# Date 2008-01-16 Time 05:16:57 PST -0800 (1200489417.36 s)
#phil __OFF__

Command line arguments: "../666.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16012
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 666

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   2.0001

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2789 [2096/2119]  1886   210  10.0%
  bin  2:  4.2789 -  3.4094 [2023/2043]  1821   202  10.0%
  bin  3:  3.4094 -  2.9823 [1990/2009]  1792   198   9.9%
  bin  4:  2.9823 -  2.7113 [1953/1983]  1757   196  10.0%
  bin  5:  2.7113 -  2.5180 [1970/1989]  1773   197  10.0%
  bin  6:  2.5180 -  2.3701 [1951/1976]  1754   197  10.1%
  bin  7:  2.3701 -  2.2518 [1926/1954]  1734   192  10.0%
  bin  8:  2.2518 -  2.1541 [1934/1970]  1740   194  10.0%
  bin  9:  2.1541 -  2.0714 [1920/1962]  1730   190   9.9%
  bin 10:  2.0714 -  2.0001 [1826/1956]  1643   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2200
        3.04 -     3.66: 4608
        3.66 -     4.28: 9049
        4.28 -     4.90: 12314
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.258 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.268 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28175 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_666/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1811   r_free= 0.1780   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.458209                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.2375 0.2331      6.2096      6.1487|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.1418 0.1250      5.8951      5.8322|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.1478 0.1518      5.7516      5.8451|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.1475 0.1715       5.602      5.6988|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.1759 0.1511      5.5322      5.4323|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.1653 0.1622      5.4201      5.3581|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.1733 0.1753      5.3863      5.4317|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.1732 0.1597      5.3582      5.3175|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.1732 0.1830      5.2814      5.2803|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.1772 0.1808      5.2755      5.2349|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.1731 0.1540      5.1991      5.1387|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.1766 0.1825      5.1781      5.2525|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.1789 0.1659      5.1087      5.0627|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.1828 0.1639      5.0742      4.9171|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7721  1371   152  0.83  22.22   0.88     0.84      31222.58|
|  2:  4.7721 -  3.8081  1299   146  0.91  13.79   1.00     0.96      19470.53|
|  3:  3.8081 -  3.3327  1286   141  0.93  12.23   1.03     1.01      12229.43|
|  4:  3.3327 -  3.0308  1281   142  0.93  12.46   1.03     1.02       9557.09|
|  5:  3.0308 -  2.8151  1260   141  0.91  14.87   1.05     1.01       7622.37|
|  6:  2.8151 -  2.6500  1268   141  0.92  14.42   1.05     1.02       6349.75|
|  7:  2.6500 -  2.5180  1264   140  0.91  14.75   1.06     1.03       5743.07|
|  8:  2.5180 -  2.4088  1249   137  0.91  14.83   1.08     1.05       5390.08|
|  9:  2.4088 -  2.3164  1241   141  0.91  15.00   1.10     1.07       4959.38|
| 10:  2.3164 -  2.2368  1243   138  0.91  15.13   1.12     1.08       4553.31|
| 11:  2.2368 -  2.1670  1249   138  0.91  15.19   1.11     1.10       4154.10|
| 12:  2.1670 -  2.1053  1240   139  0.92  14.57   1.13     1.13       3755.00|
| 13:  2.1053 -  2.0500  1247   137  0.92  14.03   1.12     1.13       3117.94|
| 14:  2.0500 -  2.0001  1132   126  0.93  13.31   1.13     1.10       2336.60|
|alpha:            min =        0.84 max =            1.13 mean =         1.04|
|beta:             min =     2336.60 max =        31222.58 mean =      8843.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.88 mean =        14.85|
|-----------------------------------------------------------------------------|

============================== 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 = 2.079801              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.601   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.855   (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 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      181 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2019 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2785 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4664 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4385 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5623 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6691 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.134 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    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: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1811   r_free= 0.1780   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.458209                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1577   r_free= 0.1563   ksol= 0.33   Bsol= 51.38   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-2.82,-0.96,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.401527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.942888              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.625   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.137151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.798   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1577      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1462          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5496 = 1.94 * 0.50 * 5.5481 + 1.00 * 0.1599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1176 = 1.94 * 0.50 * 5.1978 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1462      final r-factor (free) = 0.1463          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7190 = 0.14 * 1.00 * 5.1978 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7230 = 0.14 * 1.00 * 5.1171 + 1.00 * 0.0212                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.73   16.35    None  None   None       |
|    all(noH): 2823   0      0.00    62.73   16.35    None  None   None       |
|    Sol.    : 438    0      4.36    62.73   36.75    None  None   None       |
|    Mac.    : 2385   0      0.00    56.65   12.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.273:  131   |   5:    31.366 -  37.639:   95        |
|      1:     6.273 -  12.547: 1380   |   6:    37.639 -  43.913:  104        |
|      2:    12.547 -  18.820:  656   |   7:    43.913 -  50.186:   73        |
|      3:    18.820 -  25.093:  196   |   8:    50.186 -  56.459:   49        |
|      4:    25.093 -  31.366:  115   |   9:    56.459 -  62.732:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1463             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1460             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1460   ksol= 0.33   Bsol= 51.38   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-2.82,-0.96,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118673                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1458   ksol= 0.33   Bsol= 51.38   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.69,-1.24,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.676369              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.075  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146388              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.718   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1458      final r-factor (free) = 0.1486          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3565 = 1.68 * 0.50 * 5.1161 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3430 = 1.68 * 0.50 * 5.1077 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1486      final r-factor (free) = 0.1491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7751 = 0.15 * 1.00 * 5.1077 + 1.00 * 0.0274                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7538 = 0.15 * 1.00 * 5.1046 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    65.98   16.40    None  None   None       |
