# Date 2008-01-16 Time 04:38:56 PST -0800 (1200487136.71 s)
#phil __OFF__

Command line arguments: "../402.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8575
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 402

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.4607, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98025
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.968697

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9040
                             d_min =   1.9803

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98025
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.968697

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9044 -  4.2367 [2124/2148]  1909   215  10.1%
  bin  2:  4.2367 -  3.3757 [2032/2052]  1833   199   9.8%
  bin  3:  3.3757 -  2.9527 [2011/2030]  1810   201  10.0%
  bin  4:  2.9527 -  2.6845 [1967/1997]  1766   201  10.2%
  bin  5:  2.6845 -  2.4930 [1993/2012]  1794   199  10.0%
  bin  6:  2.4930 -  2.3466 [1967/1992]  1772   195   9.9%
  bin  7:  2.3466 -  2.2295 [1945/1973]  1750   195  10.0%
  bin  8:  2.2295 -  2.1327 [1960/1996]  1765   195   9.9%
  bin  9:  2.1327 -  2.0509 [1931/1973]  1735   196  10.2%
  bin 10:  2.0509 -  1.9803 [1659/1986]  1496   163   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2218
        3.04 -     3.66: 4737
        3.66 -     4.28: 9107
        4.28 -     4.90: 12448
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.886 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.114 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.145 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.203 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28531 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_402/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.4607 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3153   r_free= 0.3115   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 6.020960                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7251 0.99   1382  152 0.2773 0.2716      6.3307      6.2728|
|  2:  4.7251 -  3.7705 0.99   1312  151 0.2382 0.2258      6.3626      6.3329|
|  3:  3.7705 -  3.2998 0.99   1299  141 0.2650 0.2608      6.3066      6.3781|
|  4:  3.2998 -  3.0008 0.99   1296  141 0.2851 0.3243      6.1991      6.2987|
|  5:  3.0008 -  2.7872 0.99   1269  144 0.3231 0.2632      6.0722      5.9141|
|  6:  2.7872 -  2.6238 0.99   1287  144 0.3228 0.3652       6.009      5.9746|
|  7:  2.6238 -  2.4930 0.99   1267  142 0.3266 0.2900      5.9578      5.8506|
|  8:  2.4930 -  2.3849 0.98   1270  137 0.3482 0.3685      5.9584      6.0116|
|  9:  2.3849 -  2.2935 0.98   1248  142 0.3547 0.3523      5.9152      5.8882|
| 10:  2.2935 -  2.2146 1.00   1277  139 0.3627 0.3263      5.9136      5.8194|
| 11:  2.2146 -  2.1456 0.97   1246  138 0.3639 0.3831      5.8527      5.8905|
| 12:  2.1456 -  2.0844 0.98   1253  139 0.3868 0.3559      5.8372      5.8231|
| 13:  2.0844 -  2.0297 0.99   1250  139 0.3725 0.3667      5.7209      5.6856|
| 14:  2.0297 -  1.9803 0.77    974  110 0.3931 0.3764      5.7293      5.5939|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9044 -  4.7251  1382   152  0.80  24.77   0.87     0.83      39082.32|
|  2:  4.7251 -  3.7705  1312   151  0.85  20.99   0.99     0.94      42101.10|
|  3:  3.7705 -  3.2998  1299   141  0.83  23.98   1.01     0.97      40629.43|
|  4:  3.2998 -  3.0008  1296   141  0.81  26.13   1.00     0.96      35585.98|
|  5:  3.0008 -  2.7872  1269   144  0.76  30.57   1.01     0.94      28186.11|
|  6:  2.7872 -  2.6238  1287   144  0.76  30.44   0.99     0.93      24135.98|
|  7:  2.6238 -  2.4930  1267   142  0.74  31.91   1.02     0.94      22639.81|
|  8:  2.4930 -  2.3849  1270   137  0.73  33.09   1.02     0.93      22513.63|
|  9:  2.3849 -  2.2935  1248   142  0.73  33.53   1.03     0.94      21584.80|
| 10:  2.2935 -  2.2146  1277   139  0.71  34.83   1.05     0.94      20271.88|
| 11:  2.2146 -  2.1456  1246   138  0.71  35.19   1.04     0.97      19579.26|
| 12:  2.1456 -  2.0844  1253   139  0.69  36.98   1.06     0.96      18718.41|
| 13:  2.0844 -  2.0297  1250   139  0.68  37.79   1.05     0.93      16540.73|
| 14:  2.0297 -  1.9803   974   110  0.69  36.82   1.06     0.88      13159.82|
|alpha:            min =        0.83 max =            0.97 mean =         0.93|
|beta:             min =    13159.82 max =        42101.10 mean =     26456.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.99 mean =        31.02|
|phase err.(test): min =        0.00 max =           89.82 mean =        30.85|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.675525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.573   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.574582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.037   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      213 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1866 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2871 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4679 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4428 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5697 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6751 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.806 |       0.209 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3153   r_free= 0.3115   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 6.020960                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3012   r_free= 0.2968   ksol= 0.33   Bsol= 36.44   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,0.26,-1.04,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.998867                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.208409              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.403   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.944   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3012      final r-factor (work) = 0.1686          |
| start r-factor (free) = 0.2968      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8009 = 3.21 * 0.50 * 6.0076 + 1.00 * 0.1635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1703 = 3.21 * 0.50 * 5.6746 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1686      final r-factor (work) = 0.1533          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8392 = 0.32 * 1.00 * 5.6746 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7487 = 0.32 * 1.00 * 5.3868 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    69.80   17.06    None  None   None       |
|    all(noH): 2823   0      0.61    69.80   17.06    None  None   None       |
|    Sol.    : 438    0      7.38    69.80   38.89    None  None   None       |
|    Mac.    : 2385   0      0.61    68.29   13.04    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:     0.611 -   7.530:  423   |   5:    35.208 -  42.127:  109        |
|      1:     7.530 -  14.449: 1321   |   6:    42.127 -  49.046:   87        |
|      2:    14.449 -  21.369:  466   |   7:    49.046 -  55.966:   78        |
|      3:    21.369 -  28.288:  171   |   8:    55.966 -  62.885:   47        |
