closest distance to " O   HOH Z  88 " =    2.494
peak=   -3.198 closest distance to " CB  SER A 245 " =    2.505
peak=   -3.198 closest distance to " NH2 ARG A  79 " =    1.733
peak=   -3.197 closest distance to " O   HOH Z 140 " =    4.428
peak=   -3.196 closest distance to " N   VAL A  72 " =    1.378
peak=   -3.196 closest distance to " O   HOH Z 263 " =    3.239
peak=   -3.196 closest distance to " O   HOH Z 155 " =    1.288
peak=   -3.196 closest distance to " O   HOH Z 198 " =    1.633
peak=   -3.195 closest distance to " N   GLN A 122 " =    1.510
peak=   -3.194 closest distance to " O   HOH Z 377 " =    0.959
peak=   -3.193 closest distance to " CE2 PHE A 204 " =    2.190
peak=   -3.191 closest distance to " CB  PHE A 283 " =    2.628
peak=   -3.189 closest distance to " O   HOH Z 427 " =    1.377
peak=   -3.189 closest distance to " O   HOH Z 385 " =    2.061
peak=   -3.187 closest distance to " CD2 TYR A 293 " =    1.913
peak=   -3.185 closest distance to " O   GLY A 203 " =    2.426
peak=   -3.179 closest distance to " O   HOH Z 129 " =    4.720
peak=   -3.179 closest distance to " CD1 TRP A 274 " =    1.536
peak=   -3.179 closest distance to " O   HOH Z 318 " =    1.431
peak=   -3.178 closest distance to " N   THR A 264 " =    1.408
peak=   -3.168 closest distance to " O   HOH Z  40 " =    4.287
peak=   -3.166 closest distance to " O   VAL A  67 " =    2.665
peak=   -3.163 closest distance to " N   ALA A  43 " =    2.161
peak=   -3.159 closest distance to " CD  GLN A  88 " =    2.416
peak=   -3.154 closest distance to " OH  TYR A 169 " =    1.016
peak=   -3.152 closest distance to " O   HOH Z  97 " =    1.156
peak=   -3.151 closest distance to " O   ASP A 191 " =    1.529
peak=   -3.150 closest distance to " OD2 ASP A  65 " =    1.812
peak=   -3.150 closest distance to " CZ3 TRP A 123 " =    1.751
peak=   -3.149 closest distance to " CD1 ILE A 239 " =    1.892
peak=   -3.144 closest distance to " O   HOH Z 287 " =    1.257
peak=   -3.139 closest distance to " O   HOH Z 426 " =    2.186
peak=   -3.137 closest distance to " O   HOH Z 139 " =    3.427
peak=   -3.135 closest distance to " O   HOH Z   1 " =    3.715
peak=   -3.134 closest distance to " OD2 ASP A  50 " =    1.515
peak=   -3.131 closest distance to " O   HOH Z  97 " =    4.608
peak=   -3.130 closest distance to " N   ARG A 102 " =    1.327
peak=   -3.129 closest distance to " CB  ASN A  39 " =    1.960
peak=   -3.129 closest distance to " O   HOH Z 109 " =    1.132
peak=   -3.123 closest distance to " O   GLY A  80 " =    2.358
peak=   -3.117 closest distance to " CE  MET A 105 " =    2.243
peak=   -3.107 closest distance to " N   LYS A 166 " =    1.866
peak=   -3.105 closest distance to " CE1 TYR A 169 " =    2.527
peak=   -3.104 closest distance to " O   HOH Z 348 " =    1.841
peak=   -3.104 closest distance to " O   HOH Z 323 " =    1.405
peak=   -3.103 closest distance to " O   VAL A 153 " =    2.526
peak=   -3.099 closest distance to " CG1 VAL A 112 " =    2.970
peak=   -3.096 closest distance to " CG2 THR A 294 " =    2.726
peak=   -3.090 closest distance to " O   HOH Z 234 " =    4.240
peak=   -3.089 closest distance to " O   HOH Z 364 " =    2.599
peak=   -3.087 closest distance to " CG  TRP A 266 " =    1.389
peak=   -3.082 closest distance to " O   ILE A  49 " =    1.610
peak=   -3.082 closest distance to " O   HOH Z 247 " =    1.535
peak=   -3.077 closest distance to " NH2 ARG A  66 " =    4.694
peak=   -3.074 closest distance to " CD  ARG A  36 " =    1.860
peak=   -3.065 closest distance to " O   SER A 146 " =    0.906
