# Date 2008-01-16 Time 05:17:29 PST -0800 (1200489449.21 s)
#phil __OFF__

Command line arguments: "../668.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18190
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 668

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00025
Completeness in resolution range: 0.971966
Completeness with d_max=infinity: 0.968937

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0003

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00025
Completeness in resolution range: 0.971966
Completeness with d_max=infinity: 0.968937

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2795 [2124/2148]  1909   215  10.1%
  bin  2:  4.2795 -  3.4098 [2032/2052]  1833   199   9.8%
  bin  3:  3.4098 -  2.9825 [2010/2029]  1809   201  10.0%
  bin  4:  2.9825 -  2.7116 [1967/1997]  1766   201  10.2%
  bin  5:  2.7116 -  2.5182 [1992/2011]  1793   199  10.0%
  bin  6:  2.5182 -  2.3703 [1966/1991]  1771   195   9.9%
  bin  7:  2.3703 -  2.2520 [1947/1975]  1752   195  10.0%
  bin  8:  2.2520 -  2.1543 [1959/1995]  1764   195  10.0%
  bin  9:  2.1543 -  2.0716 [1930/1972]  1735   195  10.1%
  bin 10:  2.0716 -  2.0003 [1662/1984]  1498   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2181
        3.04 -     3.66: 4603
        3.66 -     4.28: 8963
        4.28 -     4.90: 12312
  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
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.845 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.956 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.032 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.104 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28069 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_668/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/model_refine_001.geo

CPU time processing inputs: 8.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2768   r_free= 0.2691   ksol= 0.00   Bsol= 0.00   scale= 0.980    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.929050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.2628 0.2590      6.2975      6.2046|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.2070 0.2070      6.2805      6.2989|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.2427 0.2247      6.2513      6.2254|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.2470 0.2747      6.1141      6.1565|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.2816 0.2284      5.9936      5.8682|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.2728 0.3064      5.8904      5.8954|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.2859 0.2762      5.8719      5.8931|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.3053 0.2552      5.8951      5.8017|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.2959 0.2858      5.8072       5.764|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.3222 0.2840      5.8385      5.7173|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.3187 0.3284      5.7614      5.8162|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.3088 0.3050      5.7041      5.7828|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.3172 0.2937      5.6229      5.5578|
| 14:  2.0502 -  2.0003 0.77    976  110 0.2923 0.3189      5.5153      5.5432|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.82  23.15   0.87     0.83      34647.92|
|  2:  4.7729 -  3.8086  1312   151  0.87  19.00   0.98     0.93      35211.30|
|  3:  3.8086 -  3.3331  1299   141  0.85  21.29   0.99     0.96      31811.02|
|  4:  3.3331 -  3.0311  1295   141  0.84  22.53   1.00     0.95      26654.05|
|  5:  3.0311 -  2.8153  1268   144  0.80  26.63   1.02     0.93      20910.50|
|  6:  2.8153 -  2.6503  1288   144  0.79  27.44   1.00     0.92      19031.27|
|  7:  2.6503 -  2.5182  1266   142  0.78  28.83   1.02     0.93      18225.34|
|  8:  2.5182 -  2.4090  1271   137  0.78  28.57   1.01     0.95      17330.12|
|  9:  2.4090 -  2.3166  1249   142  0.78  28.68   1.04     0.96      15858.21|
| 10:  2.3166 -  2.2370  1273   139  0.77  29.59   1.07     0.97      14700.08|
| 11:  2.2370 -  2.1672  1249   138  0.76  30.29   1.04     0.98      14834.32|
| 12:  2.1672 -  2.1054  1251   139  0.75  31.25   1.07     0.99      14479.25|
| 13:  2.1054 -  2.0502  1251   139  0.74  32.67   1.05     0.97      13271.96|
| 14:  2.0502 -  2.0003   976   110  0.74  32.56   1.08     0.93      11204.06|
|alpha:            min =        0.83 max =            0.99 mean =         0.94|
|beta:             min =    11204.06 max =        35211.30 mean =     20915.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.98 mean =        27.15|
|phase err.(test): min =        0.00 max =           89.97 mean =        26.81|
|-----------------------------------------------------------------------------|

============================== 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 = 3.012358              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447079              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.850   (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:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      177 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1822 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2781 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4624 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4339 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5627 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6685 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.169 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2768   r_free= 0.2691   ksol= 0.00   Bsol= 0.00   scale= 0.980    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.929050                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2565   r_free= 0.2525   ksol= 0.32   Bsol= 53.57   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-3.06,2.58,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.890156                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.686756              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.321   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.258408              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.669   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2565      final r-factor (work) = 0.1611          |
| start r-factor (free) = 0.2525      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0931 = 2.69 * 0.50 * 5.9032 + 1.00 * 0.1629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5654 = 2.69 * 0.50 * 5.5858 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1611      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.1836      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4504 = 0.26 * 1.00 * 5.5858 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5061 = 0.26 * 1.00 * 5.3672 + 1.00 * 0.1192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.44   16.21    None  None   None       |
|    all(noH): 2823   0      0.00    84.44   16.21    None  None   None       |
|    Sol.    : 438    0      6.41    62.88   37.08    None  None   None       |
|    Mac.    : 2385   0      0.00    84.44   12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.445:  533   |   5:    42.222 -  50.667:  101        |
|      1:     8.445 -  16.889: 1549   |   6:    50.667 -  59.111:   62        |
|      2:    16.889 -  25.333:  290   |   7:    59.111 -  67.556:    7        |
|      3:    25.333 -  33.778:  149   |   8:    67.556 -  76.000:    0        |
