# Date 2008-01-16 Time 04:24:59 PST -0800 (1200486299.25 s)
#phil __OFF__

Command line arguments: "../304.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21104
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 304

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.93, 87.2539, 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: (69.1963, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97074
Completeness in resolution range: 0.948758
Completeness with d_max=infinity: 0.945826

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8679
                             d_min =   1.9707

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97074
Completeness in resolution range: 0.948758
Completeness with d_max=infinity: 0.945826

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8683 -  4.2166 [2174/2201]  1954   220  10.1%
  bin  2:  4.2166 -  3.3595 [2073/2089]  1866   207  10.0%
  bin  3:  3.3595 -  2.9386 [2064/2083]  1859   205   9.9%
  bin  4:  2.9386 -  2.6716 [2039/2069]  1834   205  10.1%
  bin  5:  2.6716 -  2.4811 [2007/2026]  1809   198   9.9%
  bin  6:  2.4811 -  2.3354 [2021/2057]  1815   206  10.2%
  bin  7:  2.3354 -  2.2188 [2011/2044]  1814   197   9.8%
  bin  8:  2.2188 -  2.1225 [1989/2024]  1783   206  10.4%
  bin  9:  2.1225 -  2.0410 [1990/2017]  1799   191   9.6%
  bin 10:  2.0410 -  1.9707 [1221/2037]  1097   124  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/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: 0.14 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:
        1.74 -     2.37: 20
        2.37 -     3.00: 1966
        3.00 -     3.64: 4610
        3.64 -     4.27: 9144
        4.27 -     4.90: 12664
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.741 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.759 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.814 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.881 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28399 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_304/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/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 = 69.19625 46.93 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3028   r_free= 0.2993   ksol= 0.00   Bsol= 0.00   scale= 0.982    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.987465                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7028 0.99   1408  156 0.2643 0.2677      6.3121      6.3016|
|  2:  4.7028 -  3.7525 0.99   1360  153 0.2283 0.2133      6.3221      6.3209|
|  3:  3.7525 -  3.2840 0.99   1324  147 0.2642 0.2510      6.2769      6.2902|
|  4:  3.2840 -  2.9864 0.99   1316  139 0.2761 0.3127      6.1525      6.2628|
|  5:  2.9864 -  2.7738 0.99   1313  149 0.3062 0.2687      6.0327      5.9458|
|  6:  2.7738 -  2.6112 0.99   1313  145 0.3177 0.3551      5.9613      5.9492|
|  7:  2.6112 -  2.4811 0.99   1288  146 0.3121 0.2680      5.9218       5.824|
|  8:  2.4811 -  2.3735 0.98   1294  145 0.3357 0.3147      5.9308      5.8841|
|  9:  2.3735 -  2.2825 0.98   1305  144 0.3447 0.3375      5.8661      5.8774|
| 10:  2.2825 -  2.2040 0.98   1274  136 0.3452 0.3253      5.8709      5.7504|
| 11:  2.2040 -  2.1353 1.00   1300  150 0.3544 0.3650      5.8068      5.8665|
| 12:  2.1353 -  2.0744 0.97   1267  137 0.3537 0.3739      5.7569      5.8312|
| 13:  2.0744 -  2.0199 0.98   1277  140 0.3738 0.3699      5.7034      5.6397|
| 14:  2.0199 -  1.9707 0.46    591   72 0.3562 0.3638      5.6776      5.5735|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7028  1408   156  0.79  25.60   0.87     0.81      40943.24|
|  2:  4.7028 -  3.7525  1360   153  0.86  20.61   0.99     0.93      40794.31|
|  3:  3.7525 -  3.2840  1324   147  0.83  23.66   1.00     0.96      38155.89|
|  4:  3.2840 -  2.9864  1316   139  0.80  26.32   1.00     0.94      33926.05|
|  5:  2.9864 -  2.7738  1313   149  0.74  31.46   1.01     0.92      28697.63|
|  6:  2.7738 -  2.6112  1313   145  0.74  31.93   1.00     0.92      24375.27|
|  7:  2.6112 -  2.4811  1288   146  0.76  30.40   1.02     0.94      20932.66|
|  8:  2.4811 -  2.3735  1294   145  0.76  30.06   1.02     0.95      18665.14|
|  9:  2.3735 -  2.2825  1305   144  0.76  30.78   1.03     0.97      17742.77|
| 10:  2.2825 -  2.2040  1274   136  0.74  32.50   1.06     0.97      17651.79|
| 11:  2.2040 -  2.1353  1300   150  0.71  34.61   1.03     0.99      18573.67|
| 12:  2.1353 -  2.0744  1267   137  0.69  36.68   1.07     0.98      18533.75|
| 13:  2.0744 -  2.0199  1277   140  0.67  38.50   1.04     0.95      16641.46|
| 14:  2.0199 -  1.9707   591    72  0.70  35.87   1.05     0.86      13158.02|
|alpha:            min =        0.81 max =            0.99 mean =         0.94|
|beta:             min =    13158.02 max =        40943.24 mean =     25603.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.96 mean =        30.33|
|phase err.(test): min =        0.00 max =           89.96 mean =        30.18|
|-----------------------------------------------------------------------------|

============================== 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 = 2.434430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.382   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.494265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.903   (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 |  1.741 -  2.057:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.057 -  2.373:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.373 -  2.689:      110 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.689 -  3.005:     1856 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.005 -  3.321:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.321 -  3.637:     2725 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.637 -  3.952:     4715 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.952 -  4.268:     4429 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.268 -  4.584:     5784 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.584 -  4.900:     6880 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.741 |       0.288 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3028   r_free= 0.2993   ksol= 0.00   Bsol= 0.00   scale= 0.982    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.987465                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2888   r_free= 0.2870   ksol= 0.32   Bsol= 40.93   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-2.83,0.53,-0.00,0.00,0.00); trace/3= -1.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.959310                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.169139              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.060   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.643   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2888      final r-factor (work) = 0.1816          |
| start r-factor (free) = 0.2870      final r-factor (free) = 0.2041          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6513 = 2.17 * 0.50 * 5.9764 + 1.00 * 0.1695                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2240 = 2.17 * 0.50 * 5.6846 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1816      final r-factor (work) = 0.1702          |
| start r-factor (free) = 0.2041      final r-factor (free) = 0.2061          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6075 = 0.28 * 1.00 * 5.6846 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6466 = 0.28 * 1.00 * 5.4787 + 1.00 * 0.1039                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.01   16.22    None  None   None       |
|    all(noH): 2823   0      0.00    85.01   16.22    None  None   None       |
