# Date 2008-01-16 Time 04:44:01 PST -0800 (1200487441.64 s)
#phil __OFF__

Command line arguments: "../440.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4224
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 440

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 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: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95142
Completeness in resolution range: 0.940603
Completeness with d_max=infinity: 0.937721

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7930
                             d_min =   1.9514

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: (69.5475, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95142
Completeness in resolution range: 0.940603
Completeness with d_max=infinity: 0.937721

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7934 -  4.1756 [2194/2222]  1975   219  10.0%
  bin  2:  4.1756 -  3.3267 [2089/2112]  1880   209  10.0%
  bin  3:  3.3267 -  2.9098 [2075/2100]  1865   210  10.1%
  bin  4:  2.9098 -  2.6454 [2052/2068]  1854   198   9.6%
  bin  5:  2.6454 -  2.4568 [2042/2086]  1831   211  10.3%
  bin  6:  2.4568 -  2.3125 [2032/2060]  1833   199   9.8%
  bin  7:  2.3125 -  2.1971 [2008/2044]  1805   203  10.1%
  bin  8:  2.1971 -  2.1017 [2004/2046]  1806   198   9.9%
  bin  9:  2.1017 -  2.0210 [2016/2062]  1815   201  10.0%
  bin 10:  2.0210 -  1.9514 [1077/2026]   966   111  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 26
        2.11 -     2.81: 803
        2.81 -     3.50: 4525
        3.50 -     4.20: 9435
        4.20 -     4.90: 13920
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.409 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.546 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.575 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.680 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.699 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28704 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_440/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/model_refine_001.geo

CPU time processing inputs: 8.22


============================ 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 = 69.5475 47.3993 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 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4229   r_free= 0.4169   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.225335                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1421  158 0.3379 0.3485      6.4886      6.5029|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.3532 0.3342      6.6961      6.6577|
|  3:  3.7159 -  3.2519 0.99   1339  153 0.3753 0.3765      6.5658       6.682|
|  4:  3.2519 -  2.9572 0.99   1330  144 0.3981 0.3952       6.426      6.4262|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.4325 0.3899      6.2978      6.2409|
|  6:  2.7467 -  2.5856 0.99   1307  146 0.4480 0.4384      6.2082      6.1215|
|  7:  2.5856 -  2.4568 0.98   1311  148 0.4552 0.3909      6.1997      6.1328|
|  8:  2.4568 -  2.3502 0.99   1292  140 0.4662 0.5006      6.1293      6.1732|
|  9:  2.3502 -  2.2601 0.99   1316  150 0.4800 0.4788      6.0931      6.1045|
| 10:  2.2601 -  2.1824 0.98   1303  137 0.4823 0.5092      6.0768      6.1299|
| 11:  2.1824 -  2.1143 0.97   1273  143 0.4965 0.5108      6.0174      6.0244|
| 12:  2.1143 -  2.0540 0.99   1288  148 0.4783 0.5153      5.9347      5.9806|
| 13:  2.0540 -  2.0001 0.94   1253  138 0.5015 0.4917       5.854       5.843|
| 14:  2.0001 -  1.9514 0.38    500   56 0.5393 0.4710      5.8575      5.7174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6573  1421   158  0.72  32.52   0.85     0.74      62167.77|
|  2:  4.6573 -  3.7159  1365   150  0.75  30.91   0.94     0.85      82081.99|
|  3:  3.7159 -  3.2519  1339   153  0.68  37.10   0.95     0.87      85004.51|
|  4:  3.2519 -  2.9572  1330   144  0.62  42.34   0.96     0.84      74492.79|
|  5:  2.9572 -  2.7467  1332   148  0.58  45.83   0.92     0.80      58930.14|
|  6:  2.7467 -  2.5856  1307   146  0.56  47.45   0.95     0.77      50105.26|
|  7:  2.5856 -  2.4568  1311   148  0.55  47.92   0.95     0.74      47202.42|
|  8:  2.4568 -  2.3502  1292   140  0.48  53.36   0.94     0.68      47628.98|
|  9:  2.3502 -  2.2601  1316   150  0.42  58.00   0.96     0.61      47591.74|
| 10:  2.2601 -  2.1824  1303   137  0.38  61.16   1.00     0.55      47275.14|
| 11:  2.1824 -  2.1143  1273   143  0.33  65.01   0.97     0.51      46085.75|
| 12:  2.1143 -  2.0540  1288   148  0.34  64.92   0.99     0.53      43051.69|
| 13:  2.0540 -  2.0001  1253   138  0.35  63.95   0.97     0.56      35185.97|
| 14:  2.0001 -  1.9514   500    56  0.44  56.98   0.92     0.64      25388.94|
|alpha:            min =        0.51 max =            0.87 mean =         0.70|
|beta:             min =    25388.94 max =        85004.51 mean =     55349.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.93|
|phase err.(test): min =        0.00 max =           89.61 mean =        49.70|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.114549             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.063   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.854460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.795   (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 |  1.409 -  1.758:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.758 -  2.107:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.107 -  2.456:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.456 -  2.805:      773 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.805 -  3.154:     2111 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.154 -  3.503:     2414 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.503 -  3.853:     4604 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.853 -  4.202:     4831 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.202 -  4.551:     6296 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7624 |
|-----------------------------------------------------------------------------|
|-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 |        0.193 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.409 |       0.659 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    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 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4229   r_free= 0.4169   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.225335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4120   r_free= 0.4045   ksol= 0.32   Bsol= 22.89   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.16,2.85,-0.00,0.00,0.00); trace/3= 0.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.215391                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.502931              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.883591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.722   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4120      final r-factor (work) = 0.2627          |
| start r-factor (free) = 0.4045      final r-factor (free) = 0.2896          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6158 = 8.50 * 0.50 * 6.2150 + 1.00 * 0.1931                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7297 = 8.50 * 0.50 * 6.0218 + 1.00 * 0.1282                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2627      final r-factor (work) = 0.2382          |
| start r-factor (free) = 0.2896      final r-factor (free) = 0.2999          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3284 = 0.88 * 1.00 * 6.0218 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1709 = 0.88 * 1.00 * 5.7847 + 1.00 * 0.0596                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.06   18.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.06   18.48    None  None   None       |
|    Sol.    : 438    0      3.70    89.80   41.13    None  None   None       |
|    Mac.    : 2385   0      0.00    94.06   14.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.407:  863   |   5:    47.032 -  56.439:   92        |
|      1:     9.407 -  18.813: 1053   |   6:    56.439 -  65.845:   61        |
|      2:    18.813 -  28.219:  365   |   7:    65.845 -  75.252:   34        |