|      4:    28.288 -  35.208:  105   |   9:    62.885 -  69.805:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1533 r_free = 0.2012             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1531 r_free = 0.2009             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1531   r_free= 0.2009   ksol= 0.33   Bsol= 36.44   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,0.26,-1.04,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.402281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1519   r_free= 0.1993   ksol= 0.31   Bsol= 41.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-1.93,-1.36,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.397796                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.188327              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.648   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.098307              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.375  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1519      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1993      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9756 = 2.19 * 0.50 * 5.4001 + 1.00 * 0.0670                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8528 = 2.19 * 0.50 * 5.3013 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5296 = 0.10 * 1.00 * 5.3013 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5171 = 0.10 * 1.00 * 5.1964 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    68.51   16.60    None  None   None       |
|    all(noH): 2823   0      2.12    68.51   16.60    None  None   None       |
|    Sol.    : 438    0      6.33    67.92   36.91    None  None   None       |
|    Mac.    : 2385   0      2.12    68.51   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:     2.116 -   8.756:  642   |   5:    35.315 -  41.954:  122        |
|      1:     8.756 -  15.395: 1254   |   6:    41.954 -  48.594:   82        |
|      2:    15.395 -  22.035:  384   |   7:    48.594 -  55.234:   68        |
|      3:    22.035 -  28.675:  123   |   8:    55.234 -  61.874:   29        |
|      4:    28.675 -  35.315:  106   |   9:    61.874 -  68.513:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1575             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1195 r_free = 0.1575             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1575   ksol= 0.31   Bsol= 41.63   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-1.93,-1.36,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1574   ksol= 0.32   Bsol= 43.08   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.43,-1.18,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172112                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.567780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.692  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.485362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1247 = 1.57 * 0.50 * 5.1952 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0858 = 1.57 * 0.50 * 5.1466 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.9439 = 3.49 * 1.00 * 5.1466 + 1.00 * 0.0062                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.8453 = 3.49 * 1.00 * 5.1174 + 1.00 * 0.0092                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    85.39   17.23    None  None   None       |
|    all(noH): 2823   0      0.61    85.39   17.23    None  None   None       |
|    Sol.    : 438    0      3.68    77.77   40.28    None  None   None       |
|    Mac.    : 2385   0      0.61    85.39   12.99    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:     0.608 -   9.086:  804   |   5:    42.997 -  51.475:  108        |
|      1:     9.086 -  17.563: 1261   |   6:    51.475 -  59.953:   68        |
|      2:    17.563 -  26.041:  274   |   7:    59.953 -  68.430:   47        |
|      3:    26.041 -  34.519:  121   |   8:    68.430 -  76.908:   19        |
|      4:    34.519 -  42.997:  116   |   9:    76.908 -  85.386:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1532             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1533             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1533   ksol= 0.32   Bsol= 43.08   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.43,-1.18,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120733                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1531   ksol= 0.32   Bsol= 47.05   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.36,-1.01,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.848545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.217232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.325  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1053          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3403 = 2.85 * 0.50 * 5.1176 + 1.00 * 0.0514                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3283 = 2.85 * 0.50 * 5.0998 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1053      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1170 = 0.22 * 1.00 * 5.0998 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1155 = 0.22 * 1.00 * 5.1000 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    83.94   16.58    None  None   None       |
|    all(noH): 2823   0      1.26    83.94   16.58    None  None   None       |
|    Sol.    : 438    0      5.29    79.00   37.89    None  None   None       |
|    Mac.    : 2385   0      1.26    83.94   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.255 -   9.523:  943   |   5:    42.596 -  50.865:   92        |
|      1:     9.523 -  17.792: 1156   |   6:    50.865 -  59.133:   64        |
|      2:    17.792 -  26.060:  256   |   7:    59.133 -  67.401:   29        |
|      3:    26.060 -  34.328:  132   |   8:    67.401 -  75.670:   11        |
|      4:    34.328 -  42.596:  136   |   9:    75.670 -  83.938:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1516             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1058 r_free = 0.1516             target_work(ml) = 5.097         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1516   ksol= 0.32   Bsol= 47.05   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.36,-1.01,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1517   ksol= 0.32   Bsol= 47.05   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.24,-0.82,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097533                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.195037              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.784  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.389  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1057      final r-factor (work) = 0.1043          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2132 = 3.20 * 0.50 * 5.1006 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2029 = 3.20 * 0.50 * 5.0920 + 1.00 * 0.0684                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1043      final r-factor (work) = 0.1041          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0918 = 0.41 * 1.00 * 5.0920 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0924 = 0.41 * 1.00 * 5.0926 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    84.22   16.44    None  None   None       |
|    all(noH): 2823   0      1.01    84.22   16.44    None  None   None       |
|    Sol.    : 438    0      6.14    79.11   37.93    None  None   None       |
|    Mac.    : 2385   0      1.01    84.22   12.49    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:     1.013 -   9.333:  941   |   5:    42.616 -  50.937:   92        |
|      1:     9.333 -  17.654: 1155   |   6:    50.937 -  59.258:   65        |
|      2:    17.654 -  25.975:  259   |   7:    59.258 -  67.578:   29        |
|      3:    25.975 -  34.295:  130   |   8:    67.578 -  75.899:   11        |
|      4:    34.295 -  42.616:  137   |   9:    75.899 -  84.220:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1041 r_free = 0.1532             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1041 r_free = 0.1531             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1041   r_free= 0.1531   ksol= 0.32   Bsol= 47.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.24,-0.82,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094762                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7251 0.99   1382  152 0.0981 0.1263      5.3739      5.5221|
