# Date 2008-01-16 Time 04:10:19 PST -0800 (1200485419.50 s)
#phil __OFF__

Command line arguments: "../210.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10611
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 210

-------------------------------------------------------------------------------
  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: (68.845, 47.6339, 84.6622, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96053
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8666
                             d_min =   1.9605

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: (68.845, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96053
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8670 -  4.1952 [2162/2191]  1945   217  10.0%
  bin  2:  4.1952 -  3.3423 [2064/2087]  1858   206  10.0%
  bin  3:  3.3423 -  2.9234 [2054/2079]  1845   209  10.2%
  bin  4:  2.9234 -  2.6578 [2010/2026]  1814   196   9.8%
  bin  5:  2.6578 -  2.4682 [2005/2049]  1800   205  10.2%
  bin  6:  2.4682 -  2.3233 [2011/2039]  1819   192   9.5%
  bin  7:  2.3233 -  2.2073 [1977/2013]  1776   201  10.2%
  bin  8:  2.2073 -  2.1115 [1993/2035]  1796   197   9.9%
  bin  9:  2.1115 -  2.0304 [1969/2015]  1770   199  10.1%
  bin 10:  2.0304 -  1.9605 [1344/2004]  1207   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 20
        2.04 -     2.76: 426
        2.76 -     3.47: 4666
        3.47 -     4.19: 9484
        4.19 -     4.90: 14145
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.328 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.418 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.496 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.515 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.619 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28736 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_210/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 68.845 47.63395 84.6622 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: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4614   r_free= 0.4610   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.264541                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6791 0.99   1400  158 0.3647 0.3763      6.5361      6.5878|
|  2:  4.6791 -  3.7333 0.99   1345  147 0.3944 0.3812      6.7654      6.7494|
|  3:  3.7333 -  3.2671 0.99   1323  149 0.4129 0.4152      6.6393      6.7206|
|  4:  3.2671 -  2.9710 0.99   1315  137 0.4395 0.4351      6.4799      6.4649|
|  5:  2.9710 -  2.7595 0.98   1301  149 0.4707 0.4364      6.3536      6.3224|
|  6:  2.7595 -  2.5977 0.99   1299  146 0.4869 0.4866      6.2571      6.1666|
|  7:  2.5977 -  2.4682 0.98   1279  147 0.5024 0.4688      6.2492      6.1759|
|  8:  2.4682 -  2.3612 0.99   1299  137 0.5100 0.5312      6.1765      6.1802|
|  9:  2.3612 -  2.2707 0.99   1288  147 0.5323 0.5435      6.1188      6.1849|
| 10:  2.2707 -  2.1926 0.98   1277  140 0.5207 0.5569      6.1159      6.1324|
| 11:  2.1926 -  2.1242 0.97   1258  144 0.5349 0.5493      6.0361      6.0557|
| 12:  2.1242 -  2.0636 0.99   1282  142 0.5211 0.5177      5.9736      5.9859|
| 13:  2.0636 -  2.0094 0.94   1243  129 0.5312 0.5537      5.8792      5.9065|
| 14:  2.0094 -  1.9605 0.57    721   87 0.5367 0.4988      5.8645      5.7252|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6791  1400   158  0.68  36.29   0.84     0.70      76312.35|
|  2:  4.6791 -  3.7333  1345   147  0.70  35.13   0.92     0.80     102141.77|
|  3:  3.7333 -  3.2671  1323   149  0.63  41.35   0.94     0.82     105060.86|
|  4:  3.2671 -  2.9710  1315   137  0.55  47.55   0.94     0.78      90470.44|
|  5:  2.9710 -  2.7595  1301   149  0.51  51.52   0.90     0.71      72505.70|
|  6:  2.7595 -  2.5977  1299   146  0.46  55.35   0.91     0.64      62497.83|
|  7:  2.5977 -  2.4682  1279   147  0.43  57.67   0.91     0.59      60868.88|
|  8:  2.4682 -  2.3612  1299   137  0.36  62.73   0.92     0.52      59028.00|
|  9:  2.3612 -  2.2707  1288   147  0.31  67.23   0.90     0.47      57935.36|
| 10:  2.2707 -  2.1926  1277   140  0.27  69.62   0.96     0.40      54323.84|
| 11:  2.1926 -  2.1242  1258   144  0.22  73.29   0.92     0.35      52554.50|
| 12:  2.1242 -  2.0636  1282   142  0.20  74.89   0.97     0.33      49458.47|
| 13:  2.0636 -  2.0094  1243   129  0.20  75.22   0.92     0.32      41974.82|
| 14:  2.0094 -  1.9605   721    87  0.24  71.91   0.95     0.34      32998.78|
|alpha:            min =        0.32 max =            0.82 mean =         0.57|
|beta:             min =    32998.78 max =       105060.86 mean =     67028.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.77|
|phase err.(test): min =        0.00 max =           89.99 mean =        57.93|
|-----------------------------------------------------------------------------|

============================== 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 = 9.069415              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.783146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.097   (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 |  1.328 -  1.685:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.685 -  2.042:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.042 -  2.399:       42 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.399 -  2.757:      384 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.757 -  3.114:     2300 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.114 -  3.471:     2366 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.471 -  3.828:     4399 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.828 -  4.186:     5085 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.186 -  4.543:     6345 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.543 -  4.900:     7800 |
|-----------------------------------------------------------------------------|
|-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 |        0.213 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.328 |       0.950 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    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: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4614   r_free= 0.4610   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.264541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4543   r_free= 0.4526   ksol= 0.30   Bsol= 20.00   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,1.62,1.26,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.258167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.706622              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.203   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.307753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.838   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4543      final r-factor (work) = 0.3441          |
| start r-factor (free) = 0.4526      final r-factor (free) = 0.3687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3299 = 7.71 * 0.50 * 6.2589 + 1.00 * 0.2126                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7919 = 7.71 * 0.50 * 6.1451 + 1.00 * 0.1131                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3441      final r-factor (work) = 0.3081          |
| start r-factor (free) = 0.3687      final r-factor (free) = 0.3756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0425 = 1.31 * 1.00 * 6.1451 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8699 = 1.31 * 1.00 * 6.0013 + 1.00 * 0.0217                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.19  20.11    None  None   None       |
|    all(noH): 2823   0      0.00    112.19  20.11    None  None   None       |
|    Sol.    : 438    0      0.48    112.19  40.99    None  None   None       |
|    Mac.    : 2385   0      0.00    84.43   16.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.219: 1037   |   5:    56.095 -  67.314:   76        |
|      1:    11.219 -  22.438:  859   |   6:    67.314 -  78.533:   46        |
|      2:    22.438 -  33.657:  436   |   7:    78.533 -  89.752:   15        |
