# Date 2008-01-16 Time 06:47:53 PST -0800 (1200494873.92 s)
#phil __OFF__

Command line arguments: "../1289.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30289
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1289

-------------------------------------------------------------------------------
  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: (72.0062, 47.3993, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97133
Completeness in resolution range: 0.926413
Completeness with d_max=infinity: 0.923704

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9713

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: (72.0062, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97133
Completeness in resolution range: 0.926413
Completeness with d_max=infinity: 0.923704

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2197 [2218/2248]  1999   219   9.9%
  bin  2:  4.2197 -  3.3612 [2124/2147]  1911   213  10.0%
  bin  3:  3.3612 -  2.9398 [2105/2127]  1887   218  10.4%
  bin  4:  2.9398 -  2.6726 [2084/2103]  1887   197   9.5%
  bin  5:  2.6726 -  2.4819 [2069/2098]  1857   212  10.2%
  bin  6:  2.4819 -  2.3361 [2064/2106]  1860   204   9.9%
  bin  7:  2.3361 -  2.2195 [2048/2083]  1838   210  10.3%
  bin  8:  2.2195 -  2.1232 [2028/2066]  1830   198   9.8%
  bin  9:  2.1232 -  2.0416 [2049/2098]  1843   206  10.1%
  bin 10:  2.0416 -  1.9713 [ 800/2069]   718    82  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.54 -     2.21: 13
        2.21 -     2.88: 1268
        2.88 -     3.56: 4426
        3.56 -     4.23: 9170
        4.23 -     4.90: 13249
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.541 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.857 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.988 3.120 -x+1/2,-y+1,z-1/2
  " OG1 THR A 246 " - " O   HOH Z 202 "  1.996 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28121 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_1289/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/model_refine_001.geo

CPU time processing inputs: 9.16


============================ 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 = 72.00625 47.3993 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4279   r_free= 0.4273   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.226974                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7071 0.99   1435  161 0.3334 0.3448      6.4623      6.4664|
|  2:  4.7071 -  3.7547 0.99   1391  152 0.3491 0.3352      6.6958      6.7126|
|  3:  3.7547 -  3.2856 0.99   1357  154 0.3891 0.3774      6.5726      6.5492|
|  4:  3.2856 -  2.9876 0.99   1357  148 0.4123 0.3844      6.4262      6.4094|
|  5:  2.9876 -  2.7749 0.99   1332  145 0.4348 0.4518      6.2859      6.3335|
|  6:  2.7749 -  2.6121 0.98   1336  153 0.4729 0.4635      6.2294       6.181|
|  7:  2.6121 -  2.4819 0.99   1333  146 0.4676 0.4232      6.2014      6.1395|
|  8:  2.4819 -  2.3743 0.99   1316  150 0.4728 0.4942      6.1178      6.1869|
|  9:  2.3743 -  2.2832 0.98   1324  150 0.4915 0.4559      6.1088      6.0665|
| 10:  2.2832 -  2.2047 0.98   1311  147 0.4863 0.5669      6.0471      6.1022|
| 11:  2.2047 -  2.1359 0.98   1334  139 0.4999 0.5495      6.0185      6.0322|
| 12:  2.1359 -  2.0750 0.99   1298  147 0.4984 0.5375      5.9352      5.9772|
| 13:  2.0750 -  2.0205 0.87   1158  138 0.4914 0.4670      5.8527      5.8141|
| 14:  2.0205 -  1.9713 0.25    348   29 0.5232 0.4742      5.7944        5.79|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7071  1435   161  0.75  29.44   0.84     0.78      53441.71|
|  2:  4.7071 -  3.7547  1391   152  0.76  29.48   0.94     0.85      73955.04|
|  3:  3.7547 -  3.2856  1357   154  0.68  36.91   0.93     0.83      80893.20|
|  4:  3.2856 -  2.9876  1357   148  0.60  43.75   0.92     0.78      76357.97|
|  5:  2.9876 -  2.7749  1332   145  0.51  50.79   0.91     0.69      65698.96|
|  6:  2.7749 -  2.6121  1336   153  0.48  53.40   0.91     0.67      58891.99|
|  7:  2.6121 -  2.4819  1333   146  0.49  52.81   0.93     0.65      51927.31|
|  8:  2.4819 -  2.3743  1316   150  0.47  54.78   0.91     0.66      49952.38|
|  9:  2.3743 -  2.2832  1324   150  0.43  57.94   0.95     0.61      47252.98|
| 10:  2.2832 -  2.2047  1311   147  0.35  63.43   0.94     0.52      50178.19|
| 11:  2.2047 -  2.1359  1334   139  0.29  68.07   0.94     0.44      48836.76|
| 12:  2.1359 -  2.0750  1298   147  0.28  69.37   0.93     0.44      46110.75|
| 13:  2.0750 -  2.0205  1158   138  0.33  65.02   0.94     0.52      35877.02|
| 14:  2.0205 -  1.9713   348    29  0.42  58.29   0.90     0.61      24815.67|
|alpha:            min =        0.44 max =            0.85 mean =         0.65|
|beta:             min =    24815.67 max =        80893.20 mean =     56586.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.96 mean =        51.64|
|phase err.(test): min =        0.00 max =           90.00 mean =        51.60|
|-----------------------------------------------------------------------------|

