# Date 2008-01-16 Time 05:49:27 PST -0800 (1200491367.21 s)
#phil __OFF__

Command line arguments: "../895.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16603
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 895

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.6953, 85.9581, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99038
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.968745

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99038
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.968745

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2590 [2111/2136]  1901   210   9.9%
  bin  2:  4.2590 -  3.3931 [2038/2058]  1833   205  10.1%
  bin  3:  3.3931 -  2.9679 [2005/2024]  1802   203  10.1%
  bin  4:  2.9679 -  2.6983 [1989/2019]  1797   192   9.7%
  bin  5:  2.6983 -  2.5058 [1983/2002]  1786   197   9.9%
  bin  6:  2.5058 -  2.3586 [1964/1989]  1764   200  10.2%
  bin  7:  2.3586 -  2.2409 [1948/1976]  1748   200  10.3%
  bin  8:  2.2409 -  2.1437 [1958/1994]  1764   194   9.9%
  bin  9:  2.1437 -  2.0613 [1951/1993]  1761   190   9.7%
  bin 10:  2.0613 -  1.9904 [1642/1968]  1474   168  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2195
        3.04 -     3.66: 4677
        3.66 -     4.28: 9055
        4.28 -     4.90: 12319
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.255 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.255 3.040 -x+1/2,-y+1,z-1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28254 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_895/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 85.95805 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: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2603   r_free= 0.2616   ksol= 0.00   Bsol= 0.00   scale= 0.996    |
|                                                                             |
| 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:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.840236                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7502 0.99   1380  154 0.2641 0.2491      6.2824      6.2092|
|  2:  4.7502 -  3.7901 0.99   1324  145 0.2017 0.2053      6.2089      6.2062|
|  3:  3.7901 -  3.3168 0.99   1289  143 0.2108 0.2051      6.0735      6.1961|
|  4:  3.3168 -  3.0162 0.99   1283  147 0.2255 0.2463      5.9929      6.0212|
|  5:  3.0162 -  2.8015 0.99   1291  140 0.2595 0.2561      5.8902      5.9426|
|  6:  2.8015 -  2.6372 0.99   1276  142 0.2587 0.2785      5.8165      5.7931|
|  7:  2.6372 -  2.5058 0.99   1276  136 0.2782 0.2588      5.8085      5.8108|
|  8:  2.5058 -  2.3972 0.98   1254  147 0.2852 0.2666      5.7771      5.7396|
|  9:  2.3972 -  2.3052 0.98   1256  137 0.2722 0.2880      5.6922      5.6873|
| 10:  2.3052 -  2.2259 1.00   1269  141 0.2850 0.2926      5.6987      5.6954|
| 11:  2.2259 -  2.1565 0.97   1248  137 0.2970 0.2971      5.6805      5.7315|
| 12:  2.1565 -  2.0951 0.98   1242  142 0.2984 0.2934      5.6239      5.6582|
| 13:  2.0951 -  2.0400 1.00   1259  136 0.3022 0.3285      5.5578      5.5502|
| 14:  2.0400 -  1.9904 0.77    983  112 0.3056 0.3035      5.5142      5.4074|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7502  1380   154  0.82  23.64   0.87     0.83      35155.72|
|  2:  4.7502 -  3.7901  1324   145  0.88  17.85   0.99     0.94      31547.38|
|  3:  3.7901 -  3.3168  1289   143  0.86  20.22   1.02     0.99      28214.94|
|  4:  3.3168 -  3.0162  1283   147  0.85  21.44   1.02     0.99      24249.69|
|  5:  3.0162 -  2.8015  1291   140  0.81  25.62   1.01     0.97      20486.68|
|  6:  2.8015 -  2.6372  1276   142  0.82  25.09   1.03     0.97      17229.17|
|  7:  2.6372 -  2.5058  1276   136  0.81  25.40   1.03     0.99      15415.11|
|  8:  2.5058 -  2.3972  1254   147  0.81  25.55   1.04     1.00      14023.10|
|  9:  2.3972 -  2.3052  1256   137  0.82  25.33   1.06     1.02      13196.71|
| 10:  2.3052 -  2.2259  1269   141  0.80  26.76   1.08     1.03      13063.97|
| 11:  2.2259 -  2.1565  1248   137  0.78  28.46   1.10     1.02      13000.49|
| 12:  2.1565 -  2.0951  1242   142  0.78  28.56   1.08     1.03      12240.90|
| 13:  2.0951 -  2.0400  1259   136  0.77  29.42   1.09     1.01      10375.76|
| 14:  2.0400 -  1.9904   983   112  0.80  27.19   1.08     0.99       7936.20|
|alpha:            min =        0.83 max =            1.03 mean =         0.98|
|beta:             min =     7936.20 max =        35155.72 mean =     18655.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.82|
|phase err.(work): min =        0.00 max =           90.00 mean =        24.95|
|phase err.(test): min =        0.00 max =           89.90 mean =        24.69|
|-----------------------------------------------------------------------------|

============================== 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 = 3.307012              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.491   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.485   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      201 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1994 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1834 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2843 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4662 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4393 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5616 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6703 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.141 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    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: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2603   r_free= 0.2616   ksol= 0.00   Bsol= 0.00   scale= 0.996    |
|                                                                             |
| 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:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.840236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2445   r_free= 0.2464   ksol= 0.33   Bsol= 50.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.17,-1.47,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.809078                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.996521              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.763   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.275   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2445      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2464      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9123 = 3.00 * 0.50 * 5.8415 + 1.00 * 0.1601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3068 = 3.00 * 0.50 * 5.5064 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1422      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2341 = 0.22 * 1.00 * 5.5064 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2048 = 0.22 * 1.00 * 5.2401 + 1.00 * 0.0364                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.99   16.43    None  None   None       |
|    all(noH): 2823   0      0.00    66.99   16.43    None  None   None       |
|    Sol.    : 438    0      6.74    62.74   37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    66.99   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.699:  196   |   5:    33.497 -  40.196:  100        |
|      1:     6.699 -  13.399: 1436   |   6:    40.196 -  46.896:   87        |
|      2:    13.399 -  20.098:  583   |   7:    46.896 -  53.595:   74        |
|      3:    20.098 -  26.798:  170   |   8:    53.595 -  60.294:   41        |