|      4:    33.778 -  42.222:  131   |   9:    76.000 -  84.444:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1514 r_free = 0.1834             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1508 r_free = 0.1834             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1508   r_free= 0.1834   ksol= 0.32   Bsol= 53.57   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-3.06,2.58,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.366965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1483   r_free= 0.1804   ksol= 0.33   Bsol= 62.19   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.70,-0.20,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.350841                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.443565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.056   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.873   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1483      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9328 = 1.44 * 0.50 * 5.3636 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8579 = 1.44 * 0.50 * 5.2712 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4705 = 0.65 * 1.00 * 5.2712 + 1.00 * 0.0372                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3776 = 0.65 * 1.00 * 5.1713 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    79.16   17.10    None  None   None       |
|    all(noH): 2823   0      0.52    79.16   17.10    None  None   None       |
|    Sol.    : 438    0      3.59    76.56   40.09    None  None   None       |
|    Mac.    : 2385   0      0.52    79.16   12.87    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:     0.516 -   8.380:  646   |   5:    39.837 -  47.701:   89        |
|      1:     8.380 -  16.245: 1332   |   6:    47.701 -  55.565:   82        |
|      2:    16.245 -  24.109:  325   |   7:    55.565 -  63.430:   69        |
|      3:    24.109 -  31.973:  134   |   8:    63.430 -  71.294:   31        |
|      4:    31.973 -  39.837:  108   |   9:    71.294 -  79.158:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1195 r_free = 0.1584             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1583             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1583   ksol= 0.33   Bsol= 62.19   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.70,-0.20,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.177788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1579   ksol= 0.33   Bsol= 62.19   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.32,-0.44,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176741                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.333108              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.380  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.200  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5002 = 1.33 * 0.50 * 5.1714 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4912 = 1.33 * 0.50 * 5.1614 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0750 = 0.21 * 1.00 * 5.1614 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0738 = 0.21 * 1.00 * 5.1618 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.47   16.54    None  None   None       |
|    all(noH): 2823   0      0.00    78.47   16.54    None  None   None       |
|    Sol.    : 438    0      0.00    75.15   37.99    None  None   None       |
|    Mac.    : 2385   0      1.16    78.47   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.847:  535   |   5:    39.237 -  47.084:  102        |
|      1:     7.847 -  15.695: 1404   |   6:    47.084 -  54.932:   86        |
|      2:    15.695 -  23.542:  364   |   7:    54.932 -  62.779:   47        |
|      3:    23.542 -  31.390:  139   |   8:    62.779 -  70.626:   12        |
|      4:    31.390 -  39.237:  126   |   9:    70.626 -  78.474:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1564             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1565             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1565   ksol= 0.33   Bsol= 62.19   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.32,-0.44,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157626                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1558   ksol= 0.33   Bsol= 62.19   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.14,-0.47,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156378                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.319614              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.113871              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.496  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4569 = 1.32 * 0.50 * 5.1621 + 1.00 * 0.0509                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4486 = 1.32 * 0.50 * 5.1501 + 1.00 * 0.0505                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5944 = 0.11 * 1.00 * 5.1501 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5939 = 0.11 * 1.00 * 5.1575 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    75.59   16.04    None  None   None       |
|    all(noH): 2823   0      1.53    75.59   16.04    None  None   None       |
|    Sol.    : 438    0      3.02    72.08   36.08    None  None   None       |
|    Mac.    : 2385   0      1.53    75.59   12.36    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:     1.527 -   8.933:  830   |   5:    38.557 -  45.963:   95        |
|      1:     8.933 -  16.339: 1197   |   6:    45.963 -  53.369:   85        |
|      2:    16.339 -  23.745:  307   |   7:    53.369 -  60.775:   32        |
|      3:    23.745 -  31.151:  131   |   8:    60.775 -  68.181:   11        |
|      4:    31.151 -  38.557:  127   |   9:    68.181 -  75.587:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1552             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1552             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1552   ksol= 0.33   Bsol= 62.19   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.14,-0.47,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1553   ksol= 0.32   Bsol= 52.70   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.05,-0.44,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155688                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.399443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.709  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.924829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.483  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6592 = 1.40 * 0.50 * 5.1573 + 1.00 * 0.0505                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6557 = 1.40 * 0.50 * 5.1496 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7691 = 0.92 * 1.00 * 5.1496 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7646 = 0.92 * 1.00 * 5.1421 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.18   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    82.18   16.46    None  None   None       |
|    Sol.    : 438    0      4.33    77.25   38.61    None  None   None       |
|    Mac.    : 2385   0      0.00    82.18   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.219:  722   |   5:    41.092 -  49.311:  112        |
|      1:     8.219 -  16.437: 1306   |   6:    49.311 -  57.529:   83        |
|      2:    16.437 -  24.655:  297   |   7:    57.529 -  65.748:   40        |
|      3:    24.655 -  32.874:  138   |   8:    65.748 -  73.966:   15        |