|      3:    28.219 -  37.626:  190   |   8:    75.252 -  84.658:   10        |
|      4:    37.626 -  47.032:  149   |   9:    84.658 -  94.064:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2382 r_free = 0.2999             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2378 r_free = 0.3003             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.3003   ksol= 0.32   Bsol= 22.89   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.16,2.85,-0.00,0.00,0.00); trace/3= 0.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.796642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2341   r_free= 0.2966   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.39,-0.28,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.789185                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.525517              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.531   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.867610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.407   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2341      final r-factor (work) = 0.1728          |
| start r-factor (free) = 0.2966      final r-factor (free) = 0.2270          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3288 = 3.53 * 0.50 * 5.7869 + 1.00 * 0.1280                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0561 = 3.53 * 0.50 * 5.6708 + 1.00 * 0.0599                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1728      final r-factor (work) = 0.1564          |
| start r-factor (free) = 0.2270      final r-factor (free) = 0.2112          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9456 = 0.87 * 1.00 * 5.6708 + 1.00 * 0.0255                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7785 = 0.87 * 1.00 * 5.4784 + 1.00 * 0.0254                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.32   18.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.32   18.25    None  None   None       |
|    Sol.    : 438    0      6.53    88.32   43.24    None  None   None       |
|    Mac.    : 2385   0      0.00    98.32   13.67    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 -   9.832:  984   |   5:    49.158 -  58.990:  112        |
|      1:     9.832 -  19.663: 1109   |   6:    58.990 -  68.822:   64        |
|      2:    19.663 -  29.495:  253   |   7:    68.822 -  78.653:   22        |
|      3:    29.495 -  39.327:  139   |   8:    78.653 -  88.485:   15        |
|      4:    39.327 -  49.158:  120   |   9:    88.485 -  98.317:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1564 r_free = 0.2112             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1561 r_free = 0.2111             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1561   r_free= 0.2111   ksol= 0.33   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.39,-0.28,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.437691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1562   r_free= 0.2093   ksol= 0.32   Bsol= 44.01   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.54,-1.25,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.432839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.426461              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181799              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.927   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1562      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.2093      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7055 = 2.43 * 0.50 * 5.4776 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5513 = 2.43 * 0.50 * 5.3551 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9862 = 0.18 * 1.00 * 5.3551 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9639 = 0.18 * 1.00 * 5.2576 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    95.88   17.39    None  None   None       |
|    all(noH): 2823   0      1.53    95.88   17.39    None  None   None       |
|    Sol.    : 438    0      5.83    83.55   40.41    None  None   None       |
|    Mac.    : 2385   0      1.53    95.88   13.16    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:     1.526 -  10.962: 1219   |   5:    48.703 -  58.139:   89        |
|      1:    10.962 -  20.397:  973   |   6:    58.139 -  67.574:   38        |
|      2:    20.397 -  29.832:  205   |   7:    67.574 -  77.010:   24        |
|      3:    29.832 -  39.268:  124   |   8:    77.010 -  86.445:    8        |
|      4:    39.268 -  48.703:  140   |   9:    86.445 -  95.880:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1254 r_free = 0.1687             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1685             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1685   ksol= 0.32   Bsol= 44.01   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.54,-1.25,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.226702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1686   ksol= 0.32   Bsol= 43.06   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.84,-1.78,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.229069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.329437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.352  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.492952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.424  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1256      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1805 = 2.33 * 0.50 * 5.2598 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1048 = 2.33 * 0.50 * 5.1884 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5657 = 0.49 * 1.00 * 5.1884 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5447 = 0.49 * 1.00 * 5.1445 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    96.21   17.30    None  None   None       |
|    all(noH): 2823   0      1.71    96.21   17.30    None  None   None       |
|    Sol.    : 438    0      5.04    87.48   40.60    None  None   None       |
|    Mac.    : 2385   0      1.71    96.21   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:     1.707 -  11.158: 1285   |   5:    48.959 -  58.409:   92        |
|      1:    11.158 -  20.608:  923   |   6:    58.409 -  67.860:   52        |
|      2:    20.608 -  30.058:  197   |   7:    67.860 -  77.310:   15        |
|      3:    30.058 -  39.509:  120   |   8:    77.310 -  86.760:    8        |
|      4:    39.509 -  48.959:  126   |   9:    86.760 -  96.211:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1592             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1591             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1591   ksol= 0.32   Bsol= 43.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.84,-1.78,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146232                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1591   ksol= 0.32   Bsol= 43.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.83,-1.84,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146152                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.351085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.948  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.543664              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.368  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1090 = 2.35 * 0.50 * 5.1442 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0996 = 2.35 * 0.50 * 5.1376 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8018 = 0.54 * 1.00 * 5.1376 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7979 = 0.54 * 1.00 * 5.1299 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    99.65   17.12    None  None   None       |
|    all(noH): 2823   0      1.14    99.65   17.12    None  None   None       |
|    Sol.    : 438    0      5.36    87.93   40.18    None  None   None       |
|    Mac.    : 2385   0      1.14    99.65   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.144 -  10.994: 1262   |   5:    50.396 -  60.246:   94        |
|      1:    10.994 -  20.845:  960   |   6:    60.246 -  70.096:   36        |
|      2:    20.845 -  30.695:  199   |   7:    70.096 -  79.947:   13        |
|      3:    30.695 -  40.545:  125   |   8:    79.947 -  89.797:    7        |