|    all(noH): 2823   0      1.99    65.98   16.40    None  None   None       |
|    Sol.    : 438    0      4.66    65.64   36.27    None  None   None       |
|    Mac.    : 2385   0      1.99    65.98   12.75    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:     1.992 -   8.391:  554   |   5:    33.987 -  40.386:  122        |
|      1:     8.391 -  14.790: 1291   |   6:    40.386 -  46.785:   87        |
|      2:    14.790 -  21.189:  406   |   7:    46.785 -  53.184:   85        |
|      3:    21.189 -  27.588:  141   |   8:    53.184 -  59.583:   29        |
|      4:    27.588 -  33.987:  102   |   9:    59.583 -  65.982:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1491             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1491             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1491   ksol= 0.33   Bsol= 51.38   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.69,-1.24,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108110                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1491   ksol= 0.33   Bsol= 51.38   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.45,-1.16,-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: 5.108141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.822807              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.634  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1491      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7146 = 1.82 * 0.50 * 5.1054 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7134 = 1.82 * 0.50 * 5.1045 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1195 = 0.22 * 1.00 * 5.1045 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1206 = 0.22 * 1.00 * 5.1073 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    69.07   16.38    None  None   None       |
|    all(noH): 2823   0      1.44    69.07   16.38    None  None   None       |
|    Sol.    : 438    0      5.71    65.95   36.71    None  None   None       |
|    Mac.    : 2385   0      1.44    69.07   12.65    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:     1.445 -   8.207:  558   |   5:    35.255 -  42.017:  124        |
|      1:     8.207 -  14.969: 1322   |   6:    42.017 -  48.780:   90        |
|      2:    14.969 -  21.731:  384   |   7:    48.780 -  55.542:   71        |
|      3:    21.731 -  28.493:  139   |   8:    55.542 -  62.304:   27        |
|      4:    28.493 -  35.255:  102   |   9:    62.304 -  69.066:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1516             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1517             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1517   ksol= 0.33   Bsol= 51.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.45,-1.16,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1517   ksol= 0.33   Bsol= 51.38   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.26,-1.01,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109878                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.784655              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.647  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208171              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.641  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6193 = 1.78 * 0.50 * 5.1082 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6194 = 1.78 * 0.50 * 5.1112 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0711 = 0.21 * 1.00 * 5.1112 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4875 = 0.21 * 1.00 * 5.1141 + 1.00 * 0.4229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.25   16.24    None  None   None       |
|    all(noH): 2823   0      0.00    69.25   16.24    None  None   None       |
|    Sol.    : 438    0      6.27    65.96   36.65    None  None   None       |
|    Mac.    : 2385   0      0.00    69.25   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.925:  338   |   5:    34.623 -  41.547:  127        |
|      1:     6.925 -  13.849: 1432   |   6:    41.547 -  48.472:   95        |
|      2:    13.849 -  20.774:  467   |   7:    48.472 -  55.396:   74        |
|      3:    20.774 -  27.698:  157   |   8:    55.396 -  62.321:   27        |
|      4:    27.698 -  34.623:  100   |   9:    62.321 -  69.245:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1531             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1532             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1532   ksol= 0.33   Bsol= 51.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.26,-1.01,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116215                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1531   ksol= 0.33   Bsol= 51.38   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.07,-0.84,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116305                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.245851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 169.085  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.816919              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.947   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8024 = 2.25 * 0.50 * 5.1150 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8027 = 2.25 * 0.50 * 5.1104 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.0894 = 8.82 * 1.00 * 5.1104 + 1.00 * 0.0317                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.0082 = 8.82 * 1.00 * 5.1037 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.87   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    83.87   16.67    None  None   None       |
|    Sol.    : 438    0      5.90    74.50   39.23    None  None   None       |
|    Mac.    : 2385   0      0.00    83.87   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.387:  724   |   5:    41.935 -  50.321:  102        |
|      1:     8.387 -  16.774: 1304   |   6:    50.321 -  58.708:   83        |
|      2:    16.774 -  25.161:  306   |   7:    58.708 -  67.095:   44        |
|      3:    25.161 -  33.548:  131   |   8:    67.095 -  75.482:   13        |