|      3:    33.657 -  44.876:  219   |   8:    89.752 - 100.971:    1        |
|      4:    44.876 -  56.095:  133   |   9:   100.971 - 112.190:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3081 r_free = 0.3756             target_work(ml) = 6.013         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3078 r_free = 0.3759             target_work(ml) = 6.012         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3078   r_free= 0.3759   ksol= 0.30   Bsol= 20.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,1.62,1.26,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.012159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3061   r_free= 0.3729   ksol= 0.33   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.59,0.12,0.00,0.00,0.00); trace/3= -0.35                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.009380                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.663144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.745   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552970              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.305  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3061      final r-factor (work) = 0.2331          |
| start r-factor (free) = 0.3729      final r-factor (free) = 0.2842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1010 = 5.66 * 0.50 * 5.9996 + 1.00 * 0.1128                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7961 = 5.66 * 0.50 * 5.9033 + 1.00 * 0.0805                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2331      final r-factor (work) = 0.2128          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2682          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2858 = 0.55 * 1.00 * 5.9033 + 1.00 * 0.0215                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1897 = 0.55 * 1.00 * 5.7279 + 1.00 * 0.0224                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    131.39  19.30    None  None   None       |
|    all(noH): 2823   0      0.00    131.39  19.30    None  None   None       |
|    Sol.    : 438    0      4.68    106.43  41.63    None  None   None       |
|    Mac.    : 2385   0      0.00    131.39  15.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.139: 1370   |   5:    65.697 -  78.836:   51        |
|      1:    13.139 -  26.279:  805   |   6:    78.836 -  91.976:   12        |
|      2:    26.279 -  39.418:  302   |   7:    91.976 - 105.115:    1        |
|      3:    39.418 -  52.558:  182   |   8:   105.115 - 118.254:    1        |
|      4:    52.558 -  65.697:   98   |   9:   118.254 - 131.394:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2128 r_free = 0.2682             target_work(ml) = 5.700         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2125 r_free = 0.2680             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2680   ksol= 0.33   Bsol= 50.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.59,0.12,0.00,0.00,0.00); trace/3= -0.35                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.698519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2124   r_free= 0.2670   ksol= 0.32   Bsol= 40.40   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.19,-0.64,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.696762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.689867              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.097   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.698994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.864   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2124      final r-factor (work) = 0.1612          |
| start r-factor (free) = 0.2670      final r-factor (free) = 0.2121          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5115 = 4.69 * 0.50 * 5.7276 + 1.00 * 0.0805                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1666 = 4.69 * 0.50 * 5.5870 + 1.00 * 0.0655                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2121      final r-factor (free) = 0.1940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5119 = 1.70 * 1.00 * 5.5870 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1948 = 1.70 * 1.00 * 5.4045 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.48  18.57    None  None   None       |
|    all(noH): 2823   0      0.00    102.48  18.57    None  None   None       |
|    Sol.    : 438    0      5.87    102.48  44.31    None  None   None       |
|    Mac.    : 2385   0      0.00    93.54   13.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.248: 1054   |   5:    51.240 -  61.488:  101        |
|      1:    10.248 -  20.496: 1060   |   6:    61.488 -  71.736:   61        |
|      2:    20.496 -  30.744:  249   |   7:    71.736 -  81.984:   28        |
|      3:    30.744 -  40.992:  126   |   8:    81.984 -  92.232:   14        |
|      4:    40.992 -  51.240:  126   |   9:    92.232 - 102.480:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1940             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1421 r_free = 0.1940             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1421   r_free= 0.1940   ksol= 0.32   Bsol= 40.40   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.19,-0.64,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.348464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1937   ksol= 0.32   Bsol= 47.06   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.25,-1.56,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.349896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.106247              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.852  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.078  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7677 = 2.11 * 0.50 * 5.4146 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6410 = 2.11 * 0.50 * 5.3046 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1467 = 0.40 * 1.00 * 5.3046 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1213 = 0.40 * 1.00 * 5.2479 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    97.30   17.84    None  None   None       |
|    all(noH): 2823   0      1.26    97.30   17.84    None  None   None       |
|    Sol.    : 438    0      6.35    97.30   42.56    None  None   None       |
|    Mac.    : 2385   0      1.26    96.21   13.30    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 -  10.860: 1205   |   5:    49.277 -  58.882:   95        |
|      1:    10.860 -  20.464:  981   |   6:    58.882 -  68.486:   56        |
|      2:    20.464 -  30.069:  202   |   7:    68.486 -  78.091:   25        |
|      3:    30.069 -  39.673:  117   |   8:    78.091 -  87.695:   14        |
|      4:    39.673 -  49.277:  121   |   9:    87.695 -  97.300:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1719             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1720             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1720   ksol= 0.32   Bsol= 47.06   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.25,-1.56,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.227597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1720   ksol= 0.32   Bsol= 45.04   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.45,-1.63,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.227729                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.335884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.627  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.498517              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.715  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5598 = 1.34 * 0.50 * 5.2477 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5312 = 1.34 * 0.50 * 5.2155 + 1.00 * 0.0476                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6100 = 0.50 * 1.00 * 5.2155 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5984 = 0.50 * 1.00 * 5.1932 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    100.74  17.44    None  None   None       |
|    all(noH): 2823   0      1.35    100.74  17.44    None  None   None       |