|      4:    26.798 -  33.497:  130   |   9:    60.294 -  66.994:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1642             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1642             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1642   ksol= 0.33   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.17,-1.47,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.245438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1629   ksol= 0.33   Bsol= 49.99   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.80,-1.82,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.246781                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.746029              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.710   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6393 = 1.75 * 0.50 * 5.2491 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5847 = 1.75 * 0.50 * 5.1875 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2579 = 0.23 * 1.00 * 5.1875 + 1.00 * 0.0404                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2124 = 0.23 * 1.00 * 5.1345 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.83    70.69   16.79    None  None   None       |
|    all(noH): 2823   0      1.83    70.69   16.79    None  None   None       |
|    Sol.    : 438    0      5.62    68.95   37.87    None  None   None       |
|    Mac.    : 2385   0      1.83    70.69   12.92    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:     1.831 -   8.716:  632   |   5:    36.259 -  43.144:  107        |
|      1:     8.716 -  15.602: 1279   |   6:    43.144 -  50.030:   88        |
|      2:    15.602 -  22.488:  369   |   7:    50.030 -  56.915:   76        |
|      3:    22.488 -  29.373:  128   |   8:    56.915 -  63.801:   29        |
|      4:    29.373 -  36.259:  106   |   9:    63.801 -  70.686:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1522             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1522             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1522   ksol= 0.33   Bsol= 49.99   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.80,-1.82,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131285                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1522   ksol= 0.33   Bsol= 49.99   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.61,-1.58,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131275                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.286099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.989  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.291634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.508  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3579 = 1.29 * 0.50 * 5.1350 + 1.00 * 0.0559                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3488 = 1.29 * 0.50 * 5.1294 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5033 = 0.29 * 1.00 * 5.1294 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5037 = 0.29 * 1.00 * 5.1297 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    73.15   16.74    None  None   None       |
|    all(noH): 2823   0      1.51    73.15   16.74    None  None   None       |
|    Sol.    : 438    0      5.95    70.10   37.93    None  None   None       |
|    Mac.    : 2385   0      1.51    73.15   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.506 -   8.670:  679   |   5:    37.327 -  44.492:  118        |
|      1:     8.670 -  15.834: 1250   |   6:    44.492 -  51.656:   84        |
|      2:    15.834 -  22.999:  364   |   7:    51.656 -  58.820:   66        |
|      3:    22.999 -  30.163:  129   |   8:    58.820 -  65.985:   23        |
|      4:    30.163 -  37.327:  102   |   9:    65.985 -  73.149:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1534             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1534             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1534   ksol= 0.33   Bsol= 49.99   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.61,-1.58,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1534   ksol= 0.32   Bsol= 49.99   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.46,-1.41,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132042                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.603416              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.514  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.390438              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.081  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1631 = 1.60 * 0.50 * 5.1301 + 1.00 * 0.0503                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1616 = 1.60 * 0.50 * 5.1220 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0075 = 0.39 * 1.00 * 5.1220 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0068 = 0.39 * 1.00 * 5.1189 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    76.80   16.68    None  None   None       |
|    all(noH): 2823   0      1.12    76.80   16.68    None  None   None       |
|    Sol.    : 438    0      6.46    71.87   38.16    None  None   None       |
|    Mac.    : 2385   0      1.12    76.80   12.73    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:     1.119 -   8.687:  721   |   5:    38.959 -  46.527:  110        |
|      1:     8.687 -  16.255: 1247   |   6:    46.527 -  54.095:   88        |
|      2:    16.255 -  23.823:  347   |   7:    54.095 -  61.663:   48        |
|      3:    23.823 -  31.391:  127   |   8:    61.663 -  69.231:   17        |
|      4:    31.391 -  38.959:  110   |   9:    69.231 -  76.799:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1538             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1538             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1538   ksol= 0.32   Bsol= 49.99   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.46,-1.41,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119957                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1538   ksol= 0.32   Bsol= 49.99   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.22,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120072                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.328796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.912  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.605655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.376  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5766 = 3.33 * 0.50 * 5.1198 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5681 = 3.33 * 0.50 * 5.1038 + 1.00 * 0.0733                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1049      final r-factor (work) = 0.1047          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0993 = 0.61 * 1.00 * 5.1038 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0972 = 0.61 * 1.00 * 5.0995 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    81.33   16.61    None  None   None       |
|    all(noH): 2823   0      0.91    81.33   16.61    None  None   None       |
|    Sol.    : 438    0      6.23    73.57   38.48    None  None   None       |
|    Mac.    : 2385   0      0.91    81.33   12.59    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:     0.907 -   8.949:  849   |   5:    41.120 -  49.162:  106        |
|      1:     8.949 -  16.992: 1189   |   6:    49.162 -  57.205:   85        |
|      2:    16.992 -  25.035:  299   |   7:    57.205 -  65.248:   36        |
|      3:    25.035 -  33.077:  131   |   8:    65.248 -  73.290:   14        |
|      4:    33.077 -  41.120:  109   |   9:    73.290 -  81.333:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1047 r_free = 0.1548             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1046 r_free = 0.1548             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1046   r_free= 0.1548   ksol= 0.32   Bsol= 49.99   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.22,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.101475                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7502 0.99   1380  154 0.0966 0.1268      5.3674      5.5207|