|      4:    40.545 -  50.396:  123   |   9:    89.797 -  99.647:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1578             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1577             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1577   ksol= 0.32   Bsol= 43.06   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.83,-1.84,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131332                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1421  158 0.0960 0.1253      5.3581      5.5181|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.0813 0.1087      5.3961      5.6186|
|  3:  3.7159 -  3.2519 0.99   1339  153 0.1011 0.1540      5.4341      5.8246|
|  4:  3.2519 -  2.9572 0.99   1330  144 0.1217 0.1507      5.4462      5.6058|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1239 0.1756      5.2865      5.4917|
|  6:  2.7467 -  2.5856 0.99   1307  146 0.1198 0.1944      5.1943      5.4219|
|  7:  2.5856 -  2.4568 0.98   1311  148 0.1189 0.1635      5.1241      5.3716|
|  8:  2.4568 -  2.3502 0.99   1292  140 0.1141 0.1658      5.0632      5.2556|
|  9:  2.3502 -  2.2601 0.99   1316  150 0.1157 0.1883      5.0177      5.3293|
| 10:  2.2601 -  2.1824 0.98   1303  137 0.1104 0.1771      4.9625        5.23|
| 11:  2.1824 -  2.1143 0.97   1273  143 0.1088 0.1807      4.9068      5.2374|
| 12:  2.1143 -  2.0540 0.99   1288  148 0.1063 0.1621      4.8403      5.0667|
| 13:  2.0540 -  2.0001 0.94   1253  138 0.1116 0.1865      4.7747      5.0677|
| 14:  2.0001 -  1.9514 0.38    500   56 0.1083 0.1689      4.6867      4.9135|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6573  1421   158  0.94   8.65   0.98     0.96       6788.45|
|  2:  4.6573 -  3.7159  1365   150  0.95   7.69   1.02     1.01       8457.76|
|  3:  3.7159 -  3.2519  1339   153  0.94  10.92   1.03     1.03       9806.15|
|  4:  3.2519 -  2.9572  1330   144  0.92  14.16   1.01     1.00      10410.26|
|  5:  2.9572 -  2.7467  1332   148  0.90  15.55   1.00     0.97       7835.65|
|  6:  2.7467 -  2.5856  1307   146  0.90  15.68   0.98     0.96       6868.67|
|  7:  2.5856 -  2.4568  1311   148  0.91  14.84   0.99     0.96       5722.52|
|  8:  2.4568 -  2.3502  1292   140  0.91  15.60   1.00     0.97       5503.32|
|  9:  2.3502 -  2.2601  1316   150  0.90  15.80   1.00     0.97       4959.47|
| 10:  2.2601 -  2.1824  1303   137  0.91  15.35   1.00     0.96       4475.33|
| 11:  2.1824 -  2.1143  1273   143  0.90  16.24   1.00     0.97       4227.14|
| 12:  2.1143 -  2.0540  1288   148  0.92  14.59   1.00     0.99       3710.96|
| 13:  2.0540 -  2.0001  1253   138  0.90  16.27   1.00     1.00       3323.03|
| 14:  2.0001 -  1.9514   500    56  0.90  15.77   0.99     0.95       2699.27|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2699.27 max =        10410.26 mean =      6252.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.79 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1578   ksol= 0.32   Bsol= 43.02   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.66,-1.68,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131416                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1578   ksol= 0.32   Bsol= 43.02   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.66,-1.68,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131416                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1421  158 0.0961 0.1254      5.3589      5.5192|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.0813 0.1087      5.3965      5.6183|
|  3:  3.7159 -  3.2519 0.99   1339  153 0.1011 0.1540      5.4341      5.8247|
|  4:  3.2519 -  2.9572 0.99   1330  144 0.1217 0.1507      5.4461      5.6059|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1239 0.1756      5.2864      5.4916|
|  6:  2.7467 -  2.5856 0.99   1307  146 0.1198 0.1945      5.1942      5.4219|
|  7:  2.5856 -  2.4568 0.98   1311  148 0.1189 0.1636      5.1243      5.3718|
|  8:  2.4568 -  2.3502 0.99   1292  140 0.1141 0.1658      5.0632      5.2555|
|  9:  2.3502 -  2.2601 0.99   1316  150 0.1157 0.1883      5.0178      5.3293|
| 10:  2.2601 -  2.1824 0.98   1303  137 0.1104 0.1771      4.9626      5.2299|
| 11:  2.1824 -  2.1143 0.97   1273  143 0.1088 0.1807      4.9068      5.2373|
| 12:  2.1143 -  2.0540 0.99   1288  148 0.1063 0.1621      4.8401      5.0668|
| 13:  2.0540 -  2.0001 0.94   1253  138 0.1116 0.1864      4.7745      5.0671|
| 14:  2.0001 -  1.9514 0.38    500   56 0.1083 0.1689      4.6867      4.9136|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6573  1421   158  0.94   8.67   0.98     0.97       6801.18|
|  2:  4.6573 -  3.7159  1365   150  0.95   7.69   1.02     1.01       8465.19|
|  3:  3.7159 -  3.2519  1339   153  0.94  10.92   1.04     1.03       9806.99|
|  4:  3.2519 -  2.9572  1330   144  0.92  14.16   1.02     1.00      10409.11|
|  5:  2.9572 -  2.7467  1332   148  0.90  15.55   1.00     0.98       7833.49|
|  6:  2.7467 -  2.5856  1307   146  0.90  15.68   0.99     0.96       6866.86|
|  7:  2.5856 -  2.4568  1311   148  0.91  14.84   1.00     0.97       5722.38|
|  8:  2.4568 -  2.3502  1292   140  0.91  15.61   1.01     0.98       5503.29|
|  9:  2.3502 -  2.2601  1316   150  0.90  15.80   1.01     0.98       4960.34|
| 10:  2.2601 -  2.1824  1303   137  0.91  15.36   1.00     0.97       4475.02|
| 11:  2.1824 -  2.1143  1273   143  0.90  16.25   1.01     0.98       4226.76|
| 12:  2.1143 -  2.0540  1288   148  0.92  14.59   1.01     1.00       3709.69|
| 13:  2.0540 -  2.0001  1253   138  0.90  16.27   1.01     1.01       3321.96|
| 14:  2.0001 -  1.9514   500    56  0.90  15.76   0.99     0.95       2698.84|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2698.84 max =        10409.11 mean =      6253.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.79 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.576)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    99.61   17.08    None  None   None       |
|    all(noH): 2823   0      1.10    99.61   17.08    None  None   None       |
|    Sol.    : 438    0      5.32    87.89   40.14    None  None   None       |
|    Mac.    : 2385   0      1.10    99.61   12.85    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:     1.104 -  10.954: 1262   |   5:    50.356 -  60.206:   94        |
|      1:    10.954 -  20.805:  960   |   6:    60.206 -  70.056:   36        |
|      2:    20.805 -  30.655:  199   |   7:    70.056 -  79.907:   13        |
|      3:    30.655 -  40.505:  125   |   8:    79.907 -  89.757:    7        |
|      4:    40.505 -  50.356:  123   |   9:    89.757 -  99.608:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.429 - 5.871
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 305
   mapped sites are within: 0.740 - 5.871

peak=    5.859 closest distance to " NH2 ARG A  56 " =    2.200
peak=    5.487 closest distance to " CG  PRO A  54 " =    1.205
peak=    5.436 closest distance to " O   HOH Z 126 " =    1.878
peak=    5.379 closest distance to " CB  ARG A 275 " =    0.917
peak=    5.358 closest distance to " CB  SER A  63 " =    1.159
peak=    5.228 closest distance to " CB  GLN A 223 " =    1.445
peak=    5.171 closest distance to " CG  PRO A 213 " =    1.212
peak=    5.151 closest distance to " O   HOH Z 142 " =    1.662
peak=    5.079 closest distance to " O   HOH Z 124 " =    1.465
peak=    4.927 closest distance to " O   HOH Z 234 " =    3.709
peak=    4.748 closest distance to " O   HOH Z  78 " =    1.802
peak=    4.683 closest distance to " O   HOH Z 278 " =    1.041
peak=    4.658 closest distance to " O   HOH Z 232 " =    2.339
peak=    4.653 closest distance to " O   HOH Z 272 " =    1.842
peak=    4.617 closest distance to " O   HOH Z 193 " =    1.714
peak=    4.584 closest distance to " CB  GLN A 183 " =    1.331
peak=    4.581 closest distance to " CG  PRO A  90 " =    1.115
peak=    4.576 closest distance to " C   PRO A 198 " =    1.518
peak=    4.570 closest distance to " NE2 GLN A  11 " =    1.040
peak=    4.543 closest distance to " O   HOH Z 132 " =    1.226
peak=    4.501 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.482 closest distance to " O   HOH Z 108 " =    1.361
peak=    4.472 closest distance to " O   HOH Z  97 " =    2.566