|    Sol.    : 438    0      5.26    91.14   41.46    None  None   None       |
|    Mac.    : 2385   0      1.35    100.74  13.02    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:     1.350 -  11.289: 1336   |   5:    51.047 -  60.986:   90        |
|      1:    11.289 -  21.228:  892   |   6:    60.986 -  70.925:   45        |
|      2:    21.228 -  31.168:  194   |   7:    70.925 -  80.865:   14        |
|      3:    31.168 -  41.107:  114   |   8:    80.865 -  90.804:   10        |
|      4:    41.107 -  51.047:  123   |   9:    90.804 - 100.743:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1659             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1659             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1659   ksol= 0.32   Bsol= 45.04   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.45,-1.63,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189967                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6791 0.99   1400  158 0.1016 0.1302      5.4064      5.5551|
|  2:  4.6791 -  3.7333 0.99   1345  147 0.0875 0.1080      5.4458      5.6155|
|  3:  3.7333 -  3.2671 0.99   1323  149 0.1055 0.1537      5.4755      5.8498|
|  4:  3.2671 -  2.9710 0.99   1315  137 0.1307 0.1720      5.4986      5.6939|
|  5:  2.9710 -  2.7595 0.98   1301  149 0.1393 0.1661      5.3773      5.5118|
|  6:  2.7595 -  2.5977 0.99   1299  146 0.1374 0.2186      5.2826      5.5394|
|  7:  2.5977 -  2.4682 0.98   1279  147 0.1249 0.1640      5.1848      5.3723|
|  8:  2.4682 -  2.3612 0.99   1299  137 0.1267 0.1889      5.1371      5.3731|
|  9:  2.3612 -  2.2707 0.99   1288  147 0.1274 0.1954      5.0824      5.3534|
| 10:  2.2707 -  2.1926 0.98   1277  140 0.1196 0.1900      5.0285      5.2654|
| 11:  2.1926 -  2.1242 0.97   1258  144 0.1225 0.1748       4.969      5.2265|
| 12:  2.1242 -  2.0636 0.99   1282  142 0.1182 0.1857      4.9001      5.1707|
| 13:  2.0636 -  2.0094 0.94   1243  129 0.1236 0.1830      4.8431      5.1192|
| 14:  2.0094 -  1.9605 0.57    721   87 0.1172 0.2001      4.7822      5.0039|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6791  1400   158  0.94   9.44   0.98     0.96       7562.04|
|  2:  4.6791 -  3.7333  1345   147  0.95   8.05   1.02     1.01       9017.84|
|  3:  3.7333 -  3.2671  1323   149  0.94  11.12   1.04     1.03      10312.60|
|  4:  3.2671 -  2.9710  1315   137  0.91  14.41   1.02     1.01      11032.55|
|  5:  2.9710 -  2.7595  1301   149  0.89  16.59   1.01     0.97       8966.90|
|  6:  2.7595 -  2.5977  1299   146  0.89  17.13   0.99     0.94       7896.27|
|  7:  2.5977 -  2.4682  1279   147  0.90  16.01   0.99     0.96       6462.16|
|  8:  2.4682 -  2.3612  1299   137  0.90  16.16   1.01     0.99       6098.85|
|  9:  2.3612 -  2.2707  1288   147  0.90  16.71   1.00     0.97       5450.23|
| 10:  2.2707 -  2.1926  1277   140  0.90  16.38   1.00     0.96       5079.91|
| 11:  2.1926 -  2.1242  1258   144  0.90  16.68   1.01     0.97       4554.11|
| 12:  2.1242 -  2.0636  1282   142  0.91  15.36   1.00     0.99       3995.72|
| 13:  2.0636 -  2.0094  1243   129  0.89  17.17   1.00     0.99       3675.08|
| 14:  2.0094 -  1.9605   721    87  0.89  16.82   0.99     0.94       3203.12|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3203.12 max =        11032.55 mean =      6818.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.72|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1658   ksol= 0.32   Bsol= 44.99   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.39,-1.51,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.190008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1658   ksol= 0.32   Bsol= 44.99   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.39,-1.51,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.190008                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6791 0.99   1400  158 0.1009 0.1283      5.3986      5.5389|
|  2:  4.6791 -  3.7333 0.99   1345  147 0.0885 0.1089      5.4527      5.6326|
|  3:  3.7333 -  3.2671 0.99   1323  149 0.1056 0.1543      5.4822       5.851|
|  4:  3.2671 -  2.9710 0.99   1315  137 0.1309 0.1713      5.4995      5.6894|
|  5:  2.9710 -  2.7595 0.98   1301  149 0.1395 0.1660      5.3783      5.5121|
|  6:  2.7595 -  2.5977 0.99   1299  146 0.1371 0.2192      5.2816      5.5362|
|  7:  2.5977 -  2.4682 0.98   1279  147 0.1246 0.1643      5.1829      5.3747|
|  8:  2.4682 -  2.3612 0.99   1299  137 0.1265 0.1880      5.1357      5.3701|
|  9:  2.3612 -  2.2707 0.99   1288  147 0.1272 0.1954      5.0802      5.3534|
| 10:  2.2707 -  2.1926 0.98   1277  140 0.1195 0.1894       5.028      5.2648|
| 11:  2.1926 -  2.1242 0.97   1258  144 0.1223 0.1751      4.9685      5.2265|
| 12:  2.1242 -  2.0636 0.99   1282  142 0.1182 0.1861      4.9001      5.1717|
| 13:  2.0636 -  2.0094 0.94   1243  129 0.1235 0.1834      4.8435      5.1207|
| 14:  2.0094 -  1.9605 0.57    721   87 0.1172 0.1997      4.7823      5.0032|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6791  1400   158  0.94   9.04   0.98     0.96       7204.22|
|  2:  4.6791 -  3.7333  1345   147  0.95   8.10   1.02     1.01       9015.50|
|  3:  3.7333 -  3.2671  1323   149  0.93  11.23   1.04     1.03      10507.80|
|  4:  3.2671 -  2.9710  1315   137  0.91  14.43   1.02     1.01      11028.92|
|  5:  2.9710 -  2.7595  1301   149  0.89  16.55   1.01     0.98       8937.44|
|  6:  2.7595 -  2.5977  1299   146  0.89  17.13   0.99     0.95       7891.11|
|  7:  2.5977 -  2.4682  1279   147  0.90  15.96   0.99     0.96       6436.29|
|  8:  2.4682 -  2.3612  1299   137  0.90  16.13   1.01     0.99       6080.25|
|  9:  2.3612 -  2.2707  1288   147  0.90  16.69   1.00     0.97       5433.68|
| 10:  2.2707 -  2.1926  1277   140  0.90  16.37   1.00     0.97       5071.62|
| 11:  2.1926 -  2.1242  1258   144  0.90  16.68   1.01     0.97       4550.97|
| 12:  2.1242 -  2.0636  1282   142  0.91  15.37   1.01     1.00       4000.39|
| 13:  2.0636 -  2.0094  1243   129  0.89  17.18   1.01     1.00       3680.82|
| 14:  2.0094 -  1.9605   721    87  0.89  16.82   0.99     0.94       3202.02|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3202.02 max =        11028.92 mean =      6797.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.69|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    100.70  17.39    None  None   None       |
|    all(noH): 2823   0      1.30    100.70  17.39    None  None   None       |
|    Sol.    : 438    0      5.21    91.09   41.42    None  None   None       |
|    Mac.    : 2385   0      1.30    100.70  12.98    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:     1.302 -  11.241: 1336   |   5:    50.999 -  60.938:   90        |
|      1:    11.241 -  21.181:  892   |   6:    60.938 -  70.878:   45        |
|      2:    21.181 -  31.120:  194   |   7:    70.878 -  80.817:   14        |
|      3:    31.120 -  41.060:  114   |   8:    80.817 -  90.756:   10        |
|      4:    41.060 -  50.999:  123   |   9:    90.756 - 100.696:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.592 - 4.039
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 296
   mapped sites are within: 0.715 - 4.039

peak=    9.803 closest distance to " CB  SER A 216 " =    1.183
peak=    6.222 closest distance to " O   HOH Z  52 " =    1.475
peak=    5.934 closest distance to " O   HOH Z 102 " =    1.373
peak=    5.751 closest distance to " CB  ARG A 275 " =    0.993
peak=    5.594 closest distance to " O   HOH Z 124 " =    1.644
peak=    5.477 closest distance to " NH2 ARG A  56 " =    2.252
peak=    5.306 closest distance to " CG  PRO A  54 " =    1.241
peak=    5.162 closest distance to " O   HOH Z 193 " =    1.842
peak=    5.024 closest distance to " CB  GLN A 223 " =    1.452
peak=    4.999 closest distance to " CB  SER A  63 " =    1.128
peak=    4.999 closest distance to " CG  PRO A 213 " =    1.347
peak=    4.923 closest distance to " O   HOH Z 389 " =    1.972
peak=    4.862 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.849 closest distance to " O   HOH Z 272 " =    1.895
peak=    4.838 closest distance to " O   HOH Z 402 " =    1.444