|      4:    33.548 -  41.935:  111   |   9:    75.482 -  83.869:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1546             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1064 r_free = 0.1546             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1546   ksol= 0.33   Bsol= 51.38   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.07,-0.84,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109591                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.0984 0.1296       5.385      5.5187|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.0829 0.1115      5.4251      5.6272|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.1020 0.1449      5.4599      5.8236|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.1146 0.1554      5.4201      5.5987|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.1248 0.1746      5.2957      5.5401|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.1157 0.1749      5.1899      5.4421|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.1190 0.1564      5.1266      5.3239|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.1084 0.1752      5.0323       5.347|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.1078 0.1650      4.9821      5.2152|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.1045 0.1711      4.9318      5.2408|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.1086 0.1623      4.9161      5.1861|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.1064 0.1719      4.8498      5.2457|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.1035 0.1645      4.7702      5.0361|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.0971 0.1787      4.6407      4.9521|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7721  1371   152  0.94   9.35   0.97     0.94       7282.59|
|  2:  4.7721 -  3.8081  1299   146  0.95   7.78   1.01     0.99       9004.51|
|  3:  3.8081 -  3.3327  1286   141  0.94  10.87   1.02     1.01      10064.90|
|  4:  3.3327 -  3.0308  1281   142  0.93  12.87   1.00     0.98       9731.20|
|  5:  3.0308 -  2.8151  1260   141  0.91  15.28   0.99     0.97       8014.40|
|  6:  2.8151 -  2.6500  1268   141  0.90  15.47   0.98     0.95       6812.73|
|  7:  2.6500 -  2.5180  1264   140  0.91  14.98   0.98     0.96       5841.46|
|  8:  2.5180 -  2.4088  1249   137  0.92  13.98   0.99     0.97       4941.61|
|  9:  2.4088 -  2.3164  1241   141  0.91  14.61   0.99     0.96       4624.92|
| 10:  2.3164 -  2.2368  1243   138  0.91  14.80   0.98     0.94       4123.94|
| 11:  2.2368 -  2.1670  1249   138  0.91  15.60   0.98     0.95       4256.39|
| 12:  2.1670 -  2.1053  1240   139  0.91  14.96   0.99     0.98       3760.99|
| 13:  2.1053 -  2.0500  1247   137  0.91  14.93   0.98     0.97       3276.19|
| 14:  2.0500 -  2.0001  1132   126  0.92  14.32   0.96     0.92       2508.42|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2508.42 max =        10064.90 mean =      6077.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.50|
|phase err.(test): min =        0.00 max =           89.60 mean =        13.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1545   ksol= 0.32   Bsol= 51.38   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-1.79,-0.58,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1545   ksol= 0.32   Bsol= 51.38   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-1.79,-0.58,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109501                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.0982 0.1297      5.3837      5.5176|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.0830 0.1115      5.4257      5.6275|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.1021 0.1449      5.4601      5.8237|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.1146 0.1554      5.4199      5.5986|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.1247 0.1745      5.2954      5.5395|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.1157 0.1750      5.1897       5.442|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.1190 0.1563      5.1266      5.3237|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.1084 0.1751      5.0325      5.3468|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.1078 0.1651      4.9822      5.2155|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.1045 0.1711      4.9319      5.2407|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.1086 0.1622      4.9159      5.1857|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.1065 0.1718      4.8496      5.2456|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.1035 0.1645      4.7702      5.0361|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.0971 0.1787      4.6409      4.9523|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7721  1371   152  0.94   9.33   0.98     0.95       7255.18|
|  2:  4.7721 -  3.8081  1299   146  0.95   7.77   1.01     1.00       8998.12|
|  3:  3.8081 -  3.3327  1286   141  0.94  10.88   1.03     1.02      10067.19|
|  4:  3.3327 -  3.0308  1281   142  0.93  12.86   1.01     0.99       9724.60|
|  5:  3.0308 -  2.8151  1260   141  0.91  15.27   1.00     0.97       8009.57|
|  6:  2.8151 -  2.6500  1268   141  0.90  15.48   0.99     0.96       6808.58|
|  7:  2.6500 -  2.5180  1264   140  0.91  14.98   0.99     0.97       5840.57|
|  8:  2.5180 -  2.4088  1249   137  0.92  13.99   1.00     0.98       4942.25|
|  9:  2.4088 -  2.3164  1241   141  0.91  14.61   1.00     0.97       4626.56|
| 10:  2.3164 -  2.2368  1243   138  0.91  14.80   1.00     0.95       4123.58|
| 11:  2.2368 -  2.1670  1249   138  0.91  15.60   1.00     0.97       4254.18|
| 12:  2.1670 -  2.1053  1240   139  0.91  14.95   1.01     0.99       3759.30|
| 13:  2.1053 -  2.0500  1247   137  0.91  14.93   1.00     0.98       3275.63|
| 14:  2.0500 -  2.0001  1132   126  0.92  14.33   0.97     0.94       2509.38|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2509.38 max =        10067.19 mean =      6074.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.50|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.87   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    83.87   16.67    None  None   None       |
|    Sol.    : 438    0      5.90    74.51   39.23    None  None   None       |
|    Mac.    : 2385   0      0.00    83.87   12.53    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:     0.003 -   8.390:  724   |   5:    41.937 -  50.324:  102        |
|      1:     8.390 -  16.777: 1304   |   6:    50.324 -  58.711:   83        |
|      2:    16.777 -  25.164:  306   |   7:    58.711 -  67.098:   44        |
|      3:    25.164 -  33.551:  131   |   8:    67.098 -  75.485:   13        |
|      4:    33.551 -  41.937:  111   |   9:    75.485 -  83.872:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.496 - 4.790
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 270 from: 276
   mapped sites are within: 0.730 - 4.790

peak=    6.017 closest distance to " NH2 ARG A  56 " =    2.261
peak=    5.352 closest distance to " O   HOH Z 232 " =    2.332
peak=    5.163 closest distance to " CB  ARG A 275 " =    0.926
peak=    5.105 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.032 closest distance to " O   HOH Z 126 " =    1.861
peak=    4.869 closest distance to " CB  SER A  63 " =    1.187
peak=    4.867 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.834 closest distance to " NE2 GLN A  11 " =    1.033
peak=    4.791 closest distance to " O   HOH Z 142 " =    1.663
peak=    4.706 closest distance to " O   HOH Z  78 " =    1.756
peak=    4.658 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.509 closest distance to " O   HOH Z  15 " =    2.223
peak=    4.488 closest distance to " C   PRO A 198 " =    1.444
peak=    4.484 closest distance to " O   HOH Z 427 " =    2.964
peak=    4.458 closest distance to " O   HOH Z 298 " =    1.924
peak=    4.457 closest distance to " O   HOH Z 236 " =    2.058
peak=    4.437 closest distance to " CB  ARG A 190 " =    1.667
peak=    4.423 closest distance to " CB  ARG A  79 " =    1.302
peak=    4.383 closest distance to " OD1 ASN A  69 " =    2.562
peak=    4.352 closest distance to " CB  TYR A 169 " =    0.756
peak=    4.339 closest distance to " CG  PRO A 198 " =    1.266
peak=    4.324 closest distance to " CB  GLU A 152 " =    1.205
peak=    4.299 closest distance to " O   HOH Z 369 " =    2.203
peak=    4.251 closest distance to " O   HOH Z  61 " =    1.630
peak=    4.243 closest distance to " CZ  PHE A 218 " =    1.072
peak=    4.235 closest distance to " O   HOH Z 189 " =    2.441
peak=    4.220 closest distance to " CG2 VAL A 257 " =    0.859
