# Date 2008-01-16 Time 04:25:50 PST -0800 (1200486350.19 s)
#phil __OFF__

Command line arguments: "../309.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 585
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 309

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.1647, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7486 1.96127
Completeness in resolution range: 0.958788
Completeness with d_max=infinity: 0.955794

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7486
                             d_min =   1.9613

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7486 1.96127
Completeness in resolution range: 0.958788
Completeness with d_max=infinity: 0.955794

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7490 -  4.1960 [2148/2176]  1933   215  10.0%
  bin  2:  4.1960 -  3.3433 [2049/2072]  1845   204  10.0%
  bin  3:  3.3433 -  2.9244 [2040/2062]  1834   206  10.1%
  bin  4:  2.9244 -  2.6587 [2009/2028]  1815   194   9.7%
  bin  5:  2.6587 -  2.4691 [2011/2040]  1801   210  10.4%
  bin  6:  2.4691 -  2.3241 [1970/2011]  1780   190   9.6%
  bin  7:  2.3241 -  2.2081 [1984/2020]  1782   202  10.2%
  bin  8:  2.2081 -  2.1123 [1979/2017]  1779   200  10.1%
  bin  9:  2.1123 -  2.0312 [1953/1984]  1763   190   9.7%
  bin 10:  2.0312 -  1.9613 [1446/2021]  1298   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 22
        2.12 -     2.81: 840
        2.81 -     3.51: 4548
        3.51 -     4.20: 9454
        4.20 -     4.90: 13858
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.422 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.502 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.724 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.752 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28717 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_309/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3888   r_free= 0.3850   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.168339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6797 0.99   1388  156 0.3163 0.3263      6.4354      6.4628|
|  2:  4.6797 -  3.7343 0.99   1349  146 0.3172 0.2944      6.6045       6.575|
|  3:  3.7343 -  3.2681 0.99   1313  153 0.3309 0.3346      6.4813      6.6128|
|  4:  3.2681 -  2.9720 0.99   1313  137 0.3619 0.3782      6.3578      6.3799|
|  5:  2.9720 -  2.7604 0.98   1278  143 0.3941 0.3589      6.2425      6.1852|
|  6:  2.7604 -  2.5986 0.98   1291  144 0.4179 0.4229      6.1585      6.0967|
|  7:  2.5986 -  2.4691 0.99   1296  150 0.4190 0.3527       6.153      6.0523|
|  8:  2.4691 -  2.3621 0.99   1281  135 0.4197 0.4418      6.0922      6.1332|
|  9:  2.3621 -  2.2715 0.98   1289  146 0.4524 0.4427      6.0543      6.0876|
| 10:  2.2715 -  2.1934 0.97   1247  143 0.4362 0.4826      6.0283      6.0648|
| 11:  2.1934 -  2.1250 0.98   1269  142 0.4692 0.4744      5.9818      6.0482|
| 12:  2.1250 -  2.0644 0.99   1270  135 0.4451 0.4315      5.9192      5.9385|
| 13:  2.0644 -  2.0102 0.97   1258  137 0.4551 0.4736      5.8248      5.8404|
| 14:  2.0102 -  1.9613 0.61    788   92 0.4920 0.4608      5.8177      5.6919|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7490 -  4.6797  1388   156  0.74  30.77   0.86     0.76      56384.14|
|  2:  4.6797 -  3.7343  1349   146  0.78  28.06   0.96     0.88      69224.41|
|  3:  3.7343 -  3.2681  1313   153  0.73  32.73   0.98     0.91      70550.74|
|  4:  3.2681 -  2.9720  1313   137  0.67  37.64   0.99     0.89      61910.88|
|  5:  2.9720 -  2.7604  1278   143  0.63  41.71   0.95     0.85      50349.65|
|  6:  2.7604 -  2.5986  1291   144  0.61  43.48   0.96     0.84      43277.72|
|  7:  2.5986 -  2.4691  1296   150  0.62  42.10   0.96     0.83      39845.02|
|  8:  2.4691 -  2.3621  1281   135  0.58  45.44   0.99     0.80      38828.26|
|  9:  2.3621 -  2.2715  1289   146  0.53  49.42   0.99     0.75      37614.53|
| 10:  2.2715 -  2.1934  1247   143  0.52  50.75   1.02     0.72      36763.13|
| 11:  2.1934 -  2.1250  1269   142  0.49  53.16   1.00     0.72      34900.35|
| 12:  2.1250 -  2.0644  1270   135  0.51  51.39   1.03     0.76      31987.75|
| 13:  2.0644 -  2.0102  1258   137  0.51  51.84   0.99     0.76      27321.77|
| 14:  2.0102 -  1.9613   788    92  0.53  49.92   0.97     0.75      21675.46|
|alpha:            min =        0.72 max =            0.91 mean =         0.80|
|beta:             min =    21675.46 max =        70550.74 mean =     45255.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.08|
|phase err.(test): min =        0.00 max =           89.76 mean =        42.76|
|-----------------------------------------------------------------------------|

============================== 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 = 8.114688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.672   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.260068              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.845   (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 |  1.422 -  1.770:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.770 -  2.117:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.117 -  2.465:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.465 -  2.813:      805 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.813 -  3.161:     2121 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.161 -  3.509:     2427 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.509 -  3.857:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.857 -  4.204:     4818 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.204 -  4.552:     6305 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7553 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.422 |       0.582 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3888   r_free= 0.3850   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.168339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3781   r_free= 0.3724   ksol= 0.31   Bsol= 20.76   scale= 0.970   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.07,2.29,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.153366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.019059              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.483   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.643382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.791   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3781      final r-factor (work) = 0.2144          |
| start r-factor (free) = 0.3724      final r-factor (free) = 0.2335          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7965 = 7.02 * 0.50 * 6.1571 + 1.00 * 0.1878                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8268 = 7.02 * 0.50 * 5.9081 + 1.00 * 0.0920                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2144      final r-factor (work) = 0.1939          |
| start r-factor (free) = 0.2335      final r-factor (free) = 0.2442          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8073 = 0.64 * 1.00 * 5.9081 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6080 = 0.64 * 1.00 * 5.5906 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.71   17.99    None  None   None       |
|    all(noH): 2823   0      0.00    90.71   17.99    None  None   None       |