peak=    4.805 closest distance to " O   HOH Z 406 " =    1.539
peak=    4.774 closest distance to " O   HOH Z 234 " =    3.654
peak=    4.767 closest distance to " O   HOH Z 247 " =    1.402
peak=    4.734 closest distance to " CG  PRO A  90 " =    1.254
peak=    4.727 closest distance to " CA  TYR A  30 " =    0.995
peak=    4.715 closest distance to " CB  ASN A 187 " =    1.840
peak=    4.678 closest distance to " O   HOH Z  97 " =    1.664
peak=    4.620 closest distance to " O   HOH Z 209 " =    2.355
peak=    4.614 closest distance to " O   HOH Z  80 " =    1.757
peak=    4.603 closest distance to " O   HOH Z 214 " =    1.179
peak=    4.565 closest distance to " O   HOH Z 401 " =    1.079
peak=    4.556 closest distance to " CD  ARG A 269 " =    1.130
peak=    4.540 closest distance to " O   HOH Z 132 " =    1.397
peak=    4.473 closest distance to " O   HOH Z 142 " =    1.600
peak=    4.451 closest distance to " CG AARG A 275 " =    1.048
peak=    4.430 closest distance to " CG  ARG A  66 " =    1.073
peak=    4.389 closest distance to " O   SER A  87 " =    2.241
peak=    4.382 closest distance to " O   HOH Z  85 " =    1.904
peak=    4.378 closest distance to " CG AARG A 275 " =    1.186
peak=    4.368 closest distance to " O   HOH Z  15 " =    2.252
peak=    4.330 closest distance to " NZ  LYS A 117 " =    3.162
peak=    4.329 closest distance to " O   HOH Z 278 " =    1.115
peak=    4.294 closest distance to " C   PRO A 198 " =    1.594
peak=    4.290 closest distance to " O   HOH Z 130 " =    2.659
peak=    4.286 closest distance to " O   HOH Z 134 " =    1.679
peak=    4.283 closest distance to " O   HOH Z 227 " =    1.771
peak=    4.266 closest distance to " O   HOH Z 261 " =    1.673
peak=    4.254 closest distance to " CG1 ILE A  33 " =    1.258
peak=    4.252 closest distance to " O   HOH Z 403 " =    1.955
peak=    4.250 closest distance to " O   HOH Z  59 " =    2.283
peak=    4.236 closest distance to " O   HOH Z  40 " =    1.774
peak=    4.235 closest distance to " O   HOH Z 232 " =    2.260
peak=    4.201 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.182 closest distance to " O   HOH Z 154 " =    1.517
peak=    4.167 closest distance to " CG  PRO A 243 " =    1.199
peak=    4.166 closest distance to " O   HOH Z 298 " =    1.850
peak=    4.147 closest distance to " O   HOH Z 132 " =    2.135
peak=    4.146 closest distance to " O   HOH Z  47 " =    1.562
peak=    4.146 closest distance to " CB  GLU A 128 " =    1.199
peak=    4.146 closest distance to " O   HOH Z 404 " =    1.199
peak=    4.145 closest distance to " O   HOH Z 189 " =    1.746
peak=    4.144 closest distance to " O   HOH Z 411 " =    3.553
peak=    4.103 closest distance to " O   HOH Z 303 " =    2.009
peak=    4.091 closest distance to " NH2BARG A 145 " =    2.207
peak=    4.080 closest distance to " CE  LYS A 119 " =    1.174
peak=    4.065 closest distance to " O   HOH Z 426 " =    1.454
peak=    4.034 closest distance to " O   HOH Z  63 " =    1.877
peak=    4.029 closest distance to " CB  SER A   3 " =    1.267
peak=    4.022 closest distance to " N   ASN A  39 " =    1.237
peak=    3.994 closest distance to " CB  GLU A 152 " =    1.134
peak=    3.993 closest distance to " ND2 ASN A 187 " =    1.585
peak=    3.971 closest distance to " O   HOH Z 427 " =    2.685
peak=    3.969 closest distance to " O   HOH Z 316 " =    2.751
peak=    3.956 closest distance to " O   HOH Z 145 " =    2.139
peak=    3.927 closest distance to " CB  SER A 141 " =    1.043
peak=    3.926 closest distance to " CB  PRO A 198 " =    1.072
peak=    3.924 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.895 closest distance to " CB  TRP A 179 " =    1.072
peak=    3.895 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.894 closest distance to " CA  ARG A  36 " =    0.999
peak=    3.887 closest distance to " O   HOH Z 408 " =    1.693
peak=    3.884 closest distance to " O   HOH Z 369 " =    2.523
peak=    3.879 closest distance to " O   HOH Z 346 " =    1.492
peak=    3.863 closest distance to " O   HOH Z 345 " =    1.903
peak=    3.862 closest distance to " CA  ALA A  21 " =    1.230
peak=    3.862 closest distance to " CA  ARG A  66 " =    1.239
peak=    3.843 closest distance to " CG2 ILE A 120 " =    1.262
peak=    3.827 closest distance to " CB  SER A  62 " =    0.903
peak=    3.821 closest distance to " NE2 GLN A  11 " =    0.994
peak=    3.819 closest distance to " O   HOH Z 394 " =    1.530
peak=    3.818 closest distance to " O   HOH Z  78 " =    1.713
peak=    3.816 closest distance to " O   HOH Z 163 " =    2.046
peak=    3.815 closest distance to " O   HOH Z  68 " =    1.791
peak=    3.809 closest distance to " O   HOH Z 368 " =    1.971
peak=    3.803 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.787 closest distance to " O   HOH Z 279 " =    2.095
peak=    3.780 closest distance to " O   HOH Z 163 " =    1.508
peak=    3.780 closest distance to " CG2BVAL A  41 " =    0.878
peak=    3.773 closest distance to " O   HOH Z  97 " =    2.228
peak=    3.773 closest distance to " CB  PRO A  54 " =    0.915
peak=    3.771 closest distance to " O   HOH Z 132 " =    2.576
peak=    3.766 closest distance to " CA  ASN A 176 " =    1.065
peak=    3.753 closest distance to " O   HOH Z 156 " =    3.232
peak=    3.745 closest distance to " O   HOH Z  44 " =    1.965
peak=    3.732 closest distance to " CB  ARG A  79 " =    1.371
peak=    3.723 closest distance to " OE1 GLU A   2 " =    2.267
peak=    3.722 closest distance to " CB  ASN A 148 " =    1.395
peak=    3.717 closest distance to " CB  ALA A 291 " =    1.229
peak=    3.716 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.715 closest distance to " NZ  LYS A 119 " =    1.526
peak=    3.702 closest distance to " CB  ARG A 269 " =    0.831
peak=    3.701 closest distance to " O   HOH Z 203 " =    1.863
peak=    3.692 closest distance to " O   HOH Z 173 " =    2.161
peak=    3.688 closest distance to " OH  TYR A  30 " =    1.096
peak=    3.686 closest distance to " O   HOH Z 245 " =    1.355
peak=    3.686 closest distance to " O   HOH Z 236 " =    1.506
peak=    3.681 closest distance to " O   HOH Z 427 " =    3.032
peak=    3.677 closest distance to " O   HOH Z 334 " =    1.491
peak=    3.677 closest distance to " O   HOH Z 423 " =    1.929
peak=    3.677 closest distance to " O   HOH Z 108 " =    1.115
peak=    3.676 closest distance to " O   HOH Z 128 " =    1.959
peak=    3.669 closest distance to " CB  ASP A 191 " =    1.258
peak=    3.666 closest distance to " O   HOH Z 287 " =    1.724
peak=    3.661 closest distance to " O   HOH Z 108 " =    2.449
peak=    3.657 closest distance to " O   HOH Z 194 " =    1.884
peak=    3.656 closest distance to " O   HOH Z 345 " =    2.462
peak=    3.651 closest distance to " O   HOH Z 155 " =    2.810
peak=    3.649 closest distance to " O   HOH Z 173 " =    1.749
peak=    3.646 closest distance to " OG BSER A 210 " =    1.278
peak=    3.637 closest distance to " O   HOH Z  19 " =    1.411
peak=    3.633 closest distance to " O   HOH Z 433 " =    1.481
peak=    3.630 closest distance to " OD2 ASP A 286 " =    2.692
peak=    3.612 closest distance to " CA  ASP A 162 " =    1.147
peak=    3.611 closest distance to " O   HOH Z 114 " =    1.190
peak=    3.605 closest distance to " O   HOH Z  54 " =    1.661
peak=    3.602 closest distance to " CD2 PHE A 225 " =    1.101
peak=    3.602 closest distance to " CB  LEU A 228 " =    1.172
peak=    3.597 closest distance to " O   HOH Z 260 " =    1.349
peak=    3.588 closest distance to " O   HOH Z 365 " =    2.673
peak=    3.583 closest distance to " CG  GLN A  77 " =    0.918
peak=    3.580 closest distance to " CD2 TRP A 179 " =    1.460
peak=    3.579 closest distance to " O   HOH Z  88 " =    3.163
peak=    3.578 closest distance to " NH2 ARG A 156 " =    1.148
peak=    3.568 closest distance to " CD  ARG A 139 " =    1.386
peak=    3.562 closest distance to " OG  SER A  62 " =    2.894
peak=    3.560 closest distance to " O   HOH Z  43 " =    2.222
peak=    3.559 closest distance to " O   HOH Z  40 " =    2.012