peak=    4.207 closest distance to " O   HOH Z 203 " =    1.684
peak=    4.156 closest distance to " O   HOH Z 250 " =    1.493
peak=    4.150 closest distance to " O   HOH Z 234 " =    3.688
peak=    4.148 closest distance to " O   HOH Z 158 " =    3.034
peak=    4.137 closest distance to " CB  ASN A 148 " =    1.431
peak=    4.137 closest distance to " O   HOH Z 209 " =    2.313
peak=    4.133 closest distance to " O   HOH Z 303 " =    2.057
peak=    4.104 closest distance to " O   HOH Z  40 " =    1.729
peak=    4.103 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.094 closest distance to " CB  ASP A 140 " =    0.940
peak=    4.088 closest distance to " ND2 ASN A 187 " =    1.372
peak=    4.058 closest distance to " CB  TRP A 266 " =    1.005
peak=    4.030 closest distance to " O   HOH Z 193 " =    1.847
peak=    4.024 closest distance to " OG ASER A 258 " =    3.138
peak=    4.015 closest distance to " CA  ASN A 215 " =    1.168
peak=    3.996 closest distance to " O   HOH Z 346 " =    1.668
peak=    3.990 closest distance to " O   HOH Z 197 " =    3.155
peak=    3.977 closest distance to " NZ  LYS A 117 " =    3.260
peak=    3.968 closest distance to " O   HOH Z  19 " =    2.470
peak=    3.963 closest distance to " CB  VAL A 265 " =    1.267
peak=    3.925 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.921 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.919 closest distance to " O   HOH Z  43 " =    1.872
peak=    3.895 closest distance to " O   HOH Z 368 " =    2.080
peak=    3.856 closest distance to " O   HOH Z 261 " =    2.157
peak=    3.850 closest distance to " O   HOH Z  66 " =    2.073
peak=    3.842 closest distance to " CB  GLU A 128 " =    1.028
peak=    3.836 closest distance to " O   SER A  87 " =    2.282
peak=    3.814 closest distance to " CA  ARG A  36 " =    1.022
peak=    3.814 closest distance to " CB  VAL A 202 " =    1.542
peak=    3.813 closest distance to " CD2 TRP A 179 " =    1.359
peak=    3.811 closest distance to " CG  PRO A 243 " =    1.006
peak=    3.807 closest distance to " CB  SER A   3 " =    1.300
peak=    3.794 closest distance to " CD  ARG A  66 " =    2.491
peak=    3.782 closest distance to " O   HOH Z 389 " =    1.889
peak=    3.774 closest distance to " CA  ARG A 195 " =    1.184
peak=    3.774 closest distance to " O   HOH Z 423 " =    1.878
peak=    3.773 closest distance to " O   HOH Z 402 " =    1.398
peak=    3.764 closest distance to " O   HOH Z 280 " =    2.955
peak=    3.745 closest distance to " O   HOH Z 272 " =    1.872
peak=    3.731 closest distance to " O   HOH Z 403 " =    1.606
peak=    3.727 closest distance to " CB  GLU A 277 " =    3.589
peak=    3.719 closest distance to " O   HOH Z 403 " =    1.369
peak=    3.715 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.703 closest distance to " NH1AARG A 145 " =    1.218
peak=    3.681 closest distance to " N   ARG A 156 " =    1.339
peak=    3.677 closest distance to " O   HOH Z 214 " =    2.120
peak=    3.663 closest distance to " O   HOH Z 305 " =    3.581
peak=    3.662 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.654 closest distance to " O   HOH Z 172 " =    3.402
peak=    3.649 closest distance to " OG BSER A 164 " =    2.310
peak=    3.634 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.630 closest distance to " O   HOH Z 371 " =    3.181
peak=    3.624 closest distance to " O   HOH Z  97 " =    1.969
peak=    3.620 closest distance to " CD1 LEU A 300 " =    1.228
peak=    3.618 closest distance to " O   HOH Z 245 " =    1.272
peak=    3.617 closest distance to " O   HOH Z   1 " =    2.030
peak=    3.612 closest distance to " CB  SER A 212 " =    1.108
peak=    3.612 closest distance to " CA  ALA A  51 " =    0.943
peak=    3.610 closest distance to " O   HOH Z 180 " =    2.217
peak=    3.610 closest distance to " CD BLYS A 290 " =    1.033
peak=    3.598 closest distance to " CG1BVAL A  72 " =    1.664
peak=    3.592 closest distance to " O   HOH Z 417 " =    3.137
peak=    3.591 closest distance to " CB  TYR A 116 " =    0.780
peak=    3.588 closest distance to " O   HOH Z   9 " =    2.092
peak=    3.580 closest distance to " O   HOH Z 425 " =    2.004
peak=    3.575 closest distance to " O   HOH Z 248 " =    1.600
peak=    3.565 closest distance to " O   HOH Z 344 " =    3.221
peak=    3.565 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.561 closest distance to " CB  TRP A 179 " =    1.353
peak=    3.559 closest distance to " CG1 ILE A  33 " =    1.216
peak=    3.558 closest distance to " CB  ARG A 139 " =    0.951
peak=    3.552 closest distance to " O   HOH Z 148 " =    3.355
peak=    3.552 closest distance to " CB  THR A  31 " =    1.682
peak=    3.548 closest distance to " O  BHOH Z 338 " =    2.312
peak=    3.547 closest distance to " C   ILE A 106 " =    1.899
peak=    3.546 closest distance to " CB  PRO A  54 " =    0.730
peak=    3.529 closest distance to " CB  HIS A 108 " =    0.824
peak=    3.523 closest distance to " CG2 ILE A 120 " =    1.134
peak=    3.518 closest distance to " CD2 LEU A 297 " =    0.848
peak=    3.515 closest distance to " CB  ASN A 142 " =    1.088
peak=    3.514 closest distance to " O   HOH Z  44 " =    1.711
peak=    3.512 closest distance to " O   HOH Z 291 " =    1.603
peak=    3.509 closest distance to " O   HOH Z 265 " =    2.427
peak=    3.509 closest distance to " O   HOH Z 313 " =    1.970
peak=    3.508 closest distance to " CG1 VAL A 153 " =    0.979
peak=    3.508 closest distance to " O   HOH Z 359 " =    1.460
peak=    3.506 closest distance to " CA  THR A 221 " =    1.029
peak=    3.505 closest distance to " O   HOH Z  59 " =    1.949
peak=    3.498 closest distance to " CB  ALA A 291 " =    1.331
peak=    3.495 closest distance to " OD2 ASP A 286 " =    2.821
peak=    3.494 closest distance to " CB  MET A  47 " =    0.973
peak=    3.493 closest distance to " O   HOH Z  97 " =    2.607
peak=    3.486 closest distance to " CB  ASN A 110 " =    1.135
peak=    3.485 closest distance to " NH2BARG A 145 " =    2.086
peak=    3.480 closest distance to " O   HOH Z 128 " =    2.114
peak=    3.479 closest distance to " O   HOH Z 133 " =    2.569
peak=    3.474 closest distance to " CA  ALA A  21 " =    1.152
peak=    3.472 closest distance to " O   HOH Z 132 " =    2.549
peak=    3.470 closest distance to " CG2 ILE A  20 " =    1.402
peak=    3.462 closest distance to " OG1 THR A 294 " =    2.435
peak=    3.460 closest distance to " CA  MET A  40 " =    1.125
peak=    3.454 closest distance to " O   HOH Z 193 " =    1.645
peak=    3.454 closest distance to " CD1 LEU A  96 " =    0.738
peak=    3.453 closest distance to " NE2 GLN A  73 " =    3.880
peak=    3.447 closest distance to " CB  ILE A 120 " =    1.287
peak=    3.441 closest distance to " CD1 ILE A 106 " =    0.765
peak=    3.439 closest distance to " NH2 ARG A 156 " =    1.174
peak=    3.439 closest distance to " CA  ALA A 158 " =    1.287
peak=    3.437 closest distance to " O   HOH Z 213 " =    1.781
peak=    3.437 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.435 closest distance to " O   HOH Z 261 " =    1.528
peak=    3.430 closest distance to " O   HOH Z 141 " =    1.695
peak=    3.430 closest distance to " CA  SER A  87 " =    1.014
peak=    3.421 closest distance to " O   HOH Z 383 " =    1.807
peak=    3.419 closest distance to " O   HOH Z 185 " =    1.780
peak=    3.413 closest distance to " CA  ALA A 291 " =    0.808
peak=    3.412 closest distance to " CA  ALA A  43 " =    1.252
peak=    3.407 closest distance to " NE2 GLN A  77 " =    3.147
peak=    3.404 closest distance to " O   HOH Z 193 " =    2.081
peak=    3.399 closest distance to " CG2 THR A 221 " =    1.188