|    Sol.    : 438    0      7.12    79.74   40.78    None  None   None       |
|    Mac.    : 2385   0      0.00    90.71   13.80    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 -   9.071:  789   |   5:    45.353 -  54.423:  120        |
|      1:     9.071 -  18.141: 1185   |   6:    54.423 -  63.494:   56        |
|      2:    18.141 -  27.212:  337   |   7:    63.494 -  72.565:   34        |
|      3:    27.212 -  36.282:  148   |   8:    72.565 -  81.635:   13        |
|      4:    36.282 -  45.353:  140   |   9:    81.635 -  90.706:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1939 r_free = 0.2442             target_work(ml) = 5.608         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1936 r_free = 0.2443             target_work(ml) = 5.607         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1936   r_free= 0.2443   ksol= 0.31   Bsol= 20.76   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.07,2.29,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.606973                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1889   r_free= 0.2403   ksol= 0.31   Bsol= 32.47   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.45,-0.88,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.593846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.056355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.661   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.167062              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.241  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1889      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2403      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6538 = 3.06 * 0.50 * 5.6026 + 1.00 * 0.0920                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4106 = 3.06 * 0.50 * 5.4666 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1389      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1867      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9242 = 0.17 * 1.00 * 5.4666 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9060 = 0.17 * 1.00 * 5.2973 + 1.00 * 0.0210                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.66   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    90.66   17.89    None  None   None       |
|    Sol.    : 438    0      7.01    79.17   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    90.66   13.76    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 -   9.066:  684   |   5:    45.330 -  54.396:  115        |
|      1:     9.066 -  18.132: 1349   |   6:    54.396 -  63.462:   56        |
|      2:    18.132 -  27.198:  292   |   7:    63.462 -  72.528:   33        |
|      3:    27.198 -  36.264:  137   |   8:    72.528 -  81.594:    9        |
|      4:    36.264 -  45.330:  147   |   9:    81.594 -  90.660:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1766             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1310 r_free = 0.1765             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1310   r_free= 0.1765   ksol= 0.31   Bsol= 32.47   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.45,-0.88,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.264171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1751   ksol= 0.32   Bsol= 35.97   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.39,-1.69,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.260046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.758688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.310  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.388321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.992   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7139 = 1.76 * 0.50 * 5.2964 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6439 = 1.76 * 0.50 * 5.2216 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0366 = 0.39 * 1.00 * 5.2216 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0154 = 0.39 * 1.00 * 5.1689 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    94.17   17.64    None  None   None       |
|    all(noH): 2823   0      1.81    94.17   17.64    None  None   None       |
|    Sol.    : 438    0      6.28    82.69   40.36    None  None   None       |
|    Mac.    : 2385   0      1.81    94.17   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:     1.807 -  11.043: 1161   |   5:    47.989 -  57.225:  112        |
|      1:    11.043 -  20.279: 1020   |   6:    57.225 -  66.461:   49        |
|      2:    20.279 -  29.516:  206   |   7:    66.461 -  75.698:   13        |
|      3:    29.516 -  38.752:  122   |   8:    75.698 -  84.934:    7        |
|      4:    38.752 -  47.989:  131   |   9:    84.934 -  94.170:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1599             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1599             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1599   ksol= 0.32   Bsol= 35.97   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.39,-1.69,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.155609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1597   ksol= 0.32   Bsol= 35.97   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-2.39,-2.00,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.274363              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.372  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279298              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.632  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5144 = 3.27 * 0.50 * 5.1687 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4580 = 3.27 * 0.50 * 5.1223 + 1.00 * 0.0718                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1056          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4388 = 0.28 * 1.00 * 5.1223 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4331 = 0.28 * 1.00 * 5.1039 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.15    92.97   17.22    None  None   None       |
|    all(noH): 2823   0      2.15    92.97   17.22    None  None   None       |
|    Sol.    : 438    0      5.93    82.28   39.04    None  None   None       |
|    Mac.    : 2385   0      2.15    92.97   13.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.146 -  11.229: 1234   |   5:    47.559 -  56.641:   96        |
|      1:    11.229 -  20.311:  966   |   6:    56.641 -  65.724:   40        |
|      2:    20.311 -  29.394:  196   |   7:    65.724 -  74.806:   13        |
|      3:    29.394 -  38.476:  136   |   8:    74.806 -  83.889:    5        |
|      4:    38.476 -  47.559:  134   |   9:    83.889 -  92.971:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1056 r_free = 0.1538             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1538             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1538   ksol= 0.32   Bsol= 35.97   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-2.39,-2.00,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1538   ksol= 0.32   Bsol= 38.57   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.32,-1.97,-0.00,-0.00,-0.00); trace/3= -2.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101421                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.021684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328671              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.547  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2311 = 2.02 * 0.50 * 5.1039 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2219 = 2.02 * 0.50 * 5.1090 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6868 = 0.33 * 1.00 * 5.1090 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6876 = 0.33 * 1.00 * 5.1111 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    92.91   17.11    None  None   None       |