peak=    3.559 closest distance to " O   HOH Z  66 " =    2.215
peak=    3.557 closest distance to " CA  GLN A 194 " =    0.864
peak=    3.551 closest distance to " O   HOH Z 374 " =    2.544
peak=    3.548 closest distance to " NE1 TRP A 274 " =    0.893
peak=    3.547 closest distance to " CG  MET A  93 " =    1.042
peak=    3.547 closest distance to " OG1 THR A 294 " =    3.954
peak=    3.537 closest distance to " CG2 VAL A 257 " =    0.852
peak=    3.522 closest distance to " O   HOH Z 337 " =    3.610
peak=    3.521 closest distance to " CG2 VAL A  78 " =    0.973
peak=    3.516 closest distance to " CB  PHE A  16 " =    1.039
peak=    3.515 closest distance to " CB  MET A  47 " =    1.085
peak=    3.506 closest distance to " CG1BVAL A  72 " =    1.601
peak=    3.504 closest distance to " OG BSER A 164 " =    2.418
peak=    3.501 closest distance to " C   ILE A 106 " =    1.828
peak=    3.491 closest distance to " O   HOH Z 267 " =    1.985
peak=    3.490 closest distance to " CB  ARG A 190 " =    1.709
peak=    3.489 closest distance to " O   HOH Z  21 " =    1.867
peak=    3.484 closest distance to " CD  LYS A 119 " =    1.705
peak=    3.483 closest distance to " O   HOH Z 273 " =    2.735
peak=    3.479 closest distance to " CD1 LEU A  96 " =    0.798
peak=    3.478 closest distance to " CA  THR A 221 " =    0.969
peak=    3.473 closest distance to " OG1 THR A 294 " =    2.280
peak=    3.473 closest distance to " CB  ALA A  34 " =    0.994
peak=    3.461 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.459 closest distance to " CB  VAL A 265 " =    1.139
peak=    3.459 closest distance to " CB  ALA A 248 " =    1.257
peak=    3.458 closest distance to " CA  GLY A  80 " =    1.212
peak=    3.455 closest distance to " NH2AARG A 145 " =    2.058
peak=    3.439 closest distance to " CA  LYS A 117 " =    1.291
peak=    3.433 closest distance to " O   HOH Z 414 " =    1.609
peak=    3.431 closest distance to " O   HOH Z 298 " =    2.283
peak=    3.429 closest distance to " O   HOH Z 261 " =    1.912
peak=    3.417 closest distance to " CA  ASP A 140 " =    1.093
peak=    3.410 closest distance to " O   HOH Z 336 " =    1.608
peak=    3.405 closest distance to " O   HOH Z 250 " =    1.760
peak=    3.403 closest distance to " O   HOH Z  35 " =    2.266
peak=    3.403 closest distance to " CB  SER A  26 " =    1.698
peak=    3.401 closest distance to " O   SER A  26 " =    1.588
peak=    3.398 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.396 closest distance to " CA  ARG A 195 " =    1.287
peak=    3.391 closest distance to " CZ  PHE A  38 " =    1.423
peak=    3.383 closest distance to " O   HOH Z  30 " =    2.032
peak=    3.381 closest distance to " CZ2 TRP A 179 " =    1.811
peak=    3.376 closest distance to " CD  GLN A 194 " =    1.649
peak=    3.375 closest distance to " O   HOH Z  54 " =    2.287
peak=    3.370 closest distance to " CB  GLN A 278 " =    0.821
peak=    3.361 closest distance to " O   HOH Z 419 " =    1.498
peak=    3.359 closest distance to " O   HOH Z 361 " =    3.260
peak=    3.357 closest distance to " O   HOH Z 261 " =    1.870
peak=    3.356 closest distance to " O   HOH Z  71 " =    1.244
peak=    3.355 closest distance to " CB  ALA A  71 " =    1.101
peak=    3.354 closest distance to " O   HOH Z 425 " =    1.392
peak=    3.354 closest distance to " O   HOH Z 344 " =    2.805
peak=    3.350 closest distance to " OE1 GLN A  11 " =    1.834
peak=    3.348 closest distance to " O   HOH Z 185 " =    1.654
peak=    3.348 closest distance to " O   HOH Z 118 " =    1.071
peak=    3.346 closest distance to " O   HOH Z 124 " =    2.770
peak=    3.343 closest distance to " O   HOH Z 326 " =    1.492
peak=    3.339 closest distance to " O   HOH Z 402 " =    2.921
peak=    3.338 closest distance to " CD2 HIS A  81 " =    1.120
peak=    3.336 closest distance to " CG2 ILE A  20 " =    1.435
peak=    3.336 closest distance to " O   HOH Z 327 " =    1.790
peak=    3.325 closest distance to " O   HOH Z 357 " =    1.651
peak=    3.324 closest distance to " O   HOH Z  85 " =    1.790
peak=    3.316 closest distance to " O   HOH Z 421 " =    1.854
peak=    3.307 closest distance to " CG  GLN A  58 " =    2.351
peak=    3.279 closest distance to " O   HOH Z  51 " =    1.625
peak=    3.277 closest distance to " O   HOH Z 291 " =    1.693
peak=    3.277 closest distance to " CD BLYS A 290 " =    1.139
peak=    3.276 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.275 closest distance to " CA  ALA A 160 " =    0.875
peak=    3.274 closest distance to " CB  VAL A 202 " =    1.482
peak=    3.274 closest distance to " N   ARG A 156 " =    1.445
peak=    3.264 closest distance to " O   HOH Z 284 " =    2.773
peak=    3.263 closest distance to " CB  GLN A  58 " =    1.010
peak=    3.262 closest distance to " OD2 ASP A 298 " =    4.039
peak=    3.260 closest distance to " CA  GLU A 152 " =    0.863
peak=    3.258 closest distance to " O   HOH Z 111 " =    1.629
peak=    3.258 closest distance to " O   HOH Z 437 " =    1.416
peak=    3.258 closest distance to " CB  PRO A 163 " =    3.899
peak=    3.257 closest distance to " O   HOH Z 133 " =    1.069
peak=    3.256 closest distance to " CB  SER A 273 " =    0.913
peak=    3.250 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.249 closest distance to " CA  ASP A 191 " =    0.833
peak=    3.246 closest distance to " CZ2 TRP A 274 " =    1.637
peak=    3.244 closest distance to " NZ  LYS A  76 " =    1.125
peak=    3.244 closest distance to " O   HOH Z   3 " =    1.724
peak=    3.238 closest distance to " CA  ALA A  84 " =    1.109
peak=    3.237 closest distance to " O   HOH Z  11 " =    1.234
peak=    3.237 closest distance to " CE1 HIS A 108 " =    1.175
peak=    3.237 closest distance to " O  BHOH Z  74 " =    1.434
peak=    3.237 closest distance to " CA  ASN A 215 " =    1.110
peak=    3.234 closest distance to " O   HOH Z 214 " =    2.335
peak=    3.232 closest distance to " O   HOH Z  39 " =    1.135
peak=    3.232 closest distance to " O   GLY A  57 " =    0.969
peak=    3.227 closest distance to " CB  ASN A 215 " =    1.106
peak=    3.227 closest distance to " O   HOH Z 118 " =    1.142
peak=    3.227 closest distance to " CA  VAL A  41 " =    0.911
peak=    3.211 closest distance to " CB  GLN A 103 " =    0.845
peak=    3.211 closest distance to " O   HOH Z 257 " =    2.054
peak=    3.209 closest distance to " OG BSER A 134 " =    3.452
peak=    3.208 closest distance to " N   GLU A 175 " =    1.442
peak=    3.205 closest distance to " OG BSER A 258 " =    3.003
peak=    3.205 closest distance to " CA  VAL A 126 " =    1.119
peak=    3.204 closest distance to " N   CYS A 260 " =    0.749
peak=    3.201 closest distance to " O   HOH Z 155 " =    1.589
peak=    3.198 closest distance to " CB  ASN A  39 " =    0.834
peak=    3.197 closest distance to " O   HOH Z 151 " =    1.857
peak=    3.196 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.194 closest distance to " O   ASP A 124 " =    1.461
peak=    3.192 closest distance to " NH2AARG A 190 " =    1.457
peak=    3.192 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.191 closest distance to " ND2 ASN A 209 " =    1.601
peak=    3.190 closest distance to " NH1BARG A 145 " =    1.128
peak=    3.186 closest distance to " OD1 ASP A 238 " =    0.988
peak=    3.180 closest distance to " O   HOH Z 162 " =    1.732
peak=    3.172 closest distance to " O   HOH Z  61 " =    1.489
peak=    3.169 closest distance to " O   HOH Z 358 " =    2.072
peak=    3.167 closest distance to " CG1 ILE A 120 " =    0.904
peak=    3.163 closest distance to " CB  GLN A 194 " =    0.930
peak=    3.161 closest distance to " CB  TRP A 266 " =    1.114
peak=    3.157 closest distance to " CB  THR A  31 " =    1.800
peak=    3.156 closest distance to " CG2 VAL A 268 " =    0.923
peak=    3.155 closest distance to " O   HOH Z 148 " =    3.132
peak=    3.154 closest distance to " O   ALA A   1 " =    1.612
peak=    3.152 closest distance to " O   HOH Z   4 " =    1.836
peak=    3.144 closest distance to " O   THR A 251 " =    1.256
peak=    3.143 closest distance to " OG  SER A 245 " =    1.410