|      4:    32.874 -  41.092:  106   |   9:    73.966 -  82.184:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1571             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1572             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1572   ksol= 0.32   Bsol= 52.70   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.05,-0.44,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.1007 0.1260      5.3975      5.5095|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.0867 0.1125      5.4448       5.648|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.1053 0.1467      5.4799      5.8286|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.1205 0.1560      5.4448      5.5795|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.1328 0.1676       5.326      5.5367|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.1205 0.2025      5.2134       5.523|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.1278 0.1545      5.1746      5.3185|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.1167 0.1678      5.0826      5.3315|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.1167 0.1811      5.0344      5.3093|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.1148 0.1742      4.9732       5.246|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.1149 0.1698      4.9506       5.191|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.1157 0.1771      4.8922      5.2804|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.1083 0.1766      4.8002      5.0732|
| 14:  2.0502 -  2.0003 0.77    976  110 0.0998 0.1674       4.664      4.9161|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.94   9.10   0.97     0.94       7152.23|
|  2:  4.7729 -  3.8086  1312   151  0.95   7.87   1.00     0.99       8987.33|
|  3:  3.8086 -  3.3331  1299   141  0.94  11.04   1.02     1.01      10235.96|
|  4:  3.3331 -  3.0311  1295   141  0.93  12.98   1.00     0.98       9803.20|
|  5:  3.0311 -  2.8153  1268   144  0.91  15.35   0.99     0.96       8122.48|
|  6:  2.8153 -  2.6503  1288   144  0.90  15.93   0.98     0.95       7020.40|
|  7:  2.6503 -  2.5182  1266   142  0.90  15.60   0.98     0.95       6218.18|
|  8:  2.5182 -  2.4090  1271   137  0.91  14.78   0.98     0.96       5321.78|
|  9:  2.4090 -  2.3166  1249   142  0.91  15.26   0.99     0.96       5064.77|
| 10:  2.3166 -  2.2370  1273   139  0.90  15.70   0.98     0.94       4372.35|
| 11:  2.2370 -  2.1672  1249   138  0.90  16.09   0.98     0.94       4476.38|
| 12:  2.1672 -  2.1054  1251   139  0.90  15.88   0.99     0.97       4038.66|
| 13:  2.1054 -  2.0502  1251   139  0.90  15.83   0.98     0.95       3458.92|
| 14:  2.0502 -  2.0003   976   110  0.92  14.18   0.95     0.92       2563.37|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2563.37 max =        10235.96 mean =      6296.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.36 mean =        13.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1570   ksol= 0.32   Bsol= 54.30   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.80,-0.23,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146234                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1570   ksol= 0.32   Bsol= 54.30   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.80,-0.23,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146234                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.1007 0.1264      5.3971      5.5098|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.0869 0.1127      5.4463      5.6491|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.1054 0.1467      5.4804      5.8289|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.1204 0.1559      5.4441       5.579|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.1327 0.1674       5.325      5.5358|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.1205 0.2024      5.2127      5.5223|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.1278 0.1544       5.174      5.3179|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.1166 0.1676      5.0824       5.331|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.1167 0.1813      5.0342      5.3095|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.1148 0.1740      4.9731       5.245|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.1149 0.1697      4.9503      5.1904|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.1157 0.1769       4.892      5.2798|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.1083 0.1768      4.8001      5.0736|
| 14:  2.0502 -  2.0003 0.77    976  110 0.0999 0.1673      4.6641      4.9157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.94   9.10   0.97     0.94       7151.77|
|  2:  4.7729 -  3.8086  1312   151  0.95   7.88   1.01     0.99       8997.76|
|  3:  3.8086 -  3.3331  1299   141  0.94  11.05   1.02     1.01      10242.00|
|  4:  3.3331 -  3.0311  1295   141  0.93  12.97   1.00     0.98       9790.87|
|  5:  3.0311 -  2.8153  1268   144  0.91  15.33   1.00     0.97       8108.74|
|  6:  2.8153 -  2.6503  1288   144  0.90  15.91   0.98     0.96       7008.48|
|  7:  2.6503 -  2.5182  1266   142  0.90  15.59   0.99     0.96       6209.25|
|  8:  2.5182 -  2.4090  1271   137  0.91  14.79   0.99     0.97       5318.67|
|  9:  2.4090 -  2.3166  1249   142  0.91  15.26   1.00     0.97       5063.29|
| 10:  2.3166 -  2.2370  1273   139  0.90  15.70   0.99     0.95       4369.81|
| 11:  2.2370 -  2.1672  1249   138  0.90  16.08   0.99     0.96       4471.45|
| 12:  2.1672 -  2.1054  1251   139  0.90  15.87   1.00     0.99       4035.36|
| 13:  2.1054 -  2.0502  1251   139  0.90  15.83   0.99     0.97       3457.15|
| 14:  2.0502 -  2.0003   976   110  0.92  14.18   0.97     0.93       2563.36|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2563.36 max =        10242.00 mean =      6293.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.29 mean =        13.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.19   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    82.19   16.46    None  None   None       |
|    Sol.    : 438    0      4.33    77.25   38.61    None  None   None       |
|    Mac.    : 2385   0      0.00    82.19   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.221:  722   |   5:    41.095 -  49.314:  112        |
|      1:     8.221 -  16.440: 1306   |   6:    49.314 -  57.532:   83        |
|      2:    16.440 -  24.658:  297   |   7:    57.532 -  65.751:   40        |
|      3:    24.658 -  32.877:  138   |   8:    65.751 -  73.969:   15        |
|      4:    32.877 -  41.095:  106   |   9:    73.969 -  82.187:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 290         
Filter by distance & map next to the model:
   mapped sites are within: 0.600 - 4.046
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 290
   mapped sites are within: 0.703 - 4.046

peak=    5.637 closest distance to " NH2 ARG A  56 " =    2.208
peak=    5.372 closest distance to " CG  PRO A  54 " =    1.376
peak=    5.348 closest distance to " CB  GLN A 223 " =    1.409
peak=    5.334 closest distance to " O   HOH Z 232 " =    2.319
peak=    5.069 closest distance to " CB  ARG A 275 " =    0.935
peak=    5.032 closest distance to " O   HOH Z 126 " =    1.912
peak=    4.747 closest distance to " O   HOH Z 298 " =    1.912
peak=    4.731 closest distance to " CB  SER A  63 " =    1.187
peak=    4.722 closest distance to " CG  PRO A  90 " =    1.219
peak=    4.691 closest distance to " CG  PRO A 213 " =    1.229
peak=    4.648 closest distance to " O   HOH Z 142 " =    1.744
peak=    4.602 closest distance to " CB  PRO A  54 " =    0.975
peak=    4.592 closest distance to " CG  PRO A 198 " =    1.304
peak=    4.586 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.579 closest distance to " CZ  PHE A 218 " =    1.098
peak=    4.533 closest distance to " NE2 GLN A  11 " =    1.060
peak=    4.510 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.488 closest distance to " CB  ARG A  79 " =    1.357
peak=    4.482 closest distance to " CB  ARG A 190 " =    1.655
peak=    4.433 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.405 closest distance to " CG2 VAL A 257 " =    0.884
peak=    4.377 closest distance to " C   PRO A 198 " =    1.492
peak=    4.367 closest distance to " CB  TYR A 169 " =    0.736
peak=    4.338 closest distance to " CE  LYS A  76 " =    0.863
peak=    4.307 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.297 closest distance to " O   HOH Z  15 " =    2.167