|    all(noH): 2823   0      1.73    92.91   17.11    None  None   None       |
|    Sol.    : 438    0      5.91    81.86   38.92    None  None   None       |
|    Mac.    : 2385   0      1.73    92.91   13.11    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:     1.733 -  10.851: 1177   |   5:    47.322 -  56.440:   98        |
|      1:    10.851 -  19.969: 1010   |   6:    56.440 -  65.558:   40        |
|      2:    19.969 -  29.086:  207   |   7:    65.558 -  74.676:   14        |
|      3:    29.086 -  38.204:  134   |   8:    74.676 -  83.794:    4        |
|      4:    38.204 -  47.322:  136   |   9:    83.794 -  92.912:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1547             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1546             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1546   ksol= 0.32   Bsol= 38.57   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.32,-1.97,-0.00,-0.00,-0.00); trace/3= -2.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112791                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6797 0.99   1388  156 0.0994 0.1246      5.3717      5.5234|
|  2:  4.6797 -  3.7343 0.99   1349  146 0.0828 0.1073      5.4028      5.5848|
|  3:  3.7343 -  3.2681 0.99   1313  153 0.0998 0.1510      5.4268      5.8334|
|  4:  3.2681 -  2.9720 0.99   1313  137 0.1162 0.1550      5.4237      5.6059|
|  5:  2.9720 -  2.7604 0.98   1278  143 0.1211 0.1592      5.2812      5.4666|
|  6:  2.7604 -  2.5986 0.98   1291  144 0.1189 0.1847      5.1808      5.4019|
|  7:  2.5986 -  2.4691 0.99   1296  150 0.1132 0.1580      5.0972       5.349|
|  8:  2.4691 -  2.3621 0.99   1281  135 0.1104 0.1726      5.0447      5.2973|
|  9:  2.3621 -  2.2715 0.98   1289  146 0.1141 0.1813      5.0006      5.3073|
| 10:  2.2715 -  2.1934 0.97   1247  143 0.1082 0.1740      4.9535      5.1769|
| 11:  2.1934 -  2.1250 0.98   1269  142 0.1103 0.1739         4.9      5.2513|
| 12:  2.1250 -  2.0644 0.99   1270  135 0.1040 0.1642       4.832      5.1147|
| 13:  2.0644 -  2.0102 0.97   1258  137 0.1064 0.1683      4.7543      5.0251|
| 14:  2.0102 -  1.9613 0.61    788   92 0.1045 0.1660      4.6738       4.892|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7490 -  4.6797  1388   156  0.94   8.80   0.98     0.96       6760.28|
|  2:  4.6797 -  3.7343  1349   146  0.95   7.68   1.02     1.01       8389.00|
|  3:  3.7343 -  3.2681  1313   153  0.94  10.53   1.03     1.02       9539.56|
|  4:  3.2681 -  2.9720  1313   137  0.92  13.12   1.01     1.00       9897.82|
|  5:  2.9720 -  2.7604  1278   143  0.91  14.93   1.00     0.97       7689.18|
|  6:  2.7604 -  2.5986  1291   144  0.90  15.59   0.98     0.95       6633.83|
|  7:  2.5986 -  2.4691  1296   150  0.91  14.51   0.99     0.96       5489.15|
|  8:  2.4691 -  2.3621  1281   135  0.91  14.56   1.00     0.98       5234.34|
|  9:  2.3621 -  2.2715  1289   146  0.91  15.10   1.01     0.98       4709.68|
| 10:  2.2715 -  2.1934  1247   143  0.91  15.29   1.00     0.97       4423.10|
| 11:  2.1934 -  2.1250  1269   142  0.91  15.52   1.00     0.97       4000.30|
| 12:  2.1250 -  2.0644  1270   135  0.92  14.30   1.01     1.00       3624.34|
| 13:  2.0644 -  2.0102  1258   137  0.91  15.33   1.01     1.00       3166.15|
| 14:  2.0102 -  1.9613   788    92  0.91  14.79   0.99     0.96       2606.84|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2606.84 max =         9897.82 mean =      5997.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.48|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1547   ksol= 0.32   Bsol= 38.51   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-2.13,-1.82,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1547   ksol= 0.32   Bsol= 38.51   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-2.13,-1.82,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114171                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6797 0.99   1388  156 0.0982 0.1256      5.3723      5.5124|
|  2:  4.6797 -  3.7343 0.99   1349  146 0.0840 0.1075      5.4096      5.5901|
|  3:  3.7343 -  3.2681 0.99   1313  153 0.1004 0.1511      5.4314      5.8295|
|  4:  3.2681 -  2.9720 0.99   1313  137 0.1165 0.1540      5.4247      5.6015|
|  5:  2.9720 -  2.7604 0.98   1278  143 0.1215 0.1597      5.2831      5.4688|
|  6:  2.7604 -  2.5986 0.98   1291  144 0.1182 0.1843      5.1821      5.4035|
|  7:  2.5986 -  2.4691 0.99   1296  150 0.1129 0.1593      5.0981      5.3556|
|  8:  2.4691 -  2.3621 0.99   1281  135 0.1104 0.1730      5.0458      5.2986|
|  9:  2.3621 -  2.2715 0.98   1289  146 0.1138 0.1813      4.9997      5.3098|
| 10:  2.2715 -  2.1934 0.97   1247  143 0.1076 0.1741      4.9534      5.1771|
| 11:  2.1934 -  2.1250 0.98   1269  142 0.1102 0.1742      4.9013      5.2534|
| 12:  2.1250 -  2.0644 0.99   1270  135 0.1040 0.1639      4.8321      5.1165|
| 13:  2.0644 -  2.0102 0.97   1258  137 0.1062 0.1685      4.7544      5.0257|
| 14:  2.0102 -  1.9613 0.61    788   92 0.1045 0.1657      4.6735      4.8921|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7490 -  4.6797  1388   156  0.94   8.56   0.99     0.96       6589.85|
|  2:  4.6797 -  3.7343  1349   146  0.95   7.73   1.03     1.01       8391.34|
|  3:  3.7343 -  3.2681  1313   153  0.94  10.57   1.04     1.03       9588.89|
|  4:  3.2681 -  2.9720  1313   137  0.92  13.12   1.02     1.01       9865.82|
|  5:  2.9720 -  2.7604  1278   143  0.91  14.96   1.00     0.97       7689.87|
|  6:  2.7604 -  2.5986  1291   144  0.90  15.71   0.99     0.96       6699.34|
|  7:  2.5986 -  2.4691  1296   150  0.91  14.54   0.99     0.97       5513.53|
|  8:  2.4691 -  2.3621  1281   135  0.91  14.61   1.01     0.99       5259.78|
|  9:  2.3621 -  2.2715  1289   146  0.91  15.12   1.01     0.98       4713.84|
| 10:  2.2715 -  2.1934  1247   143  0.91  15.34   1.01     0.97       4444.45|
| 11:  2.1934 -  2.1250  1269   142  0.90  15.57   1.01     0.97       4007.43|
| 12:  2.1250 -  2.0644  1270   135  0.92  14.34   1.02     1.01       3637.17|
| 13:  2.0644 -  2.0102  1258   137  0.91  15.34   1.01     1.00       3171.99|
| 14:  2.0102 -  1.9613   788    92  0.91  14.79   1.00     0.96       2607.74|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2607.74 max =         9865.82 mean =      5997.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.50|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.528)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    92.85   17.05    None  None   None       |
|    all(noH): 2823   0      1.67    92.85   17.05    None  None   None       |
|    Sol.    : 438    0      5.84    81.80   38.85    None  None   None       |