peak=    3.398 closest distance to " CE1 TYR A 186 " =    1.329
peak=    3.398 closest distance to " O   HOH Z 298 " =    2.514
peak=    3.390 closest distance to " O   HOH Z 411 " =    3.920
peak=    3.387 closest distance to " CA  THR A 264 " =    0.908
peak=    3.383 closest distance to " O   HOH Z 285 " =    2.802
peak=    3.378 closest distance to " O   HOH Z 368 " =    3.572
peak=    3.377 closest distance to " O   HOH Z 173 " =    1.830
peak=    3.371 closest distance to " CD2 LEU A 255 " =    1.423
peak=    3.367 closest distance to " O   HOH Z 175 " =    2.144
peak=    3.364 closest distance to " O   HOH Z 407 " =    2.485
peak=    3.362 closest distance to " O   HOH Z 419 " =    1.994
peak=    3.361 closest distance to " O   HOH Z 426 " =    1.660
peak=    3.357 closest distance to " OG  SER A  22 " =    2.685
peak=    3.356 closest distance to " O   HOH Z 435 " =    1.949
peak=    3.355 closest distance to " CD  LYS A 119 " =    1.334
peak=    3.354 closest distance to " O   THR A 251 " =    1.218
peak=    3.353 closest distance to " O   HOH Z  21 " =    1.775
peak=    3.351 closest distance to " O   HOH Z  44 " =    3.097
peak=    3.351 closest distance to " O   HOH Z 273 " =    2.816
peak=    3.350 closest distance to " ND1 HIS A  86 " =    1.778
peak=    3.348 closest distance to " CB  SER A 216 " =    0.847
peak=    3.343 closest distance to " CG  LEU A 167 " =    1.259
peak=    3.342 closest distance to " O   HOH Z  88 " =    3.142
peak=    3.338 closest distance to " CB  MET A  40 " =    0.790
peak=    3.337 closest distance to " O   ALA A 165 " =    1.507
peak=    3.336 closest distance to " O   THR A 220 " =    1.252
peak=    3.331 closest distance to " O   HOH Z 337 " =    3.657
peak=    3.319 closest distance to " CB  GLN A  89 " =    1.347
peak=    3.319 closest distance to " O   HOH Z 234 " =    1.923
peak=    3.313 closest distance to " O   HOH Z 421 " =    1.816
peak=    3.313 closest distance to " CG2 ILE A 234 " =    0.812
peak=    3.309 closest distance to " O   HOH Z 219 " =    1.914
peak=    3.308 closest distance to " N   ASN A 127 " =    1.233
peak=    3.306 closest distance to " CA  TYR A 116 " =    1.355
peak=    3.304 closest distance to " O   HOH Z 391 " =    2.903
peak=    3.302 closest distance to " CB  THR A 157 " =    1.050
peak=    3.301 closest distance to " O   HOH Z 329 " =    3.943
peak=    3.298 closest distance to " ND2 ASN A 110 " =    1.653
peak=    3.297 closest distance to " O   HOH Z 258 " =    1.644
peak=    3.292 closest distance to " N   ASN A  39 " =    1.269
peak=    3.286 closest distance to " CD  ARG A  66 " =    2.400
peak=    3.286 closest distance to " CB  SER A  26 " =    1.676
peak=    3.286 closest distance to " CB  ALA A   9 " =    1.515
peak=    3.284 closest distance to " O   HOH Z 128 " =    2.297
peak=    3.284 closest distance to " N   TYR A 116 " =    1.517
peak=    3.280 closest distance to " CB  ALA A 248 " =    1.316
peak=    3.280 closest distance to " O   HOH Z 187 " =    2.273
peak=    3.277 closest distance to " CZ2 TRP A 179 " =    1.712
peak=    3.276 closest distance to " O   HOH Z 353 " =    2.635
peak=    3.275 closest distance to " CB  ALA A  34 " =    0.987
peak=    3.274 closest distance to " CB  GLN A  88 " =    1.190
peak=    3.272 closest distance to " OE1 GLU A   2 " =    2.187
peak=    3.270 closest distance to " O   HOH Z 163 " =    1.756
peak=    3.270 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.268 closest distance to " CD  LYS A 166 " =    1.230
peak=    3.266 closest distance to " O   HOH Z 406 " =    1.479
peak=    3.263 closest distance to " CG2 VAL A 197 " =    1.083
peak=    3.260 closest distance to " O   HOH Z 365 " =    2.951
peak=    3.254 closest distance to " O   HOH Z 433 " =    1.781
peak=    3.252 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.247 closest distance to " CA  ASP A 162 " =    1.087
peak=    3.246 closest distance to " O   HOH Z 325 " =    2.435
peak=    3.244 closest distance to " CA  MET A 105 " =    1.012
peak=    3.242 closest distance to " O   ASN A  74 " =    1.535
peak=    3.241 closest distance to " O   HOH Z  61 " =    1.437
peak=    3.240 closest distance to " O   HOH Z 357 " =    1.917
peak=    3.238 closest distance to " CB  PRO A  90 " =    1.216
peak=    3.233 closest distance to " CG  LYS A  76 " =    0.959
peak=    3.233 closest distance to " O   HOH Z 345 " =    3.389
peak=    3.231 closest distance to " O   HOH Z 299 " =    4.560
peak=    3.230 closest distance to " CD1AILE A 234 " =    0.906
peak=    3.217 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.209 closest distance to " CE  LYS A  48 " =    1.066
peak=    3.207 closest distance to " O   HOH Z 188 " =    2.085
peak=    3.204 closest distance to " CB  ASN A 224 " =    1.010
peak=    3.204 closest distance to " CB  ASN A 215 " =    1.133
peak=    3.203 closest distance to " CA  ALA A 160 " =    0.874
peak=    3.197 closest distance to " CB  SER A 141 " =    1.015
peak=    3.192 closest distance to " O   HOH Z 258 " =    2.236
peak=    3.189 closest distance to " CA  ILE A 234 " =    0.970
peak=    3.185 closest distance to " CA  ALA A  84 " =    1.209
peak=    3.182 closest distance to " O   TRP A 274 " =    1.821
peak=    3.181 closest distance to " CB  SER A  62 " =    1.263
peak=    3.180 closest distance to " O   HOH Z  88 " =    1.970
peak=    3.180 closest distance to " ND2 ASN A 249 " =    0.853
peak=    3.179 closest distance to " O   HOH Z 371 " =    1.753
peak=    3.176 closest distance to " NH1BARG A 145 " =    1.035
peak=    3.173 closest distance to " CB  LEU A 255 " =    0.779
peak=    3.166 closest distance to " CB  SER A  62 " =    0.816
peak=    3.164 closest distance to " O   HOH Z 279 " =    2.176
peak=    3.163 closest distance to " O   HOH Z 437 " =    1.223
peak=    3.161 closest distance to " CE ALYS A 290 " =    1.174
peak=    3.157 closest distance to " CZ  PHE A  38 " =    1.303
peak=    3.157 closest distance to " O   HOH Z 271 " =    2.383
peak=    3.151 closest distance to " CA  ASN A 217 " =    1.165
peak=    3.146 closest distance to " NZ  LYS A  48 " =    1.259
peak=    3.139 closest distance to " CG  GLN A  11 " =    1.581
peak=    3.137 closest distance to " O   HOH Z 285 " =    1.628
peak=    3.134 closest distance to " CG1 ILE A  49 " =    1.487
peak=    3.131 closest distance to " O   HOH Z  62 " =    2.091
peak=    3.126 closest distance to " O   HOH Z 290 " =    0.884
peak=    3.121 closest distance to " ND1 HIS A  81 " =    1.644
peak=    3.120 closest distance to " CB  ALA A   1 " =    4.790
peak=    3.116 closest distance to " CG  PRO A 213 " =    0.971
peak=    3.113 closest distance to " CA  VAL A 125 " =    1.109
peak=    3.112 closest distance to " N   CYS A 260 " =    0.896
peak=    3.108 closest distance to " CB  VAL A 126 " =    1.076
peak=    3.107 closest distance to " CD  ARG A  36 " =    0.958
peak=    3.101 closest distance to " CB  ALA A 114 " =    1.066
peak=    3.097 closest distance to " O   HOH Z  85 " =    2.335
peak=    3.094 closest distance to " CB  ALA A 248 " =    0.885
peak=    3.091 closest distance to " OD1BASN A 224 " =    2.374
peak=    3.090 closest distance to " CA  ARG A 159 " =    1.231
peak=    3.089 closest distance to " CB  LEU A 300 " =    0.905
peak=    3.089 closest distance to " O   HOH Z 409 " =    3.075
peak=    3.088 closest distance to " O   HOH Z 171 " =    2.118
peak=    3.083 closest distance to " NE2 HIS A 207 " =    1.335
peak=    3.075 closest distance to " CA  ASP A 140 " =    1.136
peak=    3.075 closest distance to " CB  LYS A 290 " =    1.147
peak=    3.073 closest distance to " N   SER A 135 " =    1.245
peak=    3.055 closest distance to " CB  ARG A 138 " =    0.916