peak=    4.466 closest distance to " CB  SER A   3 " =    1.298
peak=    4.458 closest distance to " O   HOH Z  15 " =    2.105
peak=    4.451 closest distance to " O   SER A  87 " =    2.211
peak=    4.440 closest distance to " O   HOH Z 298 " =    1.899
peak=    4.429 closest distance to " O   HOH Z 236 " =    1.951
peak=    4.400 closest distance to " O   HOH Z 389 " =    1.887
peak=    4.390 closest distance to " O   HOH Z  59 " =    2.301
peak=    4.373 closest distance to " O   HOH Z 403 " =    1.752
peak=    4.347 closest distance to " OD2 ASP A 286 " =    2.726
peak=    4.345 closest distance to " O   HOH Z 134 " =    1.500
peak=    4.338 closest distance to " O   HOH Z 203 " =    1.761
peak=    4.326 closest distance to " NZ  LYS A 117 " =    3.123
peak=    4.313 closest distance to " CB  GLU A 128 " =    1.211
peak=    4.312 closest distance to " CB  ASN A 148 " =    1.589
peak=    4.301 closest distance to " CA  ALA A  21 " =    1.159
peak=    4.291 closest distance to " CB  ARG A  79 " =    1.400
peak=    4.287 closest distance to " O   HOH Z 316 " =    2.841
peak=    4.281 closest distance to " O   HOH Z  97 " =    1.849
peak=    4.266 closest distance to " O   HOH Z 207 " =    1.859
peak=    4.266 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.253 closest distance to " O   HOH Z 326 " =    1.571
peak=    4.251 closest distance to " CB  GLU A 277 " =    3.492
peak=    4.250 closest distance to " CB  TYR A 169 " =    0.759
peak=    4.213 closest distance to " OD1 ASN A  69 " =    2.544
peak=    4.203 closest distance to " NH2BARG A 145 " =    2.004
peak=    4.191 closest distance to " O   HOH Z 344 " =    2.818
peak=    4.144 closest distance to " CB  TRP A 179 " =    1.303
peak=    4.142 closest distance to " O   HOH Z 427 " =    2.763
peak=    4.136 closest distance to " CB  LEU A 228 " =    1.160
peak=    4.126 closest distance to " O   HOH Z 279 " =    2.108
peak=    4.111 closest distance to " O   HOH Z 368 " =    2.030
peak=    4.109 closest distance to " O   HOH Z  49 " =    2.100
peak=    4.106 closest distance to " CG1 ILE A  33 " =    1.308
peak=    4.102 closest distance to " O   HOH Z 180 " =    2.253
peak=    4.095 closest distance to " O   HOH Z 313 " =    1.764
peak=    4.092 closest distance to " O   HOH Z 416 " =    2.693
peak=    4.091 closest distance to " O   HOH Z 128 " =    1.974
peak=    4.090 closest distance to " O   HOH Z 426 " =    1.541
peak=    4.057 closest distance to " CB  PRO A  54 " =    0.898
peak=    4.052 closest distance to " O   HOH Z 144 " =    2.161
peak=    4.051 closest distance to " O   HOH Z  54 " =    1.715
peak=    4.048 closest distance to " O   HOH Z   6 " =    2.165
peak=    4.030 closest distance to " O   HOH Z 374 " =    2.482
peak=    4.025 closest distance to " O   HOH Z 260 " =    1.140
peak=    4.004 closest distance to " CG  PRO A 198 " =    1.221
peak=    3.997 closest distance to " CA  THR A 221 " =    0.934
peak=    3.975 closest distance to " O   HOH Z 197 " =    2.549
peak=    3.967 closest distance to " ND2 ASN A 187 " =    1.557
peak=    3.952 closest distance to " CG2 ILE A 120 " =    1.217
peak=    3.952 closest distance to " O   HOH Z 334 " =    1.358
peak=    3.947 closest distance to " O   HOH Z 371 " =    3.423
peak=    3.946 closest distance to " OG BSER A 164 " =    2.494
peak=    3.943 closest distance to " CG  PRO A 243 " =    1.194
peak=    3.940 closest distance to " NZ  LYS A 119 " =    1.830
peak=    3.935 closest distance to " CG  ARG A  66 " =    2.730
peak=    3.914 closest distance to " O   HOH Z 261 " =    1.672
peak=    3.896 closest distance to " CD2 LEU A 297 " =    0.921
peak=    3.886 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.884 closest distance to " CA  ASN A 176 " =    1.150
peak=    3.872 closest distance to " O   HOH Z 402 " =    1.387
peak=    3.849 closest distance to " O   HOH Z  43 " =    2.099
peak=    3.827 closest distance to " CA  ARG A  36 " =    1.069
peak=    3.824 closest distance to " CB  VAL A 202 " =    1.611
peak=    3.821 closest distance to " O   HOH Z 369 " =    1.999
peak=    3.816 closest distance to " O   HOH Z 423 " =    2.005
peak=    3.815 closest distance to " O   HOH Z 183 " =    1.555
peak=    3.812 closest distance to " O   MET A 105 " =    1.834
peak=    3.810 closest distance to " O   HOH Z  40 " =    1.582
peak=    3.808 closest distance to " O   HOH Z  80 " =    1.630
peak=    3.786 closest distance to " CG2BVAL A  41 " =    0.837
peak=    3.782 closest distance to " O   HOH Z 193 " =    2.203
peak=    3.776 closest distance to " O   HOH Z  85 " =    1.701
peak=    3.770 closest distance to " CB  ARG A 190 " =    1.682
peak=    3.767 closest distance to " O   HOH Z 132 " =    2.111
peak=    3.755 closest distance to " O   HOH Z 132 " =    2.479
peak=    3.747 closest distance to " O   HOH Z 173 " =    2.013
peak=    3.729 closest distance to " O   HOH Z 411 " =    3.746
peak=    3.724 closest distance to " CG1BVAL A  72 " =    1.595
peak=    3.720 closest distance to " CB  ARG A 139 " =    0.927
peak=    3.718 closest distance to " CB  SER A 141 " =    1.070
peak=    3.715 closest distance to " O   HOH Z  61 " =    1.517
peak=    3.713 closest distance to " O   HOH Z 357 " =    1.946
peak=    3.710 closest distance to " N   ASN A  39 " =    1.268
peak=    3.703 closest distance to " O   HOH Z 284 " =    2.833
peak=    3.701 closest distance to " NH2 ARG A 156 " =    1.162
peak=    3.671 closest distance to " O   HOH Z  67 " =    1.828
peak=    3.668 closest distance to " CA  ASP A 140 " =    1.104
peak=    3.663 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.662 closest distance to " O   HOH Z 346 " =    1.633
peak=    3.652 closest distance to " O   HOH Z 102 " =    1.237
peak=    3.639 closest distance to " O   HOH Z 214 " =    2.179
peak=    3.636 closest distance to " O   HOH Z  71 " =    1.286
peak=    3.635 closest distance to " O   HOH Z  19 " =    1.803
peak=    3.626 closest distance to " CD  ARG A 269 " =    1.027
peak=    3.624 closest distance to " O   HOH Z 247 " =    1.254
peak=    3.620 closest distance to " OD2 ASP A 298 " =    4.013
peak=    3.614 closest distance to " O   HOH Z  63 " =    1.940
peak=    3.609 closest distance to " CG  ARG A  66 " =    0.997
peak=    3.609 closest distance to " O   HOH Z 345 " =    2.883
peak=    3.592 closest distance to " O   HOH Z 128 " =    2.243
peak=    3.584 closest distance to " CG  GLN A  58 " =    2.502
peak=    3.574 closest distance to " CB  ASN A 148 " =    1.131
peak=    3.567 closest distance to " O   HOH Z 273 " =    2.809
peak=    3.563 closest distance to " O   HOH Z  21 " =    1.754
peak=    3.561 closest distance to " CZ2 TRP A 179 " =    1.656
peak=    3.558 closest distance to " CA  MET A  40 " =    1.026
peak=    3.556 closest distance to " CD BLYS A 290 " =    1.166
peak=    3.555 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.552 closest distance to " CB  SER A  26 " =    1.606
peak=    3.546 closest distance to " O   HOH Z 353 " =    2.644
peak=    3.546 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.545 closest distance to " O   HOH Z 108 " =    2.006
peak=    3.542 closest distance to " O   HOH Z 263 " =    2.302
peak=    3.534 closest distance to " CB  VAL A 265 " =    1.258
peak=    3.531 closest distance to " O   HOH Z  88 " =    3.165
peak=    3.526 closest distance to " O   HOH Z 118 " =    1.226
peak=    3.526 closest distance to " O   HOH Z 427 " =    3.069
peak=    3.521 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.518 closest distance to " O   HOH Z  44 " =    2.060
peak=    3.514 closest distance to " NH1AARG A 145 " =    1.174
peak=    3.513 closest distance to " O   HOH Z 163 " =    1.956
peak=    3.512 closest distance to " O   HOH Z 147 " =    1.724
peak=    3.508 closest distance to " O   HOH Z 408 " =    1.513
peak=    3.505 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.504 closest distance to " CA  ALA A  51 " =    0.864
peak=    3.503 closest distance to " O   HOH Z 250 " =    1.333
peak=    3.492 closest distance to " O   HOH Z 303 " =    1.926
peak=    3.491 closest distance to " O   HOH Z 327 " =    1.756
peak=    3.483 closest distance to " O   HOH Z 366 " =    2.883
peak=    3.482 closest distance to " O   HOH Z 209 " =    2.390