peak=    3.143 closest distance to " CB  PRO A 243 " =    1.198
peak=    3.141 closest distance to " CB  ARG A 102 " =    0.758
peak=    3.141 closest distance to " CG1 VAL A 153 " =    1.075
peak=    3.133 closest distance to " NH1AARG A 145 " =    1.130
peak=    3.129 closest distance to " O   ALA A 165 " =    1.353
peak=    3.129 closest distance to " O   HOH Z 197 " =    2.467
peak=    3.126 closest distance to " OD1 ASN A  45 " =    1.228
peak=    3.124 closest distance to " O   HOH Z 412 " =    3.374
peak=    3.124 closest distance to " O   SER A 164 " =    1.073
peak=    3.105 closest distance to " O   HOH Z 195 " =    2.123
peak=    3.101 closest distance to " O   HOH Z 211 " =    2.527
peak=    3.100 closest distance to " N   ASP A 162 " =    1.430
peak=    3.100 closest distance to " CA  ASP A 124 " =    0.715
peak=    3.094 closest distance to " N   TYR A  15 " =    0.868
peak=    3.093 closest distance to " O   HOH Z   1 " =    2.398
peak=    3.088 closest distance to " O   HOH Z  20 " =    1.188
peak=    3.087 closest distance to " OD1 ASP A 286 " =    1.784
peak=    3.073 closest distance to " CD2 LEU A 297 " =    0.786
peak=    3.067 closest distance to " OH  TYR A 116 " =    1.078
peak=    3.058 closest distance to " O   HOH Z 264 " =    1.588
peak=    3.048 closest distance to " O   HOH Z  48 " =    1.782
peak=    3.002 closest distance to " OD2 ASP A 286 " =    2.957

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.589 - 5.778
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.761 - 5.778

peak=   -4.892 closest distance to " O   HOH Z 266 " =    4.273
peak=   -4.732 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.530 closest distance to " OXT GLY A 302 " =    2.947
peak=   -4.434 closest distance to " O   HOH Z  13 " =    1.607
peak=   -4.394 closest distance to " CG  LYS A 193 " =    2.345
peak=   -4.342 closest distance to " CG  MET A  93 " =    2.493
peak=   -4.263 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.045 closest distance to " O   PRO A 163 " =    1.972
peak=   -4.019 closest distance to " O   TRP A  92 " =    1.840
peak=   -4.001 closest distance to " OG BSER A 134 " =    1.364
peak=   -4.000 closest distance to " O   HOH Z  52 " =    1.654
peak=   -3.967 closest distance to " O   HOH Z 165 " =    1.883
peak=   -3.955 closest distance to " O   HOH Z 377 " =    1.946
peak=   -3.937 closest distance to " CA  VAL A  67 " =    2.923
peak=   -3.926 closest distance to " O   HOH Z 407 " =    3.087
peak=   -3.921 closest distance to " N   ALA A 248 " =    1.883
peak=   -3.904 closest distance to " O   HOH Z 418 " =    1.366
peak=   -3.897 closest distance to " C   THR A 279 " =    1.232
peak=   -3.874 closest distance to " O   HOH Z 234 " =    4.025
peak=   -3.862 closest distance to " CD2 LEU A 300 " =    2.870
peak=   -3.859 closest distance to " NH2 ARG A  66 " =    4.897
peak=   -3.859 closest distance to " CD2 LEU A 237 " =    2.559
peak=   -3.846 closest distance to " O   HOH Z  52 " =    0.917
peak=   -3.840 closest distance to " O   HOH Z 210 " =    0.761
peak=   -3.817 closest distance to " O   PRO A 198 " =    1.320
peak=   -3.809 closest distance to " CB  ALA A 161 " =    2.537
peak=   -3.801 closest distance to " O   HOH Z  71 " =    1.237
peak=   -3.797 closest distance to " O   ASN A 187 " =    1.429
peak=   -3.796 closest distance to " CD  ARG A 195 " =    5.044
peak=   -3.786 closest distance to " O   PHE A 218 " =    1.505
peak=   -3.785 closest distance to " OD2 ASP A 191 " =    1.472
peak=   -3.781 closest distance to " O   GLY A  80 " =    2.340
peak=   -3.771 closest distance to " ND2 ASN A  69 " =    1.633
peak=   -3.761 closest distance to " ND2 ASN A  45 " =    0.943
peak=   -3.752 closest distance to " CD  GLN A  58 " =    1.355
peak=   -3.752 closest distance to " OD2 ASP A  50 " =    1.294
peak=   -3.737 closest distance to " O   HOH Z  97 " =    1.229
peak=   -3.710 closest distance to " O   HOH Z 118 " =    3.265
peak=   -3.710 closest distance to " O   GLN A  11 " =    1.134
peak=   -3.708 closest distance to " O  BHOH Z 338 " =    1.484
peak=   -3.700 closest distance to " O   HOH Z 423 " =    2.399
peak=   -3.681 closest distance to " O   HOH Z 250 " =    1.423
peak=   -3.678 closest distance to " O   HOH Z 150 " =    2.296
peak=   -3.673 closest distance to " OD2 ASP A 171 " =    2.315
peak=   -3.666 closest distance to " N   GLY A 133 " =    1.798
peak=   -3.647 closest distance to " SG  CYS A 254 " =    3.228
peak=   -3.638 closest distance to " O   HOH Z 251 " =    1.318
peak=   -3.633 closest distance to " CD1 PHE A  59 " =    1.943
peak=   -3.604 closest distance to " O   HOH Z  11 " =    1.753
peak=   -3.600 closest distance to " O   ALA A 161 " =    1.445
peak=   -3.598 closest distance to " C   ALA A 158 " =    1.164
peak=   -3.596 closest distance to " CB  TYR A  15 " =    2.234
peak=   -3.589 closest distance to " O   HOH Z  11 " =    1.747
peak=   -3.589 closest distance to " N   SER A 276 " =    1.404
peak=   -3.580 closest distance to " O   HOH Z  92 " =    1.792
peak=   -3.576 closest distance to " O   HOH Z 424 " =    3.059
peak=   -3.549 closest distance to " O   HOH Z 384 " =    1.934
peak=   -3.544 closest distance to " O   HOH Z 384 " =    3.455
peak=   -3.543 closest distance to " O   HOH Z 197 " =    1.939
peak=   -3.542 closest distance to " O   ALA A  34 " =    2.426
peak=   -3.542 closest distance to " CG1AVAL A  41 " =    2.513
peak=   -3.536 closest distance to " O   VAL A 174 " =    1.833
peak=   -3.523 closest distance to " O   HOH Z  88 " =    4.319
peak=   -3.519 closest distance to " NH2 ARG A  79 " =    1.971
peak=   -3.519 closest distance to " O   HOH Z 166 " =    2.005
peak=   -3.515 closest distance to " ND2 ASN A  45 " =    1.361
peak=   -3.506 closest distance to " O   HOH Z 396 " =    1.926
peak=   -3.501 closest distance to " O   SER A 146 " =    0.829
peak=   -3.495 closest distance to " OG  SER A   3 " =    1.493
peak=   -3.494 closest distance to " CD2 TYR A  30 " =    2.876
peak=   -3.483 closest distance to " CZ  TYR A 169 " =    1.886
peak=   -3.467 closest distance to " CG  PRO A 243 " =    1.572
peak=   -3.459 closest distance to " OD1 ASP A 200 " =    1.240
peak=   -3.457 closest distance to " O   ALA A 160 " =    1.541
peak=   -3.453 closest distance to " CH2 TRP A 274 " =    1.165
peak=   -3.446 closest distance to " CB  PHE A 192 " =    1.958
peak=   -3.446 closest distance to " CB  ALA A 291 " =    2.300
peak=   -3.442 closest distance to " O   HOH Z 126 " =    1.840
peak=   -3.435 closest distance to " O   GLN A 194 " =    1.486
peak=   -3.430 closest distance to " OE2 GLU A   2 " =    1.717
peak=   -3.427 closest distance to " N   GLN A  58 " =    1.753
peak=   -3.423 closest distance to " O   THR A  52 " =    1.655
peak=   -3.417 closest distance to " CA  ASP A 298 " =    1.093
peak=   -3.414 closest distance to " OG  SER A  97 " =    2.053
peak=   -3.407 closest distance to " CH2 TRP A 179 " =    1.327
peak=   -3.404 closest distance to " O   HOH Z 422 " =    1.306
peak=   -3.395 closest distance to " O   HOH Z  38 " =    1.532
peak=   -3.395 closest distance to " O   SER A  26 " =    1.183
peak=   -3.392 closest distance to " CG2 VAL A 202 " =    2.209
peak=   -3.392 closest distance to " O   HOH Z 290 " =    0.867
peak=   -3.389 closest distance to " O   GLN A 205 " =    1.699
peak=   -3.383 closest distance to " O   HOH Z 191 " =    5.778
peak=   -3.370 closest distance to " CB  PHE A 208 " =    2.272
peak=   -3.368 closest distance to " CG  GLU A  53 " =    1.268
peak=   -3.366 closest distance to " ND2 ASN A  39 " =    1.242
peak=   -3.363 closest distance to " O   HOH Z 119 " =    2.025
peak=   -3.360 closest distance to " O   HOH Z 287 " =    2.187
peak=   -3.354 closest distance to " O   HOH Z 311 " =    3.263
peak=   -3.353 closest distance to " N   ASP A 286 " =    2.238
peak=   -3.350 closest distance to " O   HOH Z  52 " =    1.881
peak=   -3.350 closest distance to " O   HOH Z 353 " =    2.260
peak=   -3.347 closest distance to " N   ALA A 248 " =    2.275
peak=   -3.347 closest distance to " O   HOH Z 166 " =    1.497