|  2:  4.7502 -  3.7901 0.99   1324  145 0.0825 0.1136       5.416      5.6231|
|  3:  3.7901 -  3.3168 0.99   1289  143 0.1010 0.1476      5.4485      5.8333|
|  4:  3.3168 -  3.0162 0.99   1283  147 0.1144 0.1554      5.4243      5.5751|
|  5:  3.0162 -  2.8015 0.99   1291  140 0.1249 0.1754      5.2975      5.5629|
|  6:  2.8015 -  2.6372 0.99   1276  142 0.1109 0.1803      5.1733       5.405|
|  7:  2.6372 -  2.5058 0.99   1276  136 0.1189 0.1548      5.1272      5.3454|
|  8:  2.5058 -  2.3972 0.98   1254  147 0.1060 0.1680      4.9977      5.3164|
|  9:  2.3972 -  2.3052 0.98   1256  137 0.1076 0.1619      4.9817       5.223|
| 10:  2.3052 -  2.2259 1.00   1269  141 0.1004 0.1748      4.9038      5.2568|
| 11:  2.2259 -  2.1565 0.97   1248  137 0.1035 0.1649      4.9034      5.2123|
| 12:  2.1565 -  2.0951 0.98   1242  142 0.1037 0.1665      4.8384      5.1709|
| 13:  2.0951 -  2.0400 1.00   1259  136 0.1024 0.1732      4.7499      5.0747|
| 14:  2.0400 -  1.9904 0.77    983  112 0.0982 0.1689      4.6188      4.8747|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7502  1380   154  0.94   9.03   0.98     0.95       6996.11|
|  2:  4.7502 -  3.7901  1324   145  0.95   7.80   1.01     1.00       8914.52|
|  3:  3.7901 -  3.3168  1289   143  0.94  10.91   1.02     1.01      10058.50|
|  4:  3.3168 -  3.0162  1283   147  0.92  13.20   1.01     0.98       9938.31|
|  5:  3.0162 -  2.8015  1291   140  0.90  15.87   0.99     0.96       8203.86|
|  6:  2.8015 -  2.6372  1276   142  0.91  15.23   0.99     0.96       6852.62|
|  7:  2.6372 -  2.5058  1276   136  0.91  15.02   0.98     0.95       5850.08|
|  8:  2.5058 -  2.3972  1254   147  0.92  14.20   0.99     0.97       4714.46|
|  9:  2.3972 -  2.3052  1256   137  0.92  14.32   1.00     0.97       4571.28|
| 10:  2.3052 -  2.2259  1269   141  0.91  14.44   0.99     0.95       4001.75|
| 11:  2.2259 -  2.1565  1248   137  0.90  16.13   0.99     0.96       4232.16|
| 12:  2.1565 -  2.0951  1242   142  0.92  14.22   1.00     0.98       3716.64|
| 13:  2.0951 -  2.0400  1259   136  0.91  15.25   1.00     0.99       3186.61|
| 14:  2.0400 -  1.9904   983   112  0.92  13.91   0.97     0.93       2362.96|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2362.96 max =        10058.50 mean =      6065.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.48|
|phase err.(test): min =        0.00 max =           88.58 mean =        13.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1542   ksol= 0.32   Bsol= 49.96   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.09,-1.03,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1542   ksol= 0.32   Bsol= 49.96   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.09,-1.03,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7502 0.99   1380  154 0.0988 0.1252      5.3813      5.5068|
|  2:  4.7502 -  3.7901 0.99   1324  145 0.0831 0.1121      5.4182      5.6146|
|  3:  3.7901 -  3.3168 0.99   1289  143 0.1004 0.1457      5.4436      5.8228|
|  4:  3.3168 -  3.0162 0.99   1283  147 0.1145 0.1552      5.4207       5.578|
|  5:  3.0162 -  2.8015 0.99   1291  140 0.1252 0.1731      5.2952      5.5556|
|  6:  2.8015 -  2.6372 0.99   1276  142 0.1107 0.1788      5.1706      5.4001|
|  7:  2.6372 -  2.5058 0.99   1276  136 0.1190 0.1555      5.1278      5.3476|
|  8:  2.5058 -  2.3972 0.98   1254  147 0.1061 0.1687      4.9988      5.3199|
|  9:  2.3972 -  2.3052 0.98   1256  137 0.1076 0.1618      4.9828      5.2232|
| 10:  2.3052 -  2.2259 1.00   1269  141 0.1007 0.1753      4.9049      5.2592|
| 11:  2.2259 -  2.1565 0.97   1248  137 0.1036 0.1655      4.9049      5.2142|
| 12:  2.1565 -  2.0951 0.98   1242  142 0.1037 0.1670      4.8394      5.1732|
| 13:  2.0951 -  2.0400 1.00   1259  136 0.1023 0.1734      4.7509      5.0753|
| 14:  2.0400 -  1.9904 0.77    983  112 0.0982 0.1692      4.6194      4.8763|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7502  1380   154  0.94   9.11   0.98     0.95       6983.74|
|  2:  4.7502 -  3.7901  1324   145  0.95   7.70   1.01     1.01       8786.40|
|  3:  3.7901 -  3.3168  1289   143  0.94  10.80   1.02     1.02       9898.68|
|  4:  3.3168 -  3.0162  1283   147  0.92  13.15   1.01     0.99       9853.21|
|  5:  3.0162 -  2.8015  1291   140  0.90  15.78   1.00     0.97       8129.39|
|  6:  2.8015 -  2.6372  1276   142  0.91  15.18   0.99     0.96       6800.40|
|  7:  2.6372 -  2.5058  1276   136  0.91  15.02   0.99     0.96       5846.20|
|  8:  2.5058 -  2.3972  1254   147  0.92  14.24   1.00     0.97       4733.22|
|  9:  2.3972 -  2.3052  1256   137  0.92  14.36   1.00     0.98       4587.24|
| 10:  2.3052 -  2.2259  1269   141  0.91  14.47   1.00     0.96       4014.28|
| 11:  2.2259 -  2.1565  1248   137  0.90  16.17   1.00     0.97       4247.08|
| 12:  2.1565 -  2.0951  1242   142  0.92  14.25   1.01     0.99       3730.74|
| 13:  2.0951 -  2.0400  1259   136  0.91  15.28   1.00     0.99       3198.26|
| 14:  2.0400 -  1.9904   983   112  0.92  13.93   0.98     0.94       2370.01|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2370.01 max =         9898.68 mean =      6034.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.47|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.04|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.931)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    81.30   16.58    None  None   None       |
|    all(noH): 2823   0      0.88    81.30   16.58    None  None   None       |
|    Sol.    : 438    0      6.20    73.53   38.45    None  None   None       |
|    Mac.    : 2385   0      0.88    81.30   12.56    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:     0.876 -   8.918:  849   |   5:    41.089 -  49.131:  106        |
|      1:     8.918 -  16.961: 1189   |   6:    49.131 -  57.174:   85        |
|      2:    16.961 -  25.003:  299   |   7:    57.174 -  65.216:   36        |
|      3:    25.003 -  33.046:  131   |   8:    65.216 -  73.259:   14        |
|      4:    33.046 -  41.089:  109   |   9:    73.259 -  81.302:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.476 - 4.680
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 279
   mapped sites are within: 0.727 - 4.680

peak=    5.878 closest distance to " NH2 ARG A  56 " =    2.229
peak=    5.483 closest distance to " CG  PRO A  54 " =    1.226
peak=    5.352 closest distance to " NE2 GLN A  11 " =    1.142
peak=    5.306 closest distance to " O   HOH Z 232 " =    2.343
peak=    5.290 closest distance to " O   HOH Z 126 " =    1.952
peak=    5.264 closest distance to " CB  SER A  63 " =    1.225
peak=    5.044 closest distance to " O   HOH Z 144 " =    1.753
peak=    4.862 closest distance to " CB  GLN A 223 " =    1.497
peak=    4.836 closest distance to " CB  GLN A 183 " =    1.208
peak=    4.748 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.699 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.655 closest distance to " CB  GLU A 152 " =    1.236
peak=    4.629 closest distance to " O   HOH Z  78 " =    1.743
peak=    4.612 closest distance to " C   PRO A 198 " =    1.477
peak=    4.584 closest distance to " O   HOH Z  15 " =    2.223
peak=    4.538 closest distance to " O   HOH Z 298 " =    1.890
peak=    4.439 closest distance to " CB  PRO A  54 " =    0.905
peak=    4.398 closest distance to " OD1 ASN A  69 " =    2.584
peak=    4.380 closest distance to " CB  ARG A  79 " =    1.390
peak=    4.360 closest distance to " ND2 ASN A 187 " =    1.457
peak=    4.352 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.328 closest distance to " O   HOH Z 427 " =    2.926
peak=    4.304 closest distance to " CB  ASN A 148 " =    1.534