peak=    3.478 closest distance to " O   SER A  26 " =    1.700
peak=    3.464 closest distance to " CB  ASN A  39 " =    0.860
peak=    3.462 closest distance to " NH2AARG A 190 " =    1.212
peak=    3.457 closest distance to " O   ALA A 165 " =    1.375
peak=    3.457 closest distance to " O   HOH Z 380 " =    2.074
peak=    3.454 closest distance to " CA  ALA A 248 " =    1.170
peak=    3.453 closest distance to " O   HOH Z  20 " =    2.275
peak=    3.449 closest distance to " NE2 GLN A  58 " =    4.409
peak=    3.448 closest distance to " CA  ALA A  84 " =    1.320
peak=    3.443 closest distance to " O   HOH Z 189 " =    1.575
peak=    3.439 closest distance to " CD2 TRP A 179 " =    1.406
peak=    3.433 closest distance to " O   HOH Z 250 " =    1.616
peak=    3.430 closest distance to " O   HOH Z 417 " =    3.030
peak=    3.430 closest distance to " O   TRP A 274 " =    1.886
peak=    3.430 closest distance to " CD  LYS A 119 " =    1.347
peak=    3.429 closest distance to " O   HOH Z 291 " =    1.509
peak=    3.426 closest distance to " CB  SER A  62 " =    1.260
peak=    3.418 closest distance to " O   HOH Z  66 " =    2.187
peak=    3.415 closest distance to " OE1 GLN A  11 " =    1.868
peak=    3.414 closest distance to " CB  ALA A 291 " =    1.272
peak=    3.414 closest distance to " C   ALA A   1 " =    1.619
peak=    3.403 closest distance to " O   HOH Z 133 " =    1.336
peak=    3.400 closest distance to " CG2 ILE A  20 " =    1.422
peak=    3.396 closest distance to " CE  LYS A 119 " =    1.097
peak=    3.395 closest distance to " O   HOH Z 261 " =    1.975
peak=    3.394 closest distance to " O   HOH Z 214 " =    2.248
peak=    3.388 closest distance to " O   HOH Z 419 " =    1.489
peak=    3.381 closest distance to " OG  SER A  22 " =    2.674
peak=    3.380 closest distance to " O   HOH Z 227 " =    1.579
peak=    3.362 closest distance to " OG BSER A 258 " =    3.450
peak=    3.352 closest distance to " O   HOH Z 194 " =    1.995
peak=    3.351 closest distance to " O   HOH Z 362 " =    3.642
peak=    3.349 closest distance to " OG  SER A  62 " =    2.974
peak=    3.347 closest distance to " CG AARG A 275 " =    0.996
peak=    3.345 closest distance to " O   HOH Z 292 " =    1.642
peak=    3.340 closest distance to " O   HOH Z 281 " =    4.285
peak=    3.336 closest distance to " O   HOH Z   1 " =    2.211
peak=    3.335 closest distance to " O   HOH Z 280 " =    2.383
peak=    3.335 closest distance to " CG  GLN A  11 " =    1.366
peak=    3.325 closest distance to " CG  GLU A 277 " =    2.164
peak=    3.322 closest distance to " O   HOH Z 345 " =    1.642
peak=    3.317 closest distance to " O   HOH Z 368 " =    2.515
peak=    3.315 closest distance to " CD2 LEU A 255 " =    1.235
peak=    3.313 closest distance to " O   HOH Z 358 " =    2.143
peak=    3.310 closest distance to " O   HOH Z  11 " =    1.256
peak=    3.309 closest distance to " CD1 LEU A 300 " =    1.250
peak=    3.308 closest distance to " O   HOH Z 185 " =    1.688
peak=    3.305 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.304 closest distance to " SD AMET A  47 " =    1.360
peak=    3.296 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.292 closest distance to " OH  TYR A  30 " =    1.096
peak=    3.289 closest distance to " CB  SER A  62 " =    0.823
peak=    3.282 closest distance to " CA  GLY A  80 " =    0.942
peak=    3.280 closest distance to " O   HOH Z 276 " =    1.231
peak=    3.278 closest distance to " NH2 ARG A 219 " =    1.907
peak=    3.277 closest distance to " O   HOH Z 409 " =    3.408
peak=    3.277 closest distance to " CE1 TYR A 186 " =    1.223
peak=    3.273 closest distance to " OE1 GLN A  58 " =    5.871
peak=    3.270 closest distance to " NH1BARG A 145 " =    1.228
peak=    3.267 closest distance to " CG  GLN A  89 " =    1.492
peak=    3.260 closest distance to " O   HOH Z 341 " =    1.757
peak=    3.258 closest distance to " CA  ALA A 233 " =    1.215
peak=    3.257 closest distance to " CG2 VAL A 202 " =    1.217
peak=    3.256 closest distance to " NZ  LYS A  76 " =    1.282
peak=    3.256 closest distance to " O   HOH Z 417 " =    2.279
peak=    3.254 closest distance to " O   HOH Z 438 " =    1.997
peak=    3.252 closest distance to " O   HOH Z 425 " =    2.031
peak=    3.251 closest distance to " O   HOH Z  30 " =    1.973
peak=    3.251 closest distance to " O   HOH Z 211 " =    2.483
peak=    3.249 closest distance to " O   HOH Z 368 " =    2.522
peak=    3.249 closest distance to " CB  ASN A 285 " =    0.946
peak=    3.245 closest distance to " CG  MET A 185 " =    1.151
peak=    3.240 closest distance to " CA  ALA A 160 " =    0.785
peak=    3.240 closest distance to " O   HOH Z 411 " =    1.681
peak=    3.238 closest distance to " O   HOH Z 251 " =    1.584
peak=    3.230 closest distance to " O   HOH Z  35 " =    2.490
peak=    3.229 closest distance to " O   HOH Z 286 " =    2.145
peak=    3.226 closest distance to " O   HOH Z 125 " =    2.303
peak=    3.226 closest distance to " CA  ARG A 195 " =    1.305
peak=    3.224 closest distance to " CG2 VAL A 197 " =    1.117
peak=    3.219 closest distance to " O   HOH Z 155 " =    2.858
peak=    3.219 closest distance to " O   HOH Z 421 " =    1.443
peak=    3.216 closest distance to " O   HOH Z 245 " =    1.314
peak=    3.215 closest distance to " O   SER A 164 " =    1.425
peak=    3.213 closest distance to " O   HOH Z 189 " =    1.376
peak=    3.213 closest distance to " O   HOH Z 126 " =    2.150
peak=    3.211 closest distance to " C   ALA A 299 " =    0.910
peak=    3.210 closest distance to " CA  LEU A 282 " =    1.228
peak=    3.209 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.207 closest distance to " CA  ASP A 191 " =    0.956
peak=    3.205 closest distance to " O   HOH Z  48 " =    1.471
peak=    3.204 closest distance to " CG  GLN A  77 " =    2.111
peak=    3.202 closest distance to " CA  ALA A 291 " =    0.870
peak=    3.201 closest distance to " O   GLY A  91 " =    1.400
peak=    3.200 closest distance to " CB  PRO A 198 " =    1.173
peak=    3.197 closest distance to " CB  PRO A  90 " =    1.944
peak=    3.196 closest distance to " CA  ALA A 158 " =    1.137
peak=    3.196 closest distance to " O   HOH Z 313 " =    2.155
peak=    3.196 closest distance to " CB  SER A 273 " =    0.782
peak=    3.195 closest distance to " CG  MET A  93 " =    0.963
peak=    3.191 closest distance to " CA  VAL A 126 " =    1.098
peak=    3.185 closest distance to " CB  ALA A   9 " =    1.546
peak=    3.180 closest distance to " OD1 ASP A 238 " =    0.976
peak=    3.180 closest distance to " CA  ASP A 162 " =    1.172
peak=    3.179 closest distance to " O   HOH Z  44 " =    3.586
peak=    3.176 closest distance to " CB  THR A  31 " =    1.765
peak=    3.173 closest distance to " CD1AILE A 234 " =    0.989
peak=    3.171 closest distance to " O   HOH Z 337 " =    3.578
peak=    3.168 closest distance to " O   HOH Z 435 " =    1.834
peak=    3.167 closest distance to " CB  MET A  47 " =    1.164
peak=    3.166 closest distance to " O   HOH Z  85 " =    1.999
peak=    3.165 closest distance to " O   HOH Z 163 " =    1.646
peak=    3.164 closest distance to " CA  THR A 264 " =    0.817
peak=    3.162 closest distance to " O   HOH Z  59 " =    2.260
peak=    3.161 closest distance to " O   HOH Z 367 " =    3.406
peak=    3.160 closest distance to " O   HOH Z 325 " =    2.138
peak=    3.156 closest distance to " O   HOH Z 336 " =    1.762
peak=    3.151 closest distance to " CB  THR A  52 " =    1.100
peak=    3.146 closest distance to " O   ALA A   1 " =    1.415
peak=    3.141 closest distance to " CB  GLN A 278 " =    0.852
peak=    3.140 closest distance to " CA  ILE A  33 " =    1.430
peak=    3.140 closest distance to " O   HOH Z 267 " =    2.089
peak=    3.132 closest distance to " CH2 TRP A 274 " =    2.167
peak=    3.123 closest distance to " CB  TRP A 266 " =    1.063
peak=    3.123 closest distance to " N   ASN A 127 " =    1.266
peak=    3.121 closest distance to " O   HOH Z 430 " =    5.580
peak=    3.121 closest distance to " CB  ALA A 100 " =    1.170
peak=    3.120 closest distance to " CB  ALA A   1 " =    1.177
peak=    3.117 closest distance to " O   HOH Z 207 " =    1.956
peak=    3.113 closest distance to " N   ARG A 156 " =    1.330