============================== 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 = 13.721479             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.129   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.090713              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.185   (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 |  1.541 -  1.877:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.877 -  2.213:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.213 -  2.549:       40 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.549 -  2.885:     1228 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.885 -  3.221:     1906 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.221 -  3.556:     2520 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.556 -  3.892:     4650 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.892 -  4.228:     4520 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.228 -  4.564:     6067 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7182 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.541 |       0.286 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4279   r_free= 0.4273   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.226974                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4193   r_free= 0.4185   ksol= 0.29   Bsol= 26.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,-0.20,0.36,-0.00,0.00,0.00); trace/3= 0.86                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.219926                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.071169             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.446   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.023176              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.722   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4193      final r-factor (work) = 0.2549          |
| start r-factor (free) = 0.4185      final r-factor (free) = 0.2897          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5927 = 11.07 * 0.50 * 6.2183 + 1.00 * 0.1707                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.4902 = 11.07 * 0.50 * 6.0291 + 1.00 * 0.1158                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2549      final r-factor (work) = 0.2318          |
| start r-factor (free) = 0.2897      final r-factor (free) = 0.2929          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1752 = 1.02 * 1.00 * 6.0291 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9140 = 1.02 * 1.00 * 5.7655 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.79   18.37    None  None   None       |
|    all(noH): 2823   0      0.00    99.79   18.37    None  None   None       |
|    Sol.    : 438    0      2.70    99.79   42.95    None  None   None       |
|    Mac.    : 2385   0      0.00    81.87   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 -   9.979:  965   |   5:    49.895 -  59.874:   89        |
|      1:     9.979 -  19.958: 1053   |   6:    59.874 -  69.853:   58        |
|      2:    19.958 -  29.937:  331   |   7:    69.853 -  79.832:   23        |
|      3:    29.937 -  39.916:  172   |   8:    79.832 -  89.812:   12        |
|      4:    39.916 -  49.895:  117   |   9:    89.812 -  99.791:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2318 r_free = 0.2929             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2314 r_free = 0.2930             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2314   r_free= 0.2930   ksol= 0.29   Bsol= 26.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,-0.20,0.36,-0.00,0.00,0.00); trace/3= 0.86                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.770133                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2283   r_free= 0.2892   ksol= 0.32   Bsol= 55.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-1.61,-1.22,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.766954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.997045              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.837   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351437              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.174  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2283      final r-factor (work) = 0.1650          |
| start r-factor (free) = 0.2892      final r-factor (free) = 0.2143          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5494 = 5.00 * 0.50 * 5.7769 + 1.00 * 0.1158                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1886 = 5.00 * 0.50 * 5.6512 + 1.00 * 0.0691                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1650      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.2143      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0008 = 0.35 * 1.00 * 5.6512 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9212 = 0.35 * 1.00 * 5.4386 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    95.85   17.99    None  None   None       |
|    all(noH): 2823   0      1.69    95.85   17.99    None  None   None       |
|    Sol.    : 438    0      5.92    95.85   42.63    None  None   None       |
|    Mac.    : 2385   0      1.69    83.09   13.47    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:     1.695 -  11.110: 1185   |   5:    48.772 -  58.188:   97        |
|      1:    11.110 -  20.526:  975   |   6:    58.188 -  67.603:   58        |
|      2:    20.526 -  29.941:  218   |   7:    67.603 -  77.019:   19        |
|      3:    29.941 -  39.357:  127   |   8:    77.019 -  86.434:   18        |
|      4:    39.357 -  48.772:  123   |   9:    86.434 -  95.849:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1505 r_free = 0.1989             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1503 r_free = 0.1987             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.1987   ksol= 0.32   Bsol= 55.55   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-1.61,-1.22,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.399577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.1979   ksol= 0.33   Bsol= 59.14   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.21,-1.92,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.399147                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.400608              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.293  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1503      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.1979      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6033 = 2.40 * 0.50 * 5.4434 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4739 = 2.40 * 0.50 * 5.3429 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5643 = 0.67 * 1.00 * 5.3429 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5070 = 0.67 * 1.00 * 5.2558 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    96.55   18.06    None  None   None       |
|    all(noH): 2823   0      1.26    96.55   18.06    None  None   None       |
|    Sol.    : 438    0      6.27    96.55   43.31    None  None   None       |
|    Mac.    : 2385   0      1.26    92.62   13.42    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:     1.257 -  10.786: 1124   |   5:    48.904 -  58.434:  113        |
|      1:    10.786 -  20.316: 1040   |   6:    58.434 -  67.963:   54        |
|      2:    20.316 -  29.845:  213   |   7:    67.963 -  77.492:   30        |
|      3:    29.845 -  39.375:  126   |   8:    77.492 -  87.022:   14        |
|      4:    39.375 -  48.904:  103   |   9:    87.022 -  96.551:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1248 r_free = 0.1706             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1248 r_free = 0.1705             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1705   ksol= 0.33   Bsol= 59.14   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.21,-1.92,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.243760                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1707   ksol= 0.33   Bsol= 60.37   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.45,-2.11,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.244778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.332745              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572641              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.542  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1707      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1926 = 2.33 * 0.50 * 5.2571 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1518 = 2.33 * 0.50 * 5.2183 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9985 = 0.57 * 1.00 * 5.2183 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9858 = 0.57 * 1.00 * 5.1963 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    97.95   17.82    None  None   None       |
|    all(noH): 2823   0      1.01    97.95   17.82    None  None   None       |
|    Sol.    : 438    0      5.94    97.15   42.52    None  None   None       |
|    Mac.    : 2385   0      1.01    97.95   13.28    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:     1.012 -  10.705: 1124   |   5:    49.479 -  59.173:  111        |