peak=    4.260 closest distance to " O   HOH Z 203 " =    1.780
peak=    4.242 closest distance to " O   HOH Z 272 " =    1.870
peak=    4.235 closest distance to " O   HOH Z 236 " =    2.075
peak=    4.204 closest distance to " CB  LEU A 228 " =    1.068
peak=    4.202 closest distance to " O   HOH Z 303 " =    2.122
peak=    4.200 closest distance to " O   HOH Z 234 " =    3.749
peak=    4.199 closest distance to " CB  TYR A 169 " =    0.751
peak=    4.198 closest distance to " O   HOH Z 209 " =    2.334
peak=    4.085 closest distance to " CB  ARG A 190 " =    1.596
peak=    4.084 closest distance to " CB  SER A   3 " =    1.345
peak=    4.082 closest distance to " O   HOH Z  61 " =    1.624
peak=    4.080 closest distance to " O   HOH Z 158 " =    3.042
peak=    4.076 closest distance to " O   HOH Z 193 " =    1.851
peak=    4.068 closest distance to " NZ  LYS A 117 " =    3.258
peak=    4.067 closest distance to " O   HOH Z 346 " =    1.624
peak=    4.039 closest distance to " CB  ASN A 187 " =    1.057
peak=    4.034 closest distance to " O   HOH Z 368 " =    2.037
peak=    4.030 closest distance to " O   HOH Z  66 " =    2.218
peak=    4.024 closest distance to " O   HOH Z  40 " =    1.734
peak=    4.012 closest distance to " OG ASER A 258 " =    3.101
peak=    4.005 closest distance to " CD  ARG A  66 " =    2.470
peak=    3.997 closest distance to " O   HOH Z 189 " =    2.356
peak=    3.996 closest distance to " CG2 VAL A 257 " =    0.933
peak=    3.993 closest distance to " O   HOH Z 144 " =    2.222
peak=    3.989 closest distance to " O   HOH Z 250 " =    1.491
peak=    3.954 closest distance to " CB  TRP A 266 " =    0.960
peak=    3.939 closest distance to " O   HOH Z 197 " =    3.169
peak=    3.910 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.892 closest distance to " O   HOH Z  43 " =    1.803
peak=    3.887 closest distance to " CB  GLU A 128 " =    1.040
peak=    3.884 closest distance to " CB  VAL A 265 " =    1.281
peak=    3.843 closest distance to " O   SER A  87 " =    2.209
peak=    3.842 closest distance to " OD2 ASP A 286 " =    2.830
peak=    3.832 closest distance to " CD  ARG A  66 " =    2.413
peak=    3.829 closest distance to " CA  ASN A 215 " =    1.205
peak=    3.807 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.802 closest distance to " O   HOH Z   1 " =    1.985
peak=    3.786 closest distance to " O   HOH Z  10 " =    1.811
peak=    3.780 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.768 closest distance to " O   HOH Z 344 " =    3.227
peak=    3.757 closest distance to " O   HOH Z 133 " =    2.402
peak=    3.754 closest distance to " ND1 HIS A  86 " =    1.719
peak=    3.753 closest distance to " CG1 ILE A  33 " =    1.190
peak=    3.748 closest distance to " O   HOH Z  59 " =    1.938
peak=    3.724 closest distance to " CA  THR A 264 " =    0.891
peak=    3.724 closest distance to " O   HOH Z 132 " =    2.524
peak=    3.717 closest distance to " O   HOH Z 248 " =    1.648
peak=    3.716 closest distance to " O   HOH Z 214 " =    2.028
peak=    3.715 closest distance to " O   MET A 105 " =    1.840
peak=    3.715 closest distance to " O   HOH Z  53 " =    2.564
peak=    3.712 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.709 closest distance to " O   HOH Z 425 " =    2.123
peak=    3.698 closest distance to " O   HOH Z 291 " =    1.569
peak=    3.697 closest distance to " O   HOH Z 419 " =    1.951
peak=    3.692 closest distance to " O   HOH Z 180 " =    2.176
peak=    3.690 closest distance to " CG  PRO A 243 " =    1.114
peak=    3.686 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.680 closest distance to " CD2 LEU A 255 " =    1.531
peak=    3.679 closest distance to " CB  SER A 212 " =    1.084
peak=    3.677 closest distance to " O   HOH Z  44 " =    1.667
peak=    3.672 closest distance to " NH1AARG A 145 " =    1.154
peak=    3.669 closest distance to " OD1BASN A 224 " =    2.409
peak=    3.669 closest distance to " ND2 ASN A 110 " =    1.808
peak=    3.666 closest distance to " O   HOH Z 135 " =    1.692
peak=    3.665 closest distance to " CD BLYS A 290 " =    1.194
peak=    3.661 closest distance to " CB  VAL A 202 " =    1.614
peak=    3.654 closest distance to " O   HOH Z  21 " =    1.723
peak=    3.654 closest distance to " CB  TRP A 179 " =    1.375
peak=    3.652 closest distance to " O   HOH Z 368 " =    3.636
peak=    3.647 closest distance to " CG  PRO A 198 " =    1.259
peak=    3.643 closest distance to " O   HOH Z 133 " =    1.632
peak=    3.640 closest distance to " O   HOH Z  54 " =    2.430
peak=    3.629 closest distance to " NH2 ARG A 156 " =    1.197
peak=    3.629 closest distance to " CD2 TRP A 179 " =    1.328
peak=    3.625 closest distance to " CB  ARG A 139 " =    0.976
peak=    3.623 closest distance to " CZ  PHE A 218 " =    1.022
peak=    3.614 closest distance to " CB  TYR A 169 " =    0.737
peak=    3.611 closest distance to " O   HOH Z 128 " =    2.247
peak=    3.607 closest distance to " O   HOH Z 245 " =    1.311
peak=    3.605 closest distance to " CA  THR A 221 " =    0.994
peak=    3.602 closest distance to " O   HOH Z 128 " =    2.152
peak=    3.597 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.592 closest distance to " N   ARG A 156 " =    1.297
peak=    3.591 closest distance to " O   HOH Z 213 " =    1.767
peak=    3.577 closest distance to " O   HOH Z 280 " =    3.073
peak=    3.571 closest distance to " CA  MET A  40 " =    1.128
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.683
peak=    3.563 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.559 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.556 closest distance to " O   HOH Z 147 " =    1.757
peak=    3.549 closest distance to " O   HOH Z 172 " =    3.275
peak=    3.546 closest distance to " O   HOH Z 295 " =    1.573
peak=    3.542 closest distance to " CD1 LEU A 300 " =    1.251
peak=    3.537 closest distance to " CD  ARG A 159 " =    0.756
peak=    3.536 closest distance to " CB  MET A  47 " =    1.098
peak=    3.534 closest distance to " CB  ASN A 142 " =    0.986
peak=    3.534 closest distance to " O   HOH Z 426 " =    1.671
peak=    3.533 closest distance to " O   HOH Z   1 " =    1.731
peak=    3.532 closest distance to " O   HOH Z  64 " =    2.121
peak=    3.522 closest distance to " NH2BARG A 145 " =    2.086
peak=    3.516 closest distance to " O   HOH Z 305 " =    3.598
peak=    3.502 closest distance to " O   HOH Z 437 " =    1.361
peak=    3.486 closest distance to " OG BSER A 164 " =    2.306
peak=    3.486 closest distance to " O   HOH Z 371 " =    3.113
peak=    3.474 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.471 closest distance to " OE1 GLN A  11 " =    2.128
peak=    3.468 closest distance to " O   HOH Z 175 " =    2.182
peak=    3.468 closest distance to " O   HOH Z 193 " =    1.987
peak=    3.463 closest distance to " O   HOH Z  88 " =    3.287
peak=    3.456 closest distance to " CA  ALA A  51 " =    0.933
peak=    3.455 closest distance to " CB  THR A 157 " =    1.120
peak=    3.454 closest distance to " CA  ARG A 195 " =    1.199
peak=    3.449 closest distance to " O   HOH Z 345 " =    3.472
peak=    3.447 closest distance to " CB  TYR A 116 " =    0.787
peak=    3.443 closest distance to " CB  ALA A   9 " =    1.533
peak=    3.440 closest distance to " O   HOH Z 313 " =    1.933
peak=    3.436 closest distance to " CB  ALA A  34 " =    1.022
peak=    3.436 closest distance to " CB  LEU A 143 " =    1.110
peak=    3.435 closest distance to " O   HOH Z  93 " =    2.634
peak=    3.431 closest distance to " ND2 ASN A 249 " =    1.888
peak=    3.428 closest distance to " NE2 GLN A  73 " =    3.792
peak=    3.417 closest distance to " CG  LEU A 167 " =    1.251
peak=    3.415 closest distance to " O   HOH Z 407 " =    2.378