peak=    3.110 closest distance to " N   SER A 135 " =    1.300
peak=    3.110 closest distance to " O   HOH Z  39 " =    2.742
peak=    3.109 closest distance to " CA  VAL A  41 " =    0.903
peak=    3.107 closest distance to " O   ALA A 158 " =    1.246
peak=    3.106 closest distance to " O   HOH Z 154 " =    1.251
peak=    3.105 closest distance to " CG  MET A 185 " =    1.097
peak=    3.103 closest distance to " O   HOH Z 422 " =    2.634
peak=    3.099 closest distance to " O   HOH Z 128 " =    1.678
peak=    3.088 closest distance to " O   HOH Z 192 " =    1.806
peak=    3.081 closest distance to " O   HOH Z 291 " =    1.793
peak=    3.081 closest distance to " O   HOH Z 423 " =    3.184
peak=    3.081 closest distance to " CG1 ILE A 120 " =    1.188
peak=    3.075 closest distance to " O   HOH Z 106 " =    2.394
peak=    3.046 closest distance to " CE  MET A 188 " =    2.231
peak=    3.041 closest distance to " O   HOH Z 329 " =    3.279
peak=    3.039 closest distance to " CB  TYR A  30 " =    1.452
peak=    3.033 closest distance to " O   HOH Z 217 " =    1.074
peak=    3.023 closest distance to " O   HOH Z 406 " =    2.951

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.845 - 5.084
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.845 - 5.084

peak=   -4.621 closest distance to " O   HOH Z 266 " =    4.114
peak=   -4.361 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.337 closest distance to " O   HOH Z  13 " =    1.487
peak=   -4.308 closest distance to " OXT GLY A 302 " =    2.800
peak=   -4.200 closest distance to " CA  TYR A  68 " =    2.815
peak=   -4.181 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.158 closest distance to " CD1 LEU A 101 " =    2.471
peak=   -4.077 closest distance to " SG  CYS A 254 " =    3.312
peak=   -4.076 closest distance to " N   GLN A  58 " =    1.657
peak=   -4.074 closest distance to " O   HOH Z 372 " =    2.301
peak=   -4.074 closest distance to " ND2 ASN A 187 " =    1.510
peak=   -4.031 closest distance to " CB  TYR A  15 " =    2.250
peak=   -4.022 closest distance to " O   PRO A 163 " =    2.040
peak=   -3.962 closest distance to " N   ALA A 248 " =    1.680
peak=   -3.937 closest distance to " NE2 GLN A  58 " =    1.126
peak=   -3.930 closest distance to " O   HOH Z 292 " =    4.443
peak=   -3.912 closest distance to " O   HOH Z 234 " =    4.090
peak=   -3.912 closest distance to " O   VAL A  67 " =    2.774
peak=   -3.910 closest distance to " O   HOH Z  10 " =    1.534
peak=   -3.907 closest distance to " O   HOH Z 377 " =    1.904
peak=   -3.895 closest distance to " O   HOH Z 388 " =    2.029
peak=   -3.894 closest distance to " CH2 TRP A 179 " =    1.349
peak=   -3.873 closest distance to " OG BSER A 134 " =    1.321
peak=   -3.867 closest distance to " CZ  TYR A 169 " =    1.855
peak=   -3.867 closest distance to " OG  SER A  97 " =    2.111
peak=   -3.862 closest distance to " OG ASER A 134 " =    1.278
peak=   -3.851 closest distance to " ND2 ASN A  45 " =    0.927
peak=   -3.842 closest distance to " O   HOH Z  92 " =    1.731
peak=   -3.837 closest distance to " C   ALA A 158 " =    1.170
peak=   -3.836 closest distance to " CD1 PHE A 130 " =    2.214
peak=   -3.831 closest distance to " CB  ALA A 161 " =    2.568
peak=   -3.831 closest distance to " O   HOH Z 198 " =    2.202
peak=   -3.827 closest distance to " O   HOH Z  11 " =    1.735
peak=   -3.808 closest distance to " CB  ASN A  39 " =    2.314
peak=   -3.807 closest distance to " OG BSER A 134 " =    1.697
peak=   -3.800 closest distance to " NH2 ARG A  79 " =    1.919
peak=   -3.795 closest distance to " O   HOH Z  52 " =    1.570
peak=   -3.792 closest distance to " CG  ASP A 231 " =    0.845
peak=   -3.790 closest distance to " CB  PRO A 243 " =    2.567
peak=   -3.785 closest distance to " CB  ALA A 291 " =    2.420
peak=   -3.782 closest distance to " O   HOH Z  43 " =    1.600
peak=   -3.773 closest distance to " O   HOH Z 407 " =    3.096
peak=   -3.764 closest distance to " N   SER A 276 " =    1.309
peak=   -3.761 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.756 closest distance to " O   HOH Z 290 " =    0.962
peak=   -3.737 closest distance to " CD1 LEU A 228 " =    2.156
peak=   -3.736 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.734 closest distance to " O   TRP A  92 " =    1.835
peak=   -3.730 closest distance to " O   SER A 210 " =    1.843
peak=   -3.727 closest distance to " O   HOH Z 353 " =    2.201
peak=   -3.724 closest distance to " CD2 LEU A 300 " =    2.832
peak=   -3.715 closest distance to " O   HOH Z 166 " =    1.532
peak=   -3.714 closest distance to " O   HOH Z 126 " =    1.897
peak=   -3.708 closest distance to " O   HOH Z 385 " =    1.981
peak=   -3.702 closest distance to " CE2 TYR A  30 " =    2.832
peak=   -3.680 closest distance to " O   HOH Z 165 " =    2.035
peak=   -3.667 closest distance to " O   HOH Z 118 " =    2.878
peak=   -3.665 closest distance to " O   VAL A 153 " =    2.326
peak=   -3.656 closest distance to " O   ASN A  45 " =    1.844
peak=   -3.643 closest distance to " NH1 ARG A 195 " =    2.580
peak=   -3.641 closest distance to " N   GLN A 122 " =    1.551
peak=   -3.629 closest distance to " OE2 GLU A   2 " =    1.958
peak=   -3.608 closest distance to " O   MET A  40 " =    2.689
peak=   -3.600 closest distance to " CA  GLY A 133 " =    1.820
peak=   -3.590 closest distance to " NH2 ARG A  66 " =    4.751
peak=   -3.590 closest distance to " OE1 GLN A 223 " =    2.194
peak=   -3.587 closest distance to " O   HOH Z 423 " =    2.254
peak=   -3.587 closest distance to " O   HOH Z 427 " =    1.393
peak=   -3.586 closest distance to " O   ALA A 161 " =    1.668
peak=   -3.579 closest distance to " O   HOH Z 395 " =    5.084
peak=   -3.534 closest distance to " O   HOH Z 311 " =    3.510
peak=   -3.519 closest distance to " CD  LYS A 289 " =    2.528
peak=   -3.517 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.515 closest distance to " O   HOH Z 166 " =    2.017
peak=   -3.497 closest distance to " O   HOH Z 435 " =    2.628
peak=   -3.493 closest distance to " OG  SER A  62 " =    1.420
peak=   -3.486 closest distance to " CG  ASP A  50 " =    2.447
peak=   -3.486 closest distance to " CG  PHE A 283 " =    2.570
peak=   -3.483 closest distance to " O   HOH Z  38 " =    1.595
peak=   -3.476 closest distance to " O   GLY A 196 " =    0.944
peak=   -3.469 closest distance to " CD2 LEU A 237 " =    2.504
peak=   -3.458 closest distance to " O   HOH Z  11 " =    1.833
peak=   -3.458 closest distance to " O   HOH Z  17 " =    1.536
peak=   -3.457 closest distance to " O   VAL A 174 " =    2.029
peak=   -3.454 closest distance to " O   SER A 135 " =    1.604
peak=   -3.453 closest distance to " CB  PHE A 208 " =    2.231
peak=   -3.452 closest distance to " ND2 ASN A  39 " =    1.293
peak=   -3.446 closest distance to " ND2 ASN A 209 " =    1.499
peak=   -3.444 closest distance to " OD1 ASN A 187 " =    1.617
peak=   -3.438 closest distance to " CB  PHE A 192 " =    1.871
peak=   -3.435 closest distance to " N   GLN A  58 " =    1.440
peak=   -3.430 closest distance to " CE  MET A 105 " =    1.891
peak=   -3.425 closest distance to " O   HOH Z  93 " =    1.483
peak=   -3.421 closest distance to " N   ASP A 286 " =    2.324
peak=   -3.414 closest distance to " O   HOH Z 384 " =    2.446
peak=   -3.409 closest distance to " CD1 PHE A  59 " =    1.896
peak=   -3.407 closest distance to " N   HIS A 115 " =    1.888
peak=   -3.406 closest distance to " C   LEU A 143 " =    1.151
peak=   -3.404 closest distance to " O   HOH Z 196 " =    1.885
peak=   -3.398 closest distance to " NH2 ARG A  66 " =    1.844
peak=   -3.397 closest distance to " N   ALA A  43 " =    2.549
peak=   -3.394 closest distance to " CG  GLU A  53 " =    1.473
peak=   -3.394 closest distance to " CG2 VAL A 189 " =    2.187
peak=   -3.392 closest distance to " O   HOH Z 185 " =    2.208
peak=   -3.391 closest distance to " CG2 ILE A 263 " =    2.177
peak=   -3.389 closest distance to " O   ALA A 160 " =    1.487
peak=   -3.381 closest distance to " O   PHE A 218 " =    1.537
peak=   -3.379 closest distance to " O   HOH Z  19 " =    1.989
peak=   -3.377 closest distance to " O   HOH Z 360 " =    2.549