|    Sol.    : 438    0      4.92    62.82   37.03    None  None   None       |
|    Mac.    : 2385   0      0.00    85.01   12.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.501:  577   |   5:    42.505 -  51.006:   97        |
|      1:     8.501 -  17.002: 1501   |   6:    51.006 -  59.507:   61        |
|      2:    17.002 -  25.503:  302   |   7:    59.507 -  68.008:    5        |
|      3:    25.503 -  34.004:  145   |   8:    68.008 -  76.508:    0        |
|      4:    34.004 -  42.505:  134   |   9:    76.508 -  85.009:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1702 r_free = 0.2061             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1698 r_free = 0.2059             target_work(ml) = 5.481         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1698   r_free= 0.2059   ksol= 0.32   Bsol= 40.93   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-2.83,0.53,-0.00,0.00,0.00); trace/3= -1.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.481360                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2038   ksol= 0.32   Bsol= 49.52   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.66,-0.78,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.475888                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.501895              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.023   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.628315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.438   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.2038      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6707 = 3.50 * 0.50 * 5.4896 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4113 = 3.50 * 0.50 * 5.3384 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5671 = 0.63 * 1.00 * 5.3384 + 1.00 * 0.2129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2440 = 0.63 * 1.00 * 5.1489 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.21   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    75.21   16.97    None  None   None       |
|    Sol.    : 438    0      4.22    71.11   39.41    None  None   None       |
|    Mac.    : 2385   0      0.00    75.21   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.521:  436   |   5:    37.605 -  45.126:  109        |
|      1:     7.521 -  15.042: 1438   |   6:    45.126 -  52.647:   87        |
|      2:    15.042 -  22.563:  391   |   7:    52.647 -  60.168:   75        |
|      3:    22.563 -  30.084:  136   |   8:    60.168 -  67.689:   34        |
|      4:    30.084 -  37.605:  109   |   9:    67.689 -  75.210:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1556             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1555             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1555   ksol= 0.32   Bsol= 49.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.66,-0.78,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1553   ksol= 0.32   Bsol= 50.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.29,-0.75,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.046604              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.303  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.190110              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.160  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3332 = 2.05 * 0.50 * 5.1493 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3137 = 2.05 * 0.50 * 5.1364 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1217 = 1.19 * 1.00 * 5.1364 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1111 = 1.19 * 1.00 * 5.1269 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.63   16.93    None  None   None       |
|    all(noH): 2823   0      0.00    83.63   16.93    None  None   None       |
|    Sol.    : 438    0      0.00    77.35   39.76    None  None   None       |
|    Mac.    : 2385   0      0.00    83.63   12.74    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 -   8.363:  687   |   5:    41.814 -  50.177:  100        |
|      1:     8.363 -  16.726: 1328   |   6:    50.177 -  58.540:   85        |
|      2:    16.726 -  25.088:  307   |   7:    58.540 -  66.902:   40        |
|      3:    25.088 -  33.451:  130   |   8:    66.902 -  75.265:   22        |
|      4:    33.451 -  41.814:  119   |   9:    75.265 -  83.628:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1542             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1543             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1543   ksol= 0.32   Bsol= 50.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.29,-0.75,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1542   ksol= 0.32   Bsol= 50.62   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.99,-0.58,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129927                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.506903              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.776  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.092459              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.150  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4840 = 2.51 * 0.50 * 5.1270 + 1.00 * 0.0576                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4809 = 2.51 * 0.50 * 5.1199 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4829 = 0.09 * 1.00 * 5.1199 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4808 = 0.09 * 1.00 * 5.1332 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    76.62   15.89    None  None   None       |
|    all(noH): 2823   0      1.79    76.62   15.89    None  None   None       |
|    Sol.    : 438    0      2.38    70.82   35.23    None  None   None       |
|    Mac.    : 2385   0      1.79    76.62   12.34    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:     1.792 -   9.275:  884   |   5:    39.205 -  46.688:   89        |
|      1:     9.275 -  16.757: 1175   |   6:    46.688 -  54.170:   71        |
|      2:    16.757 -  24.240:  281   |   7:    54.170 -  61.653:   27        |
|      3:    24.240 -  31.722:  131   |   8:    61.653 -  69.136:    7        |
|      4:    31.722 -  39.205:  155   |   9:    69.136 -  76.618:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1527             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1527             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1527   ksol= 0.32   Bsol= 50.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.99,-0.58,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126800                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1527   ksol= 0.33   Bsol= 50.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.99,-0.58,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.275074              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.664  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.431606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.013  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3358 = 1.28 * 0.50 * 5.1329 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3266 = 1.28 * 0.50 * 5.1402 + 1.00 * 0.0495                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2247 = 0.43 * 1.00 * 5.1402 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2241 = 0.43 * 1.00 * 5.1341 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    83.19   16.29    None  None   None       |
|    all(noH): 2823   0      0.65    83.19   16.29    None  None   None       |
|    Sol.    : 438    0      3.25    71.99   37.74    None  None   None       |
|    Mac.    : 2385   0      0.65    83.19   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.649 -   8.903:  863   |   5:    41.918 -  50.172:  106        |
|      1:     8.903 -  17.157: 1219   |   6:    50.172 -  58.426:   75        |