peak=    3.414 closest distance to " CG  LYS A  76 " =    0.987
peak=    3.412 closest distance to " O   HOH Z 417 " =    3.198
peak=    3.406 closest distance to " CB  ASN A 224 " =    1.000
peak=    3.402 closest distance to " O   HOH Z 273 " =    2.718
peak=    3.397 closest distance to " O   HOH Z  44 " =    3.076
peak=    3.389 closest distance to " O   HOH Z 148 " =    3.311
peak=    3.385 closest distance to " CD  LYS A 166 " =    1.195
peak=    3.384 closest distance to " O   HOH Z 163 " =    1.747
peak=    3.379 closest distance to " CD  LYS A 119 " =    1.336
peak=    3.376 closest distance to " CA  ALA A 233 " =    1.158
peak=    3.368 closest distance to " CB  ALA A 291 " =    1.452
peak=    3.361 closest distance to " N   PHE A 130 " =    1.277
peak=    3.358 closest distance to " O   HOH Z 391 " =    2.878
peak=    3.356 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.353 closest distance to " CB  GLU A  46 " =    1.018
peak=    3.340 closest distance to " O   HOH Z 329 " =    3.789
peak=    3.338 closest distance to " O   HOH Z 411 " =    3.896
peak=    3.333 closest distance to " CB  GLN A  89 " =    1.374
peak=    3.325 closest distance to " CA  LYS A 117 " =    1.195
peak=    3.324 closest distance to " CB  SER A 216 " =    0.801
peak=    3.320 closest distance to " O   HOH Z 402 " =    1.430
peak=    3.319 closest distance to " O   HOH Z 281 " =    4.129
peak=    3.319 closest distance to " O   HOH Z   6 " =    2.071
peak=    3.316 closest distance to " O   HOH Z 409 " =    2.820
peak=    3.312 closest distance to " NH2AARG A 275 " =    3.610
peak=    3.311 closest distance to " ND1 HIS A  81 " =    1.600
peak=    3.311 closest distance to " O   HOH Z 203 " =    1.239
peak=    3.310 closest distance to " CA  ALA A  84 " =    1.387
peak=    3.307 closest distance to " CG  ARG A 159 " =    0.859
peak=    3.305 closest distance to " CG1 VAL A 153 " =    0.912
peak=    3.302 closest distance to " CB  ALA A   1 " =    4.680
peak=    3.301 closest distance to " CA  LEU A 101 " =    1.466
peak=    3.301 closest distance to " OG  SER A  22 " =    2.777
peak=    3.301 closest distance to " CB  ILE A 120 " =    1.230
peak=    3.299 closest distance to " N   ASN A 127 " =    1.228
peak=    3.299 closest distance to " CB  THR A 235 " =    1.098
peak=    3.299 closest distance to " O   HOH Z  97 " =    2.003
peak=    3.296 closest distance to " O   HOH Z  85 " =    2.205
peak=    3.291 closest distance to " CB  HIS A 108 " =    0.799
peak=    3.291 closest distance to " NE2 HIS A 207 " =    1.416
peak=    3.285 closest distance to " O  BHOH Z 338 " =    2.325
peak=    3.284 closest distance to " O   HOH Z 435 " =    1.890
peak=    3.283 closest distance to " CB  LEU A 255 " =    0.776
peak=    3.281 closest distance to " CG  GLN A  11 " =    1.785
peak=    3.281 closest distance to " OG1 THR A 294 " =    2.451
peak=    3.280 closest distance to " CA  ALA A 158 " =    1.257
peak=    3.279 closest distance to " CA  ALA A 291 " =    0.933
peak=    3.276 closest distance to " O   HOH Z 263 " =    1.698
peak=    3.276 closest distance to " O   HOH Z 271 " =    2.428
peak=    3.275 closest distance to " O   ALA A 165 " =    1.482
peak=    3.273 closest distance to " CB  MET A  40 " =    0.819
peak=    3.273 closest distance to " O   HOH Z 234 " =    1.724
peak=    3.269 closest distance to " O   HOH Z 188 " =    2.086
peak=    3.258 closest distance to " CA  ALA A 154 " =    0.968
peak=    3.257 closest distance to " O   HOH Z 423 " =    1.799
peak=    3.256 closest distance to " O   HOH Z  66 " =    2.112
peak=    3.253 closest distance to " O   HOH Z 299 " =    4.446
peak=    3.252 closest distance to " O   HOH Z 183 " =    1.283
peak=    3.249 closest distance to " CB  TRP A 150 " =    1.252
peak=    3.246 closest distance to " O   HOH Z 173 " =    1.709
peak=    3.246 closest distance to " CG1BVAL A  72 " =    1.570
peak=    3.245 closest distance to " CB  THR A  31 " =    1.763
peak=    3.245 closest distance to " O   HOH Z 261 " =    2.248
peak=    3.241 closest distance to " CG BARG A 275 " =    1.466
peak=    3.240 closest distance to " CD1 ILE A 106 " =    0.779
peak=    3.236 closest distance to " O   HOH Z 303 " =    1.759
peak=    3.233 closest distance to " CA  TYR A 116 " =    1.332
peak=    3.231 closest distance to " N   SER A 134 " =    1.392
peak=    3.231 closest distance to " O   HOH Z 406 " =    1.551
peak=    3.223 closest distance to " N   VAL A 126 " =    1.326
peak=    3.221 closest distance to " O   HOH Z 261 " =    1.577
peak=    3.218 closest distance to " O   HOH Z 108 " =    2.408
peak=    3.216 closest distance to " O   HOH Z 213 " =    2.296
peak=    3.212 closest distance to " O   HOH Z 286 " =    2.324
peak=    3.211 closest distance to " O   HOH Z 185 " =    1.826
peak=    3.206 closest distance to " CE BLYS A 290 " =    1.110
peak=    3.206 closest distance to " N   TRP A 177 " =    1.736
peak=    3.205 closest distance to " O   HOH Z 292 " =    1.677
peak=    3.202 closest distance to " O   HOH Z 327 " =    1.763
peak=    3.199 closest distance to " CG  MET A 113 " =    1.331
peak=    3.198 closest distance to " O   HOH Z 171 " =    2.002
peak=    3.190 closest distance to " O   HOH Z 365 " =    2.924
peak=    3.188 closest distance to " CD1 ILE A 263 " =    1.295
peak=    3.184 closest distance to " CG  GLN A  89 " =    1.456
peak=    3.182 closest distance to " O   HOH Z 353 " =    2.718
peak=    3.181 closest distance to " O   GLY A  57 " =    2.598
peak=    3.180 closest distance to " NH1BARG A 145 " =    1.106
peak=    3.177 closest distance to " O   HOH Z 411 " =    1.802
peak=    3.175 closest distance to " O   HOH Z 410 " =    1.870
peak=    3.170 closest distance to " O   HOH Z 219 " =    2.095
peak=    3.169 closest distance to " CG2 ILE A  20 " =    1.301
peak=    3.166 closest distance to " CA  GLY A 267 " =    1.168
peak=    3.165 closest distance to " N   ASN A  39 " =    1.237
peak=    3.160 closest distance to " CZ2 TRP A 179 " =    1.718
peak=    3.159 closest distance to " O   ALA A 158 " =    1.330
peak=    3.157 closest distance to " NH2 ARG A 219 " =    1.801
peak=    3.157 closest distance to " O   HOH Z  30 " =    2.331
peak=    3.154 closest distance to " CA  ARG A  36 " =    1.061
peak=    3.152 closest distance to " O   HOH Z  49 " =    2.886
peak=    3.148 closest distance to " CA  MET A 105 " =    0.963
peak=    3.131 closest distance to " OG  SER A 206 " =    1.330
peak=    3.130 closest distance to " O   HOH Z 327 " =    1.747
peak=    3.129 closest distance to " CB  ASN A 215 " =    1.093
peak=    3.127 closest distance to " CD2 HIS A  81 " =    1.046
peak=    3.127 closest distance to " O   HOH Z 425 " =    1.201
peak=    3.125 closest distance to " CB  ARG A 138 " =    0.987
peak=    3.121 closest distance to " CA  SER A  87 " =    1.033
peak=    3.121 closest distance to " CB  SER A 273 " =    0.824
peak=    3.113 closest distance to " CB  ASP A 171 " =    0.840
peak=    3.112 closest distance to " O   THR A 251 " =    1.238
peak=    3.111 closest distance to " CB  SER A  62 " =    1.219
peak=    3.109 closest distance to " CG2 ILE A 120 " =    1.123
peak=    3.108 closest distance to " OG1 THR A 246 " =    3.206
peak=    3.105 closest distance to " CA  ALA A 248 " =    1.252
peak=    3.095 closest distance to " O   HOH Z 374 " =    2.667
peak=    3.095 closest distance to " O   HOH Z 358 " =    3.717
peak=    3.094 closest distance to " O   TYR A 116 " =    1.257
peak=    3.092 closest distance to " O   HOH Z  88 " =    1.970
peak=    3.090 closest distance to " CB  ASN A 110 " =    1.141
peak=    3.088 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.085 closest distance to " O   HOH Z 359 " =    1.384
peak=    3.074 closest distance to " O   HOH Z 285 " =    2.912