peak=    3.051 closest distance to " O   HOH Z 423 " =    3.016

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.791 - 5.293
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.791 - 5.293

peak=   -4.629 closest distance to " CD  ARG A 156 " =    2.036
peak=   -4.604 closest distance to " O   HOH Z 266 " =    5.169
peak=   -4.541 closest distance to " SG  CYS A 254 " =    3.543
peak=   -4.498 closest distance to " CD  GLN A  58 " =    1.034
peak=   -4.446 closest distance to " CG  GLN A 223 " =    2.025
peak=   -4.361 closest distance to " O   VAL A  67 " =    2.735
peak=   -4.332 closest distance to " CB  PRO A 243 " =    2.661
peak=   -4.293 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.281 closest distance to " O   HOH Z 231 " =    2.244
peak=   -4.281 closest distance to " O   HOH Z 377 " =    2.114
peak=   -4.228 closest distance to " OG BSER A 134 " =    1.226
peak=   -4.114 closest distance to " O   HOH Z 198 " =    2.039
peak=   -4.095 closest distance to " CE  MET A 105 " =    2.395
peak=   -4.035 closest distance to " O   ILE A 109 " =    2.579
peak=   -3.993 closest distance to " CD2 PHE A 192 " =    2.029
peak=   -3.991 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.970 closest distance to " O   HOH Z 372 " =    2.283
peak=   -3.946 closest distance to " CG2 ILE A 263 " =    2.314
peak=   -3.921 closest distance to " CB  ALA A 291 " =    2.256
peak=   -3.919 closest distance to " CB  ASN A  39 " =    2.350
peak=   -3.907 closest distance to " O   VAL A  67 " =    2.896
peak=   -3.907 closest distance to " O   HOH Z 389 " =    1.926
peak=   -3.900 closest distance to " O   HOH Z 114 " =    3.051
peak=   -3.897 closest distance to " N   ALA A  43 " =    2.667
peak=   -3.888 closest distance to " CE2 TYR A  30 " =    2.726
peak=   -3.886 closest distance to " ND2 ASN A  45 " =    1.731
peak=   -3.854 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.850 closest distance to " OG  SER A  97 " =    2.199
peak=   -3.837 closest distance to " CZ3 TRP A 179 " =    1.141
peak=   -3.813 closest distance to " O   HOH Z 196 " =    2.029
peak=   -3.804 closest distance to " CB  ASP A 132 " =    2.314
peak=   -3.757 closest distance to " O   HOH Z  73 " =    2.186
peak=   -3.737 closest distance to " O   HOH Z 435 " =    2.864
peak=   -3.726 closest distance to " OXT GLY A 302 " =    2.854
peak=   -3.719 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.709 closest distance to " OD1 ASP A 171 " =    1.640
peak=   -3.709 closest distance to " CB  ALA A  43 " =    2.605
peak=   -3.699 closest distance to " O   PRO A 163 " =    2.079
peak=   -3.687 closest distance to " O   PRO A 198 " =    1.302
peak=   -3.680 closest distance to " O   HOH Z 185 " =    2.300
peak=   -3.672 closest distance to " CD  ARG A 139 " =    1.544
peak=   -3.671 closest distance to " CB  ALA A 291 " =    2.417
peak=   -3.659 closest distance to " O   HOH Z 211 " =    1.675
peak=   -3.648 closest distance to " NH2AARG A 275 " =    5.293
peak=   -3.642 closest distance to " O   HOH Z 126 " =    1.901
peak=   -3.640 closest distance to " O   HOH Z 407 " =    3.062
peak=   -3.635 closest distance to " CD1 PHE A  59 " =    1.918
peak=   -3.612 closest distance to " OD1 ASN A 187 " =    1.614
peak=   -3.607 closest distance to " ND2 ASN A  45 " =    1.096
peak=   -3.605 closest distance to " CE2 PHE A 218 " =    2.444
peak=   -3.597 closest distance to " O   HOH Z 313 " =    1.882
peak=   -3.589 closest distance to " CG  PHE A 283 " =    2.562
peak=   -3.586 closest distance to " O   HOH Z  43 " =    1.614
peak=   -3.581 closest distance to " CZ  PHE A  59 " =    1.553
peak=   -3.576 closest distance to " CG  ARG A 269 " =    2.386
peak=   -3.570 closest distance to " O   HOH Z 353 " =    2.101
peak=   -3.566 closest distance to " CA  GLY A 203 " =    2.361
peak=   -3.565 closest distance to " OD2 ASP A 191 " =    1.468
peak=   -3.532 closest distance to " O   HOH Z  44 " =    2.270
peak=   -3.529 closest distance to " O   HOH Z 311 " =    3.704
peak=   -3.523 closest distance to " CD1 LEU A 101 " =    2.310
peak=   -3.515 closest distance to " O   HOH Z 290 " =    1.347
peak=   -3.503 closest distance to " CG1 VAL A 250 " =    2.642
peak=   -3.502 closest distance to " O   HOH Z  51 " =    1.622
peak=   -3.500 closest distance to " NE2 GLN A  88 " =    1.860
peak=   -3.495 closest distance to " O   HOH Z 394 " =    1.489
peak=   -3.494 closest distance to " CD2 PHE A  61 " =    2.529
peak=   -3.490 closest distance to " N   ALA A 248 " =    1.601
peak=   -3.489 closest distance to " O   HOH Z 166 " =    1.980
peak=   -3.487 closest distance to " CB  TYR A  15 " =    2.173
peak=   -3.483 closest distance to " CA  GLY A 241 " =    3.049
peak=   -3.483 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.474 closest distance to " ND2 ASN A 249 " =    2.089
peak=   -3.473 closest distance to " OG  SER A  62 " =    1.743
peak=   -3.471 closest distance to " CA  ASP A 298 " =    1.051
peak=   -3.467 closest distance to " CB  ALA A 248 " =    2.337
peak=   -3.456 closest distance to " O   HOH Z  13 " =    1.610
peak=   -3.453 closest distance to " CB  ALA A 248 " =    2.151
peak=   -3.442 closest distance to " OD1 ASN A 148 " =    1.540
peak=   -3.436 closest distance to " O   HOH Z 292 " =    4.593
peak=   -3.428 closest distance to " NH2 ARG A  79 " =    1.552
peak=   -3.426 closest distance to " O   PHE A 218 " =    1.560
peak=   -3.424 closest distance to " O   HOH Z 351 " =    1.502
peak=   -3.413 closest distance to " CD1 LEU A 228 " =    2.195
peak=   -3.413 closest distance to " NH1 ARG A 195 " =    2.591
peak=   -3.411 closest distance to " C   LEU A 143 " =    1.037
peak=   -3.408 closest distance to " CD  ARG A 195 " =    5.187
peak=   -3.407 closest distance to " CG  GLN A  11 " =    1.811
peak=   -3.400 closest distance to " O   HOH Z  52 " =    1.327
peak=   -3.399 closest distance to " N   SER A 212 " =    1.996
peak=   -3.396 closest distance to " O   HOH Z  11 " =    1.724
peak=   -3.395 closest distance to " C   ALA A 158 " =    1.277
peak=   -3.383 closest distance to " NE2 GLN A 278 " =    1.786
peak=   -3.378 closest distance to " CB  PHE A 208 " =    2.244
peak=   -3.370 closest distance to " O   HOH Z  60 " =    2.300
peak=   -3.370 closest distance to " O   HOH Z 243 " =    2.057
peak=   -3.365 closest distance to " CG  GLU A 277 " =    1.166
peak=   -3.362 closest distance to " CG  ARG A  66 " =    2.405
peak=   -3.362 closest distance to " CZ  TYR A 169 " =    1.750
peak=   -3.361 closest distance to " O   HOH Z 298 " =    1.294
peak=   -3.360 closest distance to " O   SER A 135 " =    1.465
peak=   -3.358 closest distance to " O   ALA A 161 " =    1.720
peak=   -3.356 closest distance to " CA  GLY A 133 " =    2.010
peak=   -3.354 closest distance to " O   HOH Z  38 " =    1.516
peak=   -3.354 closest distance to " SG ACYS A 201 " =    1.882
peak=   -3.348 closest distance to " O   HOH Z 134 " =    3.011
peak=   -3.338 closest distance to " O   HOH Z 102 " =    1.559
peak=   -3.337 closest distance to " O   HOH Z 123 " =    2.264
peak=   -3.328 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.325 closest distance to " CD1 LEU A 297 " =    2.392
peak=   -3.324 closest distance to " O   HOH Z   6 " =    1.426
peak=   -3.317 closest distance to " O   HOH Z 253 " =    3.954
peak=   -3.316 closest distance to " N   THR A 157 " =    1.556
peak=   -3.311 closest distance to " O   ALA A  10 " =    1.679
peak=   -3.309 closest distance to " O   HOH Z 198 " =    1.412
peak=   -3.308 closest distance to " CD1 ILE A 239 " =    2.305
peak=   -3.296 closest distance to " O   GLY A  80 " =    2.469
peak=   -3.290 closest distance to " CB  ASP A 286 " =    2.148
peak=   -3.287 closest distance to " NH2BARG A 275 " =    1.963