|  2:  4.7251 -  3.7705 0.99   1312  151 0.0823 0.1126      5.4234      5.6382|
|  3:  3.7705 -  3.2998 0.99   1299  141 0.0996 0.1515      5.4421       5.855|
|  4:  3.2998 -  3.0008 0.99   1296  141 0.1119 0.1490      5.3972      5.5317|
|  5:  3.0008 -  2.7872 0.99   1269  144 0.1208 0.1680      5.2713      5.5375|
|  6:  2.7872 -  2.6238 0.99   1287  144 0.1112 0.1933      5.1658       5.472|
|  7:  2.6238 -  2.4930 0.99   1267  142 0.1180 0.1515      5.1209      5.3005|
|  8:  2.4930 -  2.3849 0.98   1270  137 0.1077 0.1613      5.0182      5.2974|
|  9:  2.3849 -  2.2935 0.98   1248  142 0.1066 0.1699      4.9701      5.2326|
| 10:  2.2935 -  2.2146 1.00   1277  139 0.1025 0.1680      4.9056      5.2034|
| 11:  2.2146 -  2.1456 0.97   1246  138 0.1028 0.1666      4.8911      5.1782|
| 12:  2.1456 -  2.0844 0.98   1253  139 0.1051 0.1657      4.8261      5.2269|
| 13:  2.0844 -  2.0297 0.99   1250  139 0.0985 0.1686      4.7313       5.022|
| 14:  2.0297 -  1.9803 0.77    974  110 0.0930 0.1590      4.6126      4.8604|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9044 -  4.7251  1382   152  0.94   9.12   0.98     0.95       7083.74|
|  2:  4.7251 -  3.7705  1312   151  0.95   7.85   1.02     1.01       9108.15|
|  3:  3.7705 -  3.2998  1299   141  0.94  10.82   1.03     1.02       9973.12|
|  4:  3.2998 -  3.0008  1296   141  0.93  12.66   1.00     0.99       9425.26|
|  5:  3.0008 -  2.7872  1269   144  0.91  14.94   1.00     0.97       7690.38|
|  6:  2.7872 -  2.6238  1287   144  0.90  15.39   0.98     0.95       6614.88|
|  7:  2.6238 -  2.4930  1267   142  0.91  15.24   0.98     0.95       5843.04|
|  8:  2.4930 -  2.3849  1270   137  0.92  14.00   0.99     0.98       4826.63|
|  9:  2.3849 -  2.2935  1248   142  0.92  14.49   1.01     0.98       4585.23|
| 10:  2.2935 -  2.2146  1277   139  0.91  14.76   1.00     0.96       4004.10|
| 11:  2.2146 -  2.1456  1246   138  0.91  15.30   1.00     0.96       4138.08|
| 12:  2.1456 -  2.0844  1253   139  0.91  14.97   1.01     0.99       3650.25|
| 13:  2.0844 -  2.0297  1250   139  0.91  14.70   1.00     0.98       3075.06|
| 14:  2.0297 -  1.9803   974   110  0.93  13.31   0.98     0.95       2355.53|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2355.53 max =         9973.12 mean =      5979.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.35|
|phase err.(test): min =        0.00 max =           89.50 mean =        12.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1040   r_free= 0.1532   ksol= 0.32   Bsol= 47.02   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.08,-0.62,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1040   r_free= 0.1532   ksol= 0.32   Bsol= 47.02   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.08,-0.62,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094832                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7251 0.99   1382  152 0.0981 0.1265      5.3748      5.5232|
|  2:  4.7251 -  3.7705 0.99   1312  151 0.0823 0.1126      5.4238       5.638|
|  3:  3.7705 -  3.2998 0.99   1299  141 0.0996 0.1515      5.4421      5.8553|
|  4:  3.2998 -  3.0008 0.99   1296  141 0.1119 0.1490      5.3972      5.5318|
|  5:  3.0008 -  2.7872 0.99   1269  144 0.1208 0.1679      5.2712      5.5374|
|  6:  2.7872 -  2.6238 0.99   1287  144 0.1112 0.1932      5.1658      5.4717|
|  7:  2.6238 -  2.4930 0.99   1267  142 0.1180 0.1516      5.1209      5.3007|
|  8:  2.4930 -  2.3849 0.98   1270  137 0.1077 0.1613      5.0182      5.2973|
|  9:  2.3849 -  2.2935 0.98   1248  142 0.1066 0.1698      4.9702      5.2323|
| 10:  2.2935 -  2.2146 1.00   1277  139 0.1025 0.1681      4.9056      5.2041|
| 11:  2.2146 -  2.1456 0.97   1246  138 0.1028 0.1666      4.8912      5.1782|
| 12:  2.1456 -  2.0844 0.98   1253  139 0.1051 0.1657      4.8261       5.227|
| 13:  2.0844 -  2.0297 0.99   1250  139 0.0985 0.1685      4.7312      5.0215|
| 14:  2.0297 -  1.9803 0.77    974  110 0.0930 0.1589      4.6123      4.8601|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9044 -  4.7251  1382   152  0.94   9.13   0.98     0.95       7098.17|
|  2:  4.7251 -  3.7705  1312   151  0.95   7.86   1.02     1.01       9117.36|
|  3:  3.7705 -  3.2998  1299   141  0.94  10.82   1.03     1.02       9972.72|
|  4:  3.2998 -  3.0008  1296   141  0.93  12.66   1.01     0.99       9424.05|
|  5:  3.0008 -  2.7872  1269   144  0.91  14.93   1.00     0.98       7688.13|
|  6:  2.7872 -  2.6238  1287   144  0.90  15.39   0.99     0.96       6613.89|
|  7:  2.6238 -  2.4930  1267   142  0.91  15.24   0.99     0.96       5842.66|
|  8:  2.4930 -  2.3849  1270   137  0.92  14.00   1.00     0.98       4825.80|
|  9:  2.3849 -  2.2935  1248   142  0.92  14.50   1.01     0.98       4585.92|
| 10:  2.2935 -  2.2146  1277   139  0.91  14.76   1.00     0.97       4004.65|
| 11:  2.2146 -  2.1456  1246   138  0.91  15.31   1.00     0.97       4139.78|
| 12:  2.1456 -  2.0844  1253   139  0.91  14.97   1.02     1.00       3650.35|
| 13:  2.0844 -  2.0297  1250   139  0.91  14.70   1.01     0.99       3073.84|
| 14:  2.0297 -  1.9803   974   110  0.93  13.30   0.99     0.96       2353.26|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2353.26 max =         9972.72 mean =      5980.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.35|
|phase err.(test): min =        0.00 max =           89.50 mean =        12.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    84.18   16.40    None  None   None       |
|    all(noH): 2823   0      0.98    84.18   16.40    None  None   None       |
|    Sol.    : 438    0      6.11    79.07   37.89    None  None   None       |
|    Mac.    : 2385   0      0.98    84.18   12.46    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:     0.978 -   9.298:  941   |   5:    42.581 -  50.902:   92        |
|      1:     9.298 -  17.619: 1155   |   6:    50.902 -  59.223:   65        |
|      2:    17.619 -  25.940:  259   |   7:    59.223 -  67.543:   29        |
|      3:    25.940 -  34.260:  130   |   8:    67.543 -  75.864:   11        |
|      4:    34.260 -  42.581:  137   |   9:    75.864 -  84.185:    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)= 273         
Filter by distance & map next to the model:
   mapped sites are within: 0.410 - 4.641
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 273
   mapped sites are within: 0.723 - 4.641

peak=    5.644 closest distance to " NE2 GLN A  11 " =    1.185
peak=    5.540 closest distance to " O   HOH Z 144 " =    1.804
peak=    5.434 closest distance to " O   HOH Z 126 " =    1.914
peak=    5.241 closest distance to " O   HOH Z 232 " =    2.412
peak=    5.228 closest distance to " CB  ARG A 275 " =    0.914
peak=    5.220 closest distance to " NH2 ARG A  56 " =    2.126
peak=    4.863 closest distance to " CB  GLN A 223 " =    1.470
peak=    4.858 closest distance to " CG  PRO A  54 " =    1.221
peak=    4.821 closest distance to " CB  ARG A  79 " =    1.369
peak=    4.707 closest distance to " CB  GLN A 183 " =    1.192
peak=    4.649 closest distance to " CB  GLU A 152 " =    1.237
peak=    4.581 closest distance to " O   HOH Z 236 " =    2.146
peak=    4.546 closest distance to " O   HOH Z 427 " =    2.841
peak=    4.539 closest distance to " O   HOH Z  78 " =    1.826
peak=    4.527 closest distance to " O   HOH Z 303 " =    2.113
peak=    4.509 closest distance to " CB  SER A  63 " =    1.143
peak=    4.503 closest distance to " O   HOH Z  15 " =    2.297
peak=    4.465 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.450 closest distance to " CB  VAL A 265 " =    1.296
peak=    4.431 closest distance to " O   HOH Z 158 " =    3.016
peak=    4.385 closest distance to " C   PRO A 198 " =    1.409
peak=    4.361 closest distance to " O   HOH Z 272 " =    1.826
peak=    4.335 closest distance to " O   HOH Z 209 " =    2.247