peak=    3.071 closest distance to " NH2AARG A 190 " =    1.190
peak=    3.063 closest distance to " CA  THR A  82 " =    1.496
peak=    3.060 closest distance to " CA  GLU A  46 " =    0.727
peak=    3.054 closest distance to " O   HOH Z 423 " =    2.898
peak=    3.052 closest distance to " CG  GLN A  77 " =    2.115
peak=    3.048 closest distance to " CB  LYS A 290 " =    1.131
peak=    3.034 closest distance to " O   GLN A 278 " =    1.524
peak=    3.014 closest distance to " CB  VAL A 126 " =    1.112

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.434
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.732 - 5.434

peak=   -4.611 closest distance to " CD  ARG A 156 " =    1.998
peak=   -4.577 closest distance to " CG  GLN A 223 " =    1.924
peak=   -4.573 closest distance to " CB  PRO A 243 " =    2.609
peak=   -4.566 closest distance to " O   VAL A  67 " =    2.760
peak=   -4.561 closest distance to " O   HOH Z 266 " =    4.947
peak=   -4.284 closest distance to " O   HOH Z 377 " =    2.089
peak=   -4.263 closest distance to " SG  CYS A 254 " =    3.440
peak=   -4.197 closest distance to " OG BSER A 134 " =    1.206
peak=   -4.154 closest distance to " O   HOH Z 389 " =    1.968
peak=   -4.148 closest distance to " O   HOH Z 231 " =    2.215
peak=   -4.052 closest distance to " O   HOH Z 372 " =    2.422
peak=   -4.052 closest distance to " C   HIS A 108 " =    1.124
peak=   -4.011 closest distance to " N   ALA A  43 " =    2.602
peak=   -3.944 closest distance to " O   ILE A 109 " =    2.616
peak=   -3.931 closest distance to " CA  VAL A  67 " =    2.735
peak=   -3.928 closest distance to " O   HOH Z 313 " =    1.916
peak=   -3.910 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.901 closest distance to " CB  ALA A 291 " =    2.405
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    1.476
peak=   -3.890 closest distance to " CB  ALA A 291 " =    2.190
peak=   -3.868 closest distance to " O   HOH Z 435 " =    2.855
peak=   -3.865 closest distance to " CE2 TYR A  30 " =    2.776
peak=   -3.864 closest distance to " O   HOH Z 290 " =    1.229
peak=   -3.857 closest distance to " O   HOH Z 198 " =    2.091
peak=   -3.853 closest distance to " CZ3 TRP A 179 " =    1.110
peak=   -3.839 closest distance to " CD  GLN A  58 " =    1.022
peak=   -3.836 closest distance to " O   HOH Z  10 " =    1.512
peak=   -3.834 closest distance to " O   HOH Z 126 " =    1.892
peak=   -3.810 closest distance to " O   HOH Z 114 " =    3.195
peak=   -3.807 closest distance to " CE  MET A 105 " =    2.304
peak=   -3.800 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.785 closest distance to " N   ASP A 286 " =    2.511
peak=   -3.784 closest distance to " C   ALA A 158 " =    1.330
peak=   -3.769 closest distance to " O   HOH Z 185 " =    2.258
peak=   -3.763 closest distance to " CD2 PHE A 192 " =    2.044
peak=   -3.752 closest distance to " O   PRO A 163 " =    2.034
peak=   -3.747 closest distance to " CD  ARG A 139 " =    1.561
peak=   -3.744 closest distance to " O   HOH Z 211 " =    1.660
peak=   -3.730 closest distance to " CZ  PHE A  59 " =    1.577
peak=   -3.728 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.728 closest distance to " O   HOH Z 353 " =    2.124
peak=   -3.727 closest distance to " CG1 VAL A 112 " =    2.850
peak=   -3.716 closest distance to " O   HOH Z 196 " =    2.133
peak=   -3.714 closest distance to " OD1 ASP A 171 " =    1.634
peak=   -3.710 closest distance to " CG  PHE A 283 " =    2.678
peak=   -3.709 closest distance to " CE2 PHE A 218 " =    2.448
peak=   -3.704 closest distance to " CG2 ILE A 263 " =    2.295
peak=   -3.691 closest distance to " OXT GLY A 302 " =    2.908
peak=   -3.691 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.686 closest distance to " O   HOH Z  43 " =    1.575
peak=   -3.677 closest distance to " O   HOH Z 407 " =    3.152
peak=   -3.649 closest distance to " CD1 LEU A 228 " =    2.273
peak=   -3.647 closest distance to " O   PRO A 198 " =    1.318
peak=   -3.633 closest distance to " OD1 ASN A 187 " =    1.543
peak=   -3.620 closest distance to " SG ACYS A 201 " =    1.795
peak=   -3.605 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.588 closest distance to " NH2BARG A 275 " =    1.788
peak=   -3.565 closest distance to " NH2AARG A 275 " =    5.434
peak=   -3.562 closest distance to " CG1 VAL A 250 " =    2.660
peak=   -3.559 closest distance to " O   HOH Z 311 " =    3.683
peak=   -3.556 closest distance to " N   GLN A  58 " =    1.700
peak=   -3.556 closest distance to " O   VAL A 189 " =    2.575
peak=   -3.543 closest distance to " CB  CYS A 201 " =    2.586
peak=   -3.533 closest distance to " CD2 PHE A  61 " =    2.510
peak=   -3.520 closest distance to " CZ  TYR A 169 " =    1.681
peak=   -3.513 closest distance to " CD1 LEU A 101 " =    2.315
peak=   -3.511 closest distance to " CB  ASN A  39 " =    2.302
peak=   -3.504 closest distance to " NH1 ARG A 195 " =    2.548
peak=   -3.493 closest distance to " CB  PRO A 163 " =    2.487
peak=   -3.489 closest distance to " O   HOH Z 198 " =    1.400
peak=   -3.485 closest distance to " O   HOH Z  38 " =    1.444
peak=   -3.483 closest distance to " O   HOH Z  11 " =    1.811
peak=   -3.483 closest distance to " C   LEU A 143 " =    1.161
peak=   -3.482 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.473 closest distance to " CG  TRP A 266 " =    1.760
peak=   -3.470 closest distance to " O   HOH Z  13 " =    1.589
peak=   -3.469 closest distance to " O   HOH Z 253 " =    3.941
peak=   -3.468 closest distance to " CD1 LEU A 297 " =    2.406
peak=   -3.461 closest distance to " O   HOH Z 298 " =    1.271
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.289
peak=   -3.456 closest distance to " O   HOH Z 426 " =    1.636
peak=   -3.447 closest distance to " O   ARG A 145 " =    1.567
peak=   -3.446 closest distance to " CB  ALA A 248 " =    2.427
peak=   -3.446 closest distance to " O   HOH Z 348 " =    2.178
peak=   -3.443 closest distance to " O   HOH Z 395 " =    5.264
peak=   -3.428 closest distance to " O   HOH Z  51 " =    1.590
peak=   -3.428 closest distance to " O   HOH Z 394 " =    1.387
peak=   -3.423 closest distance to " NH1 ARG A  36 " =    1.990
peak=   -3.417 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.412 closest distance to " CA  GLY A  98 " =    1.936
peak=   -3.405 closest distance to " NH2 ARG A  79 " =    1.946
peak=   -3.404 closest distance to " O   ALA A 161 " =    1.749
peak=   -3.402 closest distance to " O   HOH Z  60 " =    2.586
peak=   -3.398 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.390 closest distance to " CA  GLY A 241 " =    3.064
peak=   -3.387 closest distance to " O   HOH Z  52 " =    1.331
peak=   -3.383 closest distance to " CG1 VAL A 197 " =    2.184
peak=   -3.374 closest distance to " CD2 TYR A 247 " =    2.407
peak=   -3.368 closest distance to " O   HOH Z 111 " =    2.143
peak=   -3.368 closest distance to " O   HOH Z  44 " =    2.147
peak=   -3.352 closest distance to " OD1 ASN A 148 " =    1.658
peak=   -3.351 closest distance to " O   HOH Z 193 " =    1.899
peak=   -3.351 closest distance to " OXT GLY A 302 " =    3.316
peak=   -3.349 closest distance to " O   HOH Z  98 " =    2.329
peak=   -3.347 closest distance to " OD2 ASP A 191 " =    1.456
peak=   -3.346 closest distance to " O   GLY A  80 " =    2.450
peak=   -3.346 closest distance to " O   PHE A 218 " =    1.592
peak=   -3.343 closest distance to " O   LYS A 117 " =    1.735
peak=   -3.342 closest distance to " O   HOH Z 174 " =    2.974
peak=   -3.342 closest distance to " O   HOH Z 348 " =    1.812
peak=   -3.341 closest distance to " CE  LYS A  76 " =    2.854
peak=   -3.334 closest distance to " O   SER A 135 " =    1.503
peak=   -3.331 closest distance to " CD2 LEU A 237 " =    2.661