peak=   -3.285 closest distance to " OD2 ASP A 171 " =    2.393
peak=   -3.285 closest distance to " CA  GLY A 241 " =    2.818
peak=   -3.284 closest distance to " O   SER A  95 " =    1.565
peak=   -3.280 closest distance to " NE2 GLN A 194 " =    1.732
peak=   -3.272 closest distance to " CZ  PHE A 155 " =    1.262
peak=   -3.270 closest distance to " CD1 ILE A 151 " =    2.409
peak=   -3.269 closest distance to " CB  ASP A 286 " =    1.782
peak=   -3.266 closest distance to " CE3 TRP A 150 " =    2.196
peak=   -3.265 closest distance to " NH2 ARG A  79 " =    2.042
peak=   -3.265 closest distance to " CG2 VAL A 189 " =    2.096
peak=   -3.264 closest distance to " CD2 TYR A 293 " =    2.027
peak=   -3.256 closest distance to " O   HOH Z 295 " =    1.619
peak=   -3.256 closest distance to " C   MET A 188 " =    1.325
peak=   -3.254 closest distance to " O   HOH Z 426 " =    1.574
peak=   -3.244 closest distance to " O   PRO A 198 " =    1.337
peak=   -3.243 closest distance to " ND2 ASN A 187 " =    1.552
peak=   -3.238 closest distance to " O   HOH Z 317 " =    1.580
peak=   -3.237 closest distance to " CZ  PHE A 192 " =    2.901
peak=   -3.231 closest distance to " CA  GLY A 241 " =    2.255
peak=   -3.228 closest distance to " N   ALA A 226 " =    2.046
peak=   -3.225 closest distance to " CG1 VAL A 125 " =    2.007
peak=   -3.219 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.217 closest distance to " O   ALA A  51 " =    1.350
peak=   -3.202 closest distance to " OD2 ASP A 171 " =    1.823
peak=   -3.201 closest distance to " CB  PRO A 163 " =    2.463
peak=   -3.200 closest distance to " N   ASP A 286 " =    2.415
peak=   -3.200 closest distance to " OG BSER A 134 " =    1.791
peak=   -3.197 closest distance to " NH1 ARG A  36 " =    2.079
peak=   -3.193 closest distance to " CD2 HIS A 207 " =    2.414
peak=   -3.188 closest distance to " CG  GLU A   2 " =    1.911
peak=   -3.187 closest distance to " O   HOH Z 322 " =    1.645
peak=   -3.186 closest distance to " OE1 GLN A  88 " =    1.154
peak=   -3.179 closest distance to " O   LYS A 117 " =    1.743
peak=   -3.175 closest distance to " CG2 THR A 221 " =    2.249
peak=   -3.172 closest distance to " O   HOH Z 310 " =    1.733
peak=   -3.170 closest distance to " CG  ASN A 252 " =    1.662
peak=   -3.169 closest distance to " CG  GLU A 152 " =    1.380
peak=   -3.168 closest distance to " CG1AVAL A  41 " =    2.963
peak=   -3.166 closest distance to " O   ALA A 292 " =    2.206
peak=   -3.164 closest distance to " O   PRO A 198 " =    1.795
peak=   -3.162 closest distance to " N   SER A 276 " =    1.258
peak=   -3.161 closest distance to " O   TRP A  70 " =    1.479
peak=   -3.161 closest distance to " CG1 VAL A 197 " =    2.355
peak=   -3.160 closest distance to " OE2 GLU A 152 " =    1.222
peak=   -3.158 closest distance to " CG1 VAL A 125 " =    2.363
peak=   -3.157 closest distance to " OH  TYR A 247 " =    1.866
peak=   -3.154 closest distance to " O   HOH Z 207 " =    2.194
peak=   -3.149 closest distance to " CA  GLY A  98 " =    1.954
peak=   -3.148 closest distance to " O   HOH Z 421 " =    3.080
peak=   -3.144 closest distance to " O   LEU A 101 " =    2.838
peak=   -3.140 closest distance to " CB  PRO A  54 " =    2.400
peak=   -3.136 closest distance to " OG  SER A 206 " =    1.820
peak=   -3.129 closest distance to " C   TRP A 274 " =    1.462
peak=   -3.129 closest distance to " OE1 GLU A  44 " =    2.016
peak=   -3.128 closest distance to " CG1 VAL A  67 " =    3.129
peak=   -3.128 closest distance to " CD1 TYR A 247 " =    2.760
peak=   -3.126 closest distance to " O   HOH Z 414 " =    1.620
peak=   -3.123 closest distance to " CG  PRO A 163 " =    2.480
peak=   -3.115 closest distance to " OD2 ASP A  50 " =    1.584
peak=   -3.104 closest distance to " CG  TRP A 266 " =    1.927
peak=   -3.098 closest distance to " O   HOH Z 111 " =    2.000
peak=   -3.095 closest distance to " ND2 ASN A  60 " =    1.454
peak=   -3.095 closest distance to " O   HOH Z 396 " =    1.695
peak=   -3.095 closest distance to " O   HOH Z  91 " =    1.646
peak=   -3.088 closest distance to " OD1 ASP A 200 " =    1.437
peak=   -3.087 closest distance to " O   HOH Z  11 " =    2.134
peak=   -3.083 closest distance to " O   ARG A 145 " =    1.540
peak=   -3.073 closest distance to " O   HOH Z 357 " =    2.086
peak=   -3.071 closest distance to " O   HOH Z  41 " =    2.488
peak=   -3.064 closest distance to " O   HOH Z 357 " =    2.231
peak=   -3.061 closest distance to " CD1 TRP A  70 " =    1.114
peak=   -3.061 closest distance to " SD  MET A 188 " =    2.192
peak=   -3.050 closest distance to " OD1AASN A 224 " =    1.787
peak=   -3.032 closest distance to " O   HOH Z 175 " =    4.287
peak=   -3.021 closest distance to " O   HOH Z 193 " =    1.745
peak=   -3.015 closest distance to " CD2 LEU A 300 " =    2.914
peak=   -3.003 closest distance to " O   HOH Z 407 " =    3.154

================= 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    :  0.1811 0.1780   5.458209e+00   5.436032e+00
   1_bss:  0.1577 0.1563   5.401527e+00   5.371130e+00
   1_xyz:  0.1248 0.1462   5.174474e+00   5.303560e+00
   1_adp:  0.1151 0.1463   5.120738e+00   5.312727e+00
   1_occ:  0.1146 0.1460   5.118673e+00   5.311824e+00
   2_bss:  0.1149 0.1458   5.119827e+00   5.312018e+00
   2_xyz:  0.1123 0.1486   5.116375e+00   5.332196e+00
   2_adp:  0.1100 0.1491   5.108408e+00   5.337823e+00
   2_occ:  0.1099 0.1491   5.108110e+00   5.338046e+00
   3_bss:  0.1098 0.1491   5.108141e+00   5.338113e+00
   3_xyz:  0.1091 0.1513   5.111518e+00   5.351609e+00
   3_adp:  0.1086 0.1516   5.109673e+00   5.353790e+00
   3_occ:  0.1085 0.1517   5.109918e+00   5.354400e+00
   4_bss:  0.1084 0.1517   5.109878e+00   5.354341e+00
   4_xyz:  0.1088 0.1529   5.115714e+00   5.362910e+00
   4_adp:  0.1088 0.1531   5.116101e+00   5.364368e+00
   4_occ:  0.1088 0.1532   5.116215e+00   5.364698e+00
   5_bss:  0.1087 0.1531   5.116305e+00   5.364763e+00
   5_xyz:  0.1073 0.1531   5.109569e+00   5.363845e+00
   5_adp:  0.1065 0.1546   5.109558e+00   5.370020e+00
   5_occ:  0.1064 0.1546   5.109591e+00   5.370211e+00
   5_bss:  0.1063 0.1545   5.109501e+00   5.370069e+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:  0.328  51.377  -3.191  -2.819  -0.957  -0.000  -0.000  -0.000
   1_xyz:  0.328  51.377  -3.191  -2.819  -0.957  -0.000  -0.000  -0.000
   1_adp:  0.328  51.377  -3.191  -2.819  -0.957  -0.000  -0.000  -0.000
   1_occ:  0.328  51.377  -3.191  -2.819  -0.957  -0.000  -0.000  -0.000
   2_bss:  0.328  51.377  -3.057  -2.691  -1.242  -0.000  -0.000  -0.000
   2_xyz:  0.328  51.377  -3.057  -2.691  -1.242  -0.000  -0.000  -0.000
   2_adp:  0.328  51.377  -3.057  -2.691  -1.242  -0.000  -0.000  -0.000
   2_occ:  0.328  51.377  -3.057  -2.691  -1.242  -0.000  -0.000  -0.000
   3_bss:  0.328  51.377  -2.803  -2.448  -1.160  -0.000  -0.000  -0.000
   3_xyz:  0.328  51.377  -2.803  -2.448  -1.160  -0.000  -0.000  -0.000
   3_adp:  0.328  51.377  -2.803  -2.448  -1.160  -0.000  -0.000  -0.000
   3_occ:  0.328  51.377  -2.803  -2.448  -1.160  -0.000  -0.000  -0.000
   4_bss:  0.325  51.377  -2.597  -2.264  -1.006  -0.000  -0.000  -0.000
   4_xyz:  0.325  51.377  -2.597  -2.264  -1.006  -0.000  -0.000  -0.000
   4_adp:  0.325  51.377  -2.597  -2.264  -1.006  -0.000  -0.000  -0.000
   4_occ:  0.325  51.377  -2.597  -2.264  -1.006  -0.000  -0.000  -0.000
   5_bss:  0.325  51.377  -2.404  -2.072  -0.836  -0.000  -0.000  -0.000
   5_xyz:  0.325  51.377  -2.404  -2.072  -0.836  -0.000  -0.000  -0.000
   5_adp:  0.325  51.377  -2.404  -2.072  -0.836  -0.000  -0.000  -0.000
   5_occ:  0.325  51.377  -2.404  -2.072  -0.836  -0.000  -0.000  -0.000