|      1:    10.705 -  20.399: 1050   |   6:    59.173 -  68.866:   43        |
|      2:    20.399 -  30.092:  222   |   7:    68.866 -  78.560:   31        |
|      3:    30.092 -  39.786:  129   |   8:    78.560 -  88.253:   10        |
|      4:    39.786 -  49.479:   97   |   9:    88.253 -  97.947:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1643             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1642             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1642   ksol= 0.33   Bsol= 60.37   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.45,-2.11,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.192856                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1642   ksol= 0.33   Bsol= 60.37   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.31,-2.00,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.192910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.832055              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.508  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.938776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.805  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0220 = 3.83 * 0.50 * 5.1965 + 1.00 * 0.0653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9934 = 3.83 * 0.50 * 5.1706 + 1.00 * 0.0863                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8641 = 0.94 * 1.00 * 5.1706 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8529 = 0.94 * 1.00 * 5.1585 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    103.26  17.63    None  None   None       |
|    all(noH): 2823   0      0.57    103.26  17.63    None  None   None       |
|    Sol.    : 438    0      6.22    99.38   42.06    None  None   None       |
|    Mac.    : 2385   0      0.57    103.26  13.14    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:     0.571 -  10.840: 1213   |   5:    51.916 -  62.185:   98        |
|      1:    10.840 -  21.109:  998   |   6:    62.185 -  72.454:   38        |
|      2:    21.109 -  31.378:  205   |   7:    72.454 -  82.723:   17        |
|      3:    31.378 -  41.647:  132   |   8:    82.723 -  92.991:    8        |
|      4:    41.647 -  51.916:  109   |   9:    92.991 - 103.260:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1618             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1094 r_free = 0.1618             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1618   ksol= 0.33   Bsol= 60.37   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.31,-2.00,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.157426                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7071 0.99   1435  161 0.0925 0.1300      5.3458      5.5579|
|  2:  4.7071 -  3.7547 0.99   1391  152 0.0799 0.1032      5.3872      5.6113|
|  3:  3.7547 -  3.2856 0.99   1357  154 0.1015 0.1659      5.4395       5.879|
|  4:  3.2856 -  2.9876 0.99   1357  148 0.1233 0.1556       5.458      5.5958|
|  5:  2.9876 -  2.7749 0.99   1332  145 0.1315 0.1818      5.3346      5.5503|
|  6:  2.7749 -  2.6121 0.98   1336  153 0.1263 0.1904      5.2318      5.4773|
|  7:  2.6121 -  2.4819 0.99   1333  146 0.1227 0.1737      5.1741      5.4078|
|  8:  2.4819 -  2.3743 0.99   1316  150 0.1111 0.1714      5.0446      5.2956|
|  9:  2.3743 -  2.2832 0.98   1324  150 0.1151 0.1983       5.036      5.3589|
| 10:  2.2832 -  2.2047 0.98   1311  147 0.1108 0.1677      4.9745      5.2163|
| 11:  2.2047 -  2.1359 0.98   1334  139 0.1154 0.1943      4.9651      5.3257|
| 12:  2.1359 -  2.0750 0.99   1298  147 0.1096 0.1830      4.8925       5.147|
| 13:  2.0750 -  2.0205 0.87   1158  138 0.1140 0.1750      4.7996      5.0434|
| 14:  2.0205 -  1.9713 0.25    348   29 0.1078 0.1665      4.6568      4.9113|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7071  1435   161  0.94   8.64   0.97     0.94       6871.67|
|  2:  4.7071 -  3.7547  1391   152  0.95   7.87   1.00     0.99       8579.10|
|  3:  3.7547 -  3.2856  1357   154  0.93  11.22   1.02     1.02      10021.36|
|  4:  3.2856 -  2.9876  1357   148  0.91  14.87   1.00     0.97      10909.01|
|  5:  2.9876 -  2.7749  1332   145  0.89  16.66   0.99     0.97       8908.64|
|  6:  2.7749 -  2.6121  1336   153  0.89  17.00   0.98     0.95       7590.38|
|  7:  2.6121 -  2.4819  1333   146  0.90  16.01   0.99     0.96       6597.76|
|  8:  2.4819 -  2.3743  1316   150  0.90  15.94   0.98     0.95       5442.53|
|  9:  2.3743 -  2.2832  1324   150  0.90  16.59   0.99     0.95       5216.86|
| 10:  2.2832 -  2.2047  1311   147  0.90  16.00   0.97     0.93       4676.71|
| 11:  2.2047 -  2.1359  1334   139  0.89  17.34   0.98     0.94       4820.18|
| 12:  2.1359 -  2.0750  1298   147  0.90  16.74   0.99     0.99       4367.48|
| 13:  2.0750 -  2.0205  1158   138  0.90  16.88   0.98     0.96       3557.36|
| 14:  2.0205 -  1.9713   348    29  0.89  16.78   0.96     0.93       2708.64|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2708.64 max =        10909.01 mean =      6713.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.70|
|phase err.(test): min =        0.00 max =           89.62 mean =        14.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1617   ksol= 0.33   Bsol= 60.35   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.10,-1.78,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.157544                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1617   ksol= 0.33   Bsol= 60.35   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.10,-1.78,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.157544                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7071 0.99   1435  161 0.0926 0.1302      5.3466      5.5592|
|  2:  4.7071 -  3.7547 0.99   1391  152 0.0800 0.1032      5.3876      5.6115|
|  3:  3.7547 -  3.2856 0.99   1357  154 0.1015 0.1659      5.4393      5.8788|
|  4:  3.2856 -  2.9876 0.99   1357  148 0.1233 0.1556       5.458      5.5959|
|  5:  2.9876 -  2.7749 0.99   1332  145 0.1315 0.1818      5.3345      5.5502|
|  6:  2.7749 -  2.6121 0.98   1336  153 0.1263 0.1904      5.2318      5.4771|
|  7:  2.6121 -  2.4819 0.99   1333  146 0.1227 0.1737      5.1742       5.408|
|  8:  2.4819 -  2.3743 0.99   1316  150 0.1111 0.1714      5.0447      5.2955|
|  9:  2.3743 -  2.2832 0.98   1324  150 0.1151 0.1983      5.0362      5.3587|
| 10:  2.2832 -  2.2047 0.98   1311  147 0.1107 0.1678      4.9747      5.2165|
| 11:  2.2047 -  2.1359 0.98   1334  139 0.1154 0.1943      4.9652       5.326|
| 12:  2.1359 -  2.0750 0.99   1298  147 0.1096 0.1831      4.8924      5.1469|
| 13:  2.0750 -  2.0205 0.87   1158  138 0.1140 0.1749      4.7995      5.0431|
| 14:  2.0205 -  1.9713 0.25    348   29 0.1078 0.1664      4.6568      4.9109|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7071  1435   161  0.94   8.65   0.97     0.95       6881.50|
|  2:  4.7071 -  3.7547  1391   152  0.95   7.87   1.01     0.99       8584.92|
|  3:  3.7547 -  3.2856  1357   154  0.93  11.23   1.02     1.02      10020.22|
|  4:  3.2856 -  2.9876  1357   148  0.91  14.87   1.00     0.98      10908.61|
|  5:  2.9876 -  2.7749  1332   145  0.89  16.66   1.00     0.98       8906.30|
|  6:  2.7749 -  2.6121  1336   153  0.89  17.00   0.99     0.96       7589.16|
|  7:  2.6121 -  2.4819  1333   146  0.90  16.01   0.99     0.97       6597.44|
|  8:  2.4819 -  2.3743  1316   150  0.90  15.94   0.99     0.96       5442.06|
|  9:  2.3743 -  2.2832  1324   150  0.90  16.59   1.00     0.95       5216.46|
| 10:  2.2832 -  2.2047  1311   147  0.90  16.00   0.98     0.94       4676.77|
| 11:  2.2047 -  2.1359  1334   139  0.89  17.34   0.99     0.95       4820.17|
| 12:  2.1359 -  2.0750  1298   147  0.90  16.74   1.00     1.00       4367.64|
| 13:  2.0750 -  2.0205  1158   138  0.90  16.88   0.99     0.97       3556.62|
| 14:  2.0205 -  1.9713   348    29  0.89  16.78   0.97     0.94       2708.18|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2708.18 max =        10908.61 mean =      6714.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.70|
|phase err.(test): min =        0.00 max =           89.62 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    103.24  17.61    None  None   None       |
|    all(noH): 2823   0      0.55    103.24  17.61    None  None   None       |
|    Sol.    : 438    0      6.20    99.36   42.04    None  None   None       |
|    Mac.    : 2385   0      0.55    103.24  13.12    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:     0.553 -  10.821: 1213   |   5:    51.897 -  62.166:   98        |
|      1:    10.821 -  21.090:  998   |   6:    62.166 -  72.435:   38        |
|      2:    21.090 -  31.359:  205   |   7:    72.435 -  82.704:   17        |
|      3:    31.359 -  41.628:  132   |   8:    82.704 -  92.973:    8        |
|      4:    41.628 -  51.897:  109   |   9:    92.973 - 103.242:    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)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 4.336
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 315
   mapped sites are within: 0.703 - 4.336