peak=   -3.371 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.367 closest distance to " NE2 GLN A  88 " =    1.902
peak=   -3.367 closest distance to " O   HOH Z  90 " =    2.885
peak=   -3.365 closest distance to " O   HOH Z 418 " =    1.440
peak=   -3.364 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.349 closest distance to " O   HOH Z 417 " =    2.532
peak=   -3.346 closest distance to " CB  CYS A 254 " =    2.578
peak=   -3.342 closest distance to " O   LEU A 167 " =    1.529
peak=   -3.339 closest distance to " CD1 TYR A 247 " =    2.370
peak=   -3.335 closest distance to " O   GLY A  80 " =    2.446
peak=   -3.332 closest distance to " O   HOH Z 361 " =    3.431
peak=   -3.328 closest distance to " O   HOH Z  60 " =    1.936
peak=   -3.328 closest distance to " CD2 LEU A 237 " =    2.569
peak=   -3.325 closest distance to " O   HOH Z 250 " =    1.379
peak=   -3.319 closest distance to " O   HOH Z 145 " =    3.073
peak=   -3.312 closest distance to " CZ  PHE A  59 " =    1.600
peak=   -3.307 closest distance to " CG2AVAL A  41 " =    2.660
peak=   -3.297 closest distance to " CG1 VAL A 112 " =    2.724
peak=   -3.295 closest distance to " ND2 ASN A 215 " =    2.103
peak=   -3.294 closest distance to " CE  MET A  93 " =    1.180
peak=   -3.294 closest distance to " OE1 GLN A  77 " =    1.682
peak=   -3.291 closest distance to " O   HOH Z 148 " =    3.579
peak=   -3.289 closest distance to " O   HOH Z 263 " =    2.955
peak=   -3.285 closest distance to " O   SER A 146 " =    0.920
peak=   -3.282 closest distance to " CD  GLN A  58 " =    1.407
peak=   -3.278 closest distance to " SG ACYS A 201 " =    2.272
peak=   -3.278 closest distance to " CG  GLU A 277 " =    1.183
peak=   -3.274 closest distance to " OD2 ASP A  50 " =    1.365
peak=   -3.273 closest distance to " O   HOH Z  97 " =    1.531
peak=   -3.273 closest distance to " OD1 ASP A 191 " =    1.676
peak=   -3.273 closest distance to " CE3 TRP A 150 " =    1.906
peak=   -3.273 closest distance to " OG BSER A 210 " =    1.947
peak=   -3.268 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.266 closest distance to " N   VAL A 189 " =    1.707
peak=   -3.265 closest distance to " O   HOH Z   9 " =    1.924
peak=   -3.263 closest distance to " O   HOH Z 396 " =    1.508
peak=   -3.261 closest distance to " CD2 PHE A  59 " =    2.380
peak=   -3.260 closest distance to " O   HOH Z 378 " =    1.700
peak=   -3.256 closest distance to " O   HOH Z 283 " =    1.733
peak=   -3.256 closest distance to " O   ALA A 256 " =    1.454
peak=   -3.250 closest distance to " CD1 LEU A  25 " =    2.482
peak=   -3.248 closest distance to " ND2 ASN A  69 " =    1.409
peak=   -3.248 closest distance to " CG1AVAL A  41 " =    2.777
peak=   -3.247 closest distance to " O   HOH Z 210 " =    0.949
peak=   -3.244 closest distance to " O   HOH Z  41 " =    2.307
peak=   -3.239 closest distance to " O   ASN A 187 " =    1.442
peak=   -3.234 closest distance to " CB  ASP A 286 " =    2.055
peak=   -3.230 closest distance to " CE3 TRP A 123 " =    1.258
peak=   -3.219 closest distance to " O   HOH Z 281 " =    2.755
peak=   -3.219 closest distance to " CB  SER A 258 " =    1.996
peak=   -3.217 closest distance to " OD1 ASP A 200 " =    1.264
peak=   -3.214 closest distance to " O   VAL A 125 " =    2.207
peak=   -3.214 closest distance to " O   HOH Z  76 " =    1.980
peak=   -3.210 closest distance to " OD1 ASN A 148 " =    1.659
peak=   -3.206 closest distance to " O   ALA A   1 " =    1.849
peak=   -3.201 closest distance to " O   GLY A 118 " =    2.233
peak=   -3.201 closest distance to " O   HOH Z 405 " =    2.469
peak=   -3.199 closest distance to " O   ASP A 231 " =    2.480
peak=   -3.199 closest distance to " OG1 THR A  82 " =    1.422
peak=   -3.198 closest distance to " CG  GLU A 152 " =    2.345
peak=   -3.198 closest distance to " O   HOH Z  15 " =    1.604
peak=   -3.198 closest distance to " CD1 PHE A  38 " =    2.630
peak=   -3.197 closest distance to " OD1 ASP A 171 " =    1.581
peak=   -3.196 closest distance to " OXT GLY A 302 " =    2.997
peak=   -3.190 closest distance to " O   HOH Z  88 " =    1.751
peak=   -3.188 closest distance to " O   HOH Z 151 " =    1.415
peak=   -3.170 closest distance to " CZ3 TRP A 274 " =    2.449
peak=   -3.167 closest distance to " O   HOH Z 407 " =    3.530
peak=   -3.165 closest distance to " O   HOH Z 265 " =    1.980
peak=   -3.164 closest distance to " O   HOH Z 411 " =    3.469
peak=   -3.163 closest distance to " O   HOH Z  71 " =    1.484
peak=   -3.162 closest distance to " CB  ALA A 248 " =    1.907
peak=   -3.159 closest distance to " O   HOH Z 266 " =    4.579
peak=   -3.159 closest distance to " O   HOH Z 431 " =    1.890
peak=   -3.155 closest distance to " O   HOH Z 422 " =    1.443
peak=   -3.155 closest distance to " CB  CYS A 201 " =    2.563
peak=   -3.140 closest distance to " N   ALA A 226 " =    1.954
peak=   -3.140 closest distance to " O   ALA A  34 " =    2.494
peak=   -3.139 closest distance to " OG1 THR A 279 " =    1.331
peak=   -3.137 closest distance to " OG  SER A 206 " =    1.685
peak=   -3.134 closest distance to " OH  TYR A 214 " =    1.331
peak=   -3.133 closest distance to " CB  ALA A  10 " =    2.170
peak=   -3.132 closest distance to " O   HOH Z 137 " =    1.438
peak=   -3.128 closest distance to " O   HOH Z 377 " =    1.631
peak=   -3.122 closest distance to " N   SER A 206 " =    1.839
peak=   -3.120 closest distance to " OE1 GLN A  88 " =    1.143
peak=   -3.104 closest distance to " CG  ASN A 110 " =    1.139
peak=   -3.094 closest distance to " NH2 ARG A  66 " =    4.628
peak=   -3.089 closest distance to " O   HOH Z  61 " =    1.645
peak=   -3.086 closest distance to " CG  ARG A 259 " =    2.769
peak=   -3.084 closest distance to " CE1 HIS A  81 " =    1.408
peak=   -3.063 closest distance to " CG  ARG A 269 " =    2.214
peak=   -3.063 closest distance to " O   HOH Z  43 " =    1.422
peak=   -3.034 closest distance to " CB  ASP A 124 " =    2.104
peak=   -3.031 closest distance to " O   ALA A  51 " =    1.419
peak=   -3.009 closest distance to " OG  SER A 273 " =    2.038

================= 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    :  0.4229 0.4169   6.225335e+00   6.223443e+00
   1_bss:  0.4120 0.4045   6.215391e+00   6.202235e+00
   1_xyz:  0.2627 0.2896   5.850994e+00   5.933553e+00
   1_adp:  0.2382 0.2999   5.797438e+00   5.958355e+00
   1_occ:  0.2378 0.3003   5.796642e+00   5.957612e+00
   2_bss:  0.2341 0.2966   5.789185e+00   5.951094e+00
   2_xyz:  0.1728 0.2270   5.522526e+00   5.723965e+00
   2_adp:  0.1564 0.2112   5.438221e+00   5.648880e+00
   2_occ:  0.1561 0.2111   5.437691e+00   5.648394e+00
   3_bss:  0.1562 0.2093   5.432839e+00   5.641918e+00
   3_xyz:  0.1304 0.1780   5.270212e+00   5.495714e+00
   3_adp:  0.1254 0.1687   5.227710e+00   5.440838e+00
   3_occ:  0.1252 0.1685   5.226702e+00   5.439940e+00
   4_bss:  0.1256 0.1686   5.229069e+00   5.440797e+00
   4_xyz:  0.1140 0.1583   5.155198e+00   5.382336e+00
   4_adp:  0.1114 0.1592   5.146679e+00   5.384155e+00
   4_occ:  0.1113 0.1591   5.146232e+00   5.384031e+00
   5_bss:  0.1113 0.1591   5.146152e+00   5.383959e+00
   5_xyz:  0.1089 0.1575   5.132427e+00   5.376924e+00
   5_adp:  0.1084 0.1578   5.131368e+00   5.378677e+00
   5_occ:  0.1084 0.1577   5.131332e+00   5.378982e+00
   5_bss:  0.1083 0.1578   5.131416e+00   5.379023e+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:  0.320  22.894  -2.609  -0.159   2.854  -0.000   0.000   0.000
   1_xyz:  0.320  22.894  -2.609  -0.159   2.854  -0.000   0.000   0.000
   1_adp:  0.320  22.894  -2.609  -0.159   2.854  -0.000   0.000   0.000
   1_occ:  0.320  22.894  -2.609  -0.159   2.854  -0.000   0.000   0.000
   2_bss:  0.331  50.001  -2.973  -1.387  -0.281  -0.000  -0.000  -0.000
   2_xyz:  0.331  50.001  -2.973  -1.387  -0.281  -0.000  -0.000  -0.000
   2_adp:  0.331  50.001  -2.973  -1.387  -0.281  -0.000  -0.000  -0.000
   2_occ:  0.331  50.001  -2.973  -1.387  -0.281  -0.000  -0.000  -0.000
   3_bss:  0.321  44.009  -2.656  -1.536  -1.253  -0.000  -0.000  -0.000
   3_xyz:  0.321  44.009  -2.656  -1.536  -1.253  -0.000  -0.000  -0.000
   3_adp:  0.321  44.009  -2.656  -1.536  -1.253  -0.000  -0.000  -0.000
   3_occ:  0.321  44.009  -2.656  -1.536  -1.253  -0.000  -0.000  -0.000