peak=    4.327 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.327 closest distance to " ND2 ASN A 187 " =    1.539
peak=    4.314 closest distance to " O   HOH Z 369 " =    2.087
peak=    4.297 closest distance to " CG2 VAL A 257 " =    0.857
peak=    4.238 closest distance to " O   HOH Z 250 " =    1.492
peak=    4.215 closest distance to " O   HOH Z 193 " =    1.801
peak=    4.197 closest distance to " O   HOH Z 298 " =    1.860
peak=    4.189 closest distance to " CB  ARG A 190 " =    1.656
peak=    4.182 closest distance to " O   HOH Z  61 " =    1.656
peak=    4.137 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.131 closest distance to " CD2 TRP A 179 " =    1.329
peak=    4.127 closest distance to " O   SER A  87 " =    2.147
peak=    4.117 closest distance to " O   HOH Z 346 " =    1.696
peak=    4.108 closest distance to " CA  ASN A 215 " =    1.088
peak=    4.101 closest distance to " O   HOH Z 189 " =    2.426
peak=    4.086 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.069 closest distance to " O   HOH Z 371 " =    1.767
peak=    4.038 closest distance to " O   HOH Z 392 " =    3.136
peak=    4.019 closest distance to " O   HOH Z 389 " =    1.830
peak=    4.004 closest distance to " O   HOH Z 234 " =    3.609
peak=    3.985 closest distance to " NZ  LYS A 117 " =    3.250
peak=    3.969 closest distance to " O   HOH Z 132 " =    2.337
peak=    3.942 closest distance to " O   HOH Z 265 " =    2.347
peak=    3.939 closest distance to " O   HOH Z  93 " =    2.534
peak=    3.924 closest distance to " O   HOH Z 419 " =    2.157
peak=    3.911 closest distance to " OG ASER A 258 " =    3.072
peak=    3.899 closest distance to " OD1 ASN A  69 " =    2.617
peak=    3.898 closest distance to " CB  TRP A 266 " =    1.043
peak=    3.890 closest distance to " O   HOH Z 133 " =    2.662
peak=    3.883 closest distance to " O   HOH Z  10 " =    1.862
peak=    3.879 closest distance to " O   HOH Z 407 " =    2.333
peak=    3.870 closest distance to " O   HOH Z 203 " =    1.755
peak=    3.869 closest distance to " O   HOH Z 403 " =    1.621
peak=    3.864 closest distance to " O   HOH Z   9 " =    2.034
peak=    3.862 closest distance to " CZ  PHE A 218 " =    1.047
peak=    3.841 closest distance to " O   HOH Z 128 " =    2.139
peak=    3.839 closest distance to " O   HOH Z 368 " =    2.052
peak=    3.827 closest distance to " CD  ARG A  66 " =    2.322
peak=    3.821 closest distance to " O   HOH Z 193 " =    1.957
peak=    3.819 closest distance to " O   HOH Z 327 " =    1.557
peak=    3.814 closest distance to " O   HOH Z  40 " =    1.567
peak=    3.811 closest distance to " O   HOH Z   1 " =    1.912
peak=    3.806 closest distance to " O   HOH Z 417 " =    3.371
peak=    3.785 closest distance to " O   HOH Z 402 " =    1.415
peak=    3.783 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.777 closest distance to " O   HOH Z 425 " =    2.067
peak=    3.774 closest distance to " OG BSER A 164 " =    2.281
peak=    3.771 closest distance to " O   HOH Z 245 " =    1.334
peak=    3.768 closest distance to " O   HOH Z 248 " =    1.568
peak=    3.759 closest distance to " CB  ASP A 140 " =    0.996
peak=    3.756 closest distance to " O   HOH Z  61 " =    1.474
peak=    3.748 closest distance to " O   HOH Z  44 " =    1.712
peak=    3.744 closest distance to " O   HOH Z 423 " =    1.883
peak=    3.740 closest distance to " O   HOH Z 406 " =    1.604
peak=    3.738 closest distance to " O   HOH Z 261 " =    2.226
peak=    3.729 closest distance to " CB  LEU A 228 " =    1.093
peak=    3.724 closest distance to " O   HOH Z 128 " =    2.037
peak=    3.702 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.689 closest distance to " CB  SER A   3 " =    1.306
peak=    3.683 closest distance to " O   HOH Z 213 " =    1.885
peak=    3.682 closest distance to " O   HOH Z 371 " =    3.015
peak=    3.674 closest distance to " CB  VAL A 202 " =    1.563
peak=    3.672 closest distance to " O   HOH Z 214 " =    2.139
peak=    3.671 closest distance to " O   HOH Z  66 " =    2.124
peak=    3.667 closest distance to " O   HOH Z 344 " =    3.213
peak=    3.664 closest distance to " CG  PRO A 243 " =    1.067
peak=    3.660 closest distance to " CG1 ILE A  33 " =    1.223
peak=    3.653 closest distance to " O   HOH Z 291 " =    1.542
peak=    3.653 closest distance to " CB  ARG A 139 " =    1.003
peak=    3.644 closest distance to " OD2 ASP A 286 " =    2.770
peak=    3.623 closest distance to " CG2 ILE A 120 " =    1.079
peak=    3.621 closest distance to " CG1BVAL A  72 " =    1.505
peak=    3.619 closest distance to " O   HOH Z 337 " =    3.576
peak=    3.603 closest distance to " CB  SER A 212 " =    1.102
peak=    3.600 closest distance to " O   HOH Z 325 " =    3.906
peak=    3.598 closest distance to " O   HOH Z 173 " =    1.917
peak=    3.587 closest distance to " O   HOH Z 353 " =    2.622
peak=    3.584 closest distance to " O   HOH Z 359 " =    1.483
peak=    3.578 closest distance to " CA  ALA A  84 " =    1.264
peak=    3.574 closest distance to " CB  ASN A 142 " =    1.020
peak=    3.563 closest distance to " CB  SER A  26 " =    1.618
peak=    3.561 closest distance to " O   HOH Z 313 " =    1.970
peak=    3.560 closest distance to " O   HOH Z   1 " =    1.634
peak=    3.544 closest distance to " O   HOH Z 433 " =    1.810
peak=    3.544 closest distance to " CB  GLU A 277 " =    3.500
peak=    3.537 closest distance to " O   HOH Z  88 " =    2.520
peak=    3.535 closest distance to " O   HOH Z  40 " =    1.964
peak=    3.535 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.532 closest distance to " CD1 ILE A 106 " =    0.831
peak=    3.531 closest distance to " O   HOH Z  43 " =    2.002
peak=    3.530 closest distance to " O   HOH Z 305 " =    3.588
peak=    3.529 closest distance to " CG  PRO A 198 " =    1.235
peak=    3.528 closest distance to " O   HOH Z 368 " =    3.555
peak=    3.523 closest distance to " O   HOH Z 287 " =    2.327
peak=    3.517 closest distance to " O   HOH Z  21 " =    1.749
peak=    3.517 closest distance to " NH1AARG A 145 " =    1.214
peak=    3.515 closest distance to " O   HOH Z  88 " =    2.435
peak=    3.514 closest distance to " O   HOH Z 180 " =    2.183
peak=    3.505 closest distance to " NH2BARG A 145 " =    2.031
peak=    3.494 closest distance to " O   HOH Z 421 " =    1.877
peak=    3.490 closest distance to " N   PHE A 130 " =    1.255
peak=    3.485 closest distance to " ND1 HIS A  86 " =    1.784
peak=    3.479 closest distance to " O   HOH Z 261 " =    2.327
peak=    3.478 closest distance to " CB  ILE A 120 " =    1.285
peak=    3.477 closest distance to " CB  ASN A 110 " =    1.080
peak=    3.476 closest distance to " CA  ALA A 233 " =    0.991
peak=    3.467 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.463 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.461 closest distance to " CD1 ILE A 263 " =    1.354
peak=    3.456 closest distance to " O   HOH Z 172 " =    3.127
peak=    3.455 closest distance to " O   HOH Z   6 " =    2.104
peak=    3.455 closest distance to " CA  ASP A 162 " =    1.033
peak=    3.454 closest distance to " CB  GLN A  89 " =    1.390
peak=    3.451 closest distance to " CD  ARG A  66 " =    2.332
peak=    3.451 closest distance to " CB  LYS A 117 " =    1.280
peak=    3.449 closest distance to " CB  GLU A 128 " =    0.962
peak=    3.448 closest distance to " CB  ALA A  34 " =    1.102
peak=    3.446 closest distance to " N   ASN A  39 " =    1.216
peak=    3.439 closest distance to " O   HOH Z 147 " =    1.806
peak=    3.437 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.436 closest distance to " O   HOH Z  97 " =    1.958
peak=    3.432 closest distance to " CG  MET A 185 " =    1.183
peak=    3.430 closest distance to " O   HOH Z 148 " =    3.365
peak=    3.427 closest distance to " NE2 GLN A  73 " =    3.793