|      2:    17.157 -  25.411:  268   |   7:    58.426 -  66.679:   30        |
|      3:    25.411 -  33.664:  133   |   8:    66.679 -  74.933:    8        |
|      4:    33.664 -  41.918:  119   |   9:    74.933 -  83.187:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1546             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1546             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1546   ksol= 0.33   Bsol= 50.62   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.99,-0.58,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7028 0.99   1408  156 0.1028 0.1304      5.4233      5.5542|
|  2:  4.7028 -  3.7525 0.99   1360  153 0.0875 0.1076      5.4494      5.6024|
|  3:  3.7525 -  3.2840 0.99   1324  147 0.1050 0.1544      5.4583      5.8584|
|  4:  3.2840 -  2.9864 0.99   1316  139 0.1187 0.1478      5.4262      5.5771|
|  5:  2.9864 -  2.7738 0.99   1313  149 0.1273 0.1568      5.2924      5.4769|
|  6:  2.7738 -  2.6112 0.99   1313  145 0.1222 0.2022      5.1881      5.4803|
|  7:  2.6112 -  2.4811 0.99   1288  146 0.1234 0.1572      5.1526      5.3025|
|  8:  2.4811 -  2.3735 0.98   1294  145 0.1120 0.1612      5.0568      5.2815|
|  9:  2.3735 -  2.2825 0.98   1305  144 0.1172 0.1907      5.0118      5.3327|
| 10:  2.2825 -  2.2040 0.98   1274  136 0.1127 0.1528      4.9421      5.1108|
| 11:  2.2040 -  2.1353 1.00   1300  150 0.1121 0.1714      4.9092       5.252|
| 12:  2.1353 -  2.0744 0.97   1267  137 0.1116 0.1645      4.8625      5.1834|
| 13:  2.0744 -  2.0199 0.98   1277  140 0.1071 0.1783      4.7651      5.0179|
| 14:  2.0199 -  1.9707 0.46    591   72 0.0970 0.1679      4.6609      4.9327|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7028  1408   156  0.94   9.61   0.98     0.95       7723.38|
|  2:  4.7028 -  3.7525  1360   153  0.95   7.91   1.01     1.00       9017.54|
|  3:  3.7525 -  3.2840  1324   147  0.94  10.91   1.02     1.01       9864.18|
|  4:  3.2840 -  2.9864  1316   139  0.93  12.95   1.00     1.00       9739.99|
|  5:  2.9864 -  2.7738  1313   149  0.91  15.17   0.99     0.96       7671.96|
|  6:  2.7738 -  2.6112  1313   145  0.90  16.13   0.98     0.95       6698.86|
|  7:  2.6112 -  2.4811  1288   146  0.91  14.95   0.98     0.95       5904.07|
|  8:  2.4811 -  2.3735  1294   145  0.91  14.77   0.99     0.97       5229.42|
|  9:  2.3735 -  2.2825  1305   144  0.91  15.29   1.00     0.96       4771.75|
| 10:  2.2825 -  2.2040  1274   136  0.90  15.54   0.99     0.95       4222.69|
| 11:  2.2040 -  2.1353  1300   150  0.90  15.70   0.99     0.95       4130.47|
| 12:  2.1353 -  2.0744  1267   137  0.91  15.05   1.00     1.00       3799.51|
| 13:  2.0744 -  2.0199  1277   140  0.90  15.92   0.99     0.98       3276.42|
| 14:  2.0199 -  1.9707   591    72  0.92  13.99   0.97     0.92       2517.55|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2517.55 max =         9864.18 mean =      6223.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.79|
|phase err.(test): min =        0.00 max =           89.52 mean =        13.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1546   ksol= 0.32   Bsol= 50.60   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.80,-0.41,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137424                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1546   ksol= 0.32   Bsol= 50.60   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.80,-0.41,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137424                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7028 0.99   1408  156 0.1028 0.1305      5.4216      5.5524|
|  2:  4.7028 -  3.7525 0.99   1360  153 0.0876 0.1076      5.4498      5.6027|
|  3:  3.7525 -  3.2840 0.99   1324  147 0.1050 0.1544      5.4583      5.8578|
|  4:  3.2840 -  2.9864 0.99   1316  139 0.1187 0.1478       5.426      5.5769|
|  5:  2.9864 -  2.7738 0.99   1313  149 0.1272 0.1568      5.2924      5.4767|
|  6:  2.7738 -  2.6112 0.99   1313  145 0.1222 0.2022      5.1882      5.4803|
|  7:  2.6112 -  2.4811 0.99   1288  146 0.1234 0.1571      5.1526      5.3021|
|  8:  2.4811 -  2.3735 0.98   1294  145 0.1120 0.1611      5.0567      5.2812|
|  9:  2.3735 -  2.2825 0.98   1305  144 0.1172 0.1908      5.0119      5.3326|
| 10:  2.2825 -  2.2040 0.98   1274  136 0.1127 0.1527      4.9422      5.1103|
| 11:  2.2040 -  2.1353 1.00   1300  150 0.1121 0.1714      4.9093      5.2522|
| 12:  2.1353 -  2.0744 0.97   1267  137 0.1116 0.1646      4.8624      5.1836|
| 13:  2.0744 -  2.0199 0.98   1277  140 0.1071 0.1783      4.7651      5.0176|
| 14:  2.0199 -  1.9707 0.46    591   72 0.0970 0.1681      4.6609      4.9334|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7028  1408   156  0.94   9.59   0.98     0.95       7681.44|
|  2:  4.7028 -  3.7525  1360   153  0.95   7.90   1.01     1.00       9004.40|
|  3:  3.7525 -  3.2840  1324   147  0.94  10.92   1.02     1.02       9862.69|
|  4:  3.2840 -  2.9864  1316   139  0.93  12.94   1.01     1.00       9734.24|
|  5:  2.9864 -  2.7738  1313   149  0.91  15.17   0.99     0.97       7671.08|
|  6:  2.7738 -  2.6112  1313   145  0.90  16.13   0.98     0.96       6699.60|
|  7:  2.6112 -  2.4811  1288   146  0.91  14.94   0.99     0.95       5901.80|
|  8:  2.4811 -  2.3735  1294   145  0.91  14.76   1.00     0.97       5227.41|
|  9:  2.3735 -  2.2825  1305   144  0.91  15.28   1.00     0.96       4768.91|
| 10:  2.2825 -  2.2040  1274   136  0.90  15.54   1.00     0.96       4222.90|
| 11:  2.2040 -  2.1353  1300   150  0.90  15.70   1.00     0.96       4129.71|
| 12:  2.1353 -  2.0744  1267   137  0.91  15.05   1.01     1.00       3799.99|
| 13:  2.0744 -  2.0199  1277   140  0.90  15.93   1.00     0.98       3277.62|
| 14:  2.0199 -  1.9707   591    72  0.92  14.00   0.97     0.93       2519.63|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2519.63 max =         9862.69 mean =      6218.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    83.17   16.26    None  None   None       |
|    all(noH): 2823   0      0.63    83.17   16.26    None  None   None       |
|    Sol.    : 438    0      3.22    71.97   37.71    None  None   None       |
|    Mac.    : 2385   0      0.63    83.17   12.33    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:     0.628 -   8.882:  863   |   5:    41.897 -  50.151:  106        |
|      1:     8.882 -  17.135: 1219   |   6:    50.151 -  58.404:   75        |
|      2:    17.135 -  25.389:  268   |   7:    58.404 -  66.658:   30        |
|      3:    25.389 -  33.643:  133   |   8:    66.658 -  74.912:    8        |
|      4:    33.643 -  41.897:  119   |   9:    74.912 -  83.166:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.544 - 5.429
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 267 from: 275
   mapped sites are within: 0.709 - 5.429

peak=    5.686 closest distance to " CB  ARG A 275 " =    0.937
peak=    5.333 closest distance to " CG  PRO A  54 " =    1.341
peak=    5.270 closest distance to " CB  GLN A 223 " =    1.408
peak=    5.166 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.099 closest distance to " O   HOH Z 232 " =    2.390
peak=    5.007 closest distance to " O   HOH Z 126 " =    1.914
peak=    4.833 closest distance to " CG  PRO A  90 " =    1.268
peak=    4.831 closest distance to " O   HOH Z 142 " =    1.685
peak=    4.821 closest distance to " CG  PRO A 213 " =    1.272
peak=    4.776 closest distance to " CB  PRO A  54 " =    0.995
peak=    4.668 closest distance to " CB  GLU A 152 " =    1.176
peak=    4.655 closest distance to " CA  TYR A  30 " =    0.909
peak=    4.637 closest distance to " NE2 GLN A  11 " =    1.059
peak=    4.612 closest distance to " CG  PRO A 198 " =    1.257
peak=    4.547 closest distance to " CB  GLN A 183 " =    1.201