|    Mac.    : 2385   0      1.67    92.85   13.05    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:     1.671 -  10.789: 1177   |   5:    47.260 -  56.378:   98        |
|      1:    10.789 -  19.907: 1010   |   6:    56.378 -  65.496:   40        |
|      2:    19.907 -  29.024:  207   |   7:    65.496 -  74.614:   14        |
|      3:    29.024 -  38.142:  134   |   8:    74.614 -  83.732:    4        |
|      4:    38.142 -  47.260:  136   |   9:    83.732 -  92.850:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.668 - 5.970
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 291
   mapped sites are within: 0.704 - 5.970

peak=    5.791 closest distance to " NH2 ARG A  56 " =    2.200
peak=    5.730 closest distance to " CB  ARG A 275 " =    0.945
peak=    5.430 closest distance to " O   HOH Z 126 " =    1.820
peak=    5.414 closest distance to " O   HOH Z 142 " =    1.674
peak=    5.367 closest distance to " O   HOH Z 124 " =    1.466
peak=    5.157 closest distance to " O   HOH Z 272 " =    1.851
peak=    5.081 closest distance to " CG  PRO A  54 " =    1.223
peak=    5.019 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.985 closest distance to " CB  GLN A 223 " =    1.429
peak=    4.895 closest distance to " CB  SER A  63 " =    1.093
peak=    4.783 closest distance to " O   HOH Z 234 " =    3.661
peak=    4.748 closest distance to " NE2 GLN A  11 " =    1.060
peak=    4.680 closest distance to " C   PRO A 198 " =    1.494
peak=    4.672 closest distance to " O   HOH Z 209 " =    2.230
peak=    4.668 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.639 closest distance to " O   HOH Z 403 " =    1.749
peak=    4.633 closest distance to " O   HOH Z 193 " =    1.723
peak=    4.549 closest distance to " CB  GLN A 183 " =    1.283
peak=    4.529 closest distance to " O   HOH Z  54 " =    1.719
peak=    4.468 closest distance to " CB  GLU A 152 " =    1.121
peak=    4.407 closest distance to " O   HOH Z 368 " =    1.905
peak=    4.392 closest distance to " CB  ASN A 148 " =    1.715
peak=    4.373 closest distance to " O   HOH Z  15 " =    2.186
peak=    4.365 closest distance to " O   HOH Z 232 " =    2.366
peak=    4.362 closest distance to " O   HOH Z 427 " =    2.784
peak=    4.352 closest distance to " CG  ARG A  66 " =    2.743
peak=    4.332 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.325 closest distance to " O   HOH Z  40 " =    1.606
peak=    4.304 closest distance to " OE1 GLU A   2 " =    2.261
peak=    4.287 closest distance to " O   HOH Z  97 " =    1.882
peak=    4.280 closest distance to " CG  PRO A  90 " =    1.181
peak=    4.275 closest distance to " CB  ARG A  79 " =    1.378
peak=    4.275 closest distance to " NH2BARG A 145 " =    2.011
peak=    4.257 closest distance to " O   HOH Z 316 " =    2.941
peak=    4.235 closest distance to " O   HOH Z 402 " =    1.430
peak=    4.232 closest distance to " O   HOH Z 303 " =    1.950
peak=    4.208 closest distance to " CB  SER A   3 " =    1.256
peak=    4.204 closest distance to " O   HOH Z 203 " =    1.772
peak=    4.174 closest distance to " CB  PRO A  54 " =    0.903
peak=    4.171 closest distance to " O   HOH Z  78 " =    1.660
peak=    4.156 closest distance to " O   SER A  87 " =    2.180
peak=    4.151 closest distance to " ND2 ASN A 187 " =    1.538
peak=    4.132 closest distance to " CG  PRO A 243 " =    1.127
peak=    4.129 closest distance to " OD2 ASP A 286 " =    2.700
peak=    4.123 closest distance to " OD1 ASN A  69 " =    2.593
peak=    4.098 closest distance to " O   HOH Z  43 " =    2.012
peak=    4.095 closest distance to " O   HOH Z 236 " =    1.980
peak=    4.078 closest distance to " O   HOH Z 344 " =    2.905
peak=    4.075 closest distance to " CA  ALA A  21 " =    1.129
peak=    4.073 closest distance to " NZ  LYS A 117 " =    3.151
peak=    4.072 closest distance to " CG  PRO A 198 " =    1.195
peak=    4.065 closest distance to " O   HOH Z  97 " =    2.598
peak=    4.061 closest distance to " CB  TYR A 169 " =    0.750
peak=    4.053 closest distance to " CG1 ILE A  33 " =    1.269
peak=    4.044 closest distance to " O   HOH Z 426 " =    1.531
peak=    4.031 closest distance to " O   HOH Z 389 " =    1.834
peak=    4.026 closest distance to " CB  GLU A 277 " =    3.466
peak=    3.941 closest distance to " O   HOH Z 173 " =    1.970
peak=    3.935 closest distance to " O   HOH Z  44 " =    1.957
peak=    3.933 closest distance to " O   HOH Z 144 " =    2.134
peak=    3.919 closest distance to " O   HOH Z 128 " =    1.928
peak=    3.916 closest distance to " O   HOH Z  59 " =    2.039
peak=    3.898 closest distance to " NZ  LYS A 119 " =    1.585
peak=    3.895 closest distance to " O   HOH Z 227 " =    1.594
peak=    3.893 closest distance to " O   HOH Z  66 " =    2.155
peak=    3.885 closest distance to " O   HOH Z 346 " =    1.637
peak=    3.883 closest distance to " CB  SER A  26 " =    1.599
peak=    3.879 closest distance to " CB  GLU A 128 " =    1.092
peak=    3.875 closest distance to " O   HOH Z 134 " =    1.350
peak=    3.871 closest distance to " O   HOH Z 214 " =    2.182
peak=    3.869 closest distance to " O   HOH Z  63 " =    1.968
peak=    3.862 closest distance to " CG2 ILE A 120 " =    1.212
peak=    3.857 closest distance to " O   HOH Z 416 " =    2.676
peak=    3.841 closest distance to " O   HOH Z 411 " =    3.615
peak=    3.837 closest distance to " O   HOH Z 423 " =    1.965
peak=    3.828 closest distance to " O   HOH Z 365 " =    2.870
peak=    3.826 closest distance to " O   HOH Z 207 " =    1.804
peak=    3.822 closest distance to " O   HOH Z 261 " =    1.635
peak=    3.814 closest distance to " O   HOH Z 189 " =    1.691
peak=    3.813 closest distance to " CD2 TRP A 179 " =    1.400
peak=    3.813 closest distance to " O   HOH Z 197 " =    2.746
peak=    3.806 closest distance to " CA  ASN A 176 " =    1.098
peak=    3.804 closest distance to " CB  VAL A 265 " =    1.250
peak=    3.784 closest distance to " O   HOH Z  50 " =    1.390
peak=    3.778 closest distance to " O   HOH Z 327 " =    1.700
peak=    3.770 closest distance to " O   HOH Z 156 " =    3.311
peak=    3.767 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.766 closest distance to " O   HOH Z 183 " =    1.514
peak=    3.761 closest distance to " O   MET A 105 " =    1.838
peak=    3.757 closest distance to " CB  TYR A 169 " =    0.879
peak=    3.746 closest distance to " N   ASN A  39 " =    1.214
peak=    3.734 closest distance to " O   HOH Z  61 " =    1.569
peak=    3.727 closest distance to " CB  TRP A 179 " =    1.166
peak=    3.722 closest distance to " O   HOH Z 406 " =    1.676
peak=    3.713 closest distance to " O   HOH Z 132 " =    0.970
peak=    3.712 closest distance to " CB  ARG A 190 " =    1.719
peak=    3.710 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.709 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.709 closest distance to " O   HOH Z 421 " =    1.468
peak=    3.709 closest distance to " O   HOH Z  21 " =    1.713
peak=    3.707 closest distance to " CB  LEU A 228 " =    1.129
peak=    3.696 closest distance to " O   HOH Z 132 " =    2.452
peak=    3.693 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.679 closest distance to " O   HOH Z  61 " =    1.642