   4_bss:  0.321  43.061  -2.807  -1.845  -1.779  -0.000  -0.000  -0.000
   4_xyz:  0.321  43.061  -2.807  -1.845  -1.779  -0.000  -0.000  -0.000
   4_adp:  0.321  43.061  -2.807  -1.845  -1.779  -0.000  -0.000  -0.000
   4_occ:  0.321  43.061  -2.807  -1.845  -1.779  -0.000  -0.000  -0.000
   5_bss:  0.321  43.061  -2.735  -1.825  -1.840  -0.000  -0.000  -0.000
   5_xyz:  0.321  43.061  -2.735  -1.825  -1.840  -0.000  -0.000  -0.000
   5_adp:  0.321  43.061  -2.735  -1.825  -1.840  -0.000  -0.000  -0.000
   5_occ:  0.321  43.061  -2.735  -1.825  -1.840  -0.000  -0.000  -0.000
   5_bss:  0.321  43.021  -2.553  -1.661  -1.676  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.906 0.5219  0.6990    55348.619
   1_bss:  48.348 0.5394  0.7241    51033.607
   1_xyz:  29.313 0.7659  0.9719    21882.897
   1_adp:  30.888 0.7472  0.9572    23522.281
   1_occ:  30.859 0.7475  0.9572    23485.605
   2_bss:  30.389 0.7525  0.9117    22895.629
   2_xyz:  22.300 0.8383  0.9797    13154.127
   2_adp:  20.016 0.8616  0.9860    11198.929
   2_occ:  20.007 0.8616  0.9858    11189.815
   3_bss:  19.813 0.8632  0.9772    10957.924
   3_xyz:  16.610 0.8922  0.9941     7957.057
   3_adp:  15.262 0.9045  0.9980     7171.360
   3_occ:  15.236 0.9047  0.9979     7149.863
   4_bss:  15.248 0.9047  0.9856     7186.251
   4_xyz:  14.079 0.9141  0.9887     6328.506
   4_adp:  14.063 0.9146  0.9843     6347.362
   4_occ:  14.055 0.9147  0.9842     6342.936
   5_bss:  14.054 0.9147  0.9846     6343.939
   5_xyz:  13.882 0.9160  0.9849     6232.175
   5_adp:  13.897 0.9160  0.9804     6249.054
   5_occ:  13.899 0.9160  0.9803     6251.854
   5_bss:  13.901 0.9159  0.9850     6252.955
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9306e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9306e-01
   1_xyz:   1.405  0.012  0.084 15.913  0.006  4.112   1.2823e-01
   1_adp:   1.405  0.012  0.084 15.913  0.006  4.112   1.2823e-01
   1_occ:   1.405  0.012  0.084 15.913  0.006  4.112   1.2823e-01
   2_bss:   1.405  0.012  0.084 15.913  0.006  4.112   1.2823e-01
   2_xyz:   1.062  0.006  0.070 14.193  0.005  4.117   5.9881e-02
   2_adp:   1.062  0.006  0.070 14.193  0.005  4.117   5.9881e-02
   2_occ:   1.062  0.006  0.070 14.193  0.005  4.117   5.9881e-02
   3_bss:   1.062  0.006  0.070 14.193  0.005  4.117   5.9881e-02
   3_xyz:   0.965  0.006  0.067 14.384  0.004  4.118   5.4303e-02
   3_adp:   0.965  0.006  0.067 14.384  0.004  4.118   5.4303e-02
   3_occ:   0.965  0.006  0.067 14.384  0.004  4.118   5.4303e-02
   4_bss:   0.965  0.006  0.067 14.384  0.004  4.118   5.4303e-02
   4_xyz:   1.050  0.007  0.074 14.602  0.004  4.108   6.1739e-02
   4_adp:   1.050  0.007  0.074 14.602  0.004  4.108   6.1739e-02
   4_occ:   1.050  0.007  0.074 14.602  0.004  4.108   6.1739e-02
   5_bss:   1.050  0.007  0.074 14.602  0.004  4.108   6.1739e-02
   5_xyz:   1.030  0.007  0.073 14.551  0.004  4.108   6.0152e-02
   5_adp:   1.030  0.007  0.073 14.551  0.004  4.108   6.0152e-02
   5_occ:   1.030  0.007  0.073 14.551  0.004  4.108   6.0152e-02
   5_bss:   1.030  0.007  0.073 14.551  0.004  4.108   6.0152e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.409   2.3997e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.409   2.3997e-01
   1_xyz:   8.391  0.102  0.334 86.347  0.031  2.149   2.7675e-01
   1_adp:   8.391  0.102  0.334 86.347  0.031  2.149   2.7675e-01
   1_occ:   8.391  0.102  0.334 86.347  0.031  2.149   2.7675e-01
   2_bss:   8.391  0.102  0.334 86.347  0.031  2.149   2.7675e-01
   2_xyz:   7.593  0.041  0.233 82.108  0.037  2.384   4.1234e-02
   2_adp:   7.593  0.041  0.233 82.108  0.037  2.384   4.1234e-02
   2_occ:   7.593  0.041  0.233 82.108  0.037  2.384   4.1234e-02
   3_bss:   7.593  0.041  0.233 82.108  0.037  2.384   4.1234e-02
   3_xyz:   6.465  0.034  0.271 80.695  0.030  2.385   3.8362e-02
   3_adp:   6.465  0.034  0.271 80.695  0.030  2.385   3.8362e-02
   3_occ:   6.465  0.034  0.271 80.695  0.030  2.385   3.8362e-02
   4_bss:   6.465  0.034  0.271 80.695  0.030  2.385   3.8362e-02
   4_xyz:   6.922  0.036  0.233 82.168  0.040  2.323   6.4596e-02
   4_adp:   6.922  0.036  0.233 82.168  0.040  2.323   6.4596e-02
   4_occ:   6.922  0.036  0.233 82.168  0.040  2.323   6.4596e-02
   5_bss:   6.922  0.036  0.233 82.168  0.040  2.323   6.4596e-02
   5_xyz:   7.106  0.035  0.238 81.667  0.036  2.314   4.2933e-02
   5_adp:   7.106  0.035  0.238 81.667  0.036  2.314   4.2933e-02
   5_occ:   7.106  0.035  0.238 81.667  0.036  2.314   4.2933e-02
   5_bss:   7.106  0.035  0.238 81.667  0.036  2.314   4.2933e-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:  94.06   0.00  18.48  94.06   0.00  14.32  89.80   3.70  41.13
   1_occ:  94.06   0.00  18.48  94.06   0.00  14.32  89.80   3.70  41.13
   2_bss:  94.06   0.00  18.48  94.06   0.00  14.32  89.80   3.70  41.13
   2_xyz:  94.06   0.00  18.48  94.06   0.00  14.32  89.80   3.70  41.13
   2_adp:  98.32   0.00  18.25  98.32   0.00  13.67  88.32   6.53  43.24
   2_occ:  98.32   0.00  18.25  98.32   0.00  13.67  88.32   6.53  43.24
   3_bss:  98.32   0.00  18.25  98.32   0.00  13.67  88.32   6.53  43.24
   3_xyz:  98.32   0.00  18.25  98.32   0.00  13.67  88.32   6.53  43.24
   3_adp:  95.88   1.53  17.39  95.88   1.53  13.16  83.55   5.83  40.41
   3_occ:  95.88   1.53  17.39  95.88   1.53  13.16  83.55   5.83  40.41
   4_bss:  95.88   1.53  17.39  95.88   1.53  13.16  83.55   5.83  40.41
   4_xyz:  95.88   1.53  17.39  95.88   1.53  13.16  83.55   5.83  40.41
   4_adp:  96.21   1.71  17.30  96.21   1.71  13.02  87.48   5.04  40.60
   4_occ:  96.21   1.71  17.30  96.21   1.71  13.02  87.48   5.04  40.60
   5_bss:  96.21   1.71  17.30  96.21   1.71  13.02  87.48   5.04  40.60
   5_xyz:  96.21   1.71  17.30  96.21   1.71  13.02  87.48   5.04  40.60
   5_adp:  99.65   1.14  17.12  99.65   1.14  12.89  87.93   5.36  40.18
   5_occ:  99.65   1.14  17.12  99.65   1.14  12.89  87.93   5.36  40.18
   5_bss:  99.61   1.10  17.08  99.61   1.10  12.85  87.89   5.32  40.14
------------------------------------------------------------------------
 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:    1.910    0.033    0.419
   1_adp:    1.910    0.033    0.419
   1_occ:    1.910    0.033    0.419
   2_bss:    1.910    0.033    0.419
   2_xyz:    1.356    0.049    0.526
   2_adp:    1.356    0.049    0.526
   2_occ:    1.356    0.049    0.526
   3_bss:    1.356    0.049    0.526
   3_xyz:    1.457    0.042    0.589
   3_adp:    1.457    0.042    0.589
   3_occ:    1.457    0.042    0.589
   4_bss:    1.457    0.042    0.589
   4_xyz:    1.594    0.024    0.619
   4_adp:    1.594    0.024    0.619
   4_occ:    1.594    0.024    0.619
   5_bss:    1.594    0.024    0.619
   5_xyz:    1.660    0.049    0.629
   5_adp:    1.660    0.049    0.629
   5_occ:    1.660    0.049    0.629
   5_bss:    1.660    0.049    0.629
------------------------------------------------------------------------

CPU time actual refinement: 278.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/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_440/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_440/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 278.74 
  Macro-tasks:
    bulk solvent and scale       = 35.07  
    individual site refinement   = 112.02 
    weights calculation          = 25.03  
    collect and process          = 5.44   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 177.66 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 88.71  
    alpha_beta                      = 7.01   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 95.48  
    fmodel                         = 5.75   
    r_factors                      = 0.19   
    phase_errors                   = 8.82   
    foms                           = 0.17   
    TOTAL for micro-tasks          = 208.61 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.007 micro seconds
Total CPU time: 4.84 minutes
from_scatterers_fft:    628 calls, 88.49 s
gradients_fft:          573 calls, 84.47 s

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

# Date 2008-01-16 Time 04:48:51 PST -0800 (1200487731.18 s)
Start R-work = 0.4229, R-free = 0.4169 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.4120, R-free = 0.4045
Final R-work = 0.1083, R-free = 0.1578