peak=    4.503 closest distance to " O   HOH Z 250 " =    1.490
peak=    4.482 closest distance to " CZ  PHE A 218 " =    1.065
peak=    4.449 closest distance to " CB  SER A  63 " =    1.180
peak=    4.447 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.421 closest distance to " CG  PRO A 243 " =    1.037
peak=    4.421 closest distance to " O   HOH Z 287 " =    2.108
peak=    4.392 closest distance to " C   PRO A 198 " =    1.500
peak=    4.368 closest distance to " ND2 ASN A 187 " =    1.506
peak=    4.357 closest distance to " O   HOH Z 402 " =    1.404
peak=    4.332 closest distance to " CB  ARG A 190 " =    1.732
peak=    4.331 closest distance to " CB  ARG A  79 " =    1.318
peak=    4.326 closest distance to " O   HOH Z 303 " =    2.079
peak=    4.319 closest distance to " O   HOH Z 369 " =    2.323
peak=    4.268 closest distance to " O   HOH Z  15 " =    2.232
peak=    4.265 closest distance to " O   HOH Z 427 " =    2.963
peak=    4.259 closest distance to " O   HOH Z 298 " =    1.774
peak=    4.244 closest distance to " CG2 VAL A 257 " =    0.875
peak=    4.221 closest distance to " CA  ARG A  36 " =    1.037
peak=    4.212 closest distance to " CD2 TRP A 179 " =    1.336
peak=    4.155 closest distance to " O   HOH Z 158 " =    3.047
peak=    4.123 closest distance to " CB  ASN A 148 " =    1.468
peak=    4.101 closest distance to " CA  ASN A 215 " =    1.051
peak=    4.088 closest distance to " O   SER A  87 " =    2.189
peak=    4.076 closest distance to " O   HOH Z 423 " =    1.935
peak=    4.063 closest distance to " O   HOH Z 128 " =    1.986
peak=    4.056 closest distance to " CB  VAL A 265 " =    1.203
peak=    4.052 closest distance to " O   HOH Z 346 " =    1.686
peak=    4.049 closest distance to " O   HOH Z 209 " =    2.243
peak=    4.030 closest distance to " O   HOH Z  97 " =    2.412
peak=    4.022 closest distance to " O   HOH Z 189 " =    2.666
peak=    4.018 closest distance to " O   HOH Z 234 " =    3.722
peak=    3.992 closest distance to " O   HOH Z  43 " =    1.899
peak=    3.984 closest distance to " OG ASER A 258 " =    3.084
peak=    3.962 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.953 closest distance to " CE  LYS A  76 " =    0.870
peak=    3.936 closest distance to " O   HOH Z  61 " =    1.636
peak=    3.936 closest distance to " O   HOH Z 126 " =    2.053
peak=    3.932 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.931 closest distance to " O   HOH Z 272 " =    1.833
peak=    3.931 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.903 closest distance to " O   HOH Z  40 " =    1.762
peak=    3.897 closest distance to " CB  GLU A  46 " =    1.017
peak=    3.896 closest distance to " O   HOH Z 392 " =    2.965
peak=    3.894 closest distance to " NZ  LYS A 117 " =    3.142
peak=    3.876 closest distance to " CB  THR A  31 " =    1.503
peak=    3.868 closest distance to " O   HOH Z 265 " =    2.301
peak=    3.866 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.855 closest distance to " O   HOH Z  44 " =    1.818
peak=    3.852 closest distance to " O   HOH Z 313 " =    2.010
peak=    3.849 closest distance to " O   HOH Z 389 " =    1.816
peak=    3.848 closest distance to " CG2 ILE A 120 " =    1.164
peak=    3.812 closest distance to " CB  VAL A 202 " =    1.530
peak=    3.809 closest distance to " CB  ASN A 110 " =    1.066
peak=    3.809 closest distance to " CB  LEU A 228 " =    1.068
peak=    3.792 closest distance to " CB  GLU A 128 " =    0.974
peak=    3.748 closest distance to " N   ASN A  39 " =    1.221
peak=    3.748 closest distance to " OD1 ASN A  69 " =    2.540
peak=    3.745 closest distance to " ND2 ASN A 249 " =    0.903
peak=    3.737 closest distance to " CD  ARG A 159 " =    0.709
peak=    3.730 closest distance to " CG  ARG A  66 " =    2.593
peak=    3.727 closest distance to " CB  GLU A 277 " =    3.578
peak=    3.718 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.709 closest distance to " O   HOH Z 193 " =    1.830
peak=    3.708 closest distance to " NH1AARG A 145 " =    1.243
peak=    3.698 closest distance to " O   HOH Z 180 " =    2.198
peak=    3.693 closest distance to " O  BHOH Z  74 " =    1.263
peak=    3.682 closest distance to " CB  ALA A 114 " =    1.086
peak=    3.675 closest distance to " O   HOH Z 128 " =    2.175
peak=    3.671 closest distance to " O   HOH Z  97 " =    2.001
peak=    3.665 closest distance to " N   TYR A 116 " =    1.528
peak=    3.664 closest distance to " O   HOH Z 291 " =    1.534
peak=    3.660 closest distance to " O   HOH Z  66 " =    2.205
peak=    3.652 closest distance to " O   ASN A  74 " =    1.427
peak=    3.651 closest distance to " O   HOH Z 214 " =    2.151
peak=    3.651 closest distance to " CG2AVAL A  72 " =    1.623
peak=    3.649 closest distance to " O   HOH Z  19 " =    2.319
peak=    3.633 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.633 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.630 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.630 closest distance to " CD2 LEU A 297 " =    0.891
peak=    3.623 closest distance to " O   HOH Z 368 " =    3.653
peak=    3.593 closest distance to " O   HOH Z 337 " =    3.565
peak=    3.591 closest distance to " O   HOH Z 421 " =    1.813
peak=    3.591 closest distance to " CB  ALA A 291 " =    1.234
peak=    3.590 closest distance to " O   HOH Z 327 " =    1.591
peak=    3.583 closest distance to " O   HOH Z 353 " =    2.608
peak=    3.580 closest distance to " O   THR A 220 " =    1.241
peak=    3.579 closest distance to " O   HOH Z  54 " =    1.706
peak=    3.568 closest distance to " O   HOH Z 203 " =    1.705
peak=    3.566 closest distance to " O   HOH Z 245 " =    1.327
peak=    3.559 closest distance to " O   HOH Z 173 " =    1.972
peak=    3.554 closest distance to " CB  SER A   3 " =    1.267
peak=    3.552 closest distance to " O   HOH Z  21 " =    1.807
peak=    3.548 closest distance to " O   HOH Z 368 " =    2.072
peak=    3.536 closest distance to " O   HOH Z  10 " =    1.777
peak=    3.523 closest distance to " O   HOH Z 185 " =    1.807
peak=    3.517 closest distance to " O   HOH Z 261 " =    1.821
peak=    3.516 closest distance to " O   HOH Z 406 " =    1.544
peak=    3.514 closest distance to " CB  TYR A 169 " =    0.720
peak=    3.512 closest distance to " O   HOH Z 419 " =    2.136
peak=    3.509 closest distance to " O   HOH Z 227 " =    1.405
peak=    3.508 closest distance to " O   HOH Z 132 " =    2.941
peak=    3.506 closest distance to " CB  ILE A 120 " =    1.239
peak=    3.502 closest distance to " O   HOH Z 365 " =    2.807
peak=    3.500 closest distance to " NH2BARG A 145 " =    2.081
peak=    3.498 closest distance to " CD  LYS A 166 " =    1.213
peak=    3.493 closest distance to " O   HOH Z 280 " =    2.998
peak=    3.492 closest distance to " CB  SER A  26 " =    1.717
peak=    3.485 closest distance to " CB  ALA A 248 " =    1.329
peak=    3.485 closest distance to " CG AARG A 275 " =    1.098
peak=    3.483 closest distance to " CB  ALA A 242 " =    0.928
peak=    3.482 closest distance to " CA  THR A 264 " =    0.905
peak=    3.482 closest distance to " N   ARG A 156 " =    1.388
peak=    3.479 closest distance to " O   HOH Z 344 " =    3.085
peak=    3.479 closest distance to " O   HOH Z 411 " =    3.917
peak=    3.478 closest distance to " O   HOH Z  59 " =    1.988
peak=    3.478 closest distance to " CE1 PHE A  38 " =    1.258
peak=    3.472 closest distance to " OG BSER A 164 " =    2.295
peak=    3.469 closest distance to " O   HOH Z 172 " =    3.524
peak=    3.466 closest distance to " CG  GLU A  37 " =    0.926
peak=    3.465 closest distance to " O   HOH Z  88 " =    2.899
peak=    3.463 closest distance to " O   HOH Z 371 " =    3.027