peak=    4.267 closest distance to " O   HOH Z 303 " =    2.101
peak=    4.220 closest distance to " CB  GLU A 152 " =    1.231
peak=    4.215 closest distance to " O   HOH Z 189 " =    2.765
peak=    4.206 closest distance to " O   HOH Z  19 " =    2.511
peak=    4.190 closest distance to " CB  ASN A 148 " =    1.451
peak=    4.187 closest distance to " CG  PRO A 243 " =    1.051
peak=    4.166 closest distance to " O   HOH Z 369 " =    2.286
peak=    4.163 closest distance to " CB  TRP A 266 " =    1.017
peak=    4.162 closest distance to " O   HOH Z 236 " =    2.206
peak=    4.138 closest distance to " O   HOH Z  61 " =    1.623
peak=    4.129 closest distance to " ND2 ASN A 187 " =    1.485
peak=    4.086 closest distance to " CA  ASN A 215 " =    1.081
peak=    4.069 closest distance to " CB  VAL A 265 " =    1.228
peak=    4.063 closest distance to " O   HOH Z 427 " =    2.937
peak=    4.057 closest distance to " O   HOH Z 234 " =    3.788
peak=    4.034 closest distance to " O   HOH Z 158 " =    3.095
peak=    4.019 closest distance to " O   SER A  87 " =    2.217
peak=    4.008 closest distance to " O   HOH Z 250 " =    1.511
peak=    3.992 closest distance to " NH1AARG A 145 " =    1.296
peak=    3.989 closest distance to " O   HOH Z 289 " =    1.710
peak=    3.980 closest distance to " O   HOH Z 265 " =    2.340
peak=    3.977 closest distance to " OD1 ASN A  69 " =    2.565
peak=    3.949 closest distance to " CD2 TRP A 179 " =    1.313
peak=    3.947 closest distance to " O   HOH Z 313 " =    1.980
peak=    3.940 closest distance to " CB  ASN A  39 " =    0.926
peak=    3.927 closest distance to " CA  ARG A  36 " =    1.041
peak=    3.918 closest distance to " O   HOH Z 402 " =    1.386
peak=    3.912 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.892 closest distance to " CB  ASP A 124 " =    0.767
peak=    3.873 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.864 closest distance to " CB  GLU A 128 " =    1.000
peak=    3.860 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.852 closest distance to " O   HOH Z  40 " =    1.795
peak=    3.848 closest distance to " O   HOH Z 193 " =    1.995
peak=    3.828 closest distance to " CA  ALA A  51 " =    0.927
peak=    3.822 closest distance to " O   HOH Z  43 " =    1.947
peak=    3.816 closest distance to " O   HOH Z 209 " =    2.294
peak=    3.810 closest distance to " O   HOH Z 316 " =    3.189
peak=    3.799 closest distance to " NZ  LYS A 117 " =    3.175
peak=    3.797 closest distance to " O   HOH Z 368 " =    2.093
peak=    3.795 closest distance to " CA  SER A  87 " =    1.023
peak=    3.793 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.790 closest distance to " O   HOH Z 203 " =    1.745
peak=    3.789 closest distance to " O   HOH Z 423 " =    1.879
peak=    3.780 closest distance to " O   HOH Z  21 " =    1.798
peak=    3.755 closest distance to " CA  ARG A 195 " =    1.223
peak=    3.752 closest distance to " O   HOH Z 403 " =    1.536
peak=    3.750 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.747 closest distance to " O   HOH Z 128 " =    2.100
peak=    3.742 closest distance to " CA  TYR A  30 " =    1.067
peak=    3.735 closest distance to " O   HOH Z 392 " =    3.121
peak=    3.733 closest distance to " CB  ASP A 140 " =    1.024
peak=    3.717 closest distance to " O   HOH Z 389 " =    1.832
peak=    3.715 closest distance to " ND2 ASN A 249 " =    0.867
peak=    3.705 closest distance to " O   HOH Z 272 " =    1.849
peak=    3.704 closest distance to " O   HOH Z 406 " =    1.625
peak=    3.700 closest distance to " O  BHOH Z 338 " =    2.279
peak=    3.695 closest distance to " CB  SER A   3 " =    1.294
peak=    3.694 closest distance to " CB  THR A  31 " =    1.529
peak=    3.688 closest distance to " O   HOH Z 214 " =    2.104
peak=    3.685 closest distance to " O   ASN A  74 " =    1.432
peak=    3.678 closest distance to " CB  ASN A 142 " =    1.048
peak=    3.671 closest distance to " CB  ALA A 291 " =    1.225
peak=    3.669 closest distance to " CB  ALA A 104 " =    0.706
peak=    3.657 closest distance to " CB  GLU A 277 " =    3.660
peak=    3.651 closest distance to " NE2 GLN A  73 " =    3.890
peak=    3.650 closest distance to " CG2AVAL A  72 " =    1.688
peak=    3.650 closest distance to " O   HOH Z 180 " =    2.212
peak=    3.647 closest distance to " CB  PRO A  90 " =    1.069
peak=    3.642 closest distance to " CE1 PHE A  38 " =    1.220
peak=    3.632 closest distance to " O   HOH Z 185 " =    1.799
peak=    3.624 closest distance to " CG  LEU A 167 " =    1.243
peak=    3.619 closest distance to " CD  ARG A 269 " =    0.935
peak=    3.619 closest distance to " O   HOH Z 172 " =    3.396
peak=    3.616 closest distance to " O   HOH Z  59 " =    2.000
peak=    3.616 closest distance to " CA  VAL A 125 " =    1.129
peak=    3.612 closest distance to " O   HOH Z 419 " =    2.091
peak=    3.611 closest distance to " O   HOH Z   1 " =    2.095
peak=    3.611 closest distance to " N   ARG A 156 " =    1.363
peak=    3.608 closest distance to " O   THR A 220 " =    1.233
peak=    3.607 closest distance to " CA  ASP A 124 " =    0.703
peak=    3.606 closest distance to " CD1 LEU A  96 " =    0.720
peak=    3.603 closest distance to " CB  MET A  47 " =    1.100
peak=    3.601 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.599 closest distance to " O   HOH Z 261 " =    1.704
peak=    3.597 closest distance to " CD  LYS A 166 " =    1.238
peak=    3.595 closest distance to " O   HOH Z 261 " =    1.914
peak=    3.588 closest distance to " N   ASN A  39 " =    1.275
peak=    3.587 closest distance to " CE1 PHE A 218 " =    1.019
peak=    3.584 closest distance to " CB  PHE A 204 " =    0.729
peak=    3.570 closest distance to " CB  ILE A 120 " =    1.282
peak=    3.566 closest distance to " O   HOH Z 368 " =    3.531
peak=    3.557 closest distance to " CG  MET A 185 " =    1.144
peak=    3.552 closest distance to " CA  THR A 264 " =    0.909
peak=    3.541 closest distance to " CB  SER A 212 " =    1.191
peak=    3.539 closest distance to " O   HOH Z  10 " =    1.793
peak=    3.537 closest distance to " CD2 LEU A 297 " =    0.881
peak=    3.535 closest distance to " NH2 ARG A 156 " =    1.155
peak=    3.532 closest distance to " CA  THR A 221 " =    1.035
peak=    3.529 closest distance to " O   HOH Z 248 " =    1.577
peak=    3.516 closest distance to " CA  ASN A 217 " =    1.217
peak=    3.515 closest distance to " CG  ARG A  66 " =    2.499
peak=    3.510 closest distance to " CG  GLN A  11 " =    1.684
peak=    3.509 closest distance to " CB  ALA A 114 " =    0.824
peak=    3.507 closest distance to " CD BLYS A 290 " =    0.956
peak=    3.500 closest distance to " O   HOH Z 359 " =    1.505
peak=    3.499 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.494 closest distance to " C   ILE A 106 " =    1.931
peak=    3.492 closest distance to " CB  TRP A 179 " =    1.394
peak=    3.488 closest distance to " CB  ASN A 110 " =    1.127
peak=    3.485 closest distance to " O   ALA A 165 " =    1.544
peak=    3.477 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.477 closest distance to " O   HOH Z  68 " =    2.272
peak=    3.468 closest distance to " O   HOH Z 294 " =    1.549
peak=    3.464 closest distance to " CA  MET A 105 " =    1.021
peak=    3.458 closest distance to " CZ3 TRP A 266 " =    1.146
peak=    3.457 closest distance to " CB  LEU A  83 " =    0.794
peak=    3.451 closest distance to " O   HOH Z 148 " =    3.403
peak=    3.451 closest distance to " O   HOH Z 147 " =    1.799
peak=    3.450 closest distance to " O   THR A 251 " =    1.134
peak=    3.448 closest distance to " O   HOH Z 234 " =    1.927
peak=    3.445 closest distance to " CB  SER A 210 " =    0.804
peak=    3.427 closest distance to " O   HOH Z 411 " =    3.890