peak=    3.419 closest distance to " O   HOH Z 219 " =    2.038
peak=    3.418 closest distance to " O   HOH Z 336 " =    1.823
peak=    3.416 closest distance to " O   HOH Z  89 " =    2.087
peak=    3.416 closest distance to " O  BHOH Z 338 " =    2.339
peak=    3.407 closest distance to " CA  ARG A 195 " =    1.252
peak=    3.404 closest distance to " CB  ASN A  39 " =    0.861
peak=    3.402 closest distance to " CA  ALA A 291 " =    0.837
peak=    3.399 closest distance to " CB  TRP A 179 " =    1.353
peak=    3.392 closest distance to " O   HOH Z 234 " =    1.895
peak=    3.390 closest distance to " O   HOH Z 329 " =    3.963
peak=    3.388 closest distance to " O   HOH Z 302 " =    1.969
peak=    3.382 closest distance to " CG  GLN A  11 " =    1.911
peak=    3.376 closest distance to " N   ARG A 156 " =    1.305
peak=    3.376 closest distance to " O   HOH Z 286 " =    2.236
peak=    3.368 closest distance to " CG  LEU A 167 " =    1.260
peak=    3.365 closest distance to " O   HOH Z 365 " =    2.849
peak=    3.365 closest distance to " CA  ARG A  36 " =    0.973
peak=    3.361 closest distance to " O   HOH Z  92 " =    2.526
peak=    3.358 closest distance to " O   HOH Z 298 " =    2.495
peak=    3.358 closest distance to " CB  THR A 157 " =    1.110
peak=    3.355 closest distance to " CA  THR A 264 " =    0.868
peak=    3.355 closest distance to " O   ALA A   1 " =    1.662
peak=    3.354 closest distance to " CG AARG A 275 " =    1.073
peak=    3.349 closest distance to " CB  ALA A   9 " =    1.565
peak=    3.340 closest distance to " N   TYR A 116 " =    1.549
peak=    3.331 closest distance to " O   HOH Z 116 " =    1.743
peak=    3.316 closest distance to " O   HOH Z  59 " =    1.696
peak=    3.315 closest distance to " CA  THR A 221 " =    1.027
peak=    3.312 closest distance to " NE2 HIS A 207 " =    1.362
peak=    3.311 closest distance to " CA  ALA A  21 " =    1.136
peak=    3.310 closest distance to " CG  MET A 113 " =    1.118
peak=    3.309 closest distance to " O   HOH Z  54 " =    1.607
peak=    3.309 closest distance to " O   HOH Z 128 " =    1.976
peak=    3.308 closest distance to " O   HOH Z  64 " =    2.279
peak=    3.306 closest distance to " O   HOH Z 188 " =    1.917
peak=    3.305 closest distance to " O   HOH Z 391 " =    2.887
peak=    3.301 closest distance to " CZ2 TRP A 179 " =    1.735
peak=    3.300 closest distance to " O   HOH Z 193 " =    1.638
peak=    3.297 closest distance to " CG2 ILE A  20 " =    1.417
peak=    3.294 closest distance to " O   HOH Z  44 " =    2.946
peak=    3.294 closest distance to " O   HOH Z 343 " =    3.361
peak=    3.294 closest distance to " ND2 ASN A 110 " =    1.719
peak=    3.291 closest distance to " O   HOH Z 185 " =    1.825
peak=    3.290 closest distance to " CB  LYS A 290 " =    0.922
peak=    3.281 closest distance to " CB  SER A  62 " =    1.289
peak=    3.280 closest distance to " CB  ALA A   1 " =    4.641
peak=    3.279 closest distance to " OG  SER A  22 " =    2.652
peak=    3.279 closest distance to " O   ASN A  74 " =    1.533
peak=    3.279 closest distance to " O   HOH Z 285 " =    2.625
peak=    3.278 closest distance to " O   HOH Z 126 " =    1.562
peak=    3.268 closest distance to " O   HOH Z 411 " =    3.814
peak=    3.268 closest distance to " NH1BARG A 145 " =    1.264
peak=    3.268 closest distance to " CG  LYS A  76 " =    0.945
peak=    3.263 closest distance to " OD1BASN A 224 " =    2.307
peak=    3.251 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.249 closest distance to " CA  TYR A 116 " =    1.269
peak=    3.246 closest distance to " O   HOH Z 257 " =    2.161
peak=    3.244 closest distance to " O   HOH Z 423 " =    2.874
peak=    3.242 closest distance to " O   HOH Z  96 " =    2.207
peak=    3.240 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.238 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.237 closest distance to " CD  LYS A 166 " =    1.235
peak=    3.232 closest distance to " CD2 LEU A 297 " =    0.865
peak=    3.232 closest distance to " OG  SER A  62 " =    2.805
peak=    3.229 closest distance to " CB  THR A 294 " =    1.666
peak=    3.229 closest distance to " CA  MET A  40 " =    1.107
peak=    3.227 closest distance to " OG BSER A  99 " =    2.265
peak=    3.223 closest distance to " CA  SER A  87 " =    1.011
peak=    3.219 closest distance to " NZ  LYS A  48 " =    1.187
peak=    3.219 closest distance to " CG  GLN A  77 " =    2.053
peak=    3.218 closest distance to " CB  ALA A 114 " =    1.350
peak=    3.218 closest distance to " O   HOH Z 153 " =    1.597
peak=    3.216 closest distance to " O   MET A 105 " =    1.882
peak=    3.216 closest distance to " CB  ASN A 215 " =    1.097
peak=    3.212 closest distance to " CA  ALA A  51 " =    0.886
peak=    3.208 closest distance to " O   HOH Z 380 " =    1.892
peak=    3.207 closest distance to " CB  MET A  47 " =    1.175
peak=    3.206 closest distance to " CA  SER A 146 " =    1.719
peak=    3.205 closest distance to " O   HOH Z 426 " =    1.635
peak=    3.204 closest distance to " CD BLYS A 290 " =    1.197
peak=    3.199 closest distance to " O   HOH Z 261 " =    1.574
peak=    3.197 closest distance to " O   HOH Z 422 " =    2.610
peak=    3.197 closest distance to " O   HOH Z 299 " =    4.249
peak=    3.197 closest distance to " O   HOH Z 357 " =    1.891
peak=    3.191 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.190 closest distance to " CG2 VAL A 197 " =    1.090
peak=    3.188 closest distance to " O   HOH Z 409 " =    2.640
peak=    3.181 closest distance to " CB  THR A  31 " =    1.631
peak=    3.179 closest distance to " CB  ASP A 124 " =    0.723
peak=    3.176 closest distance to " O   HOH Z 273 " =    2.770
peak=    3.174 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.170 closest distance to " O   HOH Z 345 " =    1.653
peak=    3.167 closest distance to " N   ASP A 162 " =    1.198
peak=    3.163 closest distance to " CB  SER A 216 " =    0.777
peak=    3.161 closest distance to " O   HOH Z 144 " =    1.797
peak=    3.160 closest distance to " OG1 THR A 294 " =    2.408
peak=    3.159 closest distance to " O   HOH Z 294 " =    1.413
peak=    3.157 closest distance to " CD1 LEU A 300 " =    1.292
peak=    3.155 closest distance to " O   HOH Z 124 " =    2.164
peak=    3.150 closest distance to " CB  ASN A 224 " =    0.958
peak=    3.146 closest distance to " O   HOH Z 152 " =    1.708
peak=    3.136 closest distance to " CB  GLN A 278 " =    0.822
peak=    3.132 closest distance to " O   PHE A 192 " =    1.444
peak=    3.126 closest distance to " O   HOH Z 251 " =    1.585
peak=    3.125 closest distance to " O   HOH Z  50 " =    1.540
peak=    3.122 closest distance to " CG2 THR A 221 " =    1.055
peak=    3.116 closest distance to " CA  ALA A 158 " =    1.278
peak=    3.100 closest distance to " CB  ALA A 248 " =    0.894
peak=    3.098 closest distance to " CA  ALA A 233 " =    1.647
peak=    3.098 closest distance to " O   THR A 220 " =    1.304
peak=    3.097 closest distance to " N   ASN A 127 " =    1.288
peak=    3.093 closest distance to " CG1 ILE A  49 " =    1.427
peak=    3.075 closest distance to " CD1 LEU A 228 " =    1.575
peak=    3.069 closest distance to " CG BARG A 102 " =    1.719
peak=    3.067 closest distance to " O   HOH Z  85 " =    1.931
peak=    3.063 closest distance to " O   HOH Z 109 " =    2.539
peak=    3.061 closest distance to " O   HOH Z 132 " =    3.213
peak=    3.046 closest distance to " CA  ALA A 299 " =    0.881
peak=    3.026 closest distance to " CB  LEU A 255 " =    0.772
peak=    3.018 closest distance to " O   HOH Z 175 " =    2.144
peak=    3.014 closest distance to " O   HOH Z 238 " =    3.724
peak=    3.013 closest distance to " O   HOH Z 291 " =    1.808

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.743 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.743 - 5.939