peak=    3.450 closest distance to " CB  ASP A 140 " =    1.019
peak=    3.449 closest distance to " CA  MET A 105 " =    1.003
peak=    3.448 closest distance to " CB  SER A 212 " =    1.155
peak=    3.446 closest distance to " CG  MET A 185 " =    1.071
peak=    3.439 closest distance to " CE1 TYR A 186 " =    1.322
peak=    3.437 closest distance to " O   HOH Z 248 " =    1.571
peak=    3.437 closest distance to " O   HOH Z 148 " =    3.442
peak=    3.433 closest distance to " N   PHE A 130 " =    1.204
peak=    3.430 closest distance to " CB  PRO A  90 " =    1.034
peak=    3.424 closest distance to " O   HOH Z 147 " =    1.804
peak=    3.421 closest distance to " CD1 LEU A  96 " =    0.713
peak=    3.420 closest distance to " CG  LEU A 167 " =    1.253
peak=    3.418 closest distance to " O   HOH Z 407 " =    2.456
peak=    3.399 closest distance to " OD2 ASP A 286 " =    2.825
peak=    3.397 closest distance to " O   HOH Z 305 " =    3.558
peak=    3.395 closest distance to " CD1 ILE A 199 " =    1.067
peak=    3.384 closest distance to " CB  TRP A 179 " =    1.317
peak=    3.382 closest distance to " CB  GLN A  88 " =    1.123
peak=    3.381 closest distance to " O   HOH Z 403 " =    1.404
peak=    3.376 closest distance to " CA  ASN A 217 " =    1.241
peak=    3.372 closest distance to " O   TRP A 274 " =    1.877
peak=    3.370 closest distance to " CB  GLN A  89 " =    1.319
peak=    3.370 closest distance to " CA  ALA A  51 " =    0.843
peak=    3.365 closest distance to " CZ2 TRP A 179 " =    1.792
peak=    3.365 closest distance to " CA  ILE A 234 " =    0.914
peak=    3.365 closest distance to " CB  HIS A 108 " =    0.854
peak=    3.363 closest distance to " CD1AILE A 234 " =    0.933
peak=    3.346 closest distance to " O   HOH Z 336 " =    1.665
peak=    3.345 closest distance to " CB  ASN A 142 " =    1.059
peak=    3.340 closest distance to " N   HIS A 108 " =    1.912
peak=    3.339 closest distance to " CG2 ILE A  20 " =    1.430
peak=    3.337 closest distance to " CA  GLY A 133 " =    3.637
peak=    3.332 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.332 closest distance to " CG  GLN A  11 " =    1.610
peak=    3.332 closest distance to " CA  ALA A  84 " =    1.329
peak=    3.332 closest distance to " CB  LYS A 290 " =    0.995
peak=    3.329 closest distance to " O   HOH Z  88 " =    2.570
peak=    3.329 closest distance to " O   HOH Z 433 " =    1.820
peak=    3.322 closest distance to " CA  ASP A 162 " =    1.043
peak=    3.322 closest distance to " O   HOH Z 359 " =    1.438
peak=    3.321 closest distance to " CB  MET A  47 " =    1.066
peak=    3.320 closest distance to " O   HOH Z 126 " =    1.571
peak=    3.313 closest distance to " O   HOH Z 417 " =    3.289
peak=    3.312 closest distance to " OG1 THR A 264 " =    0.756
peak=    3.308 closest distance to " CD1 LEU A 300 " =    1.257
peak=    3.298 closest distance to " O   HOH Z 233 " =    1.877
peak=    3.297 closest distance to " CZ3 TRP A 266 " =    1.097
peak=    3.295 closest distance to " CA  ALA A  21 " =    1.077
peak=    3.285 closest distance to " CA  SER A  87 " =    1.012
peak=    3.284 closest distance to " NE2 GLN A  77 " =    3.151
peak=    3.278 closest distance to " O   HOH Z 425 " =    1.951
peak=    3.277 closest distance to " O   HOH Z 329 " =    4.006
peak=    3.272 closest distance to " CB  TYR A 116 " =    0.732
peak=    3.271 closest distance to " O   HOH Z  61 " =    1.435
peak=    3.269 closest distance to " O   HOH Z   1 " =    1.904
peak=    3.265 closest distance to " O   HOH Z 380 " =    1.855
peak=    3.264 closest distance to " O   HOH Z 193 " =    1.999
peak=    3.260 closest distance to " N   ASP A 162 " =    1.064
peak=    3.258 closest distance to " CG  LYS A  76 " =    0.911
peak=    3.254 closest distance to " O   HOH Z 371 " =    1.576
peak=    3.253 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.250 closest distance to " CB  SER A  62 " =    1.387
peak=    3.244 closest distance to " O   HOH Z 257 " =    2.180
peak=    3.239 closest distance to " NE2 HIS A 207 " =    1.230
peak=    3.227 closest distance to " O   HOH Z 430 " =    5.429
peak=    3.227 closest distance to " CA  LYS A 290 " =    1.223
peak=    3.226 closest distance to " CG  GLN A  77 " =    2.080
peak=    3.226 closest distance to " CB  LEU A  83 " =    0.773
peak=    3.225 closest distance to " O   HOH Z 261 " =    1.971
peak=    3.224 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.224 closest distance to " CB  SER A 141 " =    1.003
peak=    3.220 closest distance to " CD1 ILE A 106 " =    0.855
peak=    3.220 closest distance to " CB  SER A  62 " =    1.075
peak=    3.219 closest distance to " OG  SER A  22 " =    2.581
peak=    3.217 closest distance to " CB  ASP A 191 " =    1.209
peak=    3.216 closest distance to " O   ALA A   1 " =    1.682
peak=    3.215 closest distance to " CA  THR A 221 " =    1.013
peak=    3.212 closest distance to " O   HOH Z 294 " =    1.468
peak=    3.205 closest distance to " O   HOH Z 342 " =    0.943
peak=    3.197 closest distance to " CG2 VAL A 197 " =    1.059
peak=    3.195 closest distance to " O   HOH Z  80 " =    1.740
peak=    3.194 closest distance to " CB  PRO A 198 " =    1.188
peak=    3.193 closest distance to " CG1 ILE A 120 " =    1.075
peak=    3.191 closest distance to " O   HOH Z  66 " =    2.148
peak=    3.178 closest distance to " O   HOH Z 213 " =    1.798
peak=    3.176 closest distance to " CB  ALA A  34 " =    1.010
peak=    3.176 closest distance to " O   HOH Z 345 " =    3.251
peak=    3.175 closest distance to " CA  TYR A 116 " =    1.362
peak=    3.174 closest distance to " CG  MET A 113 " =    0.945
peak=    3.173 closest distance to " CB  ARG A 139 " =    0.973
peak=    3.172 closest distance to " O   HOH Z 423 " =    3.079
peak=    3.170 closest distance to " CA  ALA A 248 " =    1.117
peak=    3.170 closest distance to " CE  LYS A 119 " =    1.180
peak=    3.169 closest distance to " CA  ALA A 291 " =    0.758
peak=    3.167 closest distance to " CB  PRO A 243 " =    1.309
peak=    3.166 closest distance to " O   HOH Z 261 " =    2.377
peak=    3.165 closest distance to " CA  ASP A 140 " =    1.133
peak=    3.165 closest distance to " O   HOH Z 383 " =    1.791
peak=    3.162 closest distance to " O   HOH Z  44 " =    3.073
peak=    3.159 closest distance to " O   HOH Z 234 " =    2.292
peak=    3.155 closest distance to " O   HOH Z 273 " =    2.875
peak=    3.154 closest distance to " N   SER A 135 " =    1.254
peak=    3.151 closest distance to " O   HOH Z 394 " =    3.988
peak=    3.149 closest distance to " CB  GLN A 278 " =    0.851
peak=    3.146 closest distance to " O   HOH Z 299 " =    4.356
peak=    3.140 closest distance to " CB  GLN A 103 " =    0.833
peak=    3.138 closest distance to " CB  SER A 210 " =    0.795
peak=    3.136 closest distance to " O   HOH Z 426 " =    1.854
peak=    3.135 closest distance to " CG1 ILE A  49 " =    1.513
peak=    3.135 closest distance to " O   HOH Z 141 " =    1.587
peak=    3.133 closest distance to " CB  LEU A 300 " =    0.936
peak=    3.128 closest distance to " O   HOH Z 302 " =    1.949
peak=    3.126 closest distance to " O   HOH Z 285 " =    2.579
peak=    3.123 closest distance to " NE AARG A 190 " =    2.023
peak=    3.119 closest distance to " CB  THR A 294 " =    1.710
peak=    3.119 closest distance to " CA  ALA A 160 " =    0.905
peak=    3.115 closest distance to " OH  TYR A  30 " =    0.984
peak=    3.112 closest distance to " NE  ARG A  24 " =    0.921
peak=    3.108 closest distance to " CD  LYS A 119 " =    1.340
peak=    3.096 closest distance to " N   GLY A  98 " =    1.041
peak=    3.092 closest distance to " N   VAL A 265 " =    1.236
peak=    3.092 closest distance to " O   HOH Z  85 " =    1.911