peak=    3.678 closest distance to " CG  MET A 185 " =    1.166
peak=    3.676 closest distance to " CD2 LEU A 297 " =    0.922
peak=    3.672 closest distance to " O   HOH Z 369 " =    2.018
peak=    3.651 closest distance to " O   HOH Z  19 " =    2.087
peak=    3.650 closest distance to " O   HOH Z 265 " =    2.380
peak=    3.641 closest distance to " CG1BVAL A  72 " =    1.524
peak=    3.636 closest distance to " O   HOH Z 284 " =    2.845
peak=    3.628 closest distance to " CA  ASP A 140 " =    1.092
peak=    3.618 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.617 closest distance to " CG  ARG A  66 " =    0.941
peak=    3.616 closest distance to " CA  LYS A 117 " =    1.235
peak=    3.616 closest distance to " CG AARG A 275 " =    1.009
peak=    3.609 closest distance to " O   HOH Z 345 " =    2.902
peak=    3.602 closest distance to " CG2 ILE A  20 " =    1.405
peak=    3.586 closest distance to " O   HOH Z 273 " =    2.662
peak=    3.576 closest distance to " CB  ASN A  39 " =    0.839
peak=    3.565 closest distance to " O   HOH Z  88 " =    2.933
peak=    3.565 closest distance to " CB  SER A 141 " =    1.078
peak=    3.563 closest distance to " CA  MET A  40 " =    1.050
peak=    3.557 closest distance to " CG2BVAL A  41 " =    0.863
peak=    3.550 closest distance to " CD BLYS A 290 " =    1.178
peak=    3.547 closest distance to " NH1AARG A 145 " =    1.140
peak=    3.544 closest distance to " CA  ARG A  36 " =    1.005
peak=    3.543 closest distance to " C   ALA A   1 " =    1.676
peak=    3.540 closest distance to " OG BSER A 164 " =    2.356
peak=    3.535 closest distance to " O   HOH Z  10 " =    1.800
peak=    3.534 closest distance to " O   HOH Z 326 " =    1.477
peak=    3.531 closest distance to " CB  VAL A 202 " =    1.621
peak=    3.520 closest distance to " CG  GLN A  77 " =    1.911
peak=    3.519 closest distance to " O   HOH Z 286 " =    2.210
peak=    3.517 closest distance to " O   HOH Z 299 " =    4.269
peak=    3.516 closest distance to " O   HOH Z 172 " =    3.939
peak=    3.511 closest distance to " O   HOH Z 185 " =    1.630
peak=    3.507 closest distance to " O   HOH Z  49 " =    2.031
peak=    3.506 closest distance to " O   HOH Z 108 " =    2.233
peak=    3.505 closest distance to " CG  GLN A  58 " =    2.607
peak=    3.501 closest distance to " O   HOH Z 353 " =    2.558
peak=    3.496 closest distance to " CE  LYS A 119 " =    1.127
peak=    3.496 closest distance to " O   HOH Z 380 " =    2.156
peak=    3.492 closest distance to " O   HOH Z 425 " =    1.283
peak=    3.489 closest distance to " O   HOH Z 247 " =    1.290
peak=    3.476 closest distance to " O   HOH Z 427 " =    3.024
peak=    3.473 closest distance to " O   HOH Z 163 " =    1.873
peak=    3.472 closest distance to " O   HOH Z 337 " =    3.534
peak=    3.468 closest distance to " CB  TRP A 266 " =    0.997
peak=    3.467 closest distance to " O   HOH Z   9 " =    2.080
peak=    3.467 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.462 closest distance to " O   HOH Z 368 " =    3.653
peak=    3.459 closest distance to " CA  THR A 221 " =    0.949
peak=    3.458 closest distance to " O   HOH Z 180 " =    2.233
peak=    3.456 closest distance to " O   HOH Z 250 " =    1.690
peak=    3.453 closest distance to " N   ARG A 156 " =    1.326
peak=    3.446 closest distance to " O   HOH Z 342 " =    0.790
peak=    3.446 closest distance to " CZ2 TRP A 179 " =    1.715
peak=    3.443 closest distance to " O   HOH Z 108 " =    1.092
peak=    3.442 closest distance to " O   HOH Z 227 " =    2.231
peak=    3.439 closest distance to " CG  LYS A  76 " =    1.071
peak=    3.438 closest distance to " O   HOH Z 102 " =    1.258
peak=    3.435 closest distance to " CB  GLN A 278 " =    0.840
peak=    3.435 closest distance to " CA  GLY A  80 " =    0.765
peak=    3.434 closest distance to " CA  ALA A  84 " =    1.289
peak=    3.429 closest distance to " CB  ILE A 120 " =    1.262
peak=    3.420 closest distance to " O   HOH Z 291 " =    1.484
peak=    3.414 closest distance to " O   HOH Z 194 " =    1.890
peak=    3.406 closest distance to " O   HOH Z 417 " =    1.989
peak=    3.405 closest distance to " CD2 HIS A  81 " =    1.185
peak=    3.402 closest distance to " O   HOH Z   1 " =    1.990
peak=    3.398 closest distance to " CE1 TYR A 186 " =    1.270
peak=    3.397 closest distance to " O   HOH Z 411 " =    1.626
peak=    3.396 closest distance to " NH2 ARG A 156 " =    1.165
peak=    3.395 closest distance to " CB  ASN A 215 " =    1.108
peak=    3.389 closest distance to " NH1BARG A 145 " =    1.189
peak=    3.385 closest distance to " O   HOH Z 279 " =    2.078
peak=    3.382 closest distance to " CB  THR A  31 " =    1.743
peak=    3.379 closest distance to " O   HOH Z  30 " =    2.111
peak=    3.372 closest distance to " CB  ALA A 291 " =    1.314
peak=    3.371 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.370 closest distance to " CG2 VAL A 257 " =    0.845
peak=    3.370 closest distance to " CG  MET A 185 " =    0.987
peak=    3.364 closest distance to " O   HOH Z  40 " =    2.543
peak=    3.363 closest distance to " O   HOH Z 147 " =    1.748
peak=    3.350 closest distance to " O   HOH Z 374 " =    2.517
peak=    3.343 closest distance to " O   HOH Z 261 " =    1.592
peak=    3.343 closest distance to " O   ALA A 165 " =    1.418
peak=    3.342 closest distance to " O   HOH Z  47 " =    1.481
peak=    3.340 closest distance to " CB  GLN A  88 " =    1.125
peak=    3.339 closest distance to " O   HOH Z  71 " =    1.109
peak=    3.338 closest distance to " CB  ALA A  34 " =    0.967
peak=    3.333 closest distance to " O   HOH Z  68 " =    1.605
peak=    3.329 closest distance to " O   HOH Z 425 " =    1.992
peak=    3.328 closest distance to " O   HOH Z 417 " =    3.061
peak=    3.327 closest distance to " NH2 ARG A 219 " =    1.949
peak=    3.326 closest distance to " O   HOH Z 193 " =    2.105
peak=    3.324 closest distance to " O   HOH Z 261 " =    2.085
peak=    3.323 closest distance to " O   HOH Z 255 " =    1.613
peak=    3.321 closest distance to " NH2AARG A 190 " =    1.256
peak=    3.320 closest distance to " O   TRP A 274 " =    1.909
peak=    3.313 closest distance to " CA  ALA A 248 " =    1.413
peak=    3.312 closest distance to " OG  SER A  62 " =    2.855
peak=    3.309 closest distance to " CD  LYS A 119 " =    1.312
peak=    3.304 closest distance to " O   HOH Z 148 " =    3.100
peak=    3.301 closest distance to " O   HOH Z  85 " =    2.151
peak=    3.294 closest distance to " CA  PHE A 283 " =    1.304
peak=    3.293 closest distance to " CG2 THR A 221 " =    1.138
peak=    3.292 closest distance to " CA  ALA A  51 " =    0.868
peak=    3.292 closest distance to " O   HOH Z 334 " =    1.376
peak=    3.290 closest distance to " O   HOH Z 298 " =    2.396
peak=    3.289 closest distance to " O   HOH Z 263 " =    2.385
peak=    3.289 closest distance to " CD2 LEU A 255 " =    1.064
peak=    3.285 closest distance to " O   HOH Z 359 " =    1.791
peak=    3.285 closest distance to " CG2 THR A 294 " =    1.617
peak=    3.285 closest distance to " O   HOH Z 163 " =    1.633
peak=    3.285 closest distance to " O   HOH Z 192 " =    1.710