   5_bss:  0.321  51.380  -2.101  -1.785  -0.576  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  14.823 0.9101  1.0369     8843.445
   1_bss:  13.237 0.9227  0.9676     6111.132
   1_xyz:  12.185 0.9297  0.9752     5401.140
   1_adp:  12.402 0.9276  0.9736     5456.943
   1_occ:  12.385 0.9277  0.9734     5430.386
   2_bss:  12.387 0.9278  0.9729     5447.196
   2_xyz:  12.674 0.9259  0.9705     5681.467
   2_adp:  12.780 0.9250  0.9653     5694.840
   2_occ:  12.787 0.9249  0.9652     5695.835
   3_bss:  12.788 0.9249  0.9720     5698.554
   3_xyz:  13.050 0.9229  0.9719     5895.637
   3_adp:  13.100 0.9225  0.9663     5904.055
   3_occ:  13.112 0.9224  0.9662     5911.230
   4_bss:  13.112 0.9224  0.9726     5909.714
   4_xyz:  13.254 0.9214  0.9716     6016.508
   4_adp:  13.291 0.9211  0.9648     6024.129
   4_occ:  13.297 0.9210  0.9648     6028.890
   5_bss:  13.299 0.9210  0.9713     6030.385
   5_xyz:  13.295 0.9210  0.9718     6032.360
   5_adp:  13.455 0.9196  0.9638     6075.229
   5_occ:  13.459 0.9196  0.9638     6077.772
   5_bss:  13.457 0.9196  0.9738     6074.032
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5994e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5994e-01
   1_xyz:   1.030  0.009  0.079 15.684  0.004  4.115   6.8252e-02
   1_adp:   1.030  0.009  0.079 15.684  0.004  4.115   6.8252e-02
   1_occ:   1.030  0.009  0.079 15.684  0.004  4.115   6.8252e-02
   2_bss:   1.030  0.009  0.079 15.684  0.004  4.115   6.8252e-02
   2_xyz:   0.981  0.008  0.077 15.433  0.004  4.117   6.1727e-02
   2_adp:   0.981  0.008  0.077 15.433  0.004  4.117   6.1727e-02
   2_occ:   0.981  0.008  0.077 15.433  0.004  4.117   6.1727e-02
   3_bss:   0.981  0.008  0.077 15.433  0.004  4.117   6.1727e-02
   3_xyz:   0.976  0.008  0.077 15.413  0.004  4.120   6.1120e-02
   3_adp:   0.976  0.008  0.077 15.413  0.004  4.120   6.1120e-02
   3_occ:   0.976  0.008  0.077 15.413  0.004  4.120   6.1120e-02
   4_bss:   0.976  0.008  0.077 15.413  0.004  4.120   6.1120e-02
   4_xyz:   0.952  0.007  0.075 15.334  0.004  4.120   5.8559e-02
   4_adp:   0.952  0.007  0.075 15.334  0.004  4.120   5.8559e-02
   4_occ:   0.952  0.007  0.075 15.334  0.004  4.120   5.8559e-02
   5_bss:   0.952  0.007  0.075 15.334  0.004  4.120   5.8559e-02
   5_xyz:   1.004  0.008  0.079 15.395  0.004  4.121   6.4132e-02
   5_adp:   1.004  0.008  0.079 15.395  0.004  4.121   6.4132e-02
   5_occ:   1.004  0.008  0.079 15.395  0.004  4.121   6.4132e-02
   5_bss:   1.004  0.008  0.079 15.395  0.004  4.121   6.4132e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4164e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4164e-01
   1_xyz:   7.402  0.045  0.249 83.935  0.038  2.315   5.2501e-02
   1_adp:   7.402  0.045  0.249 83.935  0.038  2.315   5.2501e-02
   1_occ:   7.402  0.045  0.249 83.935  0.038  2.315   5.2501e-02
   2_bss:   7.402  0.045  0.249 83.935  0.038  2.315   5.2501e-02
   2_xyz:   6.675  0.040  0.250 83.718  0.035  2.335   4.2085e-02
   2_adp:   6.675  0.040  0.250 83.718  0.035  2.335   4.2085e-02
   2_occ:   6.675  0.040  0.250 83.718  0.035  2.335   4.2085e-02
   3_bss:   6.675  0.040  0.250 83.718  0.035  2.335   4.2085e-02
   3_xyz:   6.740  0.043  0.250 83.674  0.034  2.340   4.2134e-02
   3_adp:   6.740  0.043  0.250 83.674  0.034  2.340   4.2134e-02
   3_occ:   6.740  0.043  0.250 83.674  0.034  2.340   4.2134e-02
   4_bss:   6.740  0.043  0.250 83.674  0.034  2.340   4.2134e-02
   4_xyz:   6.513  0.043  0.237 83.499  0.034  2.350   3.7691e-02
   4_adp:   6.513  0.043  0.237 83.499  0.034  2.350   3.7691e-02
   4_occ:   6.513  0.043  0.237 83.499  0.034  2.350   3.7691e-02
   5_bss:   6.513  0.043  0.237 83.499  0.034  2.350   3.7691e-02
   5_xyz:   6.818  0.047  0.258 83.618  0.034  2.320   4.4629e-02
   5_adp:   6.818  0.047  0.258 83.618  0.034  2.320   4.4629e-02
   5_occ:   6.818  0.047  0.258 83.618  0.034  2.320   4.4629e-02
   5_bss:   6.818  0.047  0.258 83.618  0.034  2.320   4.4629e-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:  62.73   0.00  16.35  56.65   0.00  12.60  62.73   4.36  36.75
   1_occ:  62.73   0.00  16.35  56.65   0.00  12.60  62.73   4.36  36.75
   2_bss:  62.73   0.00  16.35  56.65   0.00  12.60  62.73   4.36  36.75
   2_xyz:  62.73   0.00  16.35  56.65   0.00  12.60  62.73   4.36  36.75
   2_adp:  65.98   1.99  16.40  65.98   1.99  12.75  65.64   4.66  36.27
   2_occ:  65.98   1.99  16.40  65.98   1.99  12.75  65.64   4.66  36.27
   3_bss:  65.98   1.99  16.40  65.98   1.99  12.75  65.64   4.66  36.27
   3_xyz:  65.98   1.99  16.40  65.98   1.99  12.75  65.64   4.66  36.27
   3_adp:  69.07   1.44  16.38  69.07   1.44  12.65  65.95   5.71  36.71
   3_occ:  69.07   1.44  16.38  69.07   1.44  12.65  65.95   5.71  36.71
   4_bss:  69.07   1.44  16.38  69.07   1.44  12.65  65.95   5.71  36.71
   4_xyz:  69.07   1.44  16.38  69.07   1.44  12.65  65.95   5.71  36.71
   4_adp:  69.25   0.00  16.24  69.25   0.00  12.50  65.96   6.27  36.65
   4_occ:  69.25   0.00  16.24  69.25   0.00  12.50  65.96   6.27  36.65
   5_bss:  69.25   0.00  16.24  69.25   0.00  12.50  65.96   6.27  36.65
   5_xyz:  69.25   0.00  16.24  69.25   0.00  12.50  65.96   6.27  36.65
   5_adp:  83.87   0.00  16.67  83.87   0.00  12.52  74.50   5.90  39.23
   5_occ:  83.87   0.00  16.67  83.87   0.00  12.52  74.50   5.90  39.23
   5_bss:  83.87   0.00  16.67  83.87   0.00  12.53  74.51   5.90  39.23
------------------------------------------------------------------------
 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:    0.472    0.004    0.108
   1_adp:    0.472    0.004    0.108
   1_occ:    0.472    0.004    0.108
   2_bss:    0.472    0.004    0.108
   2_xyz:    0.819    0.003    0.124
   2_adp:    0.819    0.003    0.124
   2_occ:    0.819    0.003    0.124
   3_bss:    0.819    0.003    0.124
   3_xyz:    0.956    0.008    0.132
   3_adp:    0.956    0.008    0.132
   3_occ:    0.956    0.008    0.132
   4_bss:    0.956    0.008    0.132
   4_xyz:    1.032    0.008    0.136
   4_adp:    1.032    0.008    0.136
   4_occ:    1.032    0.008    0.136
   5_bss:    1.032    0.008    0.136
   5_xyz:    1.060    0.006    0.137
   5_adp:    1.060    0.006    0.137
   5_occ:    1.060    0.006    0.137
   5_bss:    1.060    0.006    0.137
------------------------------------------------------------------------

CPU time actual refinement: 319.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/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_666/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_666/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.58 
  Macro-tasks:
    bulk solvent and scale       = 36.53  
    individual site refinement   = 133.23 
    weights calculation          = 29.49  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 205.85 
  Micro-tasks:
    mask                            = 0.58   
    f_calc                          = 101.90 
    alpha_beta                      = 7.93   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.22 
    fmodel                         = 6.36   
    r_factors                      = 0.20   
    phase_errors                   = 11.30  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 240.91 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.527 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    645 calls, 101.57 s
gradients_fft:          590 calls,  97.49 s

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

# Date 2008-01-16 Time 05:22:30 PST -0800 (1200489750.17 s)
Start R-work = 0.1811, R-free = 0.1780 (no bulk solvent and anisotropic scale)
Final R-work = 0.1291, R-free = 0.1723 (no bulk solvent and anisotropic scale)

Start R-work = 0.1577, R-free = 0.1563
Final R-work = 0.1063, R-free = 0.1545