peak=    3.073 closest distance to " CA  ARG A 102 " =    1.082
peak=    3.059 closest distance to " CD  ARG A  36 " =    0.973
peak=    3.057 closest distance to " CE AMET A  47 " =    1.438
peak=    3.054 closest distance to " CB  VAL A 126 " =    1.068
peak=    3.054 closest distance to " O   HOH Z 361 " =    3.114
peak=    3.036 closest distance to " CB  ALA A 227 " =    1.130
peak=    3.034 closest distance to " O   SER A 164 " =    1.204
peak=    3.029 closest distance to " CD1 LEU A 261 " =    1.136

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.787 - 5.881
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.787 - 5.881

peak=   -4.902 closest distance to " CD  GLN A  58 " =    1.046
peak=   -4.624 closest distance to " O   HOH Z 266 " =    5.326
peak=   -4.579 closest distance to " CD  ARG A  14 " =    3.411
peak=   -4.424 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.423 closest distance to " OG BSER A 134 " =    1.233
peak=   -4.362 closest distance to " CB  PHE A 192 " =    2.076
peak=   -4.318 closest distance to " CG1 VAL A 112 " =    2.833
peak=   -4.311 closest distance to " CD  ARG A 156 " =    2.097
peak=   -4.297 closest distance to " O   VAL A  67 " =    2.577
peak=   -4.294 closest distance to " O   HOH Z 198 " =    1.635
peak=   -4.286 closest distance to " O   HOH Z 372 " =    2.242
peak=   -4.199 closest distance to " CG  GLN A 223 " =    1.988
peak=   -4.193 closest distance to " O   HOH Z 231 " =    2.297
peak=   -4.182 closest distance to " CB  PRO A 243 " =    2.677
peak=   -4.148 closest distance to " O   PRO A 198 " =    1.226
peak=   -4.134 closest distance to " CB  PRO A 280 " =    2.129
peak=   -4.120 closest distance to " CZ3 TRP A 179 " =    1.222
peak=   -3.986 closest distance to " CA  VAL A  67 " =    2.920
peak=   -3.951 closest distance to " CE  MET A 105 " =    2.551
peak=   -3.950 closest distance to " O   HOH Z 290 " =    1.139
peak=   -3.879 closest distance to " ND2 ASN A  45 " =    1.458
peak=   -3.865 closest distance to " O   HOH Z 351 " =    1.437
peak=   -3.849 closest distance to " CB  ASN A  39 " =    2.326
peak=   -3.838 closest distance to " O   HOH Z 407 " =    2.866
peak=   -3.837 closest distance to " OXT GLY A 302 " =    2.780
peak=   -3.835 closest distance to " CB  ALA A 161 " =    2.551
peak=   -3.826 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.816 closest distance to " CE2 TYR A  30 " =    2.805
peak=   -3.803 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.778 closest distance to " ND2 ASN A 187 " =    1.468
peak=   -3.775 closest distance to " N   ALA A  43 " =    2.587
peak=   -3.774 closest distance to " N   SER A 212 " =    2.043
peak=   -3.764 closest distance to " OD2 ASP A 191 " =    1.393
peak=   -3.754 closest distance to " ND2 ASN A  45 " =    1.050
peak=   -3.703 closest distance to " CD1 LEU A 255 " =    2.778
peak=   -3.699 closest distance to " OD2 ASP A 171 " =    2.391
peak=   -3.693 closest distance to " CA  GLY A 203 " =    2.377
peak=   -3.681 closest distance to " ND2 ASN A 249 " =    2.358
peak=   -3.680 closest distance to " CB  ALA A  43 " =    2.507
peak=   -3.670 closest distance to " O   HOH Z 114 " =    3.163
peak=   -3.661 closest distance to " CG2 ILE A 263 " =    2.291
peak=   -3.646 closest distance to " CD2 TYR A 293 " =    1.987
peak=   -3.621 closest distance to " CB  ALA A 248 " =    2.281
peak=   -3.612 closest distance to " CD1 LEU A 101 " =    2.337
peak=   -3.597 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.579 closest distance to " O   HOH Z  73 " =    2.445
peak=   -3.576 closest distance to " CG  PHE A 283 " =    2.655
peak=   -3.576 closest distance to " O   HOH Z 196 " =    2.029
peak=   -3.572 closest distance to " OD1 ASN A 148 " =    1.478
peak=   -3.569 closest distance to " CZ  TYR A 169 " =    1.807
peak=   -3.562 closest distance to " O   HOH Z 389 " =    1.888
peak=   -3.550 closest distance to " CG  GLU A 277 " =    1.278
peak=   -3.534 closest distance to " O   HOH Z 185 " =    2.354
peak=   -3.533 closest distance to " O   HOH Z 211 " =    1.603
peak=   -3.531 closest distance to " CB  ASP A 132 " =    2.271
peak=   -3.531 closest distance to " O   HOH Z  63 " =    1.590
peak=   -3.527 closest distance to " O   HOH Z 102 " =    1.615
peak=   -3.524 closest distance to " CZ  ARG A  66 " =    1.273
peak=   -3.523 closest distance to " NH2AARG A 275 " =    5.101
peak=   -3.521 closest distance to " NE  ARG A 156 " =    1.936
peak=   -3.517 closest distance to " O   HOH Z 353 " =    2.157
peak=   -3.516 closest distance to " CG  ARG A  66 " =    2.484
peak=   -3.513 closest distance to " CB  ALA A 291 " =    2.268
peak=   -3.505 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.491 closest distance to " CD1 ILE A 239 " =    2.359
peak=   -3.484 closest distance to " CB  ASP A 286 " =    1.788
peak=   -3.477 closest distance to " O   HOH Z 166 " =    2.004
peak=   -3.476 closest distance to " CG2 THR A 178 " =    2.285
peak=   -3.472 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.471 closest distance to " NE2 GLN A 194 " =    1.865
peak=   -3.470 closest distance to " CD1 PHE A  59 " =    1.944
peak=   -3.469 closest distance to " CB  ALA A 248 " =    2.204
peak=   -3.468 closest distance to " O   PHE A 218 " =    1.576
peak=   -3.454 closest distance to " O   HOH Z 394 " =    1.475
peak=   -3.448 closest distance to " O   HOH Z 313 " =    1.875
peak=   -3.447 closest distance to " O   HOH Z  13 " =    1.639
peak=   -3.434 closest distance to " CG1 VAL A  78 " =    3.194
peak=   -3.432 closest distance to " CD  ARG A 195 " =    5.171
peak=   -3.427 closest distance to " O   PRO A 163 " =    2.020
peak=   -3.426 closest distance to " O   SER A  95 " =    1.567
peak=   -3.420 closest distance to " O   HOH Z 292 " =    4.554
peak=   -3.419 closest distance to " N   MET A 188 " =    1.971
peak=   -3.413 closest distance to " O   HOH Z 421 " =    3.228
peak=   -3.411 closest distance to " CE BMET A  47 " =    1.356
peak=   -3.411 closest distance to " O   HOH Z 165 " =    2.003
peak=   -3.405 closest distance to " N   GLN A  58 " =    1.717
peak=   -3.403 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.398 closest distance to " N   THR A  52 " =    1.719
peak=   -3.396 closest distance to " NE2 GLN A 278 " =    1.754
peak=   -3.394 closest distance to " OG  SER A   3 " =    1.712
peak=   -3.392 closest distance to " O   GLN A 240 " =    2.101
peak=   -3.389 closest distance to " O   ALA A 292 " =    2.027
peak=   -3.388 closest distance to " CG  ARG A 269 " =    2.250
peak=   -3.388 closest distance to " CA  ILE A 263 " =    1.119
peak=   -3.381 closest distance to " O   ALA A 161 " =    1.666
peak=   -3.378 closest distance to " CD  GLU A 236 " =    1.060
peak=   -3.378 closest distance to " OD1 ASP A 171 " =    1.560
peak=   -3.377 closest distance to " O   HOH Z 243 " =    1.944
peak=   -3.371 closest distance to " CA  GLY A 241 " =    3.221
peak=   -3.362 closest distance to " CZ  PHE A 155 " =    1.093
peak=   -3.361 closest distance to " O   VAL A 174 " =    2.104
peak=   -3.353 closest distance to " O   HOH Z 348 " =    2.268
peak=   -3.351 closest distance to " O   GLN A  89 " =    1.508
peak=   -3.340 closest distance to " O   ARG A 145 " =    1.610
peak=   -3.338 closest distance to " CG  ASP A 231 " =    0.787
peak=   -3.338 closest distance to " CE2 PHE A 218 " =    2.509
peak=   -3.332 closest distance to " CG1 VAL A 230 " =    2.031
peak=   -3.327 closest distance to " O   ALA A  10 " =    1.721
peak=   -3.323 closest distance to " CB  ALA A   7 " =    2.174
peak=   -3.320 closest distance to " O   HOH Z  10 " =    1.463
peak=   -3.314 closest distance to " OD2 ASP A  50 " =    2.172
peak=   -3.313 closest distance to " CE2 PHE A  61 " =    2.618
peak=   -3.307 closest distance to " CD2 LEU A 237 " =    2.811