peak=   -3.325 closest distance to " CB  ASP A 132 " =    2.254
peak=   -3.307 closest distance to " N   ASP A 171 " =    2.421
peak=   -3.304 closest distance to " O   GLY A 211 " =    1.460
peak=   -3.304 closest distance to " CD2 LEU A 300 " =    2.875
peak=   -3.299 closest distance to " O   HOH Z  70 " =    2.156
peak=   -3.297 closest distance to " OG  SER A  87 " =    1.348
peak=   -3.291 closest distance to " O   SER A  22 " =    2.368
peak=   -3.289 closest distance to " O   HOH Z  73 " =    2.214
peak=   -3.289 closest distance to " CB  ALA A 131 " =    2.061
peak=   -3.286 closest distance to " N   THR A 235 " =    1.361
peak=   -3.280 closest distance to " NH2 ARG A  79 " =    1.594
peak=   -3.279 closest distance to " OH  TYR A 214 " =    1.239
peak=   -3.275 closest distance to " CG1 VAL A 112 " =    2.600
peak=   -3.268 closest distance to " CB  ASP A 286 " =    2.230
peak=   -3.257 closest distance to " NE2 GLN A  88 " =    1.908
peak=   -3.257 closest distance to " OG BSER A 134 " =    1.654
peak=   -3.255 closest distance to " CG1 VAL A 230 " =    2.082
peak=   -3.250 closest distance to " N   ALA A 248 " =    1.550
peak=   -3.246 closest distance to " O   HOH Z 359 " =    3.166
peak=   -3.242 closest distance to " OG  SER A  62 " =    1.690
peak=   -3.236 closest distance to " O   HOH Z  63 " =    1.546
peak=   -3.232 closest distance to " C   LEU A 222 " =    0.732
peak=   -3.231 closest distance to " OD1AASN A 224 " =    1.742
peak=   -3.229 closest distance to " CG  GLU A 152 " =    1.189
peak=   -3.224 closest distance to " CB  TRP A  85 " =    2.491
peak=   -3.223 closest distance to " O   HOH Z 166 " =    2.016
peak=   -3.222 closest distance to " CG  GLU A   2 " =    1.921
peak=   -3.221 closest distance to " OE1 GLN A 223 " =    2.048
peak=   -3.220 closest distance to " O   MET A  40 " =    2.812
peak=   -3.220 closest distance to " O   HOH Z 123 " =    2.266
peak=   -3.219 closest distance to " CB  ALA A 248 " =    2.026
peak=   -3.219 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.219 closest distance to " CA  GLY A 133 " =    2.060
peak=   -3.218 closest distance to " O   HOH Z 282 " =    1.278
peak=   -3.218 closest distance to " CB  ALA A  43 " =    2.503
peak=   -3.213 closest distance to " NE  ARG A  36 " =    1.907
peak=   -3.206 closest distance to " O   HOH Z 385 " =    2.056
peak=   -3.204 closest distance to " OD2 ASP A 171 " =    1.778
peak=   -3.203 closest distance to " ND2 ASN A 249 " =    2.340
peak=   -3.201 closest distance to " OG  SER A  26 " =    1.289
peak=   -3.198 closest distance to " CA  GLY A 241 " =    2.261
peak=   -3.198 closest distance to " N   SER A 212 " =    2.045
peak=   -3.196 closest distance to " O   GLY A  80 " =    2.474
peak=   -3.188 closest distance to " C   MET A 188 " =    1.362
peak=   -3.187 closest distance to " O   VAL A 174 " =    2.078
peak=   -3.186 closest distance to " CG  MET A 105 " =    0.982
peak=   -3.180 closest distance to " OD2 ASP A 171 " =    2.269
peak=   -3.178 closest distance to " C   VAL A 174 " =    1.817
peak=   -3.176 closest distance to " O   HOH Z 234 " =    4.152
peak=   -3.175 closest distance to " ND2 ASN A  60 " =    1.454
peak=   -3.169 closest distance to " O   HOH Z 114 " =    1.688
peak=   -3.169 closest distance to " OE1 GLN A  88 " =    1.239
peak=   -3.154 closest distance to " CE3 TRP A 150 " =    2.049
peak=   -3.152 closest distance to " O   HOH Z 263 " =    3.147
peak=   -3.151 closest distance to " CE BMET A  47 " =    1.926
peak=   -3.151 closest distance to " O   ALA A  10 " =    1.642
peak=   -3.144 closest distance to " O   HOH Z 298 " =    2.509
peak=   -3.131 closest distance to " O   HOH Z 414 " =    1.797
peak=   -3.131 closest distance to " N   MET A 105 " =    2.768
peak=   -3.130 closest distance to " O   ALA A  51 " =    1.384
peak=   -3.124 closest distance to " SD  MET A 188 " =    2.259
peak=   -3.119 closest distance to " O   HOH Z 137 " =    1.499
peak=   -3.118 closest distance to " CG  ASN A 301 " =    1.943
peak=   -3.117 closest distance to " O   ALA A 292 " =    2.008
peak=   -3.115 closest distance to " O   HOH Z 357 " =    2.040
peak=   -3.115 closest distance to " CA  GLY A 241 " =    2.801
peak=   -3.111 closest distance to " CB  ASP A 286 " =    1.846
peak=   -3.110 closest distance to " CD1 ILE A 199 " =    2.535
peak=   -3.103 closest distance to " CG  ARG A 269 " =    2.547
peak=   -3.101 closest distance to " ND2 ASN A  60 " =    1.798
peak=   -3.097 closest distance to " CG  GLU A 277 " =    1.216
peak=   -3.096 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.096 closest distance to " O   HOH Z 281 " =    2.708
peak=   -3.089 closest distance to " O   HOH Z 174 " =    2.547
peak=   -3.084 closest distance to " O   HOH Z 323 " =    1.400
peak=   -3.080 closest distance to " O   GLN A 240 " =    1.902
peak=   -3.079 closest distance to " O   HOH Z 168 " =    1.811
peak=   -3.068 closest distance to " O   HOH Z 423 " =    2.074
peak=   -3.055 closest distance to " O   HOH Z 166 " =    1.417
peak=   -3.055 closest distance to " CG2 VAL A 189 " =    1.992
peak=   -3.050 closest distance to " O   HOH Z 175 " =    4.269

================= 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    :  0.2603 0.2616   5.840236e+00   5.843384e+00
   1_bss:  0.2445 0.2464   5.809078e+00   5.805853e+00
   1_xyz:  0.1422 0.1613   5.298410e+00   5.412887e+00
   1_adp:  0.1320 0.1642   5.248023e+00   5.432311e+00
   1_occ:  0.1316 0.1642   5.245438e+00   5.431146e+00
   2_bss:  0.1313 0.1629   5.246781e+00   5.431055e+00
   2_xyz:  0.1170 0.1531   5.152677e+00   5.364494e+00
   2_adp:  0.1130 0.1522   5.131410e+00   5.358182e+00
   2_occ:  0.1130 0.1522   5.131285e+00   5.358317e+00
   3_bss:  0.1129 0.1522   5.131275e+00   5.358130e+00
   3_xyz:  0.1122 0.1531   5.133363e+00   5.365127e+00
   3_adp:  0.1115 0.1534   5.132061e+00   5.368137e+00
   3_occ:  0.1115 0.1534   5.132113e+00   5.368366e+00
   4_bss:  0.1114 0.1534   5.132042e+00   5.368264e+00
   4_xyz:  0.1092 0.1538   5.121326e+00   5.367644e+00
   4_adp:  0.1089 0.1538   5.119975e+00   5.367557e+00
   4_occ:  0.1089 0.1538   5.119957e+00   5.367607e+00
   5_bss:  0.1088 0.1538   5.120072e+00   5.367661e+00
   5_xyz:  0.1049 0.1543   5.102005e+00   5.366465e+00
   5_adp:  0.1047 0.1548   5.101429e+00   5.367557e+00
   5_occ:  0.1046 0.1548   5.101475e+00   5.367675e+00
   5_bss:  0.1049 0.1542   5.102309e+00   5.365569e+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:  0.326  50.000  -1.341  -2.174  -1.469  -0.000  -0.000  -0.000
   1_xyz:  0.326  50.000  -1.341  -2.174  -1.469  -0.000  -0.000  -0.000
   1_adp:  0.326  50.000  -1.341  -2.174  -1.469  -0.000  -0.000  -0.000
   1_occ:  0.326  50.000  -1.341  -2.174  -1.469  -0.000  -0.000  -0.000
   2_bss:  0.327  49.993  -2.441  -2.804  -1.823  -0.000  -0.000  -0.000
   2_xyz:  0.327  49.993  -2.441  -2.804  -1.823  -0.000  -0.000  -0.000
   2_adp:  0.327  49.993  -2.441  -2.804  -1.823  -0.000  -0.000  -0.000
   2_occ:  0.327  49.993  -2.441  -2.804  -1.823  -0.000  -0.000  -0.000
   3_bss:  0.327  49.993  -2.422  -2.608  -1.581  -0.000  -0.000  -0.000
   3_xyz:  0.327  49.993  -2.422  -2.608  -1.581  -0.000  -0.000  -0.000
   3_adp:  0.327  49.993  -2.422  -2.608  -1.581  -0.000  -0.000  -0.000
   3_occ:  0.327  49.993  -2.422  -2.608  -1.581  -0.000  -0.000  -0.000
   4_bss:  0.322  49.993  -2.324  -2.462  -1.415  -0.000  -0.000  -0.000
   4_xyz:  0.322  49.993  -2.324  -2.462  -1.415  -0.000  -0.000  -0.000
   4_adp:  0.322  49.993  -2.324  -2.462  -1.415  -0.000  -0.000  -0.000
   4_occ:  0.322  49.993  -2.324  -2.462  -1.415  -0.000  -0.000  -0.000
   5_bss:  0.322  49.993  -2.148  -2.276  -1.220  -0.000  -0.000  -0.000
   5_xyz:  0.322  49.993  -2.148  -2.276  -1.220  -0.000  -0.000  -0.000