peak=   -3.345 closest distance to " CD1 PHE A 130 " =    2.258
peak=   -3.343 closest distance to " CB  LEU A 167 " =    2.130
peak=   -3.343 closest distance to " OG BSER A  99 " =    1.035
peak=   -3.338 closest distance to " O   ASN A  45 " =    1.797
peak=   -3.336 closest distance to " O   HOH Z 109 " =    5.674
peak=   -3.335 closest distance to " O   HOH Z  15 " =    1.543
peak=   -3.335 closest distance to " ND2 ASN A 187 " =    1.450
peak=   -3.333 closest distance to " CD1 LEU A 228 " =    2.125
peak=   -3.320 closest distance to " CD1 TYR A 247 " =    2.325
peak=   -3.319 closest distance to " CG  ARG A 219 " =    2.337
peak=   -3.318 closest distance to " O   HOH Z 265 " =    1.970
peak=   -3.317 closest distance to " O   HOH Z 222 " =    1.233
peak=   -3.317 closest distance to " O   PRO A 198 " =    1.307
peak=   -3.315 closest distance to " O   HOH Z 435 " =    2.481
peak=   -3.307 closest distance to " O   HOH Z 401 " =    0.856
peak=   -3.300 closest distance to " C   GLY A  91 " =    1.232
peak=   -3.295 closest distance to " C   ALA A 242 " =    1.837
peak=   -3.288 closest distance to " CZ2 TRP A  92 " =    2.558
peak=   -3.282 closest distance to " O   VAL A 197 " =    1.137
peak=   -3.279 closest distance to " O   GLY A 196 " =    0.941
peak=   -3.278 closest distance to " O   HOH Z 198 " =    1.751
peak=   -3.272 closest distance to " O   ALA A  51 " =    1.483
peak=   -3.270 closest distance to " O   HOH Z 172 " =    5.054
peak=   -3.269 closest distance to " O   HOH Z 380 " =    4.578
peak=   -3.265 closest distance to " CG  ASP A 132 " =    2.233
peak=   -3.264 closest distance to " O   LEU A 167 " =    1.563
peak=   -3.264 closest distance to " O   HOH Z 360 " =    2.534
peak=   -3.262 closest distance to " NE2 GLN A 223 " =    1.284
peak=   -3.260 closest distance to " O   HOH Z 150 " =    1.636
peak=   -3.258 closest distance to " O   HOH Z 193 " =    1.725
peak=   -3.255 closest distance to " CB  ALA A 244 " =    1.985
peak=   -3.253 closest distance to " N   ALA A 226 " =    1.859
peak=   -3.253 closest distance to " CD1 TRP A 179 " =    1.220
peak=   -3.251 closest distance to " CD2 TYR A 293 " =    2.027
peak=   -3.250 closest distance to " O   HOH Z 351 " =    1.526
peak=   -3.245 closest distance to " C   PHE A 218 " =    1.390
peak=   -3.244 closest distance to " O   HOH Z 100 " =    0.915
peak=   -3.241 closest distance to " O   HOH Z   6 " =    1.838
peak=   -3.237 closest distance to " O   HOH Z 369 " =    2.149
peak=   -3.234 closest distance to " O   VAL A  67 " =    2.698
peak=   -3.228 closest distance to " NH2 ARG A  66 " =    1.714
peak=   -3.227 closest distance to " O   HOH Z 377 " =    1.350
peak=   -3.227 closest distance to " O   ARG A  56 " =    1.452
peak=   -3.224 closest distance to " O   MET A  40 " =    2.617
peak=   -3.221 closest distance to " O   HOH Z 202 " =    1.646
peak=   -3.220 closest distance to " O   LEU A 143 " =    1.479
peak=   -3.219 closest distance to " O   ALA A 256 " =    1.399
peak=   -3.218 closest distance to " OD1 ASP A 191 " =    1.556
peak=   -3.216 closest distance to " C   PRO A  90 " =    1.552
peak=   -3.210 closest distance to " O   HOH Z 427 " =    1.491
peak=   -3.209 closest distance to " O   HOH Z  41 " =    2.159
peak=   -3.209 closest distance to " SG ACYS A 201 " =    2.247
peak=   -3.206 closest distance to " N   ALA A  43 " =    2.524
peak=   -3.204 closest distance to " CG1 VAL A 112 " =    2.540
peak=   -3.204 closest distance to " CG  GLU A 277 " =    1.316
peak=   -3.204 closest distance to " OG  SER A  62 " =    1.375
peak=   -3.203 closest distance to " O   HOH Z 411 " =    3.428
peak=   -3.199 closest distance to " NH2AARG A 275 " =    4.717
peak=   -3.198 closest distance to " O   ALA A  10 " =    1.656
peak=   -3.197 closest distance to " N   VAL A 189 " =    1.666
peak=   -3.193 closest distance to " OG ASER A 134 " =    1.175
peak=   -3.174 closest distance to " CG  ASP A  50 " =    2.493
peak=   -3.170 closest distance to " O   LEU A 222 " =    1.354
peak=   -3.168 closest distance to " OXT GLY A 302 " =    3.112
peak=   -3.168 closest distance to " O   HOH Z  56 " =    1.490
peak=   -3.166 closest distance to " O   HOH Z 174 " =    4.253
peak=   -3.164 closest distance to " N   THR A  52 " =    1.681
peak=   -3.161 closest distance to " CG  GLU A 152 " =    1.139
peak=   -3.159 closest distance to " CG1BVAL A  72 " =    2.415
peak=   -3.158 closest distance to " CD  PRO A 198 " =    1.187
peak=   -3.156 closest distance to " OG BSER A 134 " =    1.683
peak=   -3.154 closest distance to " O   SER A 210 " =    1.928
peak=   -3.142 closest distance to " NE2 GLN A  88 " =    1.928
peak=   -3.140 closest distance to " CD  ARG A 139 " =    1.525
peak=   -3.138 closest distance to " O   SER A 135 " =    1.545
peak=   -3.133 closest distance to " O   HOH Z 392 " =    1.608
peak=   -3.133 closest distance to " O   THR A 182 " =    1.164
peak=   -3.125 closest distance to " O   HOH Z 111 " =    3.272
peak=   -3.122 closest distance to " NE2 GLN A  88 " =    1.020
peak=   -3.119 closest distance to " CG1AVAL A  72 " =    1.928
peak=   -3.110 closest distance to " O   ALA A 161 " =    2.665
peak=   -3.094 closest distance to " O   HOH Z 397 " =    1.143
peak=   -3.093 closest distance to " CA  GLY A 241 " =    2.284
peak=   -3.078 closest distance to " C   SER A 271 " =    1.224
peak=   -3.078 closest distance to " O   HOH Z  93 " =    1.343
peak=   -3.069 closest distance to " O   ARG A 219 " =    1.759
peak=   -3.064 closest distance to " CE  MET A 105 " =    1.977
peak=   -3.054 closest distance to " NE  ARG A 259 " =    0.986
peak=   -3.049 closest distance to " CB  CYS A 254 " =    2.576
peak=   -3.019 closest distance to " O   HOH Z 109 " =    3.439

================= 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    :  0.4614 0.4610   6.264541e+00   6.261746e+00
   1_bss:  0.4543 0.4526   6.258167e+00   6.248367e+00
   1_xyz:  0.3441 0.3687   6.070723e+00   6.111940e+00
   1_adp:  0.3081 0.3756   6.012527e+00   6.135732e+00
   1_occ:  0.3078 0.3759   6.012159e+00   6.135786e+00
   2_bss:  0.3061 0.3729   6.009380e+00   6.135222e+00
   2_xyz:  0.2331 0.2842   5.765162e+00   5.937317e+00
   2_adp:  0.2128 0.2682   5.699563e+00   5.883623e+00
   2_occ:  0.2125 0.2680   5.698519e+00   5.883078e+00
   3_bss:  0.2124 0.2670   5.696762e+00   5.879098e+00
   3_xyz:  0.1612 0.2121   5.458653e+00   5.675332e+00
   3_adp:  0.1422 0.1940   5.348586e+00   5.574978e+00
   3_occ:  0.1421 0.1940   5.348464e+00   5.575105e+00
   4_bss:  0.1423 0.1937   5.349896e+00   5.572737e+00
   4_xyz:  0.1270 0.1775   5.258552e+00   5.490996e+00
   4_adp:  0.1235 0.1719   5.228018e+00   5.455442e+00
   4_occ:  0.1234 0.1720   5.227597e+00   5.455416e+00
   5_bss:  0.1234 0.1720   5.227729e+00   5.455431e+00
   5_xyz:  0.1193 0.1665   5.198407e+00   5.425019e+00
   5_adp:  0.1180 0.1659   5.190162e+00   5.419636e+00
   5_occ:  0.1180 0.1659   5.189967e+00   5.419797e+00
   5_bss:  0.1180 0.1658   5.190008e+00   5.419411e+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:  0.300  20.000  -1.044   1.616   1.259   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -1.044   1.616   1.259   0.000   0.000   0.000
   1_adp:  0.300  20.000  -1.044   1.616   1.259   0.000   0.000   0.000
   1_occ:  0.300  20.000  -1.044   1.616   1.259   0.000   0.000   0.000
   2_bss:  0.326  50.001  -1.779   0.594   0.123   0.000   0.000   0.000
   2_xyz:  0.326  50.001  -1.779   0.594   0.123   0.000   0.000   0.000
   2_adp:  0.326  50.001  -1.779   0.594   0.123   0.000   0.000   0.000
   2_occ:  0.326  50.001  -1.779   0.594   0.123   0.000   0.000   0.000
   3_bss:  0.317  40.404  -2.029  -0.185  -0.642  -0.000  -0.000  -0.000
   3_xyz:  0.317  40.404  -2.029  -0.185  -0.642  -0.000  -0.000  -0.000
   3_adp:  0.317  40.404  -2.029  -0.185  -0.642  -0.000  -0.000  -0.000
   3_occ:  0.317  40.404  -2.029  -0.185  -0.642  -0.000  -0.000  -0.000
   4_bss:  0.320  47.057  -2.850  -1.245  -1.561  -0.000  -0.000  -0.000
   4_xyz:  0.320  47.057  -2.850  -1.245  -1.561  -0.000  -0.000  -0.000
   4_adp:  0.320  47.057  -2.850  -1.245  -1.561  -0.000  -0.000  -0.000