peak=   -3.063 closest distance to " CA  TYR A 247 " =    1.392
peak=   -3.058 closest distance to " CG1 VAL A 197 " =    2.195

================= 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    :  0.4819 0.4868   6.284655e+00   6.283132e+00
   1_bss:  0.4746 0.4802   6.283758e+00   6.275059e+00
   1_xyz:  0.3818 0.4138   6.147808e+00   6.200333e+00
   1_adp:  0.3473 0.4213   6.102924e+00   6.208963e+00
   1_occ:  0.3468 0.4210   6.101725e+00   6.207778e+00
   2_bss:  0.3466 0.4203   6.101977e+00   6.205696e+00
   2_xyz:  0.2724 0.3487   5.915474e+00   6.075952e+00
   2_adp:  0.2530 0.3277   5.862955e+00   6.035119e+00
   2_occ:  0.2527 0.3273   5.862127e+00   6.034499e+00
   3_bss:  0.2524 0.3263   5.860138e+00   6.032451e+00
   3_xyz:  0.1840 0.2400   5.579698e+00   5.788048e+00
   3_adp:  0.1617 0.2181   5.470875e+00   5.694745e+00
   3_occ:  0.1616 0.2176   5.469204e+00   5.692657e+00
   4_bss:  0.1612 0.2166   5.466871e+00   5.690187e+00
   4_xyz:  0.1388 0.1862   5.323417e+00   5.549179e+00
   4_adp:  0.1323 0.1807   5.288080e+00   5.519551e+00
   4_occ:  0.1323 0.1805   5.287541e+00   5.519075e+00
   5_bss:  0.1325 0.1807   5.287200e+00   5.519765e+00
   5_xyz:  0.1209 0.1700   5.214966e+00   5.460303e+00
   5_adp:  0.1189 0.1655   5.194822e+00   5.436419e+00
   5_occ:  0.1187 0.1652   5.193343e+00   5.435052e+00
   5_bss:  0.1187 0.1652   5.193357e+00   5.435097e+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:  0.310  13.692   0.188  -0.021   1.577  -0.000   0.000   0.000
   1_xyz:  0.310  13.692   0.188  -0.021   1.577  -0.000   0.000   0.000
   1_adp:  0.310  13.692   0.188  -0.021   1.577  -0.000   0.000   0.000
   1_occ:  0.310  13.692   0.188  -0.021   1.577  -0.000   0.000   0.000
   2_bss:  0.343  50.000  -0.088  -0.633   0.796  -0.000   0.000   0.000
   2_xyz:  0.343  50.000  -0.088  -0.633   0.796  -0.000   0.000   0.000
   2_adp:  0.343  50.000  -0.088  -0.633   0.796  -0.000   0.000   0.000
   2_occ:  0.343  50.000  -0.088  -0.633   0.796  -0.000   0.000   0.000
   3_bss:  0.343  50.000  -0.784  -1.424  -0.229  -0.000  -0.000  -0.000
   3_xyz:  0.343  50.000  -0.784  -1.424  -0.229  -0.000  -0.000  -0.000
   3_adp:  0.343  50.000  -0.784  -1.424  -0.229  -0.000  -0.000  -0.000
   3_occ:  0.343  50.000  -0.784  -1.424  -0.229  -0.000  -0.000  -0.000
   4_bss:  0.330  48.990  -1.751  -2.534  -1.623  -0.000  -0.000  -0.000
   4_xyz:  0.330  48.990  -1.751  -2.534  -1.623  -0.000  -0.000  -0.000
   4_adp:  0.330  48.990  -1.751  -2.534  -1.623  -0.000  -0.000  -0.000
   4_occ:  0.330  48.990  -1.751  -2.534  -1.623  -0.000  -0.000  -0.000
   5_bss:  0.322  50.041  -1.966  -2.747  -1.901  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.041  -1.966  -2.747  -1.901  -0.000  -0.000  -0.000
   5_adp:  0.322  50.041  -1.966  -2.747  -1.901  -0.000  -0.000  -0.000
   5_occ:  0.322  50.041  -1.966  -2.747  -1.901  -0.000  -0.000  -0.000
   5_bss:  0.322  50.010  -1.942  -2.659  -1.898  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.734 0.3700  0.5067    75472.261
   1_bss:  60.985 0.3780  0.5302    72459.581
   1_xyz:  47.198 0.5544  0.7641    50793.351
   1_adp:  48.325 0.5397  0.7555    51997.889
   1_occ:  48.267 0.5403  0.7551    51806.132
   2_bss:  47.954 0.5442  0.7495    51483.855
   2_xyz:  37.548 0.6700  0.9080    32932.388
   2_adp:  34.652 0.7042  0.9280    29064.430
   2_occ:  34.624 0.7045  0.9273    29006.714
   3_bss:  34.440 0.7063  0.9015    28677.592
   3_xyz:  24.284 0.8186  0.9993    15436.003
   3_adp:  21.358 0.8489  1.0098    12668.543