peak=    3.416 closest distance to " O   HOH Z 365 " =    2.819
peak=    3.415 closest distance to " CB  TYR A 116 " =    0.777
peak=    3.410 closest distance to " N   PHE A 130 " =    1.251
peak=    3.407 closest distance to " O   HOH Z 280 " =    2.961
peak=    3.407 closest distance to " CA  ASP A 162 " =    0.996
peak=    3.402 closest distance to " O   HOH Z 133 " =    2.572
peak=    3.400 closest distance to " NE2 HIS A 207 " =    1.198
peak=    3.395 closest distance to " O   HOH Z 285 " =    2.492
peak=    3.394 closest distance to " CG2 ILE A  20 " =    1.405
peak=    3.389 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.388 closest distance to " O   HOH Z 291 " =    1.612
peak=    3.386 closest distance to " CA  TYR A 116 " =    1.362
peak=    3.382 closest distance to " O   HOH Z 325 " =    2.340
peak=    3.379 closest distance to " CD1 ILE A 106 " =    0.796
peak=    3.377 closest distance to " O   HOH Z 371 " =    3.023
peak=    3.377 closest distance to " CA  ILE A 234 " =    0.949
peak=    3.376 closest distance to " O   HOH Z 305 " =    3.640
peak=    3.375 closest distance to " O   HOH Z 213 " =    2.019
peak=    3.375 closest distance to " N   TYR A 116 " =    1.487
peak=    3.375 closest distance to " O   HOH Z 273 " =    2.911
peak=    3.373 closest distance to " CB  ALA A 242 " =    0.887
peak=    3.372 closest distance to " NZ  LYS A  48 " =    1.292
peak=    3.370 closest distance to " CD1 ILE A 199 " =    0.868
peak=    3.369 closest distance to " CB  PRO A 198 " =    1.103
peak=    3.366 closest distance to " O   HOH Z  88 " =    3.240
peak=    3.360 closest distance to " O   HOH Z 128 " =    2.133
peak=    3.358 closest distance to " CG AARG A 275 " =    1.143
peak=    3.355 closest distance to " CG  GLU A  37 " =    0.832
peak=    3.354 closest distance to " CZ2 TRP A 179 " =    1.779
peak=    3.351 closest distance to " O   HOH Z   9 " =    2.043
peak=    3.350 closest distance to " O   HOH Z 425 " =    2.018
peak=    3.345 closest distance to " OG BSER A 164 " =    2.373
peak=    3.343 closest distance to " CG1 ILE A 120 " =    1.000
peak=    3.336 closest distance to " O   HOH Z 116 " =    3.049
peak=    3.332 closest distance to " O   HOH Z 132 " =    2.631
peak=    3.331 closest distance to " OH  TYR A 116 " =    1.053
peak=    3.320 closest distance to " O   HOH Z  97 " =    2.460
peak=    3.320 closest distance to " CE1 TYR A 186 " =    1.369
peak=    3.318 closest distance to " O   HOH Z 325 " =    3.975
peak=    3.313 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.306 closest distance to " O   HOH Z 250 " =    2.180
peak=    3.306 closest distance to " O   HOH Z  88 " =    1.929
peak=    3.305 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.303 closest distance to " O   HOH Z  40 " =    1.409
peak=    3.302 closest distance to " CG2 THR A 221 " =    1.042
peak=    3.299 closest distance to " CG2 ILE A 234 " =    0.796
peak=    3.298 closest distance to " CA  ALA A  84 " =    1.271
peak=    3.294 closest distance to " CB  SER A  62 " =    0.789
peak=    3.290 closest distance to " O   HOH Z 344 " =    3.172
peak=    3.287 closest distance to " NE2 GLN A  77 " =    3.247
peak=    3.287 closest distance to " O   HOH Z 175 " =    2.187
peak=    3.284 closest distance to " OG BSER A  99 " =    2.308
peak=    3.283 closest distance to " CB  ASN A 215 " =    1.141
peak=    3.281 closest distance to " CD1AILE A 234 " =    0.933
peak=    3.281 closest distance to " O   TYR A 116 " =    1.418
peak=    3.280 closest distance to " CB  ALA A 248 " =    1.346
peak=    3.276 closest distance to " CB  SER A 216 " =    0.833
peak=    3.272 closest distance to " N   GLY A  98 " =    1.074
peak=    3.268 closest distance to " CE  LYS A  48 " =    1.094
peak=    3.266 closest distance to " CB  GLN A  89 " =    1.315
peak=    3.264 closest distance to " O   HOH Z 337 " =    3.583
peak=    3.263 closest distance to " O   HOH Z 421 " =    1.925
peak=    3.262 closest distance to " CA  GLU A  46 " =    0.859
peak=    3.257 closest distance to " CB  MET A  40 " =    0.818
peak=    3.249 closest distance to " ND2 ASN A 110 " =    1.587
peak=    3.245 closest distance to " OD2 ASP A 286 " =    2.907
peak=    3.245 closest distance to " O   PHE A  61 " =    1.384
peak=    3.244 closest distance to " OG  SER A  22 " =    2.696
peak=    3.244 closest distance to " N   ASN A 127 " =    1.253
peak=    3.243 closest distance to " CA  ALA A 154 " =    0.992
peak=    3.237 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.236 closest distance to " CA  ASN A 110 " =    1.140
peak=    3.235 closest distance to " CB  LYS A 290 " =    0.993
peak=    3.235 closest distance to " O   HOH Z   1 " =    1.634
peak=    3.233 closest distance to " CA  ALA A 158 " =    1.371
peak=    3.233 closest distance to " CB  SER A  62 " =    1.112
peak=    3.230 closest distance to " O   SER A 164 " =    1.357
peak=    3.229 closest distance to " O   THR A 182 " =    1.344
peak=    3.229 closest distance to " O   HOH Z 403 " =    1.576
peak=    3.225 closest distance to " CB  LEU A 300 " =    0.896
peak=    3.225 closest distance to " CB  ALA A   9 " =    1.527
peak=    3.219 closest distance to " O   ASP A 191 " =    1.514
peak=    3.218 closest distance to " CA  ARG A 139 " =    0.984
peak=    3.215 closest distance to " O   HOH Z 339 " =    2.178
peak=    3.215 closest distance to " O   HOH Z 193 " =    1.732
peak=    3.209 closest distance to " CB  GLN A 103 " =    0.883
peak=    3.207 closest distance to " O   HOH Z  88 " =    2.581
peak=    3.207 closest distance to " CB  LYS A 117 " =    1.261
peak=    3.202 closest distance to " CA  ARG A 159 " =    1.289
peak=    3.202 closest distance to " O   HOH Z 258 " =    1.682
peak=    3.199 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.196 closest distance to " O   PHE A 192 " =    1.429
peak=    3.192 closest distance to " O   HOH Z 329 " =    4.046
peak=    3.190 closest distance to " CB  ALA A  34 " =    0.961
peak=    3.189 closest distance to " CB  TYR A 169 " =    1.217
peak=    3.187 closest distance to " CG  LYS A  76 " =    1.007
peak=    3.183 closest distance to " O   HOH Z 417 " =    3.279
peak=    3.183 closest distance to " OG BSER A 134 " =    2.822
peak=    3.182 closest distance to " CB  ARG A 139 " =    0.986
peak=    3.182 closest distance to " O   HOH Z 426 " =    1.931
peak=    3.182 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.171 closest distance to " O   HOH Z   6 " =    2.164
peak=    3.170 closest distance to " O   HOH Z 383 " =    1.876
peak=    3.170 closest distance to " O   HOH Z  44 " =    3.024
peak=    3.167 closest distance to " CB  ASP A 298 " =    1.146
peak=    3.164 closest distance to " O   HOH Z 261 " =    2.411
peak=    3.162 closest distance to " CA  ALA A 233 " =    1.449
peak=    3.161 closest distance to " CG2 VAL A 197 " =    1.062
peak=    3.161 closest distance to " O   HOH Z 271 " =    2.042
peak=    3.156 closest distance to " O   HOH Z 173 " =    1.842
peak=    3.155 closest distance to " N   SER A 135 " =    1.272
peak=    3.148 closest distance to " O   HOH Z  62 " =    2.100
peak=    3.147 closest distance to " O   HOH Z 152 " =    2.343
peak=    3.138 closest distance to " CB  SER A 141 " =    1.012
peak=    3.137 closest distance to " NH1BARG A 145 " =    0.971
peak=    3.137 closest distance to " O   HOH Z 384 " =    2.979
peak=    3.133 closest distance to " CG BARG A 102 " =    1.747
peak=    3.123 closest distance to " O   ALA A   1 " =    1.680
peak=    3.123 closest distance to " ND1 HIS A  86 " =    1.662
peak=    3.121 closest distance to " O   HOH Z 371 " =    1.625
peak=    3.118 closest distance to " CB  PRO A 243 " =    1.505
peak=    3.117 closest distance to " CD  ARG A 195 " =    3.451
peak=    3.111 closest distance to " CB  ASN A 173 " =    1.114
peak=    3.109 closest distance to " CD  ARG A 219 " =    1.112