peak=    3.284 closest distance to " CA  ASP A 162 " =    1.128
peak=    3.282 closest distance to " CB  ALA A   1 " =    1.163
peak=    3.281 closest distance to " OG  SER A  22 " =    2.609
peak=    3.280 closest distance to " CA  ALA A 233 " =    1.194
peak=    3.279 closest distance to " CB  SER A  62 " =    0.891
peak=    3.271 closest distance to " O   HOH Z 214 " =    2.379
peak=    3.266 closest distance to " O   HOH Z 158 " =    2.913
peak=    3.265 closest distance to " O   HOH Z  48 " =    1.624
peak=    3.259 closest distance to " CD1 ILE A 106 " =    0.870
peak=    3.259 closest distance to " CG  GLU A 277 " =    2.216
peak=    3.256 closest distance to " CB  TYR A 116 " =    0.841
peak=    3.256 closest distance to " CG2 VAL A  67 " =    1.058
peak=    3.252 closest distance to " O   HOH Z 359 " =    1.474
peak=    3.249 closest distance to " O   GLY A  91 " =    1.511
peak=    3.247 closest distance to " CD  GLN A  58 " =    5.970
peak=    3.243 closest distance to " O   HOH Z 132 " =    2.290
peak=    3.243 closest distance to " O   HOH Z 281 " =    4.407
peak=    3.243 closest distance to " CD  ARG A 159 " =    0.704
peak=    3.241 closest distance to " O   HOH Z 313 " =    1.679
peak=    3.241 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.239 closest distance to " O   HOH Z 257 " =    2.243
peak=    3.233 closest distance to " O   HOH Z 430 " =    5.529
peak=    3.224 closest distance to " CE  LYS A  48 " =    1.191
peak=    3.222 closest distance to " O   HOH Z 367 " =    3.550
peak=    3.216 closest distance to " O   HOH Z 211 " =    2.712
peak=    3.214 closest distance to " CB  ALA A   9 " =    1.566
peak=    3.213 closest distance to " N   PHE A 130 " =    1.396
peak=    3.210 closest distance to " O   HOH Z 267 " =    2.005
peak=    3.204 closest distance to " CG  GLN A  11 " =    1.535
peak=    3.202 closest distance to " O   HOH Z 250 " =    1.893
peak=    3.198 closest distance to " CB  SER A 273 " =    0.777
peak=    3.196 closest distance to " O   HOH Z 189 " =    1.291
peak=    3.195 closest distance to " CE BLYS A 290 " =    1.031
peak=    3.187 closest distance to " O   HOH Z 251 " =    1.599
peak=    3.187 closest distance to " CG2 VAL A 202 " =    1.199
peak=    3.183 closest distance to " ND1 HIS A  81 " =    1.507
peak=    3.177 closest distance to " O   HOH Z 410 " =    1.836
peak=    3.175 closest distance to " CB  ARG A 139 " =    1.777
peak=    3.170 closest distance to " O   HOH Z 435 " =    1.868
peak=    3.170 closest distance to " CA  THR A 264 " =    0.821
peak=    3.167 closest distance to " CA  ILE A  33 " =    1.357
peak=    3.166 closest distance to " CB  ARG A 269 " =    0.734
peak=    3.156 closest distance to " C   TYR A 214 " =    1.383
peak=    3.154 closest distance to " N   ASP A 162 " =    1.218
peak=    3.151 closest distance to " CB  ALA A 114 " =    1.133
peak=    3.147 closest distance to " CB  SER A 216 " =    0.730
peak=    3.143 closest distance to " O   HOH Z  64 " =    2.289
peak=    3.143 closest distance to " N   ASN A 127 " =    1.239
peak=    3.142 closest distance to " O   HOH Z 305 " =    3.576
peak=    3.142 closest distance to " CB  THR A 279 " =    1.618
peak=    3.140 closest distance to " O   HOH Z  73 " =    1.464
peak=    3.133 closest distance to " O   HOH Z 409 " =    3.116
peak=    3.133 closest distance to " CB  ASP A 140 " =    0.888
peak=    3.130 closest distance to " CG1 VAL A 153 " =    1.025
peak=    3.122 closest distance to " CG  MET A 113 " =    1.095
peak=    3.121 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.119 closest distance to " CB  GLU A  46 " =    1.009
peak=    3.104 closest distance to " O   HOH Z 422 " =    2.660
peak=    3.103 closest distance to " CA  LEU A 282 " =    1.180
peak=    3.097 closest distance to " O   HOH Z  59 " =    2.267
peak=    3.095 closest distance to " O   HOH Z 222 " =    2.380
peak=    3.088 closest distance to " CA  MET A 105 " =    0.986
peak=    3.087 closest distance to " NE2 GLN A  58 " =    2.402
peak=    3.075 closest distance to " O   HOH Z 189 " =    2.163
peak=    3.073 closest distance to " CG2 VAL A  78 " =    0.900
peak=    3.068 closest distance to " CB  MET A  47 " =    1.009
peak=    3.064 closest distance to " CB  SER A  62 " =    1.349
peak=    3.062 closest distance to " O   HOH Z 357 " =    1.825
peak=    3.058 closest distance to " CB  ALA A  71 " =    1.255
peak=    3.058 closest distance to " CA  ARG A  56 " =    1.463
peak=    3.055 closest distance to " N   SER A 135 " =    1.291
peak=    3.050 closest distance to " O   HOH Z 403 " =    1.239
peak=    3.036 closest distance to " CG  MET A  93 " =    0.971

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.675 - 5.865
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.828 - 5.865

peak=   -4.940 closest distance to " O   HOH Z 266 " =    4.325
peak=   -4.495 closest distance to " C   HIS A 108 " =    1.098
peak=   -4.415 closest distance to " N   ALA A 248 " =    1.725
peak=   -4.311 closest distance to " OXT GLY A 302 " =    2.707
peak=   -4.260 closest distance to " SG  CYS A 254 " =    3.272
peak=   -4.183 closest distance to " CD  ARG A 156 " =    2.036
peak=   -4.161 closest distance to " O   HOH Z 290 " =    1.006
peak=   -4.160 closest distance to " CB  PRO A 243 " =    2.623
peak=   -4.112 closest distance to " O   VAL A  67 " =    2.785
peak=   -4.105 closest distance to " O   HOH Z  13 " =    1.553
peak=   -4.094 closest distance to " O   VAL A  67 " =    2.771
peak=   -4.079 closest distance to " N   GLN A  58 " =    1.666
peak=   -4.019 closest distance to " O   HOH Z  11 " =    1.908
peak=   -4.007 closest distance to " CB  ALA A 161 " =    2.472
peak=   -3.986 closest distance to " O   PRO A 163 " =    1.995
peak=   -3.959 closest distance to " CZ  TYR A 169 " =    1.766
peak=   -3.956 closest distance to " CD1 PHE A 130 " =    2.201
peak=   -3.951 closest distance to " CD1 LEU A 101 " =    2.430
peak=   -3.943 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.941 closest distance to " OG  SER A  97 " =    2.080
peak=   -3.926 closest distance to " ND2 ASN A  45 " =    0.945
peak=   -3.917 closest distance to " O   HOH Z 102 " =    1.705
peak=   -3.896 closest distance to " CD  ARG A 139 " =    1.544
peak=   -3.881 closest distance to " O   HOH Z 126 " =    1.808
peak=   -3.873 closest distance to " N   ALA A 248 " =    2.199
peak=   -3.857 closest distance to " O   HOH Z 372 " =    2.241
peak=   -3.852 closest distance to " CD1 LEU A 228 " =    2.122
peak=   -3.839 closest distance to " O   HOH Z 407 " =    2.864
peak=   -3.838 closest distance to " O   HOH Z 377 " =    1.939
peak=   -3.836 closest distance to " O   HOH Z  52 " =    1.474
peak=   -3.834 closest distance to " OG BSER A 134 " =    1.234
peak=   -3.824 closest distance to " OG  SER A   3 " =    1.567
peak=   -3.822 closest distance to " OE1 GLN A 223 " =    2.301
peak=   -3.819 closest distance to " O   GLY A  80 " =    2.404
peak=   -3.765 closest distance to " CG  PHE A 283 " =    2.611
peak=   -3.759 closest distance to " O   HOH Z 118 " =    3.088
peak=   -3.749 closest distance to " O   HOH Z 185 " =    2.221
peak=   -3.739 closest distance to " O   TRP A  92 " =    1.781
peak=   -3.737 closest distance to " O   HOH Z 165 " =    1.993