peak=    5.675 closest distance to " CB  GLN A 223 " =    1.499
peak=    5.625 closest distance to " O   HOH Z 111 " =    1.819
peak=    5.300 closest distance to " CB  SER A  63 " =    1.316
peak=    5.134 closest distance to " O   HOH Z 232 " =    2.272
peak=    4.891 closest distance to " CB  GLN A 183 " =    1.251
peak=    4.603 closest distance to " CB  LEU A 228 " =    1.100
peak=    4.594 closest distance to " NE2 GLN A  11 " =    1.062
peak=    4.522 closest distance to " O   HOH Z 368 " =    2.067
peak=    4.509 closest distance to " O   HOH Z 193 " =    1.941
peak=    4.486 closest distance to " O   HOH Z 298 " =    1.875
peak=    4.469 closest distance to " CB  GLU A 128 " =    1.118
peak=    4.413 closest distance to " O   HOH Z 180 " =    2.201
peak=    4.408 closest distance to " O   HOH Z  80 " =    1.732
peak=    4.391 closest distance to " O   HOH Z 425 " =    1.432
peak=    4.391 closest distance to " O   HOH Z 126 " =    1.584
peak=    4.368 closest distance to " CG  PRO A 213 " =    1.174
peak=    4.358 closest distance to " O   HOH Z 403 " =    1.786
peak=    4.344 closest distance to " O   HOH Z 133 " =    2.320
peak=    4.308 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.302 closest distance to " O   HOH Z  15 " =    2.073
peak=    4.298 closest distance to " O   PRO A 198 " =    1.497
peak=    4.286 closest distance to " O   HOH Z 369 " =    2.035
peak=    4.248 closest distance to " CG1 ILE A  33 " =    1.199
peak=    4.240 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.239 closest distance to " NH2 ARG A 156 " =    1.223
peak=    4.233 closest distance to " CB  GLU A 277 " =    3.687
peak=    4.218 closest distance to " CG2 THR A 221 " =    0.990
peak=    4.214 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.190 closest distance to " O   HOH Z 236 " =    1.945
peak=    4.185 closest distance to " OD1 ASN A 217 " =    1.809
peak=    4.146 closest distance to " CB  SER A   3 " =    1.357
peak=    4.141 closest distance to " CA  THR A 221 " =    0.969
peak=    4.127 closest distance to " CA  MET A  40 " =    1.121
peak=    4.112 closest distance to " CD ALYS A 290 " =    1.031
peak=    4.105 closest distance to " O   HOH Z 126 " =    1.886
peak=    4.097 closest distance to " ND2 ASN A 110 " =    1.772
peak=    4.073 closest distance to " O   HOH Z  78 " =    1.902
peak=    4.061 closest distance to " OD1 ASN A  69 " =    2.650
peak=    4.057 closest distance to " CB  VAL A 202 " =    1.657
peak=    4.054 closest distance to " CB  ARG A  79 " =    1.500
peak=    4.042 closest distance to " O   HOH Z  68 " =    1.848
peak=    4.033 closest distance to " O   HOH Z 234 " =    3.853
peak=    4.030 closest distance to " CB  ASN A 148 " =    1.425
peak=    4.027 closest distance to " CB  ARG A 190 " =    1.693
peak=    4.018 closest distance to " O   HOH Z 108 " =    2.245
peak=    4.007 closest distance to " O   HOH Z 313 " =    1.787
peak=    4.005 closest distance to " OD2 ASP A 286 " =    2.930
peak=    3.987 closest distance to " O   HOH Z 134 " =    1.376
peak=    3.968 closest distance to " O   HOH Z 132 " =    2.398
peak=    3.951 closest distance to " O   HOH Z 303 " =    2.186
peak=    3.950 closest distance to " O   HOH Z  47 " =    1.401
peak=    3.941 closest distance to " O   HOH Z 135 " =    1.812
peak=    3.940 closest distance to " O   HOH Z 261 " =    2.081
peak=    3.938 closest distance to " O   HOH Z 426 " =    1.528
peak=    3.932 closest distance to " NH1AARG A 145 " =    1.109
peak=    3.931 closest distance to " CD2 LEU A 255 " =    1.554
peak=    3.924 closest distance to " C   ILE A 106 " =    1.930
peak=    3.921 closest distance to " O   ALA A 165 " =    1.463
peak=    3.914 closest distance to " CB  TYR A 169 " =    0.845
peak=    3.914 closest distance to " O   HOH Z 247 " =    1.317
peak=    3.910 closest distance to " O   HOH Z  20 " =    2.214
peak=    3.878 closest distance to " CB  VAL A 265 " =    1.241
peak=    3.875 closest distance to " NH2BARG A 145 " =    2.101
peak=    3.853 closest distance to " CA  ALA A  21 " =    1.284
peak=    3.851 closest distance to " CD1 LEU A 300 " =    1.285
peak=    3.850 closest distance to " CA  ALA A 160 " =    0.857
peak=    3.833 closest distance to " CB  TRP A 266 " =    0.938
peak=    3.830 closest distance to " O   HOH Z 316 " =    3.060
peak=    3.818 closest distance to " O   HOH Z 193 " =    2.279
peak=    3.814 closest distance to " O   HOH Z 174 " =    2.423
peak=    3.810 closest distance to " O   HOH Z 371 " =    3.440
peak=    3.807 closest distance to " ND2 ASN A 187 " =    1.445
peak=    3.796 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.786 closest distance to " NZ  LYS A 117 " =    3.291
peak=    3.783 closest distance to " CB  ASP A 140 " =    0.928
peak=    3.779 closest distance to " O   HOH Z 374 " =    2.810
peak=    3.775 closest distance to " CG BARG A 275 " =    1.513
peak=    3.773 closest distance to " O   HOH Z  88 " =    3.795
peak=    3.768 closest distance to " O   HOH Z 112 " =    1.556
peak=    3.765 closest distance to " O   HOH Z 427 " =    3.001
peak=    3.763 closest distance to " ND1 HIS A  81 " =    1.556
peak=    3.762 closest distance to " O   HOH Z 163 " =    1.596
peak=    3.747 closest distance to " O   HOH Z 144 " =    1.556
peak=    3.742 closest distance to " CD  ARG A  66 " =    2.357
peak=    3.730 closest distance to " O   HOH Z 280 " =    3.051
peak=    3.728 closest distance to " CB  TRP A 179 " =    1.539
peak=    3.725 closest distance to " O   HOH Z  49 " =    2.251
peak=    3.720 closest distance to " O   HOH Z 118 " =    1.728
peak=    3.717 closest distance to " O   THR A 251 " =    1.258
peak=    3.717 closest distance to " O   HOH Z  40 " =    1.573
peak=    3.712 closest distance to " OG BSER A 164 " =    2.392
peak=    3.711 closest distance to " O   HOH Z 272 " =    1.970
peak=    3.709 closest distance to " CG  PRO A 243 " =    1.209
peak=    3.708 closest distance to " O   HOH Z 423 " =    1.842
peak=    3.707 closest distance to " O   HOH Z 197 " =    2.585
peak=    3.703 closest distance to " O   HOH Z 193 " =    1.646
peak=    3.702 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.683 closest distance to " O   HOH Z  97 " =    1.872
peak=    3.658 closest distance to " O   HOH Z  53 " =    2.498
peak=    3.655 closest distance to " O   HOH Z 281 " =    4.336
peak=    3.652 closest distance to " O   TRP A 274 " =    1.768
peak=    3.649 closest distance to " O   HOH Z 344 " =    3.221
peak=    3.647 closest distance to " O   HOH Z 260 " =    1.143
peak=    3.631 closest distance to " CD  ARG A 159 " =    0.857
peak=    3.614 closest distance to " O   HOH Z 183 " =    1.609
peak=    3.605 closest distance to " O   HOH Z 207 " =    1.996
peak=    3.605 closest distance to " O   HOH Z 389 " =    1.909
peak=    3.603 closest distance to " O   HOH Z  21 " =    1.683
peak=    3.599 closest distance to " O   HOH Z 411 " =    3.611
peak=    3.597 closest distance to " CB  SER A 212 " =    1.108
peak=    3.596 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.584 closest distance to " O   HOH Z 437 " =    1.376
peak=    3.583 closest distance to " CZ  PHE A 218 " =    1.039
peak=    3.581 closest distance to " CB  SER A 216 " =    0.916
peak=    3.575 closest distance to " O   HOH Z 213 " =    1.836
peak=    3.572 closest distance to " O   HOH Z 345 " =    1.695
peak=    3.571 closest distance to " O   HOH Z 147 " =    1.809
peak=    3.555 closest distance to " O   HOH Z  58 " =    1.287
peak=    3.554 closest distance to " O   HOH Z 214 " =    1.992
peak=    3.542 closest distance to " CG1 ILE A 151 " =    0.884
peak=    3.542 closest distance to " O   HOH Z 172 " =    3.936
peak=    3.536 closest distance to " CD  ARG A 269 " =    0.908
peak=    3.534 closest distance to " ND1 HIS A  86 " =    1.832
peak=    3.530 closest distance to " CA  ASP A 124 " =    0.703
peak=    3.512 closest distance to " O   HOH Z 411 " =    1.744
peak=    3.511 closest distance to " O   HOH Z  54 " =    2.252
peak=    3.510 closest distance to " OG BSER A 134 " =    2.766
peak=    3.506 closest distance to " CG1 VAL A 153 " =    1.028
peak=    3.497 closest distance to " O   HOH Z 189 " =    2.596
peak=    3.493 closest distance to " CB  MET A  47 " =    0.956
peak=    3.490 closest distance to " O   SER A  87 " =    2.272
peak=    3.486 closest distance to " CA  ASP A 191 " =    0.821
peak=    3.483 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.480 closest distance to " O   HOH Z 214 " =    2.569
peak=    3.480 closest distance to " CB  SER A 141 " =    0.999
peak=    3.473 closest distance to " O   HOH Z 227 " =    1.737
peak=    3.470 closest distance to " CB  ALA A 248 " =    0.953
peak=    3.469 closest distance to " CB  ASN A 187 " =    1.149
peak=    3.463 closest distance to " CG  PRO A 198 " =    1.297
peak=    3.463 closest distance to " O   HOH Z 409 " =    3.092
peak=    3.461 closest distance to " CB  TYR A 116 " =    1.001
peak=    3.459 closest distance to " NZ  LYS A 166 " =    3.025
peak=    3.459 closest distance to " CD  LYS A 119 " =    1.413
peak=    3.455 closest distance to " O   HOH Z 352 " =    1.926
peak=    3.452 closest distance to " CG  GLN A  58 " =    2.602
peak=    3.450 closest distance to " N   ASN A 127 " =    1.242
peak=    3.448 closest distance to " CB  LEU A 143 " =    1.086
peak=    3.447 closest distance to " O   HOH Z 346 " =    1.652
peak=    3.447 closest distance to " CB  ALA A 100 " =    1.295
peak=    3.446 closest distance to " OE1 GLN A  11 " =    2.049
peak=    3.440 closest distance to " N   ASN A  39 " =    1.370
peak=    3.439 closest distance to " O   HOH Z 391 " =    2.986
peak=    3.435 closest distance to " O   HOH Z  85 " =    2.171
peak=    3.431 closest distance to " N   ARG A 156 " =    1.347