peak=   -3.303 closest distance to " O   HOH Z  11 " =    1.695
peak=   -3.300 closest distance to " OE1 GLN A 194 " =    1.727
peak=   -3.299 closest distance to " NH2 ARG A  79 " =    1.556
peak=   -3.295 closest distance to " CG  GLN A  11 " =    1.756
peak=   -3.291 closest distance to " CE3 TRP A 150 " =    2.140
peak=   -3.285 closest distance to " O   HOH Z 317 " =    1.453
peak=   -3.284 closest distance to " O   HOH Z 200 " =    4.731
peak=   -3.277 closest distance to " CA  GLY A 241 " =    2.345
peak=   -3.274 closest distance to " O   VAL A 189 " =    2.685
peak=   -3.272 closest distance to " CB  PRO A 163 " =    2.489
peak=   -3.270 closest distance to " O   HOH Z 134 " =    3.121
peak=   -3.270 closest distance to " CD  GLN A 223 " =    0.843
peak=   -3.269 closest distance to " O   ILE A 106 " =    1.859
peak=   -3.261 closest distance to " C   ASP A 231 " =    2.623
peak=   -3.261 closest distance to " NE2 GLN A  88 " =    1.802
peak=   -3.259 closest distance to " O   HOH Z 385 " =    2.106
peak=   -3.255 closest distance to " CB  TYR A  15 " =    2.176
peak=   -3.253 closest distance to " O   HOH Z 362 " =    5.881
peak=   -3.252 closest distance to " O   VAL A 189 " =    1.634
peak=   -3.250 closest distance to " CG  TRP A 266 " =    1.975
peak=   -3.248 closest distance to " CB  TRP A  85 " =    2.550
peak=   -3.248 closest distance to " O   HOH Z  71 " =    2.103
peak=   -3.237 closest distance to " C   MET A 188 " =    1.349
peak=   -3.236 closest distance to " O   HOH Z 171 " =    1.980
peak=   -3.235 closest distance to " OE2 GLU A 152 " =    1.256
peak=   -3.233 closest distance to " O   HOH Z 174 " =    4.101
peak=   -3.227 closest distance to " ND2 ASN A  60 " =    1.273
peak=   -3.221 closest distance to " O   LEU A 167 " =    1.426
peak=   -3.219 closest distance to " O   HOH Z  37 " =    1.799
peak=   -3.216 closest distance to " CG1 VAL A 250 " =    2.627
peak=   -3.214 closest distance to " NE2 GLN A  88 " =    1.100
peak=   -3.211 closest distance to " O   HOH Z 253 " =    3.844
peak=   -3.202 closest distance to " O   HOH Z 357 " =    2.037
peak=   -3.202 closest distance to " O   HOH Z 369 " =    2.215
peak=   -3.201 closest distance to " O   HOH Z  38 " =    1.709
peak=   -3.200 closest distance to " N   ALA A 226 " =    1.952
peak=   -3.198 closest distance to " O   GLY A 196 " =    1.116
peak=   -3.196 closest distance to " C   ALA A 158 " =    1.430
peak=   -3.192 closest distance to " O   SER A 135 " =    1.479
peak=   -3.187 closest distance to " OD2 ASP A  50 " =    1.548
peak=   -3.187 closest distance to " O   ALA A 180 " =    1.285
peak=   -3.186 closest distance to " O   HOH Z 191 " =    5.769
peak=   -3.186 closest distance to " O   ALA A  34 " =    2.272
peak=   -3.182 closest distance to " N   MET A 105 " =    2.502
peak=   -3.182 closest distance to " O   HOH Z 256 " =    1.419
peak=   -3.180 closest distance to " CD1 LEU A 255 " =    2.632
peak=   -3.178 closest distance to " CB  ASP A 132 " =    2.394
peak=   -3.177 closest distance to " CG  GLU A 152 " =    1.088
peak=   -3.176 closest distance to " CD  ARG A  79 " =    1.147
peak=   -3.175 closest distance to " O   HOH Z 233 " =    2.390
peak=   -3.169 closest distance to " N   ASP A 286 " =    2.251
peak=   -3.157 closest distance to " CE3 TRP A 274 " =    2.428
peak=   -3.149 closest distance to " O   HOH Z 177 " =    1.730
peak=   -3.147 closest distance to " CG2BVAL A  41 " =    2.122
peak=   -3.145 closest distance to " O   HOH Z 210 " =    1.105
peak=   -3.144 closest distance to " O   HOH Z 298 " =    2.464
peak=   -3.139 closest distance to " O   LEU A 101 " =    2.186
peak=   -3.138 closest distance to " O   ALA A 227 " =    1.595
peak=   -3.135 closest distance to " CG  GLU A  53 " =    1.465
peak=   -3.133 closest distance to " O   HOH Z 250 " =    1.337
peak=   -3.133 closest distance to " OE1 GLN A  88 " =    1.077
peak=   -3.126 closest distance to " OG BSER A 134 " =    1.798
peak=   -3.122 closest distance to " OE1 GLN A 183 " =    1.531
peak=   -3.122 closest distance to " O   GLU A 152 " =    1.283
peak=   -3.115 closest distance to " CD1 LEU A   5 " =    2.396
peak=   -3.112 closest distance to " OD1 ASN A 301 " =    1.896
peak=   -3.107 closest distance to " CG  LEU A  83 " =    1.915
peak=   -3.102 closest distance to " CZ2 TRP A 274 " =    1.017
peak=   -3.101 closest distance to " O   ALA A  51 " =    1.232
peak=   -3.095 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.082 closest distance to " O   HOH Z 244 " =    2.023
peak=   -3.082 closest distance to " O   TRP A  92 " =    1.850
peak=   -3.081 closest distance to " CD1 ILE A 199 " =    2.457
peak=   -3.074 closest distance to " O   ALA A   1 " =    1.725
peak=   -3.068 closest distance to " N   GLY A  23 " =    2.425
peak=   -3.064 closest distance to " O   HOH Z 123 " =    2.390
peak=   -3.053 closest distance to " O   HOH Z  60 " =    2.204
peak=   -3.050 closest distance to " O   HOH Z 166 " =    1.637
peak=   -3.034 closest distance to " CG1 VAL A 197 " =    2.181
peak=   -3.033 closest distance to " O   TRP A  70 " =    1.438

================= 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    :  0.3028 0.2993   5.987465e+00   5.970146e+00
   1_bss:  0.2888 0.2870   5.959310e+00   5.938483e+00
   1_xyz:  0.1816 0.2041   5.523927e+00   5.618314e+00
   1_adp:  0.1702 0.2061   5.482931e+00   5.633324e+00
   1_occ:  0.1698 0.2059   5.481360e+00   5.632460e+00
   2_bss:  0.1681 0.2038   5.475888e+00   5.626598e+00
   2_xyz:  0.1238 0.1532   5.189260e+00   5.366767e+00
   2_adp:  0.1151 0.1556   5.153459e+00   5.373324e+00
   2_occ:  0.1150 0.1555   5.153043e+00   5.372994e+00
   3_bss:  0.1150 0.1553   5.152069e+00   5.369331e+00
   3_xyz:  0.1109 0.1536   5.132506e+00   5.364990e+00
   3_adp:  0.1098 0.1542   5.130362e+00   5.369949e+00
   3_occ:  0.1097 0.1543   5.129880e+00   5.370073e+00
   4_bss:  0.1096 0.1542   5.129927e+00   5.369988e+00
   4_xyz:  0.1071 0.1540   5.118830e+00   5.369781e+00
   4_adp:  0.1102 0.1527   5.127088e+00   5.360560e+00
   4_occ:  0.1100 0.1527   5.126800e+00   5.360841e+00
   5_bss:  0.1100 0.1527   5.126972e+00   5.361119e+00
   5_xyz:  0.1130 0.1539   5.145290e+00   5.370739e+00
   5_adp:  0.1108 0.1546   5.137498e+00   5.374598e+00
   5_occ:  0.1108 0.1546   5.137556e+00   5.374817e+00
   5_bss:  0.1107 0.1546   5.137424e+00   5.374569e+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:  0.321  40.932  -0.848  -2.827   0.528  -0.000   0.000   0.000
   1_xyz:  0.321  40.932  -0.848  -2.827   0.528  -0.000   0.000   0.000
   1_adp:  0.321  40.932  -0.848  -2.827   0.528  -0.000   0.000   0.000
   1_occ:  0.321  40.932  -0.848  -2.827   0.528  -0.000   0.000   0.000
   2_bss:  0.325  49.522  -2.734  -2.663  -0.776  -0.000  -0.000  -0.000
   2_xyz:  0.325  49.522  -2.734  -2.663  -0.776  -0.000  -0.000  -0.000
   2_adp:  0.325  49.522  -2.734  -2.663  -0.776  -0.000  -0.000  -0.000
   2_occ:  0.325  49.522  -2.734  -2.663  -0.776  -0.000  -0.000  -0.000
   3_bss:  0.324  50.618  -2.753  -2.287  -0.752  -0.000  -0.000  -0.000
   3_xyz:  0.324  50.618  -2.753  -2.287  -0.752  -0.000  -0.000  -0.000
   3_adp:  0.324  50.618  -2.753  -2.287  -0.752  -0.000  -0.000  -0.000
   3_occ:  0.324  50.618  -2.753  -2.287  -0.752  -0.000  -0.000  -0.000
   4_bss:  0.323  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   4_xyz:  0.323  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   4_adp:  0.323  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   4_occ:  0.323  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   5_bss:  0.330  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   5_xyz:  0.330  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   5_adp:  0.330  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   5_occ:  0.330  50.618  -2.594  -1.993  -0.577  -0.000  -0.000  -0.000