peak=   -3.703 closest distance to " OD1 ASN A  39 " =    2.183
peak=   -3.700 closest distance to " CD1 PHE A  59 " =    1.895
peak=   -3.687 closest distance to " O   HOH Z 166 " =    1.466
peak=   -3.680 closest distance to " O   HOH Z 198 " =    2.038
peak=   -3.677 closest distance to " OG BSER A 134 " =    1.703
peak=   -3.676 closest distance to " C   ALA A 158 " =    1.183
peak=   -3.675 closest distance to " NH2 ARG A  79 " =    1.946
peak=   -3.674 closest distance to " CB  PHE A 192 " =    1.872
peak=   -3.667 closest distance to " CB  ASN A  39 " =    2.266
peak=   -3.661 closest distance to " N   ASP A 286 " =    2.324
peak=   -3.651 closest distance to " O   HOH Z 351 " =    1.404
peak=   -3.640 closest distance to " CB  ALA A 291 " =    2.409
peak=   -3.624 closest distance to " CD2 LEU A 300 " =    2.908
peak=   -3.624 closest distance to " CE2 TYR A  30 " =    2.856
peak=   -3.623 closest distance to " O   HOH Z 362 " =    5.865
peak=   -3.610 closest distance to " O   HOH Z 234 " =    4.021
peak=   -3.609 closest distance to " CE  MET A 105 " =    2.151
peak=   -3.608 closest distance to " CD1 ILE A 239 " =    2.471
peak=   -3.598 closest distance to " O   ALA A 161 " =    1.560
peak=   -3.583 closest distance to " OE2 GLU A   2 " =    1.912
peak=   -3.575 closest distance to " O   MET A  40 " =    2.668
peak=   -3.567 closest distance to " O   VAL A 174 " =    2.019
peak=   -3.557 closest distance to " OD2 ASP A 171 " =    2.296
peak=   -3.549 closest distance to " CD  GLN A  58 " =    1.348
peak=   -3.548 closest distance to " CZ3 TRP A 179 " =    1.348
peak=   -3.547 closest distance to " O   HOH Z 388 " =    2.082
peak=   -3.544 closest distance to " O   HOH Z 250 " =    1.430
peak=   -3.534 closest distance to " O   HOH Z  11 " =    1.735
peak=   -3.525 closest distance to " O   HOH Z  10 " =    1.409
peak=   -3.523 closest distance to " CD2 LEU A 237 " =    2.476
peak=   -3.520 closest distance to " ND2 ASN A 187 " =    1.447
peak=   -3.519 closest distance to " NE2 GLN A  58 " =    1.184
peak=   -3.513 closest distance to " O   HOH Z  43 " =    1.626
peak=   -3.507 closest distance to " CG  ASP A 132 " =    2.273
peak=   -3.503 closest distance to " NH2 ARG A  66 " =    4.782
peak=   -3.500 closest distance to " C   LEU A 143 " =    1.047
peak=   -3.498 closest distance to " O   SER A 146 " =    1.029
peak=   -3.481 closest distance to " OD2 ASP A 191 " =    1.499
peak=   -3.475 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -3.473 closest distance to " O   HOH Z 116 " =    1.313
peak=   -3.473 closest distance to " CG  ASP A 231 " =    0.828
peak=   -3.472 closest distance to " O   HOH Z 196 " =    1.873
peak=   -3.454 closest distance to " CD1 LEU A 255 " =    2.681
peak=   -3.452 closest distance to " O   SER A 210 " =    1.890
peak=   -3.448 closest distance to " CG  GLU A  53 " =    1.338
peak=   -3.431 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.429 closest distance to " CZ  PHE A 130 " =    0.900
peak=   -3.428 closest distance to " N   ALA A  43 " =    2.565
peak=   -3.424 closest distance to " CB  GLN A  11 " =    1.752
peak=   -3.422 closest distance to " CA  GLY A 133 " =    1.857
peak=   -3.421 closest distance to " CG2 ILE A 263 " =    2.185
peak=   -3.418 closest distance to " O   HOH Z  97 " =    1.573
peak=   -3.407 closest distance to " OXT GLY A 302 " =    3.222
peak=   -3.407 closest distance to " OD1 ASP A 191 " =    1.619
peak=   -3.403 closest distance to " O   HOH Z  71 " =    1.376
peak=   -3.398 closest distance to " CB  PHE A 208 " =    2.207
peak=   -3.388 closest distance to " N   SER A 276 " =    1.254
peak=   -3.388 closest distance to " O   HOH Z  47 " =    1.524
peak=   -3.375 closest distance to " O   HOH Z 263 " =    2.917
peak=   -3.375 closest distance to " OD2 ASP A  50 " =    1.336
peak=   -3.371 closest distance to " CZ3 TRP A 274 " =    2.427
peak=   -3.365 closest distance to " O   HOH Z 417 " =    2.495
peak=   -3.361 closest distance to " CA  TYR A  68 " =    2.934
peak=   -3.359 closest distance to " O   HOH Z 134 " =    2.628
peak=   -3.359 closest distance to " O   HOH Z  41 " =    2.263
peak=   -3.359 closest distance to " N   HIS A 115 " =    1.988
peak=   -3.359 closest distance to " C   GLN A 205 " =    1.877
peak=   -3.357 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.357 closest distance to " C   ASP A 231 " =    2.648
peak=   -3.356 closest distance to " ND2 ASN A  39 " =    1.279
peak=   -3.353 closest distance to " O   HOH Z 353 " =    2.213
peak=   -3.349 closest distance to " CA  GLY A 203 " =    2.280
peak=   -3.346 closest distance to " C   PRO A  90 " =    1.512
peak=   -3.345 closest distance to " ND2 ASN A 209 " =    1.746
peak=   -3.340 closest distance to " O   HOH Z 311 " =    3.420
peak=   -3.336 closest distance to " O   HOH Z 427 " =    1.408
peak=   -3.336 closest distance to " O   HOH Z 423 " =    2.234
peak=   -3.328 closest distance to " CD1 TYR A 247 " =    2.434
peak=   -3.325 closest distance to " O   HOH Z 385 " =    2.029
peak=   -3.321 closest distance to " O   ALA A  34 " =    2.400
peak=   -3.320 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.318 closest distance to " O   HOH Z  15 " =    1.566
peak=   -3.311 closest distance to " O   SER A 135 " =    1.564
peak=   -3.309 closest distance to " O   ILE A 120 " =    1.360
peak=   -3.305 closest distance to " O   SER A  95 " =    1.502
peak=   -3.300 closest distance to " O   HOH Z 326 " =    1.624
peak=   -3.299 closest distance to " O   HOH Z 281 " =    2.696
peak=   -3.299 closest distance to " NH2AARG A 275 " =    5.024
peak=   -3.295 closest distance to " O   HOH Z 113 " =    2.187
peak=   -3.295 closest distance to " OD1 ASP A 191 " =    1.457
peak=   -3.294 closest distance to " O   ASN A  45 " =    1.841
peak=   -3.283 closest distance to " N   GLN A 122 " =    1.452
peak=   -3.282 closest distance to " O   HOH Z 421 " =    3.266
peak=   -3.280 closest distance to " CD1 LEU A  25 " =    2.431
peak=   -3.280 closest distance to " CG  ASP A  50 " =    2.367
peak=   -3.277 closest distance to " O   HOH Z 313 " =    2.058
peak=   -3.276 closest distance to " O   SER A  26 " =    1.165
peak=   -3.275 closest distance to " O   HOH Z 283 " =    1.803
peak=   -3.274 closest distance to " OG  SER A  62 " =    1.368
peak=   -3.274 closest distance to " CG  GLU A 152 " =    0.970
peak=   -3.274 closest distance to " CG  GLU A 277 " =    1.177
peak=   -3.272 closest distance to " O   ASN A 187 " =    1.470
peak=   -3.267 closest distance to " CG2 THR A 178 " =    2.203
peak=   -3.265 closest distance to " O   HOH Z 166 " =    2.016
peak=   -3.262 closest distance to " O   HOH Z 407 " =    3.308
peak=   -3.261 closest distance to " O   HOH Z 395 " =    5.146
peak=   -3.256 closest distance to " ND2 ASN A 249 " =    2.230
peak=   -3.253 closest distance to " O   ALA A 292 " =    1.956
peak=   -3.251 closest distance to " N   VAL A 189 " =    1.613
peak=   -3.250 closest distance to " CG2 VAL A 202 " =    2.178
peak=   -3.248 closest distance to " O   HOH Z 198 " =    1.477
peak=   -3.246 closest distance to " O   HOH Z 265 " =    1.991
peak=   -3.245 closest distance to " CA  GLY A  98 " =    1.967
peak=   -3.244 closest distance to " CD  GLN A  88 " =    1.038