peak=    3.104 closest distance to " CB  THR A  52 " =    0.843
peak=    3.101 closest distance to " O   HOH Z 188 " =    1.975
peak=    3.099 closest distance to " O   HOH Z 285 " =    1.846
peak=    3.085 closest distance to " CB  ARG A 138 " =    0.947
peak=    3.069 closest distance to " CD1 ILE A 263 " =    1.254
peak=    3.069 closest distance to " CB  PHE A 204 " =    0.721
peak=    3.068 closest distance to " O   HOH Z 171 " =    4.032
peak=    3.067 closest distance to " N   ASP A 162 " =    1.176
peak=    3.065 closest distance to " O   HOH Z 345 " =    3.388
peak=    3.065 closest distance to " O   HOH Z 421 " =    2.945
peak=    3.050 closest distance to " O   HOH Z 219 " =    1.555
peak=    3.047 closest distance to " O   HOH Z 391 " =    2.914
peak=    3.033 closest distance to " CB  ALA A  43 " =    0.798
peak=    3.016 closest distance to " O   HOH Z 371 " =    3.303

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.801 - 5.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 188
   mapped sites are within: 0.801 - 5.626

peak=   -4.702 closest distance to " CD  GLN A  58 " =    0.962
peak=   -4.702 closest distance to " CD  ARG A  14 " =    3.509
peak=   -4.547 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -4.438 closest distance to " O   HOH Z 266 " =    5.427
peak=   -4.361 closest distance to " O   HOH Z 231 " =    2.250
peak=   -4.352 closest distance to " C   HIS A 108 " =    1.088
peak=   -4.277 closest distance to " CD  ARG A 156 " =    2.027
peak=   -4.267 closest distance to " O   VAL A  67 " =    2.643
peak=   -4.240 closest distance to " OG BSER A 134 " =    1.288
peak=   -4.203 closest distance to " O   PRO A 198 " =    1.278
peak=   -4.195 closest distance to " CB  PRO A 243 " =    2.670
peak=   -4.180 closest distance to " O   HOH Z 377 " =    2.051
peak=   -4.167 closest distance to " CD2 PHE A 192 " =    2.055
peak=   -4.142 closest distance to " CZ3 TRP A 179 " =    1.196
peak=   -4.129 closest distance to " O   HOH Z 372 " =    2.361
peak=   -4.049 closest distance to " CA  VAL A  67 " =    2.913
peak=   -4.017 closest distance to " CG1 VAL A 112 " =    2.846
peak=   -4.010 closest distance to " O   HOH Z 198 " =    1.879
peak=   -3.927 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.912 closest distance to " CE2 PHE A  61 " =    2.662
peak=   -3.911 closest distance to " OD1 ASN A 148 " =    1.408
peak=   -3.893 closest distance to " CG  GLN A 223 " =    1.935
peak=   -3.888 closest distance to " O   HOH Z  73 " =    2.247
peak=   -3.881 closest distance to " OG  SER A  97 " =    2.299
peak=   -3.833 closest distance to " CE  MET A 105 " =    2.547
peak=   -3.823 closest distance to " CB  ALA A 161 " =    2.600
peak=   -3.794 closest distance to " CA  ASP A 298 " =    1.091
peak=   -3.782 closest distance to " O   HOH Z 114 " =    3.051
peak=   -3.779 closest distance to " CG1 VAL A 265 " =    2.339
peak=   -3.765 closest distance to " O   HOH Z 290 " =    1.193
peak=   -3.762 closest distance to " CB  ASN A  39 " =    2.352
peak=   -3.757 closest distance to " O   HOH Z 196 " =    2.059
peak=   -3.747 closest distance to " ND2 ASN A  45 " =    1.816
peak=   -3.742 closest distance to " OD1 ASP A 171 " =    1.618
peak=   -3.739 closest distance to " N   ALA A  43 " =    2.588
peak=   -3.738 closest distance to " O   HOH Z 407 " =    3.171
peak=   -3.734 closest distance to " O   HOH Z  10 " =    1.502
peak=   -3.733 closest distance to " CB  ALA A  43 " =    2.621
peak=   -3.732 closest distance to " CG  ARG A 269 " =    2.514
peak=   -3.726 closest distance to " OD2 ASP A 191 " =    1.463
peak=   -3.699 closest distance to " OXT GLY A 302 " =    2.914
peak=   -3.691 closest distance to " CE BMET A  47 " =    1.388
peak=   -3.678 closest distance to " CD2 TYR A 293 " =    2.011
peak=   -3.660 closest distance to " CD1 PHE A  59 " =    1.972
peak=   -3.643 closest distance to " O   HOH Z 389 " =    1.919
peak=   -3.643 closest distance to " NE2 GLN A 194 " =    1.880
peak=   -3.640 closest distance to " CB  ALA A 248 " =    2.374
peak=   -3.628 closest distance to " O   HOH Z 429 " =    2.195
peak=   -3.603 closest distance to " O   PRO A 163 " =    2.055
peak=   -3.592 closest distance to " NH2 ARG A  79 " =    1.512
peak=   -3.585 closest distance to " CA  GLY A 203 " =    2.449
peak=   -3.581 closest distance to " O   HOH Z 185 " =    2.322
peak=   -3.576 closest distance to " CB  ALA A 291 " =    2.298
peak=   -3.569 closest distance to " N   THR A  52 " =    1.657
peak=   -3.567 closest distance to " ND2 ASN A  45 " =    1.106
peak=   -3.565 closest distance to " N   ALA A 248 " =    1.694
peak=   -3.564 closest distance to " NH2AARG A 275 " =    5.345
peak=   -3.557 closest distance to " O   HOH Z  51 " =    1.709
peak=   -3.556 closest distance to " O   HOH Z 394 " =    1.498
peak=   -3.556 closest distance to " CD1 LEU A 101 " =    2.390
peak=   -3.551 closest distance to " O   PHE A 218 " =    1.533
peak=   -3.548 closest distance to " CG2 ILE A  49 " =    2.777
peak=   -3.547 closest distance to " O   HOH Z 313 " =    1.881
peak=   -3.539 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.533 closest distance to " O   VAL A 189 " =    1.589
peak=   -3.530 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.529 closest distance to " CA  GLY A 241 " =    3.387
peak=   -3.515 closest distance to " CD1 LEU A 255 " =    2.883
peak=   -3.511 closest distance to " CG  GLU A 277 " =    1.197
peak=   -3.510 closest distance to " CG1 VAL A 250 " =    2.682
peak=   -3.506 closest distance to " CZ  PHE A 155 " =    1.249
peak=   -3.503 closest distance to " ND2 ASN A 249 " =    2.401
peak=   -3.497 closest distance to " C   LEU A 143 " =    1.009
peak=   -3.494 closest distance to " NE2 GLN A  88 " =    1.928
peak=   -3.492 closest distance to " O   HOH Z 211 " =    1.614
peak=   -3.491 closest distance to " CA  GLY A 241 " =    2.327
peak=   -3.491 closest distance to " O   HOH Z 102 " =    1.552
peak=   -3.489 closest distance to " CB  ALA A   7 " =    2.308
peak=   -3.488 closest distance to " CB  ASP A 132 " =    2.299
peak=   -3.487 closest distance to " CB  GLN A  11 " =    1.726
peak=   -3.471 closest distance to " CD  ARG A 195 " =    5.127
peak=   -3.461 closest distance to " CD  ARG A 139 " =    1.548
peak=   -3.460 closest distance to " NE2 GLN A 278 " =    1.741
peak=   -3.450 closest distance to " O   ALA A  10 " =    1.668
peak=   -3.449 closest distance to " CB  ALA A 291 " =    2.469
peak=   -3.444 closest distance to " N   SER A 212 " =    1.966
peak=   -3.443 closest distance to " O   ALA A  34 " =    2.468
peak=   -3.436 closest distance to " O   HOH Z 353 " =    2.115
peak=   -3.419 closest distance to " CD2 HIS A 207 " =    2.378
peak=   -3.406 closest distance to " ND2 ASN A 187 " =    1.458
peak=   -3.393 closest distance to " CG  LEU A  83 " =    1.963
peak=   -3.393 closest distance to " O   VAL A 189 " =    2.605
peak=   -3.382 closest distance to " CG  PHE A 283 " =    2.669
peak=   -3.370 closest distance to " O   HOH Z  44 " =    2.376
peak=   -3.366 closest distance to " O   HOH Z  38 " =    1.515
peak=   -3.354 closest distance to " CG  ARG A  66 " =    2.368
peak=   -3.351 closest distance to " CD1 ILE A 151 " =    2.502
peak=   -3.350 closest distance to " O   GLY A  17 " =    1.117
peak=   -3.349 closest distance to " O   HOH Z 311 " =    3.745
peak=   -3.344 closest distance to " CB  ASP A 286 " =    1.765
peak=   -3.336 closest distance to " CG1 VAL A  67 " =    3.194
peak=   -3.336 closest distance to " C   ALA A 158 " =    1.450
peak=   -3.331 closest distance to " O   TYR A 247 " =    2.893
peak=   -3.331 closest distance to " OD1 ASN A 187 " =    1.610
peak=   -3.328 closest distance to " C   MET A 188 " =    1.405
peak=   -3.325 closest distance to " NH2BARG A 275 " =    1.992