   5_bss:  0.325  50.596  -2.464  -1.797  -0.405  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.314 0.7580  0.9366    25599.806
   1_bss:  28.917 0.7715  0.9237    22395.733
   1_xyz:  19.198 0.8705  0.9999    10568.421
   1_adp:  19.550 0.8669  0.9905    10847.991
   1_occ:  19.546 0.8669  0.9904    10823.671
   2_bss:  19.341 0.8688  0.9557    10631.773
   2_xyz:  13.896 0.9153  0.9779     6177.702
   2_adp:  13.968 0.9149  0.9732     6201.797
   2_occ:  13.963 0.9149  0.9731     6193.679
   3_bss:  13.901 0.9154  0.9773     6130.688
   3_xyz:  13.628 0.9180  0.9776     6080.476
   3_adp:  13.711 0.9175  0.9700     6122.016
   3_occ:  13.716 0.9174  0.9698     6118.360
   4_bss:  13.717 0.9174  0.9769     6117.966
   4_xyz:  13.723 0.9173  0.9780     6136.051
   4_adp:  13.521 0.9189  0.9755     6094.493
   4_occ:  13.527 0.9188  0.9754     6093.838
   5_bss:  13.532 0.9188  0.9755     6100.291
   5_xyz:  13.651 0.9181  0.9746     6204.017
   5_adp:  13.742 0.9174  0.9692     6220.833
   5_occ:  13.747 0.9174  0.9690     6222.036
   5_bss:  13.744 0.9174  0.9740     6216.752
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6945e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6945e-01
   1_xyz:   1.000  0.006  0.067 14.958  0.004  4.110   5.8635e-02
   1_adp:   1.000  0.006  0.067 14.958  0.004  4.110   5.8635e-02
   1_occ:   1.000  0.006  0.067 14.958  0.004  4.110   5.8635e-02
   2_bss:   1.000  0.006  0.067 14.958  0.004  4.110   5.8635e-02
   2_xyz:   1.044  0.008  0.076 14.945  0.004  4.118   6.3963e-02
   2_adp:   1.044  0.008  0.076 14.945  0.004  4.118   6.3963e-02
   2_occ:   1.044  0.008  0.076 14.945  0.004  4.118   6.3963e-02
   3_bss:   1.044  0.008  0.076 14.945  0.004  4.118   6.3963e-02
   3_xyz:   0.977  0.007  0.076 14.697  0.004  4.111   5.7566e-02
   3_adp:   0.977  0.007  0.076 14.697  0.004  4.111   5.7566e-02
   3_occ:   0.977  0.007  0.076 14.697  0.004  4.111   5.7566e-02
   4_bss:   0.977  0.007  0.076 14.697  0.004  4.111   5.7566e-02
   4_xyz:   1.032  0.008  0.079 14.766  0.004  4.112   6.3437e-02
   4_adp:   1.032  0.008  0.079 14.766  0.004  4.112   6.3437e-02
   4_occ:   1.032  0.008  0.079 14.766  0.004  4.112   6.3437e-02
   5_bss:   1.032  0.008  0.079 14.766  0.004  4.112   6.3437e-02
   5_xyz:   0.888  0.005  0.070 14.463  0.004  4.111   4.9547e-02
   5_adp:   0.888  0.005  0.070 14.463  0.004  4.111   4.9547e-02
   5_occ:   0.888  0.005  0.070 14.463  0.004  4.111   4.9547e-02
   5_bss:   0.888  0.005  0.070 14.463  0.004  4.111   4.9547e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.741   2.4047e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.741   2.4047e-01
   1_xyz:   7.870  0.037  0.264 83.844  0.045  2.186   5.8073e-02
   1_adp:   7.870  0.037  0.264 83.844  0.045  2.186   5.8073e-02
   1_occ:   7.870  0.037  0.264 83.844  0.045  2.186   5.8073e-02
   2_bss:   7.870  0.037  0.264 83.844  0.045  2.186   5.8073e-02
   2_xyz:   7.449  0.045  0.272 82.837  0.035  2.283   4.9327e-02
   2_adp:   7.449  0.045  0.272 82.837  0.035  2.283   4.9327e-02
   2_occ:   7.449  0.045  0.272 82.837  0.035  2.283   4.9327e-02
   3_bss:   7.449  0.045  0.272 82.837  0.035  2.283   4.9327e-02
   3_xyz:   6.747  0.046  0.245 82.482  0.038  2.369   3.9844e-02
   3_adp:   6.747  0.046  0.245 82.482  0.038  2.369   3.9844e-02
   3_occ:   6.747  0.046  0.245 82.482  0.038  2.369   3.9844e-02
   4_bss:   6.747  0.046  0.245 82.482  0.038  2.369   3.9844e-02
   4_xyz:   7.064  0.053  0.270 82.493  0.036  2.327   4.7794e-02
   4_adp:   7.064  0.053  0.270 82.493  0.036  2.327   4.7794e-02
   4_occ:   7.064  0.053  0.270 82.493  0.036  2.327   4.7794e-02
   5_bss:   7.064  0.053  0.270 82.493  0.036  2.327   4.7794e-02
   5_xyz:   6.207  0.042  0.218 82.511  0.036  2.371   2.9081e-02
   5_adp:   6.207  0.042  0.218 82.511  0.036  2.371   2.9081e-02
   5_occ:   6.207  0.042  0.218 82.511  0.036  2.371   2.9081e-02
   5_bss:   6.207  0.042  0.218 82.511  0.036  2.371   2.9081e-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:  85.01   0.00  16.22  85.01   0.00  12.40  62.82   4.92  37.03
   1_occ:  85.01   0.00  16.22  85.01   0.00  12.40  62.82   4.92  37.03
   2_bss:  85.01   0.00  16.22  85.01   0.00  12.40  62.82   4.92  37.03
   2_xyz:  85.01   0.00  16.22  85.01   0.00  12.40  62.82   4.92  37.03
   2_adp:  75.21   0.00  16.97  75.21   0.00  12.85  71.11   4.22  39.41
   2_occ:  75.21   0.00  16.97  75.21   0.00  12.85  71.11   4.22  39.41
   3_bss:  75.21   0.00  16.97  75.21   0.00  12.85  71.11   4.22  39.41
   3_xyz:  75.21   0.00  16.97  75.21   0.00  12.85  71.11   4.22  39.41
   3_adp:  83.63   0.00  16.93  83.63   0.00  12.74  77.35   0.00  39.76
   3_occ:  83.63   0.00  16.93  83.63   0.00  12.74  77.35   0.00  39.76
   4_bss:  83.63   0.00  16.93  83.63   0.00  12.74  77.35   0.00  39.76
   4_xyz:  83.63   0.00  16.93  83.63   0.00  12.74  77.35   0.00  39.76
   4_adp:  76.62   1.79  15.89  76.62   1.79  12.34  70.82   2.38  35.23
   4_occ:  76.62   1.79  15.89  76.62   1.79  12.34  70.82   2.38  35.23
   5_bss:  76.62   1.79  15.89  76.62   1.79  12.34  70.82   2.38  35.23
   5_xyz:  76.62   1.79  15.89  76.62   1.79  12.34  70.82   2.38  35.23
   5_adp:  83.19   0.65  16.29  83.19   0.65  12.35  71.99   3.25  37.74
   5_occ:  83.19   0.65  16.29  83.19   0.65  12.35  71.99   3.25  37.74
   5_bss:  83.17   0.63  16.26  83.17   0.63  12.33  71.97   3.22  37.71
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.245    0.011    0.232
   1_adp:    1.245    0.011    0.232
   1_occ:    1.245    0.011    0.232
   2_bss:    1.245    0.011    0.232
   2_xyz:    0.920    0.014    0.318
   2_adp:    0.920    0.014    0.318
   2_occ:    0.920    0.014    0.318
   3_bss:    0.920    0.014    0.318
   3_xyz:    0.969    0.023    0.336
   3_adp:    0.969    0.023    0.336
   3_occ:    0.969    0.023    0.336
   4_bss:    0.969    0.023    0.336
   4_xyz:    1.170    0.024    0.346
   4_adp:    1.170    0.024    0.346
   4_occ:    1.170    0.024    0.346
   5_bss:    1.170    0.024    0.346
   5_xyz:    1.260    0.040    0.347
   5_adp:    1.260    0.040    0.347
   5_occ:    1.260    0.040    0.347
   5_bss:    1.260    0.040    0.347
------------------------------------------------------------------------

CPU time actual refinement: 316.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/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_304/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_304/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.25 
  Macro-tasks:
    bulk solvent and scale       = 35.81  
    individual site refinement   = 131.23 
    weights calculation          = 28.48  
    collect and process          = 6.62   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.23 
  Micro-tasks:
    mask                            = 1.14   
    f_calc                          = 100.84 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.86 
    fmodel                         = 6.32   
    r_factors                      = 0.18   
    phase_errors                   = 11.17  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 239.18 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.513 micro seconds
Total CPU time: 5.49 minutes
from_scatterers_fft:    640 calls, 100.49 s
gradients_fft:          585 calls,  96.68 s

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

# Date 2008-01-16 Time 04:30:29 PST -0800 (1200486629.35 s)
Start R-work = 0.3028, R-free = 0.2993 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1733 (no bulk solvent and anisotropic scale)

Start R-work = 0.2888, R-free = 0.2870
Final R-work = 0.1107, R-free = 0.1546