   3_occ:  21.298 0.8494  1.0098    12590.364
   4_bss:  21.205 0.8501  0.9687    12477.162
   4_xyz:  17.607 0.8837  0.9872     8922.999
   4_adp:  16.801 0.8915  0.9857     8413.311
   4_occ:  16.780 0.8917  0.9857     8398.390
   5_bss:  16.789 0.8916  0.9772     8415.538
   5_xyz:  15.576 0.9016  0.9819     7307.148
   5_adp:  14.979 0.9069  0.9802     6993.665
   5_occ:  14.935 0.9072  0.9803     6960.814
   5_bss:  14.936 0.9072  0.9805     6961.091
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8321e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8321e-01
   1_xyz:   1.402  0.011  0.091 15.826  0.005  4.107   1.1202e-01
   1_adp:   1.402  0.011  0.091 15.826  0.005  4.107   1.1202e-01
   1_occ:   1.402  0.011  0.091 15.826  0.005  4.107   1.1202e-01
   2_bss:   1.402  0.011  0.091 15.826  0.005  4.107   1.1202e-01
   2_xyz:   1.279  0.009  0.078 15.037  0.005  4.106   8.9557e-02
   2_adp:   1.279  0.009  0.078 15.037  0.005  4.106   8.9557e-02
   2_occ:   1.279  0.009  0.078 15.037  0.005  4.106   8.9557e-02
   3_bss:   1.279  0.009  0.078 15.037  0.005  4.106   8.9557e-02
   3_xyz:   1.134  0.008  0.077 14.743  0.004  4.108   7.1608e-02
   3_adp:   1.134  0.008  0.077 14.743  0.004  4.108   7.1608e-02
   3_occ:   1.134  0.008  0.077 14.743  0.004  4.108   7.1608e-02
   4_bss:   1.134  0.008  0.077 14.743  0.004  4.108   7.1608e-02
   4_xyz:   0.950  0.005  0.067 14.315  0.003  4.113   5.3461e-02
   4_adp:   0.950  0.005  0.067 14.315  0.003  4.113   5.3461e-02
   4_occ:   0.950  0.005  0.067 14.315  0.003  4.113   5.3461e-02
   5_bss:   0.950  0.005  0.067 14.315  0.003  4.113   5.3461e-02
   5_xyz:   0.994  0.006  0.070 14.606  0.004  4.109   5.7766e-02
   5_adp:   0.994  0.006  0.070 14.606  0.004  4.109   5.7766e-02
   5_occ:   0.994  0.006  0.070 14.606  0.004  4.109   5.7766e-02
   5_bss:   0.994  0.006  0.070 14.606  0.004  4.109   5.7766e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.482   2.3953e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.482   2.3953e-01
   1_xyz:  10.080  0.063  0.390 85.548  0.034  2.052   9.2598e-02
   1_adp:  10.080  0.063  0.390 85.548  0.034  2.052   9.2598e-02
   1_occ:  10.080  0.063  0.390 85.548  0.034  2.052   9.2598e-02
   2_bss:  10.080  0.063  0.390 85.548  0.034  2.052   9.2598e-02
   2_xyz:   8.123  0.054  0.262 85.923  0.036  2.269   1.4288e-01
   2_adp:   8.123  0.054  0.262 85.923  0.036  2.269   1.4288e-01
   2_occ:   8.123  0.054  0.262 85.923  0.036  2.269   1.4288e-01
   3_bss:   8.123  0.054  0.262 85.923  0.036  2.269   1.4288e-01
   3_xyz:   8.222  0.060  0.395 81.292  0.024  2.276   6.6401e-02
   3_adp:   8.222  0.060  0.395 81.292  0.024  2.276   6.6401e-02
   3_occ:   8.222  0.060  0.395 81.292  0.024  2.276   6.6401e-02
   4_bss:   8.222  0.060  0.395 81.292  0.024  2.276   6.6401e-02
   4_xyz:   8.052  0.038  0.234 83.308  0.025  2.325   4.0624e-02
   4_adp:   8.052  0.038  0.234 83.308  0.025  2.325   4.0624e-02
   4_occ:   8.052  0.038  0.234 83.308  0.025  2.325   4.0624e-02
   5_bss:   8.052  0.038  0.234 83.308  0.025  2.325   4.0624e-02
   5_xyz:   7.879  0.049  0.217 84.757  0.028  2.303   3.9668e-02
   5_adp:   7.879  0.049  0.217 84.757  0.028  2.303   3.9668e-02
   5_occ:   7.879  0.049  0.217 84.757  0.028  2.303   3.9668e-02
   5_bss:   7.879  0.049  0.217 84.757  0.028  2.303   3.9668e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  95.91   0.00  19.47  95.91   0.00  16.37  95.68   0.00  36.35
   1_occ:  95.91   0.00  19.47  95.91   0.00  16.37  95.68   0.00  36.35