peak=   -3.324 closest distance to " CG1 VAL A 125 " =    1.911
peak=   -3.324 closest distance to " O   HOH Z 191 " =    5.626
peak=   -3.323 closest distance to " O   SER A  95 " =    1.658
peak=   -3.321 closest distance to " O   HOH Z 166 " =    2.057
peak=   -3.319 closest distance to " O   HOH Z  60 " =    2.224
peak=   -3.316 closest distance to " O   HOH Z 322 " =    1.235
peak=   -3.310 closest distance to " CD1 ILE A 239 " =    2.169
peak=   -3.309 closest distance to " CE3 TRP A 150 " =    2.192
peak=   -3.304 closest distance to " O   HOH Z  11 " =    1.663
peak=   -3.303 closest distance to " O   HOH Z 322 " =    1.662
peak=   -3.302 closest distance to " CG  TRP A 266 " =    1.874
peak=   -3.299 closest distance to " O   HOH Z   6 " =    1.367
peak=   -3.291 closest distance to " O   HOH Z 177 " =    1.753
peak=   -3.289 closest distance to " O   HOH Z 357 " =    2.111
peak=   -3.288 closest distance to " O   HOH Z 348 " =    2.242
peak=   -3.279 closest distance to " O   HOH Z 298 " =    1.294
peak=   -3.278 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.276 closest distance to " CG  HIS A  86 " =    1.095
peak=   -3.273 closest distance to " O   HOH Z 134 " =    3.069
peak=   -3.273 closest distance to " CD1 TRP A  70 " =    1.079
peak=   -3.272 closest distance to " O   GLY A 211 " =    1.294
peak=   -3.272 closest distance to " C   SER A 206 " =    1.494
peak=   -3.271 closest distance to " N   GLN A  58 " =    1.665
peak=   -3.267 closest distance to " CZ  PHE A 192 " =    2.803
peak=   -3.267 closest distance to " O   HOH Z 298 " =    2.526
peak=   -3.266 closest distance to " CA  ILE A 263 " =    1.101
peak=   -3.264 closest distance to " OD2 ASP A 171 " =    2.472
peak=   -3.258 closest distance to " OG BSER A 134 " =    1.873
peak=   -3.251 closest distance to " O   GLN A 240 " =    2.145
peak=   -3.251 closest distance to " O   HOH Z  43 " =    1.630
peak=   -3.243 closest distance to " CD  GLN A 223 " =    0.995
peak=   -3.241 closest distance to " O   HOH Z  37 " =    1.696
peak=   -3.240 closest distance to " N   THR A 157 " =    1.588
peak=   -3.235 closest distance to " CD2 PHE A 225 " =    1.171
peak=   -3.235 closest distance to " N   ASN A  60 " =    1.335
peak=   -3.233 closest distance to " O   HOH Z 106 " =    1.885
peak=   -3.233 closest distance to " O   HOH Z 253 " =    3.957
peak=   -3.229 closest distance to " O   ALA A 180 " =    1.211
peak=   -3.227 closest distance to " CD  GLU A 236 " =    1.081
peak=   -3.227 closest distance to " OE1 GLN A  88 " =    1.041
peak=   -3.226 closest distance to " O   HOH Z 126 " =    1.881
peak=   -3.219 closest distance to " C   GLY A 262 " =    1.927
peak=   -3.217 closest distance to " O   HOH Z 123 " =    2.463
peak=   -3.217 closest distance to " O   HOH Z  52 " =    1.444
peak=   -3.214 closest distance to " O   ILE A 106 " =    1.981
peak=   -3.212 closest distance to " O   ARG A 145 " =    1.563
peak=   -3.195 closest distance to " O   HOH Z 174 " =    4.115
peak=   -3.194 closest distance to " CA  GLY A 241 " =    2.864
peak=   -3.187 closest distance to " CD1 LEU A   5 " =    2.491
peak=   -3.187 closest distance to " O   HOH Z 281 " =    2.693
peak=   -3.184 closest distance to " O   HOH Z 421 " =    3.117
peak=   -3.183 closest distance to " O   HOH Z 171 " =    1.933
peak=   -3.175 closest distance to " OH  TYR A 247 " =    1.867
peak=   -3.175 closest distance to " CE1 PHE A 218 " =    2.700
peak=   -3.156 closest distance to " O   ALA A 180 " =    0.998
peak=   -3.153 closest distance to " CA  GLY A 133 " =    2.313
peak=   -3.149 closest distance to " O   MET A  40 " =    2.876
peak=   -3.147 closest distance to " ND2 ASN A  60 " =    1.395
peak=   -3.146 closest distance to " O   GLU A 152 " =    1.366
peak=   -3.142 closest distance to " O   HOH Z 128 " =    2.574
peak=   -3.141 closest distance to " CA  GLY A 133 " =    2.044
peak=   -3.139 closest distance to " O   TRP A  70 " =    1.418
peak=   -3.139 closest distance to " O   HOH Z 317 " =    1.501
peak=   -3.138 closest distance to " N   ALA A 226 " =    2.095
peak=   -3.136 closest distance to " CA  SER A 135 " =    1.286
peak=   -3.134 closest distance to " CZ  TYR A 169 " =    1.801
peak=   -3.133 closest distance to " CG  MET A 105 " =    0.948
peak=   -3.126 closest distance to " O   ALA A 292 " =    2.074
peak=   -3.125 closest distance to " O   HOH Z 359 " =    3.110
peak=   -3.115 closest distance to " O   HOH Z 216 " =    1.626
peak=   -3.114 closest distance to " OD2 ASP A 171 " =    1.850
peak=   -3.109 closest distance to " CB  CYS A 201 " =    2.647
peak=   -3.108 closest distance to " OE2 GLU A 152 " =    1.204
peak=   -3.106 closest distance to " CA  ASP A  27 " =    2.438
peak=   -3.102 closest distance to " CB  PRO A 163 " =    2.462
peak=   -3.097 closest distance to " OE1 GLU A  44 " =    1.909
peak=   -3.096 closest distance to " O   HOH Z  13 " =    1.624
peak=   -3.080 closest distance to " O   HOH Z 244 " =    2.037
peak=   -3.071 closest distance to " CG1AVAL A  41 " =    2.841
peak=   -3.065 closest distance to " CD  GLN A 223 " =    1.338
peak=   -3.059 closest distance to " CD2 PHE A  61 " =    2.188
peak=   -3.033 closest distance to " O   HOH Z 357 " =    2.215

================= 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    :  0.2768 0.2691   5.929050e+00   5.904862e+00
   1_bss:  0.2565 0.2525   5.890156e+00   5.863832e+00
   1_xyz:  0.1611 0.1836   5.413228e+00   5.516808e+00
   1_adp:  0.1514 0.1834   5.368721e+00   5.525631e+00
   1_occ:  0.1508 0.1834   5.366965e+00   5.525248e+00
   2_bss:  0.1483 0.1804   5.350841e+00   5.508416e+00
   2_xyz:  0.1269 0.1560   5.207267e+00   5.380432e+00
   2_adp:  0.1195 0.1584   5.178287e+00   5.389546e+00
   2_occ:  0.1194 0.1583   5.177788e+00   5.389008e+00
   3_bss:  0.1191 0.1579   5.176741e+00   5.388205e+00
   3_xyz:  0.1154 0.1581   5.161391e+00   5.389535e+00
   3_adp:  0.1155 0.1564   5.157688e+00   5.382796e+00
   3_occ:  0.1154 0.1565   5.157626e+00   5.383258e+00
   4_bss:  0.1154 0.1558   5.156378e+00   5.379478e+00
   4_xyz:  0.1139 0.1559   5.150550e+00   5.380467e+00
   4_adp:  0.1154 0.1552   5.155331e+00   5.376389e+00
   4_occ:  0.1153 0.1552   5.155541e+00   5.377018e+00
   5_bss:  0.1153 0.1553   5.155688e+00   5.377616e+00
   5_xyz:  0.1140 0.1561   5.152311e+00   5.383961e+00
   5_adp:  0.1122 0.1571   5.146191e+00   5.388212e+00
   5_occ:  0.1122 0.1572   5.146411e+00   5.388706e+00
   5_bss:  0.1120 0.1570   5.146234e+00   5.388468e+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:  0.319  53.571  -3.347  -3.056   2.584  -0.000   0.000   0.000
   1_xyz:  0.319  53.571  -3.347  -3.056   2.584  -0.000   0.000   0.000
   1_adp:  0.319  53.571  -3.347  -3.056   2.584  -0.000   0.000   0.000
   1_occ:  0.319  53.571  -3.347  -3.056   2.584  -0.000   0.000   0.000
   2_bss:  0.334  62.189  -3.110  -2.703  -0.203  -0.000  -0.000  -0.000
   2_xyz:  0.334  62.189  -3.110  -2.703  -0.203  -0.000  -0.000  -0.000
   2_adp:  0.334  62.189  -3.110  -2.703  -0.203  -0.000  -0.000  -0.000
   2_occ:  0.334  62.189  -3.110  -2.703  -0.203  -0.000  -0.000  -0.000
   3_bss:  0.334  62.189  -2.695  -2.319  -0.442  -0.000  -0.000  -0.000
   3_xyz:  0.334  62.189  -2.695  -2.319  -0.442  -0.000  -0.000  -0.000
   3_adp:  0.334  62.189  -2.695  -2.319  -0.442  -0.000  -0.000  -0.000
   3_occ:  0.334  62.189  -2.695  -2.319  -0.442  -0.000  -0.000  -0.000
   4_bss:  0.334  62.189  -2.491  -2.136  -0.468  -0.000  -0.000  -0.000
   4_xyz:  0.334  62.189  -2.491  -2.136  -0.468  -0.000  -0.000  -0.000
   4_adp:  0.334  62.189  -2.491  -2.136  -0.468  -0.000  -0.000  -0.000
   4_occ:  0.334  62.189  -2.491  -2.136  -0.468  -0.000  -0.000  -0.000
   5_bss:  0.322  52.701  -2.395  -2.054  -0.439  -0.000  -0.000  -0.000
   5_xyz:  0.322  52.701  -2.395  -2.054  -0.439  -0.000  -0.000  -0.000