peak=    3.427 closest distance to " CA  GLY A 267 " =    1.036
peak=    3.424 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.423 closest distance to " O   HOH Z  93 " =    2.655
peak=    3.423 closest distance to " O   HOH Z 133 " =    1.688
peak=    3.422 closest distance to " CA  ASP A 140 " =    1.164
peak=    3.422 closest distance to " O   ALA A 158 " =    1.301
peak=    3.416 closest distance to " O   HOH Z 295 " =    1.497
peak=    3.409 closest distance to " O   HOH Z 387 " =    2.837
peak=    3.408 closest distance to " O   HOH Z 250 " =    1.404
peak=    3.406 closest distance to " CD1 ILE A 106 " =    0.981
peak=    3.394 closest distance to " CA  TYR A 116 " =    1.463
peak=    3.392 closest distance to " O   HOH Z 298 " =    2.561
peak=    3.392 closest distance to " CG  LEU A 167 " =    1.164
peak=    3.392 closest distance to " CG1 VAL A 202 " =    1.977
peak=    3.391 closest distance to " O   HOH Z 286 " =    2.231
peak=    3.390 closest distance to " CE  MET A 113 " =    1.783
peak=    3.388 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.387 closest distance to " CD2 HIS A  81 " =    1.075
peak=    3.383 closest distance to " CB  MET A  40 " =    0.798
peak=    3.383 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.381 closest distance to " CG2 VAL A 197 " =    1.155
peak=    3.379 closest distance to " O   HOH Z 114 " =    1.678
peak=    3.375 closest distance to " O   HOH Z 345 " =    3.405
peak=    3.373 closest distance to " CA  THR A 264 " =    0.909
peak=    3.372 closest distance to " O   HOH Z   1 " =    1.989
peak=    3.368 closest distance to " O   HOH Z 128 " =    2.239
peak=    3.368 closest distance to " CB  ILE A 120 " =    1.327
peak=    3.365 closest distance to " O   HOH Z  22 " =    2.735
peak=    3.363 closest distance to " O   HOH Z  64 " =    2.213
peak=    3.360 closest distance to " O   HOH Z 109 " =    2.779
peak=    3.358 closest distance to " CG BARG A 102 " =    1.895
peak=    3.358 closest distance to " O   HOH Z  54 " =    1.672
peak=    3.358 closest distance to " CA  ASN A 215 " =    1.210
peak=    3.354 closest distance to " O   HOH Z  63 " =    1.958
peak=    3.353 closest distance to " CA  ARG A  36 " =    1.261
peak=    3.348 closest distance to " O   HOH Z 134 " =    2.725
peak=    3.344 closest distance to " CG  PRO A  90 " =    1.045
peak=    3.335 closest distance to " CZ  PHE A 192 " =    0.931
peak=    3.335 closest distance to " O   HOH Z 368 " =    3.712
peak=    3.332 closest distance to " O   GLY A  57 " =    2.603
peak=    3.329 closest distance to " O   HOH Z 425 " =    2.176
peak=    3.327 closest distance to " CG1BVAL A  72 " =    1.647
peak=    3.322 closest distance to " O   HOH Z 158 " =    2.929
peak=    3.321 closest distance to " O   HOH Z 199 " =    1.624
peak=    3.321 closest distance to " O   HOH Z 305 " =    3.679
peak=    3.320 closest distance to " O   HOH Z 108 " =    1.278
peak=    3.320 closest distance to " O   HOH Z 368 " =    2.590
peak=    3.319 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.316 closest distance to " NH2BARG A 102 " =    1.101
peak=    3.316 closest distance to " O   HOH Z 383 " =    2.015
peak=    3.313 closest distance to " O   HOH Z 255 " =    1.798
peak=    3.311 closest distance to " CA  ALA A 158 " =    1.071
peak=    3.310 closest distance to " CB  ALA A   9 " =    1.593
peak=    3.308 closest distance to " CG AARG A 275 " =    1.190
peak=    3.308 closest distance to " CB  ARG A 139 " =    0.803
peak=    3.308 closest distance to " CE1 TYR A 186 " =    1.161
peak=    3.306 closest distance to " O   HOH Z 329 " =    3.725
peak=    3.305 closest distance to " CA  ASN A  74 " =    1.186
peak=    3.304 closest distance to " CG2 THR A 220 " =    1.063
peak=    3.302 closest distance to " OG1 THR A 294 " =    1.656
peak=    3.299 closest distance to " O   HOH Z 128 " =    2.233
peak=    3.295 closest distance to " O   HOH Z 419 " =    3.041
peak=    3.294 closest distance to " CB  ILE A 199 " =    1.027
peak=    3.293 closest distance to " O   HOH Z  44 " =    3.269
peak=    3.293 closest distance to " O   HOH Z 263 " =    1.749
peak=    3.292 closest distance to " CZ  PHE A 208 " =    1.141
peak=    3.287 closest distance to " CG2BVAL A  41 " =    0.846
peak=    3.287 closest distance to " CA  LEU A 101 " =    1.461
peak=    3.281 closest distance to " CA  ALA A 154 " =    1.396
peak=    3.280 closest distance to " CB  PRO A 163 " =    4.220
peak=    3.274 closest distance to " O   HOH Z 279 " =    2.373
peak=    3.273 closest distance to " O   HOH Z 261 " =    2.194
peak=    3.271 closest distance to " O   HOH Z 116 " =    1.883
peak=    3.271 closest distance to " CB  TRP A 150 " =    1.023
peak=    3.267 closest distance to " CA  ARG A 195 " =    1.200
peak=    3.259 closest distance to " O   HOH Z 175 " =    3.631
peak=    3.258 closest distance to " O   HOH Z   6 " =    2.189
peak=    3.256 closest distance to " O   HOH Z 245 " =    1.266
peak=    3.255 closest distance to " CA  LEU A  83 " =    1.521
peak=    3.254 closest distance to " CB  ASN A 285 " =    0.868
peak=    3.254 closest distance to " O   HOH Z 156 " =    2.855
peak=    3.252 closest distance to " C   TYR A 214 " =    1.529
peak=    3.250 closest distance to " CB  ARG A 138 " =    1.099
peak=    3.250 closest distance to " NH1 ARG A  56 " =    1.234
peak=    3.247 closest distance to " CB  PHE A  16 " =    1.031
peak=    3.242 closest distance to " O   HOH Z 171 " =    3.847
peak=    3.240 closest distance to " CB  GLN A  88 " =    1.300
peak=    3.233 closest distance to " CG2 ILE A 120 " =    1.048
peak=    3.224 closest distance to " O   HOH Z  63 " =    2.240
peak=    3.223 closest distance to " O   TRP A  70 " =    1.405
peak=    3.223 closest distance to " CD  GLU A 152 " =    0.853
peak=    3.221 closest distance to " O   THR A  31 " =    1.594
peak=    3.219 closest distance to " O   HOH Z  10 " =    1.862
peak=    3.216 closest distance to " O   HOH Z 394 " =    1.703
peak=    3.212 closest distance to " O   HOH Z 301 " =    2.007
peak=    3.211 closest distance to " NH2AARG A 275 " =    3.725
peak=    3.211 closest distance to " CD  ARG A 219 " =    1.133
peak=    3.207 closest distance to " CB  ALA A  71 " =    1.305
peak=    3.206 closest distance to " CA  GLU A 152 " =    0.828
peak=    3.199 closest distance to " CD  ARG A  66 " =    2.389
peak=    3.196 closest distance to " CB  ALA A 291 " =    1.436
peak=    3.190 closest distance to " CB  TYR A  30 " =    1.417
peak=    3.189 closest distance to " CG  MET A 185 " =    1.232
peak=    3.188 closest distance to " CD  ARG A 195 " =    0.923
peak=    3.187 closest distance to " CD1AILE A 234 " =    0.979
peak=    3.181 closest distance to " CG  GLN A  89 " =    1.332
peak=    3.178 closest distance to " O   HOH Z   9 " =    1.662
peak=    3.175 closest distance to " OG  SER A  22 " =    2.890
peak=    3.172 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.170 closest distance to " CE1 HIS A 115 " =    0.985
peak=    3.165 closest distance to " CB  GLU A 152 " =    1.603
peak=    3.163 closest distance to " CA  TRP A 274 " =    0.889
peak=    3.162 closest distance to " CD1 LEU A 228 " =    1.865
peak=    3.159 closest distance to " CB  ASN A 110 " =    1.233
peak=    3.158 closest distance to " CG2 ILE A 234 " =    0.848
peak=    3.158 closest distance to " O   HOH Z 128 " =    3.608
peak=    3.156 closest distance to " O   HOH Z 217 " =    1.287
peak=    3.153 closest distance to " CB  THR A  31 " =    1.806
peak=    3.151 closest distance to " O   HOH Z 410 " =    1.878
peak=    3.150 closest distance to " CD2 LEU A 297 " =    0.789
peak=    3.145 closest distance to " O   HOH Z 166 " =    1.515
peak=    3.145 closest distance to " CG  ARG A 219 " =    1.251
peak=    3.142 closest distance to " OG  SER A  28 " =    1.568
peak=    3.139 closest distance to " O   HOH Z 417 " =    3.186
peak=    3.135 closest distance to " CD  LYS A 166 " =    1.532
peak=    3.132 closest distance to " N   SER A 134 " =    1.482
peak=    3.125 closest distance to " O  BHOH Z 338 " =    2.274
peak=    3.124 closest distance to " CB  THR A 157 " =    1.050
peak=    3.122 closest distance to " O   HOH Z 359 " =    1.579
peak=    3.122 closest distance to " O   ALA A 233 " =    1.885
peak=    3.120 closest distance to " O   HOH Z   4 " =    1.834
peak=    3.114 closest distance to " O   HOH Z 189 " =    1.478
peak=    3.113 closest distance to " CA  ASP A 162 " =    1.223
peak=    3.113 closest distance to " O   HOH Z  38 " =    1.975
peak=    3.109 closest distance to " CA  MET A 105 " =    1.098
peak=    3.108 closest distance to " O   HOH Z 139 " =    3.211
peak=    3.105 closest distance to " CA  ARG A  56 " =    2.163
peak=    3.104 closest distance to " O   HOH Z 353 " =    2.837
peak=    3.103 closest distance to " CG  LYS A  76 " =    0.998
peak=    3.103 closest distance to " CA  ALA A 299 " =    0.956
peak=    3.102 closest distance to " NE2 GLN A  58 " =    4.258
peak=    3.099 closest distance to " O   HOH Z 427 " =    3.137
peak=    3.093 closest distance to " O   HOH Z 258 " =    2.043
peak=    3.091 closest distance to " N   SER A 135 " =    1.393
peak=    3.089 closest distance to " O   HOH Z   1 " =    2.251
peak=    3.082 closest distance to " CA  ILE A  33 " =    1.691
peak=    3.082 closest distance to " NH2 ARG A 219 " =    1.878
peak=    3.075 closest distance to " O   HOH Z 392 " =    1.518
peak=    3.073 closest distance to " NH2AARG A 190 " =    1.363
peak=    3.067 closest distance to " CB  LEU A 237 " =    0.780
peak=    3.063 closest distance to " O   HOH Z  64 " =    2.254
peak=    3.062 closest distance to " O   HOH Z  59 " =    2.558
peak=    3.036 closest distance to " CG2 VAL A 257 " =    0.904