   2_bss:  95.91   0.00  19.47  95.91   0.00  16.37  95.68   0.00  36.35
   2_xyz:  95.91   0.00  19.47  95.91   0.00  16.37  95.68   0.00  36.35
   2_adp:  94.70   0.00  18.51  90.14   0.00  14.68  94.70   1.80  39.32
   2_occ:  94.70   0.00  18.51  90.14   0.00  14.68  94.70   1.80  39.32
   3_bss:  94.70   0.00  18.51  90.14   0.00  14.68  94.70   1.80  39.32
   3_xyz:  94.70   0.00  18.51  90.14   0.00  14.68  94.70   1.80  39.32
   3_adp:  89.09   0.00  17.96  88.52   0.00  13.45  89.09   6.21  42.47
   3_occ:  89.09   0.00  17.96  88.52   0.00  13.45  89.09   6.21  42.47
   4_bss:  89.09   0.00  17.96  88.52   0.00  13.45  89.09   6.21  42.47
   4_xyz:  89.09   0.00  17.96  88.52   0.00  13.45  89.09   6.21  42.47
   4_adp:  98.15   0.00  18.23  98.15   0.00  13.27  93.00   6.60  45.23
   4_occ:  98.15   0.00  18.23  98.15   0.00  13.27  93.00   6.60  45.23
   5_bss:  98.15   0.00  18.23  98.15   0.00  13.27  93.00   6.60  45.23
   5_xyz:  98.15   0.00  18.23  98.15   0.00  13.27  93.00   6.60  45.23
   5_adp: 101.45   0.89  17.70 101.45   0.89  13.05  98.62   6.29  43.03
   5_occ: 101.45   0.89  17.70 101.45   0.89  13.05  98.62   6.29  43.03
   5_bss: 101.42   0.86  17.67 101.42   0.86  13.02  98.59   6.26  43.00
------------------------------------------------------------------------
 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:    1.816    0.014    0.307
   1_adp:    1.816    0.014    0.307
   1_occ:    1.816    0.014    0.307
   2_bss:    1.816    0.014    0.307
   2_xyz:    1.356    0.054    0.526
   2_adp:    1.356    0.054    0.526
   2_occ:    1.356    0.054    0.526
   3_bss:    1.356    0.054    0.526
   3_xyz:    1.393    0.049    0.713
   3_adp:    1.393    0.049    0.713
   3_occ:    1.393    0.049    0.713
   4_bss:    1.393    0.049    0.713
   4_xyz:    1.437    0.074    0.746
   4_adp:    1.437    0.074    0.746
   4_occ:    1.437    0.074    0.746
   5_bss:    1.437    0.074    0.746
   5_xyz:    1.504    0.095    0.780
   5_adp:    1.504    0.095    0.780
   5_occ:    1.504    0.095    0.780
   5_bss:    1.504    0.095    0.780
------------------------------------------------------------------------

CPU time actual refinement: 357.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/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/noshake/run_1111/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1111/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.25 
  Macro-tasks:
    bulk solvent and scale       = 42.82  
    individual site refinement   = 145.30 
    weights calculation          = 30.59  
    collect and process          = 6.56   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 225.39 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 117.22 
    alpha_beta                      = 8.32   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 123.64 
    fmodel                         = 7.62   
    r_factors                      = 0.33   
    phase_errors                   = 10.47  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 271.40 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.126 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    630 calls, 116.89 s
gradients_fft:          575 calls, 111.04 s

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

# Date 2008-01-16 Time 06:27:48 PST -0800 (1200493668.61 s)
Start R-work = 0.4819, R-free = 0.4868 (no bulk solvent and anisotropic scale)
Final R-work = 0.1430, R-free = 0.1869 (no bulk solvent and anisotropic scale)

Start R-work = 0.4746, R-free = 0.4802
Final R-work = 0.1187, R-free = 0.1652