   5_adp:  0.322  52.701  -2.395  -2.054  -0.439  -0.000  -0.000  -0.000
   5_occ:  0.322  52.701  -2.395  -2.054  -0.439  -0.000  -0.000  -0.000
   5_bss:  0.319  54.298  -2.131  -1.801  -0.227  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.120 0.7932  0.9426    20915.814
   1_bss:  25.669 0.8069  0.9172    17951.636
   1_xyz:  16.772 0.8924  0.9863     8395.055
   1_adp:  16.940 0.8906  0.9821     8491.523
   1_occ:  16.939 0.8905  0.9817     8472.552
   2_bss:  16.491 0.8947  0.9619     8253.118
   2_xyz:  13.808 0.9168  0.9691     6251.895
   2_adp:  13.977 0.9154  0.9619     6306.874
   2_occ:  13.962 0.9155  0.9619     6298.242
   3_bss:  13.942 0.9157  0.9687     6293.465
   3_xyz:  13.897 0.9163  0.9701     6343.229
   3_adp:  13.743 0.9175  0.9649     6257.357
   3_occ:  13.752 0.9174  0.9647     6261.578
   4_bss:  13.681 0.9179  0.9688     6176.190
   4_xyz:  13.708 0.9177  0.9687     6191.631
   4_adp:  13.622 0.9185  0.9641     6164.295
   4_occ:  13.638 0.9184  0.9639     6169.559
   5_bss:  13.646 0.9183  0.9660     6168.384
   5_xyz:  13.742 0.9175  0.9668     6270.907
   5_adp:  13.855 0.9166  0.9600     6290.707
   5_occ:  13.863 0.9165  0.9598     6296.423
   5_bss:  13.859 0.9166  0.9684     6292.981
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6287e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6287e-01
   1_xyz:   1.024  0.008  0.071 15.012  0.004  4.119   6.1533e-02
   1_adp:   1.024  0.008  0.071 15.012  0.004  4.119   6.1533e-02
   1_occ:   1.024  0.008  0.071 15.012  0.004  4.119   6.1533e-02
   2_bss:   1.024  0.008  0.071 15.012  0.004  4.119   6.1533e-02
   2_xyz:   0.940  0.006  0.072 14.535  0.004  4.124   5.3182e-02
   2_adp:   0.940  0.006  0.072 14.535  0.004  4.124   5.3182e-02
   2_occ:   0.940  0.006  0.072 14.535  0.004  4.124   5.3182e-02
   3_bss:   0.940  0.006  0.072 14.535  0.004  4.124   5.3182e-02
   3_xyz:   0.911  0.006  0.073 14.371  0.003  4.126   5.0893e-02
   3_adp:   0.911  0.006  0.073 14.371  0.003  4.126   5.0893e-02
   3_occ:   0.911  0.006  0.073 14.371  0.003  4.126   5.0893e-02
   4_bss:   0.911  0.006  0.073 14.371  0.003  4.126   5.0893e-02
   4_xyz:   0.906  0.006  0.072 14.313  0.003  4.128   5.0549e-02
   4_adp:   0.906  0.006  0.072 14.313  0.003  4.128   5.0549e-02
   4_occ:   0.906  0.006  0.072 14.313  0.003  4.128   5.0549e-02
   5_bss:   0.906  0.006  0.072 14.313  0.003  4.128   5.0549e-02
   5_xyz:   0.927  0.007  0.074 14.305  0.003  4.131   5.2384e-02
   5_adp:   0.927  0.007  0.074 14.305  0.003  4.131   5.2384e-02
   5_occ:   0.927  0.007  0.074 14.305  0.003  4.131   5.2384e-02
   5_bss:   0.927  0.007  0.074 14.305  0.003  4.131   5.2384e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4243e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4243e-01
   1_xyz:   8.693  0.039  0.237 82.755  0.038  2.285   9.2103e-02
   1_adp:   8.693  0.039  0.237 82.755  0.038  2.285   9.2103e-02
   1_occ:   8.693  0.039  0.237 82.755  0.038  2.285   9.2103e-02
   2_bss:   8.693  0.039  0.237 82.755  0.038  2.285   9.2103e-02
   2_xyz:   6.502  0.033  0.224 81.535  0.039  2.402   6.9249e-02
   2_adp:   6.502  0.033  0.224 81.535  0.039  2.402   6.9249e-02
   2_occ:   6.502  0.033  0.224 81.535  0.039  2.402   6.9249e-02
   3_bss:   6.502  0.033  0.224 81.535  0.039  2.402   6.9249e-02
   3_xyz:   6.636  0.033  0.226 82.407  0.036  2.401   3.6823e-02
   3_adp:   6.636  0.033  0.226 82.407  0.036  2.401   3.6823e-02
   3_occ:   6.636  0.033  0.226 82.407  0.036  2.401   3.6823e-02
   4_bss:   6.636  0.033  0.226 82.407  0.036  2.401   3.6823e-02
   4_xyz:   6.640  0.042  0.228 82.134  0.033  2.382   2.9860e-02
   4_adp:   6.640  0.042  0.228 82.134  0.033  2.382   2.9860e-02
   4_occ:   6.640  0.042  0.228 82.134  0.033  2.382   2.9860e-02
   5_bss:   6.640  0.042  0.228 82.134  0.033  2.382   2.9860e-02
   5_xyz:   6.544  0.040  0.226 82.477  0.032  2.362   3.0700e-02
   5_adp:   6.544  0.040  0.226 82.477  0.032  2.362   3.0700e-02
   5_occ:   6.544  0.040  0.226 82.477  0.032  2.362   3.0700e-02
   5_bss:   6.544  0.040  0.226 82.477  0.032  2.362   3.0700e-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:  84.44   0.00  16.21  84.44   0.00  12.38  62.88   6.41  37.08
   1_occ:  84.44   0.00  16.21  84.44   0.00  12.38  62.88   6.41  37.08
   2_bss:  84.44   0.00  16.21  84.44   0.00  12.38  62.88   6.41  37.08
   2_xyz:  84.44   0.00  16.21  84.44   0.00  12.38  62.88   6.41  37.08
   2_adp:  79.16   0.52  17.10  79.16   0.52  12.87  76.56   3.59  40.09
   2_occ:  79.16   0.52  17.10  79.16   0.52  12.87  76.56   3.59  40.09
   3_bss:  79.16   0.52  17.10  79.16   0.52  12.87  76.56   3.59  40.09
   3_xyz:  79.16   0.52  17.10  79.16   0.52  12.87  76.56   3.59  40.09
   3_adp:  78.47   0.00  16.54  78.47   1.16  12.61  75.15   0.00  37.99
   3_occ:  78.47   0.00  16.54  78.47   1.16  12.61  75.15   0.00  37.99
   4_bss:  78.47   0.00  16.54  78.47   1.16  12.61  75.15   0.00  37.99
   4_xyz:  78.47   0.00  16.54  78.47   1.16  12.61  75.15   0.00  37.99
   4_adp:  75.59   1.53  16.04  75.59   1.53  12.36  72.08   3.02  36.08
   4_occ:  75.59   1.53  16.04  75.59   1.53  12.36  72.08   3.02  36.08
   5_bss:  75.59   1.53  16.04  75.59   1.53  12.36  72.08   3.02  36.08
   5_xyz:  75.59   1.53  16.04  75.59   1.53  12.36  72.08   3.02  36.08
   5_adp:  82.18   0.00  16.46  82.18   0.00  12.39  77.25   4.33  38.61
   5_occ:  82.18   0.00  16.46  82.18   0.00  12.39  77.25   4.33  38.61
   5_bss:  82.19   0.00  16.46  82.19   0.00  12.39  77.25   4.33  38.61
------------------------------------------------------------------------
 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:    0.912    0.009    0.252
   1_adp:    0.912    0.009    0.252
   1_occ:    0.912    0.009    0.252
   2_bss:    0.912    0.009    0.252
   2_xyz:    0.852    0.006    0.270
   2_adp:    0.852    0.006    0.270
   2_occ:    0.852    0.006    0.270
   3_bss:    0.852    0.006    0.270
   3_xyz:    1.036    0.009    0.292
   3_adp:    1.036    0.009    0.292
   3_occ:    1.036    0.009    0.292
   4_bss:    1.036    0.009    0.292
   4_xyz:    1.263    0.010    0.299
   4_adp:    1.263    0.010    0.299
   4_occ:    1.263    0.010    0.299
   5_bss:    1.263    0.010    0.299
   5_xyz:    1.387    0.003    0.308
   5_adp:    1.387    0.003    0.308
   5_occ:    1.387    0.003    0.308
   5_bss:    1.387    0.003    0.308
------------------------------------------------------------------------

CPU time actual refinement: 269.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/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_668/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_668/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 269.06 
  Macro-tasks:
    bulk solvent and scale       = 31.74  
    individual site refinement   = 112.19 
    weights calculation          = 24.44  
    collect and process          = 5.44   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 173.90 
  Micro-tasks:
    mask                            = 0.97   
    f_calc                          = 85.42  
    alpha_beta                      = 6.74   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 93.48  
    fmodel                         = 5.27   
    r_factors                      = 0.14   
    phase_errors                   = 9.33   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 202.55 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.815 micro seconds
Total CPU time: 4.68 minutes
from_scatterers_fft:    639 calls, 85.08 s
gradients_fft:          584 calls, 81.67 s

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

# Date 2008-01-16 Time 05:22:09 PST -0800 (1200489729.16 s)
Start R-work = 0.2768, R-free = 0.2691 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.2565, R-free = 0.2525
Final R-work = 0.1120, R-free = 0.1570