   5_adp:  0.322  49.993  -2.148  -2.276  -1.220  -0.000  -0.000  -0.000
   5_occ:  0.322  49.993  -2.148  -2.276  -1.220  -0.000  -0.000  -0.000
   5_bss:  0.321  49.962  -1.948  -2.091  -1.034  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  24.926 0.8166  0.9836    18654.723
   1_bss:  23.643 0.8280  0.9422    15810.134
   1_xyz:  14.295 0.9133  0.9956     6785.941
   1_adp:  14.730 0.9095  0.9944     6993.584
   1_occ:  14.700 0.9097  0.9943     6951.869
   2_bss:  14.692 0.9098  0.9694     6944.308
   2_xyz:  13.386 0.9201  0.9748     6071.409
   2_adp:  13.266 0.9209  0.9727     5945.105
   2_occ:  13.274 0.9209  0.9726     5946.099
   3_bss:  13.273 0.9209  0.9779     5944.217
   3_xyz:  13.372 0.9203  0.9765     6031.772
   3_adp:  13.411 0.9201  0.9711     6056.381
   3_occ:  13.419 0.9200  0.9710     6060.006
   4_bss:  13.416 0.9200  0.9758     6057.445
   4_xyz:  13.410 0.9200  0.9761     6063.162
   4_adp:  13.422 0.9199  0.9704     6058.417
   4_occ:  13.426 0.9199  0.9704     6059.488
   5_bss:  13.429 0.9198  0.9769     6060.963
   5_xyz:  13.404 0.9199  0.9771     6060.031
   5_adp:  13.433 0.9197  0.9705     6063.509
   5_occ:  13.436 0.9197  0.9704     6065.313
   5_bss:  13.430 0.9197  0.9757     6033.996
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6012e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6012e-01
   1_xyz:   0.953  0.007  0.071 15.185  0.004  4.113   5.6757e-02
   1_adp:   0.953  0.007  0.071 15.185  0.004  4.113   5.6757e-02
   1_occ:   0.953  0.007  0.071 15.185  0.004  4.113   5.6757e-02
   2_bss:   0.953  0.007  0.071 15.185  0.004  4.113   5.6757e-02
   2_xyz:   0.944  0.006  0.073 15.073  0.003  4.115   5.5882e-02
   2_adp:   0.944  0.006  0.073 15.073  0.003  4.115   5.5882e-02
   2_occ:   0.944  0.006  0.073 15.073  0.003  4.115   5.5882e-02
   3_bss:   0.944  0.006  0.073 15.073  0.003  4.115   5.5882e-02
   3_xyz:   0.878  0.005  0.069 14.944  0.003  4.115   5.0287e-02
   3_adp:   0.878  0.005  0.069 14.944  0.003  4.115   5.0287e-02
   3_occ:   0.878  0.005  0.069 14.944  0.003  4.115   5.0287e-02
   4_bss:   0.878  0.005  0.069 14.944  0.003  4.115   5.0287e-02
   4_xyz:   0.929  0.006  0.072 14.997  0.004  4.116   5.5269e-02
   4_adp:   0.929  0.006  0.072 14.997  0.004  4.116   5.5269e-02
   4_occ:   0.929  0.006  0.072 14.997  0.004  4.116   5.5269e-02
   5_bss:   0.929  0.006  0.072 14.997  0.004  4.116   5.5269e-02
   5_xyz:   1.080  0.010  0.083 15.286  0.005  4.117   7.3307e-02
   5_adp:   1.080  0.010  0.083 15.286  0.005  4.117   7.3307e-02
   5_occ:   1.080  0.010  0.083 15.286  0.005  4.117   7.3307e-02
   5_bss:   1.080  0.010  0.083 15.286  0.005  4.117   7.3307e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4112e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4112e-01
   1_xyz:   8.143  0.033  0.269 84.772  0.035  2.351   5.1446e-02
   1_adp:   8.143  0.033  0.269 84.772  0.035  2.351   5.1446e-02
   1_occ:   8.143  0.033  0.269 84.772  0.035  2.351   5.1446e-02
   2_bss:   8.143  0.033  0.269 84.772  0.035  2.351   5.1446e-02
   2_xyz:   7.406  0.037  0.220 83.791  0.030  2.344   3.7547e-02
   2_adp:   7.406  0.037  0.220 83.791  0.030  2.344   3.7547e-02
   2_occ:   7.406  0.037  0.220 83.791  0.030  2.344   3.7547e-02
   3_bss:   7.406  0.037  0.220 83.791  0.030  2.344   3.7547e-02
   3_xyz:   7.313  0.035  0.209 83.633  0.034  2.377   2.9249e-02
   3_adp:   7.313  0.035  0.209 83.633  0.034  2.377   2.9249e-02
   3_occ:   7.313  0.035  0.209 83.633  0.034  2.377   2.9249e-02
   4_bss:   7.313  0.035  0.209 83.633  0.034  2.377   2.9249e-02
   4_xyz:   7.007  0.039  0.227 83.834  0.033  2.342   3.5757e-02
   4_adp:   7.007  0.039  0.227 83.834  0.033  2.342   3.5757e-02
   4_occ:   7.007  0.039  0.227 83.834  0.033  2.342   3.5757e-02
   5_bss:   7.007  0.039  0.227 83.834  0.033  2.342   3.5757e-02
   5_xyz:   6.775  0.048  0.267 83.496  0.039  2.258   6.1410e-02
   5_adp:   6.775  0.048  0.267 83.496  0.039  2.258   6.1410e-02
   5_occ:   6.775  0.048  0.267 83.496  0.039  2.258   6.1410e-02
   5_bss:   6.775  0.048  0.267 83.496  0.039  2.258   6.1410e-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:  66.99   0.00  16.43  66.99   0.00  12.62  62.74   6.74  37.13
   1_occ:  66.99   0.00  16.43  66.99   0.00  12.62  62.74   6.74  37.13
   2_bss:  66.99   0.00  16.43  66.99   0.00  12.62  62.74   6.74  37.13
   2_xyz:  66.99   0.00  16.43  66.99   0.00  12.62  62.74   6.74  37.13
   2_adp:  70.69   1.83  16.79  70.69   1.83  12.92  68.95   5.62  37.87
   2_occ:  70.69   1.83  16.79  70.69   1.83  12.92  68.95   5.62  37.87
   3_bss:  70.69   1.83  16.79  70.69   1.83  12.92  68.95   5.62  37.87
   3_xyz:  70.69   1.83  16.79  70.69   1.83  12.92  68.95   5.62  37.87
   3_adp:  73.15   1.51  16.74  73.15   1.51  12.85  70.10   5.95  37.93
   3_occ:  73.15   1.51  16.74  73.15   1.51  12.85  70.10   5.95  37.93
   4_bss:  73.15   1.51  16.74  73.15   1.51  12.85  70.10   5.95  37.93
   4_xyz:  73.15   1.51  16.74  73.15   1.51  12.85  70.10   5.95  37.93
   4_adp:  76.80   1.12  16.68  76.80   1.12  12.73  71.87   6.46  38.16
   4_occ:  76.80   1.12  16.68  76.80   1.12  12.73  71.87   6.46  38.16
   5_bss:  76.80   1.12  16.68  76.80   1.12  12.73  71.87   6.46  38.16
   5_xyz:  76.80   1.12  16.68  76.80   1.12  12.73  71.87   6.46  38.16
   5_adp:  81.33   0.91  16.61  81.33   0.91  12.59  73.57   6.23  38.48
   5_occ:  81.33   0.91  16.61  81.33   0.91  12.59  73.57   6.23  38.48
   5_bss:  81.30   0.88  16.58  81.30   0.88  12.56  73.53   6.20  38.45
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.716    0.014    0.228
   1_adp:    0.716    0.014    0.228
   1_occ:    0.716    0.014    0.228
   2_bss:    0.716    0.014    0.228
   2_xyz:    0.605    0.019    0.254
   2_adp:    0.605    0.019    0.254
   2_occ:    0.605    0.019    0.254
   3_bss:    0.605    0.019    0.254
   3_xyz:    0.712    0.031    0.270
   3_adp:    0.712    0.031    0.270
   3_occ:    0.712    0.031    0.270
   4_bss:    0.712    0.031    0.270
   4_xyz:    0.803    0.034    0.276
   4_adp:    0.803    0.034    0.276
   4_occ:    0.803    0.034    0.276
   5_bss:    0.803    0.034    0.276
   5_xyz:    0.891    0.029    0.282
   5_adp:    0.891    0.029    0.282
   5_occ:    0.891    0.029    0.282
   5_bss:    0.891    0.029    0.282
------------------------------------------------------------------------

CPU time actual refinement: 321.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/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_895/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_895/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.69 
  Macro-tasks:
    bulk solvent and scale       = 37.43  
    individual site refinement   = 133.51 
    weights calculation          = 28.68  
    collect and process          = 6.57   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 206.28 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 102.34 
    alpha_beta                      = 8.16   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.00 
    fmodel                         = 6.55   
    r_factors                      = 0.22   
    phase_errors                   = 11.21  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 243.08 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.533 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    655 calls, 101.99 s
gradients_fft:          600 calls,  98.19 s

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

# Date 2008-01-16 Time 05:55:01 PST -0800 (1200491701.55 s)
Start R-work = 0.2603, R-free = 0.2616 (no bulk solvent and anisotropic scale)
Final R-work = 0.1285, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.2445, R-free = 0.2464
Final R-work = 0.1049, R-free = 0.1542