peak=   -4.778 closest distance to " CB  PRO A 243 " =    2.611
peak=   -4.698 closest distance to " O   HOH Z 266 " =    5.008
peak=   -4.540 closest distance to " CD  ARG A 156 " =    2.094
peak=   -4.478 closest distance to " O   HOH Z 377 " =    2.179
peak=   -4.427 closest distance to " OG BSER A 134 " =    1.286
peak=   -4.370 closest distance to " CG  GLN A 223 " =    1.987
peak=   -4.361 closest distance to " O   VAL A  67 " =    2.657
peak=   -4.313 closest distance to " C   HIS A 108 " =    1.163
peak=   -4.312 closest distance to " CD  GLN A  58 " =    1.053
peak=   -4.204 closest distance to " SG  CYS A 254 " =    3.420
peak=   -4.199 closest distance to " CG1 VAL A 112 " =    2.789
peak=   -4.100 closest distance to " CA  VAL A  67 " =    2.894
peak=   -4.056 closest distance to " O   HOH Z 313 " =    1.884
peak=   -4.047 closest distance to " CB  PHE A 192 " =    1.972
peak=   -4.043 closest distance to " O   HOH Z 435 " =    2.807
peak=   -4.040 closest distance to " O   HOH Z 389 " =    1.935
peak=   -4.006 closest distance to " ND2 ASN A  45 " =    1.711
peak=   -4.000 closest distance to " CZ3 TRP A 179 " =    1.174
peak=   -3.982 closest distance to " CE  MET A 105 " =    2.332
peak=   -3.975 closest distance to " O   HOH Z 290 " =    1.264
peak=   -3.948 closest distance to " CZ  TYR A 169 " =    1.738
peak=   -3.947 closest distance to " O   HOH Z 185 " =    2.181
peak=   -3.936 closest distance to " CD  ARG A 139 " =    1.522
peak=   -3.881 closest distance to " O   HOH Z 372 " =    2.306
peak=   -3.862 closest distance to " CB  ALA A 291 " =    2.294
peak=   -3.861 closest distance to " CE2 PHE A 218 " =    2.417
peak=   -3.858 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.842 closest distance to " N   ALA A  43 " =    2.574
peak=   -3.835 closest distance to " O   HOH Z 351 " =    1.506
peak=   -3.819 closest distance to " CB  ASN A  39 " =    2.316
peak=   -3.808 closest distance to " O   HOH Z 231 " =    2.356
peak=   -3.803 closest distance to " CE2 TYR A  30 " =    2.736
peak=   -3.773 closest distance to " OD1 ASP A 171 " =    1.649
peak=   -3.765 closest distance to " OD2 ASP A 171 " =    2.377
peak=   -3.759 closest distance to " N   GLN A  58 " =    1.709
peak=   -3.757 closest distance to " O   HOH Z 407 " =    2.953
peak=   -3.728 closest distance to " OG  SER A  97 " =    2.176
peak=   -3.724 closest distance to " OXT GLY A 302 " =    2.755
peak=   -3.720 closest distance to " O   HOH Z 198 " =    1.965
peak=   -3.718 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.717 closest distance to " O   HOH Z 114 " =    3.029
peak=   -3.700 closest distance to " CB  ALA A 248 " =    2.342
peak=   -3.697 closest distance to " CB  ALA A  43 " =    2.469
peak=   -3.690 closest distance to " O   ALA A 161 " =    1.690
peak=   -3.683 closest distance to " O   HOH Z 211 " =    1.710
peak=   -3.668 closest distance to " OD1 ASN A 148 " =    1.577
peak=   -3.663 closest distance to " N   ALA A 248 " =    1.715
peak=   -3.655 closest distance to " CG2 ILE A 263 " =    2.241
peak=   -3.626 closest distance to " O   HOH Z 198 " =    1.438
peak=   -3.626 closest distance to " O   ARG A 145 " =    1.501
peak=   -3.625 closest distance to " OD2 ASP A 191 " =    1.375
peak=   -3.613 closest distance to " CZ  PHE A  59 " =    1.476
peak=   -3.604 closest distance to " O   SER A  95 " =    1.506
peak=   -3.600 closest distance to " O   HOH Z  15 " =    1.539
peak=   -3.597 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.593 closest distance to " O   HOH Z 353 " =    2.214
peak=   -3.567 closest distance to " CB  PHE A 208 " =    2.237
peak=   -3.567 closest distance to " CG2 THR A 178 " =    2.256
peak=   -3.561 closest distance to " CB  ALA A 248 " =    2.148
peak=   -3.556 closest distance to " CD1 PHE A  59 " =    1.954
peak=   -3.548 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.546 closest distance to " NH2BARG A 275 " =    1.880
peak=   -3.536 closest distance to " NH2AARG A 275 " =    5.159
peak=   -3.535 closest distance to " CB  ALA A 291 " =    2.210
peak=   -3.521 closest distance to " ND2 ASN A 187 " =    1.469
peak=   -3.504 closest distance to " OD1 ASN A 187 " =    1.660
peak=   -3.497 closest distance to " O   HOH Z 298 " =    1.292
peak=   -3.496 closest distance to " CB  ASP A 132 " =    2.255
peak=   -3.496 closest distance to " O   HOH Z  38 " =    1.675
peak=   -3.493 closest distance to " ND2 ASN A 249 " =    2.177
peak=   -3.485 closest distance to " OD1 ASP A 191 " =    1.532
peak=   -3.480 closest distance to " O   HOH Z 395 " =    5.197
peak=   -3.478 closest distance to " O   PRO A 163 " =    2.050
peak=   -3.477 closest distance to " CA  GLY A  98 " =    1.834
peak=   -3.475 closest distance to " O   HOH Z 283 " =    2.387
peak=   -3.468 closest distance to " CD2 TYR A 247 " =    2.505
peak=   -3.467 closest distance to " O   SER A 210 " =    2.029
peak=   -3.466 closest distance to " CB  ALA A 161 " =    2.430
peak=   -3.463 closest distance to " O   HOH Z  13 " =    1.630
peak=   -3.463 closest distance to " CA  GLY A 133 " =    2.043
peak=   -3.457 closest distance to " CB  TRP A  85 " =    2.519
peak=   -3.451 closest distance to " O   PHE A 218 " =    1.590
peak=   -3.450 closest distance to " O   HOH Z  60 " =    2.246
peak=   -3.440 closest distance to " O   HOH Z  63 " =    1.759
peak=   -3.439 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.428 closest distance to " CA  GLY A 203 " =    2.288
peak=   -3.427 closest distance to " CB  ASP A 132 " =    2.396
peak=   -3.421 closest distance to " CB  PRO A 163 " =    2.427
peak=   -3.417 closest distance to " O   HOH Z 362 " =    5.939
peak=   -3.417 closest distance to " O   SER A 135 " =    1.438
peak=   -3.408 closest distance to " CA  ASP A 298 " =    1.107
peak=   -3.405 closest distance to " O   VAL A 189 " =    1.655
peak=   -3.402 closest distance to " O   HOH Z 102 " =    1.547
peak=   -3.397 closest distance to " O   HOH Z 126 " =    1.862
peak=   -3.395 closest distance to " O   HOH Z 394 " =    1.393
peak=   -3.393 closest distance to " O   VAL A 189 " =    2.599
peak=   -3.392 closest distance to " CG  ARG A 269 " =    2.347
peak=   -3.387 closest distance to " CG  ASP A 231 " =    0.758
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.643
peak=   -3.378 closest distance to " N   ASP A 286 " =    2.319
peak=   -3.377 closest distance to " C   PRO A  90 " =    1.502
peak=   -3.369 closest distance to " O   HOH Z 385 " =    1.989
peak=   -3.367 closest distance to " NE2 GLN A 278 " =    1.639
peak=   -3.366 closest distance to " CB  ASP A 286 " =    1.768
peak=   -3.366 closest distance to " OG  SER A  97 " =    1.764
peak=   -3.360 closest distance to " O   HOH Z 339 " =    1.838
peak=   -3.359 closest distance to " O   HOH Z 359 " =    3.332
peak=   -3.354 closest distance to " O   HOH Z 253 " =    3.822
peak=   -3.353 closest distance to " O   HOH Z 266 " =    4.825
peak=   -3.348 closest distance to " O   ALA A 292 " =    2.006
peak=   -3.348 closest distance to " O   HOH Z 140 " =    1.732
peak=   -3.344 closest distance to " OE2 GLU A 152 " =    1.181
peak=   -3.333 closest distance to " O   HOH Z  43 " =    1.775
peak=   -3.320 closest distance to " CG1 VAL A 268 " =    2.431
peak=   -3.317 closest distance to " O   HOH Z 137 " =    1.420
peak=   -3.305 closest distance to " O   ALA A  34 " =    2.420
peak=   -3.304 closest distance to " OD1 ASP A 191 " =    1.822
peak=   -3.303 closest distance to " CG  GLU A 277 " =    1.306
peak=   -3.302 closest distance to " C   LEU A 143 " =    1.000
peak=   -3.299 closest distance to " CD2 PHE A 225 " =    1.175
peak=   -3.296 closest distance to " ND2 ASN A 252 " =    1.703
peak=   -3.296 closest distance to " O   HOH Z 371 " =    1.625
peak=   -3.293 closest distance to " O   HOH Z  10 " =    1.435