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.725 - 5.597
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 222
   mapped sites are within: 0.725 - 5.597

peak=   -4.776 closest distance to " O   HOH Z 266 " =    4.433
peak=   -4.484 closest distance to " O   HOH Z 377 " =    1.804
peak=   -4.320 closest distance to " O   HOH Z 198 " =    2.551
peak=   -4.276 closest distance to " CD  ARG A 156 " =    1.975
peak=   -4.225 closest distance to " O   HOH Z  52 " =    1.498
peak=   -4.198 closest distance to " O   VAL A  67 " =    2.777
peak=   -4.186 closest distance to " N   ALA A  43 " =    2.440
peak=   -4.176 closest distance to " O   HOH Z  10 " =    1.572
peak=   -4.126 closest distance to " CB  PRO A 243 " =    2.628
peak=   -4.077 closest distance to " O   HOH Z  38 " =    1.186
peak=   -4.046 closest distance to " OG  SER A  97 " =    2.211
peak=   -4.004 closest distance to " CG1 VAL A 250 " =    2.666
peak=   -3.987 closest distance to " O   HOH Z  19 " =    2.206
peak=   -3.987 closest distance to " CD1 LEU A 228 " =    2.427
peak=   -3.979 closest distance to " O   HOH Z 372 " =    2.611
peak=   -3.943 closest distance to " CD2 LEU A 300 " =    2.869
peak=   -3.941 closest distance to " C   ASN A 187 " =    1.884
peak=   -3.936 closest distance to " OE1 GLN A 223 " =    2.050
peak=   -3.916 closest distance to " O   ILE A 109 " =    2.702
peak=   -3.916 closest distance to " O   PRO A 163 " =    2.089
peak=   -3.911 closest distance to " O   HOH Z 231 " =    2.181
peak=   -3.907 closest distance to " O   HOH Z 290 " =    1.237
peak=   -3.902 closest distance to " O   HOH Z 275 " =    1.598
peak=   -3.896 closest distance to " CD1 PHE A  59 " =    1.883
peak=   -3.891 closest distance to " O   HOH Z 353 " =    2.228
peak=   -3.888 closest distance to " C   ALA A 158 " =    1.270
peak=   -3.872 closest distance to " O   PRO A 198 " =    1.376
peak=   -3.863 closest distance to " CE2 TYR A  30 " =    2.761
peak=   -3.843 closest distance to " CD  ARG A  14 " =    3.377
peak=   -3.828 closest distance to " OD1 ASN A 148 " =    1.655
peak=   -3.809 closest distance to " CB  TRP A  85 " =    2.552
peak=   -3.788 closest distance to " O   HOH Z 283 " =    2.167
peak=   -3.784 closest distance to " OG BSER A 134 " =    1.726
peak=   -3.761 closest distance to " O   HOH Z 407 " =    3.648
peak=   -3.748 closest distance to " O   HOH Z  43 " =    1.585
peak=   -3.713 closest distance to " CD2 PHE A  59 " =    2.459
peak=   -3.706 closest distance to " CG  MET A  93 " =    2.583
peak=   -3.704 closest distance to " SG  CYS A 254 " =    3.281
peak=   -3.702 closest distance to " SG ACYS A 201 " =    1.998
peak=   -3.702 closest distance to " C   ASN A 285 " =    2.514
peak=   -3.667 closest distance to " CZ3 TRP A 179 " =    1.148
peak=   -3.664 closest distance to " OXT GLY A 302 " =    2.900
peak=   -3.657 closest distance to " CG  PHE A 283 " =    2.793
peak=   -3.635 closest distance to " CG1 VAL A 112 " =    2.582
peak=   -3.630 closest distance to " O   HOH Z 388 " =    1.963
peak=   -3.623 closest distance to " OG  SER A  87 " =    1.546
peak=   -3.621 closest distance to " O   ASN A 301 " =    1.491
peak=   -3.620 closest distance to " O   HOH Z 436 " =    1.489
peak=   -3.615 closest distance to " O   HOH Z  13 " =    1.563
peak=   -3.615 closest distance to " NH2 ARG A  66 " =    1.896
peak=   -3.594 closest distance to " O   HOH Z 292 " =    4.618
peak=   -3.590 closest distance to " CB  CYS A 254 " =    2.369
peak=   -3.589 closest distance to " OG ASER A 134 " =    1.324
peak=   -3.567 closest distance to " CD2 TYR A 293 " =    2.101
peak=   -3.565 closest distance to " CD  ARG A 139 " =    1.645
peak=   -3.559 closest distance to " ND2 ASN A  45 " =    1.671
peak=   -3.557 closest distance to " CB  ASN A  39 " =    2.188
peak=   -3.555 closest distance to " O   VAL A 125 " =    2.180
peak=   -3.551 closest distance to " CB  ALA A 291 " =    2.323
peak=   -3.549 closest distance to " N   SER A 276 " =    1.446
peak=   -3.548 closest distance to " CA  GLY A 241 " =    3.049
peak=   -3.545 closest distance to " O   HOH Z 243 " =    2.008
peak=   -3.535 closest distance to " CG  ARG A  66 " =    2.259
peak=   -3.532 closest distance to " CE  MET A  93 " =    1.302
peak=   -3.530 closest distance to " C   HIS A 108 " =    1.088
peak=   -3.527 closest distance to " O   HOH Z 189 " =    1.999
peak=   -3.524 closest distance to " ND2 ASN A  60 " =    1.426
peak=   -3.523 closest distance to " CG2 THR A 221 " =    2.277
peak=   -3.519 closest distance to " O   SER A 210 " =    1.926
peak=   -3.519 closest distance to " O   HOH Z 393 " =    1.429
peak=   -3.516 closest distance to " CD  ARG A 195 " =    5.158
peak=   -3.515 closest distance to " CG  GLU A  53 " =    1.401
peak=   -3.515 closest distance to " CG  TRP A 266 " =    1.725
peak=   -3.512 closest distance to " O   HOH Z 166 " =    1.744
peak=   -3.512 closest distance to " O   HOH Z  88 " =    2.356
peak=   -3.511 closest distance to " O   HOH Z  98 " =    2.097
peak=   -3.506 closest distance to " O   HOH Z 426 " =    1.735
peak=   -3.503 closest distance to " OE2 GLU A   2 " =    1.699
peak=   -3.493 closest distance to " CZ  PHE A  59 " =    1.910
peak=   -3.477 closest distance to " CA  VAL A 232 " =    2.438
peak=   -3.476 closest distance to " O   HOH Z 111 " =    1.995
peak=   -3.465 closest distance to " CG2 VAL A 189 " =    2.181
peak=   -3.464 closest distance to " OD1 ASP A 191 " =    1.671
peak=   -3.460 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.459 closest distance to " ND2 ASN A  45 " =    1.018
peak=   -3.459 closest distance to " CD  GLN A  88 " =    0.866
peak=   -3.457 closest distance to " O   HOH Z  98 " =    1.906
peak=   -3.456 closest distance to " O   HOH Z  93 " =    2.085
peak=   -3.453 closest distance to " OD2 ASP A  65 " =    1.837
peak=   -3.451 closest distance to " CD  LYS A 289 " =    2.399
peak=   -3.449 closest distance to " CG  PRO A 163 " =    2.396
peak=   -3.449 closest distance to " N   THR A 157 " =    1.698
peak=   -3.441 closest distance to " O   HOH Z 435 " =    2.615
peak=   -3.441 closest distance to " O   HOH Z 234 " =    4.328
peak=   -3.435 closest distance to " O   GLY A 196 " =    1.221
peak=   -3.431 closest distance to " CD  GLN A  88 " =    2.146
peak=   -3.423 closest distance to " O   HOH Z 185 " =    2.424
peak=   -3.421 closest distance to " CB  ALA A 291 " =    2.339
peak=   -3.418 closest distance to " O   VAL A  67 " =    2.797
peak=   -3.413 closest distance to " O   HOH Z 389 " =    1.978
peak=   -3.409 closest distance to " O   HOH Z  76 " =    2.005
peak=   -3.407 closest distance to " OD2 ASP A 171 " =    1.821
peak=   -3.401 closest distance to " O   HOH Z 266 " =    4.986
peak=   -3.394 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.393 closest distance to " OG BSER A 134 " =    1.302
peak=   -3.391 closest distance to " O   HOH Z 396 " =    1.653
peak=   -3.389 closest distance to " CB  SER A 258 " =    2.015
peak=   -3.388 closest distance to " NE2 GLN A  58 " =    1.040
peak=   -3.388 closest distance to " O   GLY A 211 " =    1.570