   4_occ:  0.320  47.057  -2.850  -1.245  -1.561  -0.000  -0.000  -0.000
   5_bss:  0.321  45.036  -2.930  -1.446  -1.629  -0.000  -0.000  -0.000
   5_xyz:  0.321  45.036  -2.930  -1.446  -1.629  -0.000  -0.000  -0.000
   5_adp:  0.321  45.036  -2.930  -1.446  -1.629  -0.000  -0.000  -0.000
   5_occ:  0.321  45.036  -2.930  -1.446  -1.629  -0.000  -0.000  -0.000
   5_bss:  0.321  44.988  -2.779  -1.392  -1.507  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.789 0.4212  0.5672    67016.466
   1_bss:  56.635 0.4342  0.5985    63207.368
   1_xyz:  39.167 0.6527  0.8768    36443.135
   1_adp:  41.115 0.6283  0.8580    39043.353
   1_occ:  41.165 0.6277  0.8560    39073.698
   2_bss:  40.939 0.6303  0.8333    38651.754
   2_xyz:  30.328 0.7517  0.9645    21684.375
   2_adp:  27.662 0.7822  0.9809    19104.034
   2_occ:  27.650 0.7823  0.9807    19066.511
   3_bss:  27.505 0.7837  0.9605    18839.898
   3_xyz:  20.861 0.8523  1.0132    11577.352
   3_adp:  18.277 0.8776  1.0172     9436.629
   3_occ:  18.282 0.8776  1.0172     9439.124
   4_bss:  18.216 0.8781  0.9836     9382.796
   4_xyz:  16.412 0.8943  0.9904     7829.482
   4_adp:  15.558 0.9021  0.9875     7339.397
   4_occ:  15.552 0.9022  0.9875     7336.921
   5_bss:  15.553 0.9022  0.9834     7337.044
   5_xyz:  14.874 0.9079  0.9849     6861.996
   5_adp:  14.690 0.9097  0.9797     6817.701
   5_occ:  14.690 0.9097  0.9796     6817.357
   5_bss:  14.659 0.9100  0.9821     6795.970
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.1258e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.1258e-01
   1_xyz:   1.431  0.011  0.084 15.670  0.006  4.107   1.1307e-01
   1_adp:   1.431  0.011  0.084 15.670  0.006  4.107   1.1307e-01
   1_occ:   1.431  0.011  0.084 15.670  0.006  4.107   1.1307e-01
   2_bss:   1.431  0.011  0.084 15.670  0.006  4.107   1.1307e-01
   2_xyz:   1.246  0.008  0.079 14.683  0.005  4.108   8.0544e-02
   2_adp:   1.246  0.008  0.079 14.683  0.005  4.108   8.0544e-02
   2_occ:   1.246  0.008  0.079 14.683  0.005  4.108   8.0544e-02
   3_bss:   1.246  0.008  0.079 14.683  0.005  4.108   8.0544e-02
   3_xyz:   1.078  0.007  0.070 14.602  0.004  4.112   6.5480e-02
   3_adp:   1.078  0.007  0.070 14.602  0.004  4.112   6.5480e-02
   3_occ:   1.078  0.007  0.070 14.602  0.004  4.112   6.5480e-02
   4_bss:   1.078  0.007  0.070 14.602  0.004  4.112   6.5480e-02
   4_xyz:   0.976  0.006  0.067 14.462  0.004  4.107   5.4596e-02
   4_adp:   0.976  0.006  0.067 14.462  0.004  4.107   5.4596e-02
   4_occ:   0.976  0.006  0.067 14.462  0.004  4.107   5.4596e-02
   5_bss:   0.976  0.006  0.067 14.462  0.004  4.107   5.4596e-02
   5_xyz:   0.891  0.005  0.064 14.223  0.003  4.108   4.7556e-02
   5_adp:   0.891  0.005  0.064 14.223  0.003  4.108   4.7556e-02
   5_occ:   0.891  0.005  0.064 14.223  0.003  4.108   4.7556e-02
   5_bss:   0.891  0.005  0.064 14.223  0.003  4.108   4.7556e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.328   2.4140e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.328   2.4140e-01
   1_xyz:   8.846  0.058  0.335 86.578  0.036  1.980   9.4628e-02
   1_adp:   8.846  0.058  0.335 86.578  0.036  1.980   9.4628e-02
   1_occ:   8.846  0.058  0.335 86.578  0.036  1.980   9.4628e-02
   2_bss:   8.846  0.058  0.335 86.578  0.036  1.980   9.4628e-02
   2_xyz:   7.396  0.051  0.320 80.700  0.046  2.183   1.0296e-01
   2_adp:   7.396  0.051  0.320 80.700  0.046  2.183   1.0296e-01
   2_occ:   7.396  0.051  0.320 80.700  0.046  2.183   1.0296e-01
   3_bss:   7.396  0.051  0.320 80.700  0.046  2.183   1.0296e-01
   3_xyz:   7.318  0.058  0.243 79.034  0.045  2.236   6.1885e-02
   3_adp:   7.318  0.058  0.243 79.034  0.045  2.236   6.1885e-02
   3_occ:   7.318  0.058  0.243 79.034  0.045  2.236   6.1885e-02
   4_bss:   7.318  0.058  0.243 79.034  0.045  2.236   6.1885e-02
   4_xyz:   6.656  0.039  0.225 80.883  0.034  2.360   3.5519e-02
   4_adp:   6.656  0.039  0.225 80.883  0.034  2.360   3.5519e-02
   4_occ:   6.656  0.039  0.225 80.883  0.034  2.360   3.5519e-02
   5_bss:   6.656  0.039  0.225 80.883  0.034  2.360   3.5519e-02
   5_xyz:   6.638  0.040  0.195 82.630  0.031  2.413   2.9041e-02
   5_adp:   6.638  0.040  0.195 82.630  0.031  2.413   2.9041e-02
   5_occ:   6.638  0.040  0.195 82.630  0.031  2.413   2.9041e-02
   5_bss:   6.638  0.040  0.195 82.630  0.031  2.413   2.9041e-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: 112.19   0.00  20.11  84.43   0.00  16.28 112.19   0.48  40.99
   1_occ: 112.19   0.00  20.11  84.43   0.00  16.28 112.19   0.48  40.99
   2_bss: 112.19   0.00  20.11  84.43   0.00  16.28 112.19   0.48  40.99
   2_xyz: 112.19   0.00  20.11  84.43   0.00  16.28 112.19   0.48  40.99
   2_adp: 131.39   0.00  19.30 131.39   0.00  15.20 106.43   4.68  41.63
   2_occ: 131.39   0.00  19.30 131.39   0.00  15.20 106.43   4.68  41.63
   3_bss: 131.39   0.00  19.30 131.39   0.00  15.20 106.43   4.68  41.63
   3_xyz: 131.39   0.00  19.30 131.39   0.00  15.20 106.43   4.68  41.63
   3_adp: 102.48   0.00  18.57  93.54   0.00  13.85 102.48   5.87  44.31
   3_occ: 102.48   0.00  18.57  93.54   0.00  13.85 102.48   5.87  44.31
   4_bss: 102.48   0.00  18.57  93.54   0.00  13.85 102.48   5.87  44.31
   4_xyz: 102.48   0.00  18.57  93.54   0.00  13.85 102.48   5.87  44.31
   4_adp:  97.30   1.26  17.84  96.21   1.26  13.30  97.30   6.35  42.56
   4_occ:  97.30   1.26  17.84  96.21   1.26  13.30  97.30   6.35  42.56
   5_bss:  97.30   1.26  17.84  96.21   1.26  13.30  97.30   6.35  42.56
   5_xyz:  97.30   1.26  17.84  96.21   1.26  13.30  97.30   6.35  42.56
   5_adp: 100.74   1.35  17.44 100.74   1.35  13.02  91.14   5.26  41.46
   5_occ: 100.74   1.35  17.44 100.74   1.35  13.02  91.14   5.26  41.46
   5_bss: 100.70   1.30  17.39 100.70   1.30  12.98  91.09   5.21  41.42
------------------------------------------------------------------------
 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:    2.973    0.008    0.328
   1_adp:    2.973    0.008    0.328
   1_occ:    2.973    0.008    0.328
   2_bss:    2.973    0.008    0.328
   2_xyz:    1.954    0.037    0.530
   2_adp:    1.954    0.037    0.530
   2_occ:    1.954    0.037    0.530
   3_bss:    1.954    0.037    0.530
   3_xyz:    1.870    0.042    0.654
   3_adp:    1.870    0.042    0.654
   3_occ:    1.870    0.042    0.654
   4_bss:    1.870    0.042    0.654
   4_xyz:    1.747    0.039    0.691
   4_adp:    1.747    0.039    0.691
   4_occ:    1.747    0.039    0.691
   5_bss:    1.747    0.039    0.691
   5_xyz:    1.725    0.055    0.716
   5_adp:    1.725    0.055    0.716
   5_occ:    1.725    0.055    0.716
   5_bss:    1.725    0.055    0.716
------------------------------------------------------------------------

CPU time actual refinement: 352.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/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_210/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_210/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.23 
  Macro-tasks:
    bulk solvent and scale       = 43.69  
    individual site refinement   = 144.08 
    weights calculation          = 29.76  
    collect and process          = 6.40   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 224.02 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 113.93 
    alpha_beta                      = 8.27   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.88 
    fmodel                         = 7.20   
    r_factors                      = 0.26   
    phase_errors                   = 10.26  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 265.65 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.986 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    654 calls, 113.64 s
gradients_fft:          599 calls, 108.56 s

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

# Date 2008-01-16 Time 04:16:23 PST -0800 (1200485783.73 s)
Start R-work = 0.4614, R-free = 0.4610 (no bulk solvent and anisotropic scale)
Final R-work = 0.1417, R-free = 0.1853 (no bulk solvent and anisotropic scale)

Start R-work = 0.4543, R-free = 0.4526
Final R-work = 0.1180, R-free = 0.1658