peak=   -3.291 closest distance to " CG1 VAL A 230 " =    2.010
peak=   -3.289 closest distance to " O   HOH Z 263 " =    3.017
peak=   -3.288 closest distance to " CE BMET A  47 " =    1.492
peak=   -3.284 closest distance to " O   TRP A  70 " =    1.464
peak=   -3.281 closest distance to " O   SER A  22 " =    2.417
peak=   -3.275 closest distance to " O   HOH Z 134 " =    3.151
peak=   -3.270 closest distance to " OD2 ASP A  50 " =    1.551
peak=   -3.268 closest distance to " CE3 TRP A 274 " =    1.139
peak=   -3.268 closest distance to " O   HOH Z 111 " =    2.012
peak=   -3.256 closest distance to " O   HOH Z 243 " =    1.895
peak=   -3.255 closest distance to " O   VAL A 174 " =    2.107
peak=   -3.252 closest distance to " CA  GLY A 241 " =    2.281
peak=   -3.249 closest distance to " O   HOH Z 421 " =    3.064
peak=   -3.249 closest distance to " O   ALA A  51 " =    1.307
peak=   -3.248 closest distance to " CD  GLN A 223 " =    0.743
peak=   -3.248 closest distance to " O   HOH Z 165 " =    2.057
peak=   -3.247 closest distance to " CB  GLN A  11 " =    1.839
peak=   -3.240 closest distance to " CD1 LEU A 101 " =    2.250
peak=   -3.239 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.228 closest distance to " O   HOH Z 166 " =    2.001
peak=   -3.227 closest distance to " O   HOH Z 196 " =    2.159
peak=   -3.221 closest distance to " O   HOH Z  91 " =    1.579
peak=   -3.220 closest distance to " CD1 LEU A 228 " =    2.085
peak=   -3.219 closest distance to " CB  LEU A  83 " =    2.342
peak=   -3.219 closest distance to " O   HOH Z   6 " =    1.453
peak=   -3.217 closest distance to " O   HOH Z 166 " =    1.450
peak=   -3.216 closest distance to " CA  GLY A  57 " =    2.208
peak=   -3.216 closest distance to " CD  GLN A  88 " =    0.846
peak=   -3.201 closest distance to " NE  ARG A  36 " =    1.905
peak=   -3.199 closest distance to " O   HOH Z 123 " =    2.234
peak=   -3.199 closest distance to " CD1 LEU A 297 " =    2.379
peak=   -3.197 closest distance to " CG  GLU A 152 " =    1.030
peak=   -3.193 closest distance to " CG2 THR A 157 " =    2.083
peak=   -3.193 closest distance to " O   HOH Z 281 " =    2.680
peak=   -3.188 closest distance to " O   HOH Z 131 " =    4.067
peak=   -3.180 closest distance to " O   ALA A  10 " =    1.653
peak=   -3.175 closest distance to " N   PHE A  59 " =    1.907
peak=   -3.172 closest distance to " OG  SER A  62 " =    1.521
peak=   -3.170 closest distance to " C   MET A 188 " =    1.404
peak=   -3.169 closest distance to " CG  LEU A  83 " =    1.924
peak=   -3.165 closest distance to " O   GLN A 240 " =    1.958
peak=   -3.164 closest distance to " O   GLY A  80 " =    2.522
peak=   -3.157 closest distance to " OH  TYR A 214 " =    1.242
peak=   -3.156 closest distance to " CD  PRO A  90 " =    1.855
peak=   -3.148 closest distance to " CA  TYR A  30 " =    2.895
peak=   -3.146 closest distance to " OG  SER A  87 " =    1.305
peak=   -3.144 closest distance to " O   HOH Z 244 " =    2.017
peak=   -3.143 closest distance to " CG1 VAL A 125 " =    1.946
peak=   -3.143 closest distance to " O   HOH Z 295 " =    1.585
peak=   -3.142 closest distance to " CG1 VAL A 197 " =    2.070
peak=   -3.139 closest distance to " CD2 PHE A  61 " =    2.240
peak=   -3.138 closest distance to " O   HOH Z 414 " =    1.671
peak=   -3.131 closest distance to " O   HOH Z  71 " =    2.076
peak=   -3.130 closest distance to " O   HOH Z 371 " =    1.498
peak=   -3.126 closest distance to " O   HOH Z 357 " =    2.011
peak=   -3.125 closest distance to " OE1 GLN A 223 " =    1.832
peak=   -3.124 closest distance to " SG ACYS A 201 " =    1.682
peak=   -3.121 closest distance to " CD2 TYR A 293 " =    1.929
peak=   -3.116 closest distance to " CG  PRO A 163 " =    2.667
peak=   -3.108 closest distance to " CB  ALA A 100 " =    2.382
peak=   -3.101 closest distance to " SD  MET A 188 " =    2.171
peak=   -3.099 closest distance to " CA  GLY A 241 " =    3.129
peak=   -3.099 closest distance to " CD2 PHE A  61 " =    2.532
peak=   -3.098 closest distance to " O   HOH Z 298 " =    2.418
peak=   -3.097 closest distance to " C   ASP A 231 " =    2.628
peak=   -3.094 closest distance to " O   HOH Z 369 " =    2.200
peak=   -3.091 closest distance to " O   HOH Z 174 " =    4.272
peak=   -3.089 closest distance to " NH1 ARG A 195 " =    2.621
peak=   -3.087 closest distance to " OD1AASN A 224 " =    1.822
peak=   -3.086 closest distance to " ND2 ASN A  60 " =    1.328
peak=   -3.085 closest distance to " NH2 ARG A  79 " =    1.998
peak=   -3.084 closest distance to " NH2 ARG A  56 " =    1.910
peak=   -3.083 closest distance to " O   GLN A 240 " =    2.383
peak=   -3.071 closest distance to " O   MET A  40 " =    2.799
peak=   -3.069 closest distance to " O   HOH Z 323 " =    1.400
peak=   -3.069 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.066 closest distance to " CG  GLU A   2 " =    2.006
peak=   -3.064 closest distance to " CG2 VAL A 189 " =    1.995
peak=   -3.062 closest distance to " CD2 LEU A 300 " =    2.794
peak=   -3.053 closest distance to " CA  TYR A  68 " =    2.973
peak=   -3.051 closest distance to " CE  LYS A  76 " =    2.680
peak=   -3.039 closest distance to " O   HOH Z 137 " =    1.508
peak=   -3.016 closest distance to " CD2 LEU A 143 " =    2.705

================= 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    :  0.3153 0.3115   6.020960e+00   5.991054e+00
   1_bss:  0.3012 0.2968   5.998867e+00   5.959367e+00
   1_xyz:  0.1686 0.1925   5.456776e+00   5.561252e+00
   1_adp:  0.1533 0.2012   5.403482e+00   5.600931e+00
   1_occ:  0.1531 0.2009   5.402281e+00   5.599902e+00
   2_bss:  0.1519 0.1993   5.397796e+00   5.591984e+00
   2_xyz:  0.1218 0.1648   5.203426e+00   5.420251e+00
   2_adp:  0.1197 0.1575   5.174219e+00   5.379772e+00
   2_occ:  0.1195 0.1575   5.173464e+00   5.379676e+00
   3_bss:  0.1196 0.1574   5.172112e+00   5.377424e+00
   3_xyz:  0.1133 0.1527   5.132909e+00   5.354840e+00
   3_adp:  0.1104 0.1532   5.120757e+00   5.358751e+00
   3_occ:  0.1103 0.1533   5.120733e+00   5.358863e+00
   4_bss:  0.1102 0.1531   5.120174e+00   5.358088e+00
   4_xyz:  0.1053 0.1526   5.098141e+00   5.356084e+00
   4_adp:  0.1058 0.1516   5.097553e+00   5.351102e+00
   4_occ:  0.1058 0.1516   5.097498e+00   5.351189e+00
   5_bss:  0.1057 0.1517   5.097533e+00   5.351215e+00
   5_xyz:  0.1043 0.1528   5.094752e+00   5.358093e+00
   5_adp:  0.1041 0.1532   5.094849e+00   5.360087e+00
   5_occ:  0.1041 0.1531   5.094762e+00   5.359964e+00
   5_bss:  0.1040 0.1532   5.094832e+00   5.360017e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.328  36.441  -2.086   0.261  -1.041   0.000  -0.000  -0.000
   1_xyz:  0.328  36.441  -2.086   0.261  -1.041   0.000  -0.000  -0.000
   1_adp:  0.328  36.441  -2.086   0.261  -1.041   0.000  -0.000  -0.000
   1_occ:  0.328  36.441  -2.086   0.261  -1.041   0.000  -0.000  -0.000
   2_bss:  0.311  41.633  -2.899  -1.930  -1.364  -0.000  -0.000  -0.000
   2_xyz:  0.311  41.633  -2.899  -1.930  -1.364  -0.000  -0.000  -0.000
   2_adp:  0.311  41.633  -2.899  -1.930  -1.364  -0.000  -0.000  -0.000
   2_occ:  0.311  41.633  -2.899  -1.930  -1.364  -0.000  -0.000  -0.000
   3_bss:  0.319  43.077  -2.952  -2.427  -1.181  -0.000  -0.000  -0.000
   3_xyz:  0.319  43.077  -2.952  -2.427  -1.181  -0.000  -0.000  -0.000
   3_adp:  0.319  43.077  -2.952  -2.427  -1.181  -0.000  -0.000  -0.000
   3_occ:  0.319  43.077  -2.952  -2.427  -1.181  -0.000  -0.000  -0.000
   4_bss:  0.320  47.051  -2.769  -2.358  -1.011  -0.000  -0.000  -0.000
   4_xyz:  0.320  47.051  -2.769  -2.358  -1.011  -0.000  -0.000  -0.000
   4_adp:  0.320  47.051  -2.769  -2.358  -1.011  -0.000  -0.000  -0.000
   4_occ:  0.320  47.051  -2.769  -2.358  -1.011  -0.000  -0.000  -0.000
   5_bss:  0.320  47.051  -2.611  -2.244  -0.818  -0.000  -0.000  -0.000