peak=   -3.388 closest distance to " CB  PHE A  16 " =    2.635
peak=   -3.381 closest distance to " O   HOH Z 118 " =    2.858
peak=   -3.381 closest distance to " O   HOH Z 211 " =    1.547
peak=   -3.369 closest distance to " ND2 ASN A 249 " =    2.234
peak=   -3.368 closest distance to " CG  LEU A  83 " =    2.065
peak=   -3.362 closest distance to " CA  SER A 135 " =    1.307
peak=   -3.361 closest distance to " CB  ALA A  43 " =    2.477
peak=   -3.359 closest distance to " O   HOH Z 103 " =    1.941
peak=   -3.358 closest distance to " NH2AARG A 275 " =    5.564
peak=   -3.356 closest distance to " O   HOH Z 399 " =    2.274
peak=   -3.354 closest distance to " SG ACYS A 201 " =    1.099
peak=   -3.353 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.353 closest distance to " CE3 TRP A  70 " =    1.772
peak=   -3.347 closest distance to " O   HOH Z 311 " =    3.761
peak=   -3.346 closest distance to " O   PRO A 198 " =    1.964
peak=   -3.342 closest distance to " OG  SER A  62 " =    1.643
peak=   -3.340 closest distance to " CA  GLY A 203 " =    2.253
peak=   -3.337 closest distance to " O   HOH Z  11 " =    2.002
peak=   -3.336 closest distance to " O   HOH Z 252 " =    4.100
peak=   -3.334 closest distance to " O   HOH Z 377 " =    1.423
peak=   -3.317 closest distance to " NH1 ARG A 195 " =    2.608
peak=   -3.316 closest distance to " O   HOH Z 322 " =    1.416
peak=   -3.313 closest distance to " O   HOH Z 166 " =    1.555
peak=   -3.308 closest distance to " O   HOH Z 184 " =    1.881
peak=   -3.300 closest distance to " O   VAL A 189 " =    2.552
peak=   -3.300 closest distance to " CB  ILE A 239 " =    2.038
peak=   -3.300 closest distance to " CE3 TRP A 150 " =    2.039
peak=   -3.299 closest distance to " CD1 LEU A 222 " =    2.444
peak=   -3.297 closest distance to " O   HOH Z 128 " =    2.543
peak=   -3.297 closest distance to " O   HOH Z   6 " =    1.809
peak=   -3.291 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -3.287 closest distance to " O   ASN A 187 " =    1.504
peak=   -3.282 closest distance to " OG  SER A  26 " =    1.339
peak=   -3.279 closest distance to " NH1BARG A 275 " =    2.086
peak=   -3.271 closest distance to " CA  GLY A 133 " =    2.264
peak=   -3.271 closest distance to " CD2 LEU A 237 " =    2.807
peak=   -3.271 closest distance to " O   HOH Z 196 " =    2.071
peak=   -3.270 closest distance to " N   ALA A 226 " =    2.094
peak=   -3.265 closest distance to " N   GLN A  58 " =    1.527
peak=   -3.262 closest distance to " OG1 THR A 178 " =    1.284
peak=   -3.262 closest distance to " OD2 ASP A 132 " =    2.125
peak=   -3.261 closest distance to " CG  ARG A 259 " =    2.890
peak=   -3.261 closest distance to " O   HOH Z 412 " =    5.597
peak=   -3.255 closest distance to " CG1 VAL A 197 " =    2.336
peak=   -3.253 closest distance to " CB  LEU A 167 " =    2.200
peak=   -3.249 closest distance to " C   LEU A 143 " =    1.263
peak=   -3.247 closest distance to " OH  TYR A 169 " =    1.050
peak=   -3.244 closest distance to " CG  ASP A 231 " =    0.899
peak=   -3.244 closest distance to " O   ALA A  34 " =    2.530
peak=   -3.243 closest distance to " CD2 LEU A 167 " =    1.830
peak=   -3.227 closest distance to " O   PHE A 218 " =    1.540
peak=   -3.225 closest distance to " NH2 ARG A  79 " =    1.878
peak=   -3.219 closest distance to " O   HOH Z 184 " =    1.663
peak=   -3.218 closest distance to " O   GLN A 240 " =    2.361
peak=   -3.218 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.217 closest distance to " N   GLN A 122 " =    1.559
peak=   -3.217 closest distance to " O   GLY A 118 " =    2.246
peak=   -3.215 closest distance to " O   HOH Z  71 " =    1.433
peak=   -3.211 closest distance to " O   HOH Z 387 " =    3.932
peak=   -3.210 closest distance to " CE1 TYR A 169 " =    2.426
peak=   -3.209 closest distance to " CG1 VAL A 125 " =    2.065
peak=   -3.208 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.203 closest distance to " O   HOH Z  98 " =    1.506
peak=   -3.199 closest distance to " ND2 ASN A  69 " =    1.572
peak=   -3.196 closest distance to " CE2 PHE A 218 " =    2.451
peak=   -3.192 closest distance to " CB  PRO A 163 " =    2.636
peak=   -3.192 closest distance to " NH2 ARG A  66 " =    5.367
peak=   -3.191 closest distance to " C   LEU A 222 " =    0.725
peak=   -3.185 closest distance to " O   HOH Z 350 " =    1.731
peak=   -3.183 closest distance to " OD1 ASN A 187 " =    1.670
peak=   -3.183 closest distance to " O   HOH Z 208 " =    1.728
peak=   -3.180 closest distance to " O   HOH Z 252 " =    4.150
peak=   -3.169 closest distance to " O   HOH Z 207 " =    2.137
peak=   -3.166 closest distance to " O   HOH Z 409 " =    4.537
peak=   -3.165 closest distance to " CD2 TRP A 274 " =    2.397
peak=   -3.163 closest distance to " CE2 PHE A  61 " =    2.591
peak=   -3.163 closest distance to " O   GLY A  80 " =    2.471
peak=   -3.160 closest distance to " ND2 ASN A 215 " =    2.182
peak=   -3.159 closest distance to " O   HOH Z 385 " =    2.017
peak=   -3.153 closest distance to " O   HOH Z  90 " =    3.584
peak=   -3.140 closest distance to " O   SER A 271 " =    2.144
peak=   -3.137 closest distance to " CG  GLN A  58 " =    1.420
peak=   -3.133 closest distance to " CG  ASN A 301 " =    1.963
peak=   -3.132 closest distance to " N   ALA A 248 " =    1.724
peak=   -3.132 closest distance to " CB  TYR A  15 " =    2.273
peak=   -3.132 closest distance to " CB  ALA A 114 " =    2.349
peak=   -3.128 closest distance to " NH1 ARG A 195 " =    2.341
peak=   -3.127 closest distance to " CE  MET A 105 " =    2.109
peak=   -3.124 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.123 closest distance to " CZ  TYR A 169 " =    1.860
peak=   -3.120 closest distance to " O   HOH Z  11 " =    1.933
peak=   -3.119 closest distance to " O   HOH Z 108 " =    2.003
peak=   -3.112 closest distance to " CB  ASP A 286 " =    2.298
peak=   -3.111 closest distance to " O   HOH Z 292 " =    1.790
peak=   -3.109 closest distance to " N   SER A   3 " =    2.239
peak=   -3.104 closest distance to " CG2 VAL A 189 " =    2.054
peak=   -3.102 closest distance to " OD2 ASP A 171 " =    2.266
peak=   -3.098 closest distance to " NH2 ARG A 159 " =    2.525
peak=   -3.094 closest distance to " CD1 LEU A 297 " =    2.606
peak=   -3.094 closest distance to " O   HOH Z 111 " =    1.334
peak=   -3.090 closest distance to " O   HOH Z 417 " =    2.656
peak=   -3.078 closest distance to " O   HOH Z  90 " =    1.639
peak=   -3.070 closest distance to " O   HOH Z  97 " =    1.806
peak=   -3.068 closest distance to " C   SER A 206 " =    1.487
peak=   -3.067 closest distance to " CG  GLN A 278 " =    2.348
peak=   -3.064 closest distance to " CE  MET A 105 " =    1.927
peak=   -3.056 closest distance to " O   SER A 135 " =    1.585
peak=   -3.045 closest distance to " ND2 ASN A 249 " =    1.995
peak=   -3.044 closest distance to " CB  ALA A 227 " =    2.305
peak=   -3.027 closest distance to " CD2 LEU A 237 " =    2.504
peak=   -3.025 closest distance to " CG2 ILE A  20 " =    2.795
peak=   -3.023 closest distance to " O   ASN A 209 " =    2.108