   5_xyz:  0.320  47.051  -2.611  -2.244  -0.818  -0.000  -0.000  -0.000
   5_adp:  0.320  47.051  -2.611  -2.244  -0.818  -0.000  -0.000  -0.000
   5_occ:  0.320  47.051  -2.611  -2.244  -0.818  -0.000  -0.000  -0.000
   5_bss:  0.320  47.016  -2.412  -2.076  -0.617  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.001 0.7506  0.9338    26455.319
   1_bss:  29.700 0.7625  0.9170    23199.916
   1_xyz:  17.590 0.8853  1.0135     9190.026
   1_adp:  18.562 0.8758  1.0078     9887.243
   1_occ:  18.540 0.8760  1.0077     9851.358
   2_bss:  18.300 0.8782  0.9705     9632.389
   2_xyz:  14.813 0.9079  0.9843     6735.097
   2_adp:  13.897 0.9158  0.9847     6281.284
   2_occ:  13.895 0.9158  0.9846     6272.461
   3_bss:  13.854 0.9161  0.9808     6242.403
   3_xyz:  13.289 0.9207  0.9825     5900.740
   3_adp:  13.337 0.9204  0.9762     5906.998
   3_occ:  13.339 0.9204  0.9761     5907.777
   4_bss:  13.321 0.9205  0.9814     5898.248
   4_xyz:  13.274 0.9208  0.9816     5909.901
   4_adp:  13.179 0.9216  0.9763     5857.736
   4_occ:  13.181 0.9216  0.9762     5857.637
   5_bss:  13.181 0.9216  0.9818     5858.509
   5_xyz:  13.267 0.9210  0.9814     5967.467
   5_adp:  13.307 0.9207  0.9747     5981.531
   5_occ:  13.305 0.9207  0.9746     5979.353
   5_bss:  13.307 0.9207  0.9801     5980.737
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6349e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6349e-01
   1_xyz:   1.016  0.008  0.070 15.081  0.004  4.110   6.7038e-02
   1_adp:   1.016  0.008  0.070 15.081  0.004  4.110   6.7038e-02
   1_occ:   1.016  0.008  0.070 15.081  0.004  4.110   6.7038e-02
   2_bss:   1.016  0.008  0.070 15.081  0.004  4.110   6.7038e-02
   2_xyz:   0.940  0.005  0.071 14.710  0.004  4.115   5.2234e-02
   2_adp:   0.940  0.005  0.071 14.710  0.004  4.115   5.2234e-02
   2_occ:   0.940  0.005  0.071 14.710  0.004  4.115   5.2234e-02
   3_bss:   0.940  0.005  0.071 14.710  0.004  4.115   5.2234e-02
   3_xyz:   0.910  0.006  0.071 14.567  0.004  4.109   5.1448e-02
   3_adp:   0.910  0.006  0.071 14.567  0.004  4.109   5.1448e-02
   3_occ:   0.910  0.006  0.071 14.567  0.004  4.109   5.1448e-02
   4_bss:   0.910  0.006  0.071 14.567  0.004  4.109   5.1448e-02
   4_xyz:   1.039  0.008  0.080 14.862  0.004  4.110   6.4846e-02
   4_adp:   1.039  0.008  0.080 14.862  0.004  4.110   6.4846e-02
   4_occ:   1.039  0.008  0.080 14.862  0.004  4.110   6.4846e-02
   5_bss:   1.039  0.008  0.080 14.862  0.004  4.110   6.4846e-02
   5_xyz:   1.070  0.008  0.082 14.881  0.005  4.110   6.8373e-02
   5_adp:   1.070  0.008  0.082 14.881  0.005  4.110   6.8373e-02
   5_occ:   1.070  0.008  0.082 14.881  0.005  4.110   6.8373e-02
   5_bss:   1.070  0.008  0.082 14.881  0.005  4.110   6.8373e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3932e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3932e-01
   1_xyz:   6.845  0.059  0.210 84.038  0.039  2.242   1.4956e-01
   1_adp:   6.845  0.059  0.210 84.038  0.039  2.242   1.4956e-01
   1_occ:   6.845  0.059  0.210 84.038  0.039  2.242   1.4956e-01
   2_bss:   6.845  0.059  0.210 84.038  0.039  2.242   1.4956e-01
   2_xyz:   6.545  0.040  0.207 82.909  0.041  2.349   3.5919e-02
   2_adp:   6.545  0.040  0.207 82.909  0.041  2.349   3.5919e-02
   2_occ:   6.545  0.040  0.207 82.909  0.041  2.349   3.5919e-02
   3_bss:   6.545  0.040  0.207 82.909  0.041  2.349   3.5919e-02
   3_xyz:   6.089  0.041  0.225 84.610  0.039  2.328   3.4652e-02
   3_adp:   6.089  0.041  0.225 84.610  0.039  2.328   3.4652e-02
   3_occ:   6.089  0.041  0.225 84.610  0.039  2.328   3.4652e-02
   4_bss:   6.089  0.041  0.225 84.610  0.039  2.328   3.4652e-02
   4_xyz:   6.318  0.053  0.259 83.681  0.038  2.301   5.4558e-02
   4_adp:   6.318  0.053  0.259 83.681  0.038  2.301   5.4558e-02
   4_occ:   6.318  0.053  0.259 83.681  0.038  2.301   5.4558e-02
   5_bss:   6.318  0.053  0.259 83.681  0.038  2.301   5.4558e-02
   5_xyz:   6.489  0.053  0.273 83.984  0.037  2.240   5.8323e-02
   5_adp:   6.489  0.053  0.273 83.984  0.037  2.240   5.8323e-02
   5_occ:   6.489  0.053  0.273 83.984  0.037  2.240   5.8323e-02
   5_bss:   6.489  0.053  0.273 83.984  0.037  2.240   5.8323e-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:  69.80   0.61  17.06  68.29   0.61  13.04  69.80   7.38  38.89
   1_occ:  69.80   0.61  17.06  68.29   0.61  13.04  69.80   7.38  38.89
   2_bss:  69.80   0.61  17.06  68.29   0.61  13.04  69.80   7.38  38.89
   2_xyz:  69.80   0.61  17.06  68.29   0.61  13.04  69.80   7.38  38.89
   2_adp:  68.51   2.12  16.60  68.51   2.12  12.87  67.92   6.33  36.91
   2_occ:  68.51   2.12  16.60  68.51   2.12  12.87  67.92   6.33  36.91
   3_bss:  68.51   2.12  16.60  68.51   2.12  12.87  67.92   6.33  36.91
   3_xyz:  68.51   2.12  16.60  68.51   2.12  12.87  67.92   6.33  36.91
   3_adp:  85.39   0.61  17.23  85.39   0.61  12.99  77.77   3.68  40.28
   3_occ:  85.39   0.61  17.23  85.39   0.61  12.99  77.77   3.68  40.28
   4_bss:  85.39   0.61  17.23  85.39   0.61  12.99  77.77   3.68  40.28
   4_xyz:  85.39   0.61  17.23  85.39   0.61  12.99  77.77   3.68  40.28
   4_adp:  83.94   1.26  16.58  83.94   1.26  12.67  79.00   5.29  37.89
   4_occ:  83.94   1.26  16.58  83.94   1.26  12.67  79.00   5.29  37.89
   5_bss:  83.94   1.26  16.58  83.94   1.26  12.67  79.00   5.29  37.89
   5_xyz:  83.94   1.26  16.58  83.94   1.26  12.67  79.00   5.29  37.89
   5_adp:  84.22   1.01  16.44  84.22   1.01  12.49  79.11   6.14  37.93
   5_occ:  84.22   1.01  16.44  84.22   1.01  12.49  79.11   6.14  37.93
   5_bss:  84.18   0.98  16.40  84.18   0.98  12.46  79.07   6.11  37.89
------------------------------------------------------------------------
 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:    0.968    0.010    0.283
   1_adp:    0.968    0.010    0.283
   1_occ:    0.968    0.010    0.283
   2_bss:    0.968    0.010    0.283
   2_xyz:    0.794    0.029    0.347
   2_adp:    0.794    0.029    0.347
   2_occ:    0.794    0.029    0.347
   3_bss:    0.794    0.029    0.347
   3_xyz:    0.989    0.031    0.373
   3_adp:    0.989    0.031    0.373
   3_occ:    0.989    0.031    0.373
   4_bss:    0.989    0.031    0.373
   4_xyz:    1.065    0.048    0.384
   4_adp:    1.065    0.048    0.384
   4_occ:    1.065    0.048    0.384
   5_bss:    1.065    0.048    0.384
   5_xyz:    1.177    0.040    0.392
   5_adp:    1.177    0.040    0.392
   5_occ:    1.177    0.040    0.392
   5_bss:    1.177    0.040    0.392
------------------------------------------------------------------------

CPU time actual refinement: 318.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/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_402/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_402/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.90 
  Macro-tasks:
    bulk solvent and scale       = 36.07  
    individual site refinement   = 128.69 
    weights calculation          = 28.41  
    collect and process          = 6.49   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 199.74 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 101.61 
    alpha_beta                      = 7.87   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.42 
    fmodel                         = 6.12   
    r_factors                      = 0.18   
    phase_errors                   = 11.12  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 239.91 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.520 micro seconds
Total CPU time: 5.52 minutes
from_scatterers_fft:    658 calls, 101.28 s
gradients_fft:          603 calls,  96.93 s

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

# Date 2008-01-16 Time 04:44:26 PST -0800 (1200487466.83 s)
Start R-work = 0.3153, R-free = 0.3115 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.3012, R-free = 0.2968
Final R-work = 0.1040, R-free = 0.1532