================= 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    :  0.4279 0.4273   6.226974e+00   6.228387e+00
   1_bss:  0.4193 0.4185   6.219926e+00   6.217842e+00
   1_xyz:  0.2549 0.2897   5.826763e+00   5.929040e+00
   1_adp:  0.2318 0.2929   5.771128e+00   5.946889e+00
   1_occ:  0.2314 0.2930   5.770133e+00   5.946154e+00
   2_bss:  0.2283 0.2892   5.766954e+00   5.941348e+00
   2_xyz:  0.1650 0.2143   5.476847e+00   5.693644e+00
   2_adp:  0.1505 0.1989   5.400641e+00   5.618454e+00
   2_occ:  0.1503 0.1987   5.399577e+00   5.617353e+00
   3_bss:  0.1503 0.1979   5.399147e+00   5.615658e+00
   3_xyz:  0.1304 0.1746   5.273338e+00   5.495200e+00
   3_adp:  0.1248 0.1706   5.244085e+00   5.473469e+00
   3_occ:  0.1248 0.1705   5.243760e+00   5.473191e+00
   4_bss:  0.1251 0.1707   5.244778e+00   5.474007e+00
   4_xyz:  0.1175 0.1654   5.199772e+00   5.441989e+00
   4_adp:  0.1164 0.1643   5.192988e+00   5.435997e+00
   4_occ:  0.1163 0.1642   5.192856e+00   5.435989e+00
   5_bss:  0.1163 0.1642   5.192910e+00   5.436012e+00
   5_xyz:  0.1101 0.1622   5.161280e+00   5.420543e+00
   5_adp:  0.1095 0.1618   5.157443e+00   5.417886e+00
   5_occ:  0.1094 0.1618   5.157426e+00   5.418033e+00
   5_bss:  0.1093 0.1617   5.157544e+00   5.418106e+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:  0.287  25.999   2.426  -0.196   0.361  -0.000   0.000   0.000
   1_xyz:  0.287  25.999   2.426  -0.196   0.361  -0.000   0.000   0.000
   1_adp:  0.287  25.999   2.426  -0.196   0.361  -0.000   0.000   0.000
   1_occ:  0.287  25.999   2.426  -0.196   0.361  -0.000   0.000   0.000
   2_bss:  0.324  55.545  -0.655  -1.611  -1.219  -0.000  -0.000  -0.000
   2_xyz:  0.324  55.545  -0.655  -1.611  -1.219  -0.000  -0.000  -0.000
   2_adp:  0.324  55.545  -0.655  -1.611  -1.219  -0.000  -0.000  -0.000
   2_occ:  0.324  55.545  -0.655  -1.611  -1.219  -0.000  -0.000  -0.000
   3_bss:  0.332  59.141  -1.843  -2.211  -1.918  -0.000  -0.000  -0.000
   3_xyz:  0.332  59.141  -1.843  -2.211  -1.918  -0.000  -0.000  -0.000
   3_adp:  0.332  59.141  -1.843  -2.211  -1.918  -0.000  -0.000  -0.000
   3_occ:  0.332  59.141  -1.843  -2.211  -1.918  -0.000  -0.000  -0.000
   4_bss:  0.326  60.373  -2.212  -2.450  -2.108  -0.000  -0.000  -0.000
   4_xyz:  0.326  60.373  -2.212  -2.450  -2.108  -0.000  -0.000  -0.000
   4_adp:  0.326  60.373  -2.212  -2.450  -2.108  -0.000  -0.000  -0.000
   4_occ:  0.326  60.373  -2.212  -2.450  -2.108  -0.000  -0.000  -0.000
   5_bss:  0.326  60.373  -2.106  -2.310  -2.001  -0.000  -0.000  -0.000
   5_xyz:  0.326  60.373  -2.106  -2.310  -2.001  -0.000  -0.000  -0.000
   5_adp:  0.326  60.373  -2.106  -2.310  -2.001  -0.000  -0.000  -0.000
   5_occ:  0.326  60.373  -2.106  -2.310  -2.001  -0.000  -0.000  -0.000
   5_bss:  0.326  60.355  -1.890  -2.099  -1.778  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.639 0.4991  0.6518    56590.004
   1_bss:  50.705 0.5089  0.6880    53752.009
   1_xyz:  29.444 0.7642  0.9842    21995.376
   1_adp:  30.303 0.7536  0.9798    22936.362
   1_occ:  30.293 0.7537  0.9797    22913.310
   2_bss:  30.147 0.7552  0.9159    22712.928
   2_xyz:  21.346 0.8474  0.9827    12123.211
   2_adp:  19.310 0.8682  0.9910    10474.995
   2_occ:  19.280 0.8684  0.9912    10440.208
   3_bss:  19.222 0.8689  0.9624    10370.404
   3_xyz:  16.365 0.8949  0.9773     7941.925
   3_adp:  15.827 0.9000  0.9757     7612.369
   3_occ:  15.819 0.9000  0.9756     7603.498
   4_bss:  15.827 0.9000  0.9663     7612.070
   4_xyz:  15.162 0.9054  0.9674     7058.902
   4_adp:  14.993 0.9069  0.9634     6978.044
   4_occ:  14.992 0.9070  0.9633     6976.487
   5_bss:  14.994 0.9069  0.9672     6976.993
   5_xyz:  14.710 0.9092  0.9691     6767.480
   5_adp:  14.643 0.9098  0.9635     6714.302
   5_occ:  14.643 0.9098  0.9634     6713.613
   5_bss:  14.647 0.9098  0.9701     6714.355
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7067e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7067e-01
   1_xyz:   1.446  0.011  0.091 15.894  0.005  4.120   1.1575e-01
   1_adp:   1.446  0.011  0.091 15.894  0.005  4.120   1.1575e-01
   1_occ:   1.446  0.011  0.091 15.894  0.005  4.120   1.1575e-01
   2_bss:   1.446  0.011  0.091 15.894  0.005  4.120   1.1575e-01
   2_xyz:   1.100  0.008  0.077 14.869  0.004  4.138   6.9062e-02
   2_adp:   1.100  0.008  0.077 14.869  0.004  4.138   6.9062e-02
   2_occ:   1.100  0.008  0.077 14.869  0.004  4.138   6.9062e-02
   3_bss:   1.100  0.008  0.077 14.869  0.004  4.138   6.9062e-02
   3_xyz:   1.003  0.007  0.071 14.869  0.004  4.127   6.0814e-02
   3_adp:   1.003  0.007  0.071 14.869  0.004  4.127   6.0814e-02
   3_occ:   1.003  0.007  0.071 14.869  0.004  4.127   6.0814e-02
   4_bss:   1.003  0.007  0.071 14.869  0.004  4.127   6.0814e-02
   4_xyz:   1.058  0.008  0.075 14.903  0.004  4.132   6.5331e-02
   4_adp:   1.058  0.008  0.075 14.903  0.004  4.132   6.5331e-02
   4_occ:   1.058  0.008  0.075 14.903  0.004  4.132   6.5331e-02
   5_bss:   1.058  0.008  0.075 14.903  0.004  4.132   6.5331e-02
   5_xyz:   1.209  0.012  0.085 15.290  0.005  4.137   8.6347e-02
   5_adp:   1.209  0.012  0.085 15.290  0.005  4.137   8.6347e-02
   5_occ:   1.209  0.012  0.085 15.290  0.005  4.137   8.6347e-02
   5_bss:   1.209  0.012  0.085 15.290  0.005  4.137   8.6347e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.541   2.4248e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.541   2.4248e-01
   1_xyz:   9.944  0.070  0.331 84.165  0.017  2.107   9.8265e-02
   1_adp:   9.944  0.070  0.331 84.165  0.017  2.107   9.8265e-02
   1_occ:   9.944  0.070  0.331 84.165  0.017  2.107   9.8265e-02
   2_bss:   9.944  0.070  0.331 84.165  0.017  2.107   9.8265e-02
   2_xyz:   8.030  0.047  0.232 87.280  0.044  2.352   6.9160e-02
   2_adp:   8.030  0.047  0.232 87.280  0.044  2.352   6.9160e-02
   2_occ:   8.030  0.047  0.232 87.280  0.044  2.352   6.9160e-02
   3_bss:   8.030  0.047  0.232 87.280  0.044  2.352   6.9160e-02
   3_xyz:   8.379  0.044  0.227 81.372  0.040  2.323   5.6455e-02
   3_adp:   8.379  0.044  0.227 81.372  0.040  2.323   5.6455e-02
   3_occ:   8.379  0.044  0.227 81.372  0.040  2.323   5.6455e-02
   4_bss:   8.379  0.044  0.227 81.372  0.040  2.323   5.6455e-02
   4_xyz:   8.128  0.041  0.235 84.440  0.043  2.322   4.3953e-02
   4_adp:   8.128  0.041  0.235 84.440  0.043  2.322   4.3953e-02
   4_occ:   8.128  0.041  0.235 84.440  0.043  2.322   4.3953e-02
   5_bss:   8.128  0.041  0.235 84.440  0.043  2.322   4.3953e-02
   5_xyz:   8.033  0.049  0.262 81.997  0.042  2.261   6.6109e-02
   5_adp:   8.033  0.049  0.262 81.997  0.042  2.261   6.6109e-02
   5_occ:   8.033  0.049  0.262 81.997  0.042  2.261   6.6109e-02
   5_bss:   8.033  0.049  0.262 81.997  0.042  2.261   6.6109e-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:  99.79   0.00  18.37  81.87   0.00  13.85  99.79   2.70  42.95
   1_occ:  99.79   0.00  18.37  81.87   0.00  13.85  99.79   2.70  42.95
   2_bss:  99.79   0.00  18.37  81.87   0.00  13.85  99.79   2.70  42.95
   2_xyz:  99.79   0.00  18.37  81.87   0.00  13.85  99.79   2.70  42.95
   2_adp:  95.85   1.69  17.99  83.09   1.69  13.47  95.85   5.92  42.63
   2_occ:  95.85   1.69  17.99  83.09   1.69  13.47  95.85   5.92  42.63
   3_bss:  95.85   1.69  17.99  83.09   1.69  13.47  95.85   5.92  42.63
   3_xyz:  95.85   1.69  17.99  83.09   1.69  13.47  95.85   5.92  42.63
   3_adp:  96.55   1.26  18.06  92.62   1.26  13.42  96.55   6.27  43.31
   3_occ:  96.55   1.26  18.06  92.62   1.26  13.42  96.55   6.27  43.31
   4_bss:  96.55   1.26  18.06  92.62   1.26  13.42  96.55   6.27  43.31
   4_xyz:  96.55   1.26  18.06  92.62   1.26  13.42  96.55   6.27  43.31
   4_adp:  97.95   1.01  17.82  97.95   1.01  13.28  97.15   5.94  42.52
   4_occ:  97.95   1.01  17.82  97.95   1.01  13.28  97.15   5.94  42.52
   5_bss:  97.95   1.01  17.82  97.95   1.01  13.28  97.15   5.94  42.52
   5_xyz:  97.95   1.01  17.82  97.95   1.01  13.28  97.15   5.94  42.52
   5_adp: 103.26   0.57  17.63 103.26   0.57  13.14  99.38   6.22  42.06
   5_occ: 103.26   0.57  17.63 103.26   0.57  13.14  99.38   6.22  42.06
   5_bss: 103.24   0.55  17.61 103.24   0.55  13.12  99.36   6.20  42.04
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.621    0.036    0.453
   1_adp:    1.621    0.036    0.453
   1_occ:    1.621    0.036    0.453
   2_bss:    1.621    0.036    0.453
   2_xyz:    1.214    0.024    0.548
   2_adp:    1.214    0.024    0.548
   2_occ:    1.214    0.024    0.548
   3_bss:    1.214    0.024    0.548
   3_xyz:    1.161    0.071    0.607
   3_adp:    1.161    0.071    0.607
   3_occ:    1.161    0.071    0.607
   4_bss:    1.161    0.071    0.607
   4_xyz:    1.201    0.076    0.626
   4_adp:    1.201    0.076    0.626
   4_occ:    1.201    0.076    0.626
   5_bss:    1.201    0.076    0.626
   5_xyz:    1.189    0.045    0.643
   5_adp:    1.189    0.045    0.643
   5_occ:    1.189    0.045    0.643
   5_bss:    1.189    0.045    0.643
------------------------------------------------------------------------

CPU time actual refinement: 343.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/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_1289/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1289/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.12 
  Macro-tasks:
    bulk solvent and scale       = 37.50  
    individual site refinement   = 142.09 
    weights calculation          = 29.72  
    collect and process          = 6.44   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.85 
  Micro-tasks:
    mask                            = 1.92   
    f_calc                          = 114.10 
    alpha_beta                      = 7.87   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 121.65 
    fmodel                         = 6.45   
    r_factors                      = 0.26   
    phase_errors                   = 10.84  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 264.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.875 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    646 calls, 113.67 s
gradients_fft:          591 calls, 108.35 s

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

# Date 2008-01-16 Time 06:53:50 PST -0800 (1200495230.55 s)
Start R-work = 0.4279, R-free = 0.4273 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1808 (no bulk solvent and anisotropic scale)

Start R-work = 0.4193, R-free = 0.4185
Final R-work = 0.1093, R-free = 0.1617