peak=   -3.241 closest distance to " NE2 GLN A  88 " =    1.815
peak=   -3.241 closest distance to " N   SER A  12 " =    1.405
peak=   -3.237 closest distance to " OE1 GLN A 194 " =    1.534
peak=   -3.231 closest distance to " O   ALA A 256 " =    1.498
peak=   -3.229 closest distance to " O   HOH Z 148 " =    3.692
peak=   -3.229 closest distance to " CB  ASP A 286 " =    1.958
peak=   -3.228 closest distance to " O   ALA A   1 " =    1.857
peak=   -3.225 closest distance to " OD1 ASN A 148 " =    1.595
peak=   -3.218 closest distance to " CB  PRO A 163 " =    2.660
peak=   -3.215 closest distance to " NH1 ARG A 195 " =    2.504
peak=   -3.214 closest distance to " CB  ALA A 248 " =    1.986
peak=   -3.214 closest distance to " O   HOH Z 309 " =    2.506
peak=   -3.213 closest distance to " O   HOH Z 377 " =    1.795
peak=   -3.210 closest distance to " CE  MET A  93 " =    1.105
peak=   -3.205 closest distance to " O   ALA A  51 " =    1.417
peak=   -3.200 closest distance to " OG ASER A 134 " =    1.474
peak=   -3.197 closest distance to " NE2 GLN A 103 " =    1.659
peak=   -3.194 closest distance to " O   GLY A 196 " =    0.941
peak=   -3.191 closest distance to " O   LEU A 167 " =    1.476
peak=   -3.188 closest distance to " O   HOH Z 150 " =    1.684
peak=   -3.187 closest distance to " NE2 GLN A 194 " =    1.643
peak=   -3.183 closest distance to " CG1AVAL A  41 " =    2.816
peak=   -3.175 closest distance to " O   HOH Z 210 " =    1.013
peak=   -3.174 closest distance to " O   HOH Z 197 " =    4.960
peak=   -3.162 closest distance to " SG ACYS A 201 " =    1.946
peak=   -3.159 closest distance to " OE1 GLN A  88 " =    1.120
peak=   -3.157 closest distance to " O   HOH Z 422 " =    1.432
peak=   -3.156 closest distance to " CB  PRO A 213 " =    1.618
peak=   -3.155 closest distance to " O   HOH Z  63 " =    1.399
peak=   -3.144 closest distance to " N   VAL A 296 " =    2.497
peak=   -3.144 closest distance to " CG1 VAL A 250 " =    2.631
peak=   -3.144 closest distance to " O   HOH Z 191 " =    5.544
peak=   -3.133 closest distance to " CG  GLU A 152 " =    2.272
peak=   -3.132 closest distance to " OH  TYR A 172 " =    1.747
peak=   -3.128 closest distance to " CG  ASN A 301 " =    1.946
peak=   -3.127 closest distance to " O   HOH Z 360 " =    2.567
peak=   -3.113 closest distance to " O   HOH Z 200 " =    4.893
peak=   -3.109 closest distance to " O   PRO A 198 " =    1.224
peak=   -3.109 closest distance to " N   SER A 245 " =    2.374
peak=   -3.108 closest distance to " O   LYS A 117 " =    1.598
peak=   -3.097 closest distance to " O   ASN A 249 " =    1.433
peak=   -3.095 closest distance to " O   GLY A 111 " =    1.145
peak=   -3.094 closest distance to " O   HOH Z  60 " =    1.912
peak=   -3.090 closest distance to " O   HOH Z 243 " =    2.024
peak=   -3.081 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.081 closest distance to " O   ARG A  56 " =    1.528
peak=   -3.074 closest distance to " OD1 ASP A 171 " =    1.563
peak=   -3.071 closest distance to " O   HOH Z 351 " =    1.195
peak=   -3.070 closest distance to " CE1 TYR A 247 " =    2.643
peak=   -3.056 closest distance to " O   HOH Z 378 " =    1.710
peak=   -3.053 closest distance to " O   HOH Z 396 " =    1.628
peak=   -3.038 closest distance to " CD1 PHE A 208 " =    2.597

================= 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    :  0.3888 0.3850   6.168339e+00   6.172822e+00
   1_bss:  0.3781 0.3724   6.153366e+00   6.146611e+00
   1_xyz:  0.2144 0.2335   5.661567e+00   5.745513e+00
   1_adp:  0.1939 0.2442   5.607720e+00   5.782528e+00
   1_occ:  0.1936 0.2443   5.606973e+00   5.782250e+00
   2_bss:  0.1889 0.2403   5.593846e+00   5.770207e+00
   2_xyz:  0.1389 0.1867   5.321577e+00   5.534234e+00
   2_adp:  0.1312 0.1766   5.265673e+00   5.474646e+00
   2_occ:  0.1310 0.1765   5.264171e+00   5.473454e+00
   3_bss:  0.1311 0.1751   5.260046e+00   5.466697e+00
   3_xyz:  0.1199 0.1632   5.189348e+00   5.407219e+00
   3_adp:  0.1148 0.1599   5.155919e+00   5.382810e+00
   3_occ:  0.1147 0.1599   5.155609e+00   5.382655e+00
   4_bss:  0.1147 0.1597   5.155126e+00   5.382236e+00
   4_xyz:  0.1063 0.1547   5.106848e+00   5.357751e+00
   4_adp:  0.1056 0.1538   5.101583e+00   5.353272e+00
   4_occ:  0.1055 0.1538   5.101506e+00   5.353458e+00
   5_bss:  0.1055 0.1538   5.101421e+00   5.353434e+00
   5_xyz:  0.1070 0.1543   5.112253e+00   5.359673e+00
   5_adp:  0.1069 0.1547   5.112914e+00   5.362181e+00
   5_occ:  0.1069 0.1546   5.112791e+00   5.362164e+00
   5_bss:  0.1069 0.1547   5.114171e+00   5.362450e+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:  0.310  20.758  -1.391  -2.067   2.294  -0.000   0.000   0.000
   1_xyz:  0.310  20.758  -1.391  -2.067   2.294  -0.000   0.000   0.000
   1_adp:  0.310  20.758  -1.391  -2.067   2.294  -0.000   0.000   0.000
   1_occ:  0.310  20.758  -1.391  -2.067   2.294  -0.000   0.000   0.000
   2_bss:  0.314  32.468  -2.854  -2.455  -0.876  -0.000  -0.000  -0.000
   2_xyz:  0.314  32.468  -2.854  -2.455  -0.876  -0.000  -0.000  -0.000
   2_adp:  0.314  32.468  -2.854  -2.455  -0.876  -0.000  -0.000  -0.000
   2_occ:  0.314  32.468  -2.854  -2.455  -0.876  -0.000  -0.000  -0.000
   3_bss:  0.316  35.975  -3.150  -2.391  -1.691  -0.000  -0.000  -0.000
   3_xyz:  0.316  35.975  -3.150  -2.391  -1.691  -0.000  -0.000  -0.000
   3_adp:  0.316  35.975  -3.150  -2.391  -1.691  -0.000  -0.000  -0.000
   3_occ:  0.316  35.975  -3.150  -2.391  -1.691  -0.000  -0.000  -0.000
   4_bss:  0.315  35.975  -3.214  -2.393  -1.998  -0.000  -0.000  -0.000
   4_xyz:  0.315  35.975  -3.214  -2.393  -1.998  -0.000  -0.000  -0.000
   4_adp:  0.315  35.975  -3.214  -2.393  -1.998  -0.000  -0.000  -0.000
   4_occ:  0.315  35.975  -3.214  -2.393  -1.998  -0.000  -0.000  -0.000
   5_bss:  0.322  38.568  -3.149  -2.323  -1.972  -0.000  -0.000  -0.000
   5_xyz:  0.322  38.568  -3.149  -2.323  -1.972  -0.000  -0.000  -0.000
   5_adp:  0.322  38.568  -3.149  -2.323  -1.972  -0.000  -0.000  -0.000
   5_occ:  0.322  38.568  -3.149  -2.323  -1.972  -0.000  -0.000  -0.000
   5_bss:  0.322  38.506  -2.988  -2.134  -1.820  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.045 0.6082  0.8029    45252.231
   1_bss:  41.553 0.6244  0.8143    41038.075
   1_xyz:  22.398 0.8392  1.0184    13769.881
   1_adp:  23.788 0.8242  1.0121    14981.838
   1_occ:  23.777 0.8243  1.0119    14969.529
   2_bss:  23.298 0.8289  0.9568    14440.014
   2_xyz:  17.455 0.8846  0.9902     8568.361
   2_adp:  16.019 0.8980  1.0007     7677.898
   2_occ:  15.993 0.8982  1.0007     7649.134
   3_bss:  15.807 0.8997  0.9888     7506.363
   3_xyz:  14.482 0.9109  0.9951     6583.496
   3_adp:  13.961 0.9153  0.9943     6286.560
   3_occ:  13.954 0.9154  0.9942     6281.221
   4_bss:  13.946 0.9154  0.9896     6278.044
   4_xyz:  13.469 0.9190  0.9891     5946.156
   4_adp:  13.352 0.9202  0.9848     5899.831
   4_occ:  13.349 0.9202  0.9848     5900.258
   5_bss:  13.349 0.9202  0.9868     5905.446
   5_xyz:  13.417 0.9198  0.9867     5970.248
   5_adp:  13.456 0.9195  0.9825     5998.183
   5_occ:  13.453 0.9196  0.9824     5996.488
   5_bss:  13.471 0.9194  0.9856     5996.754
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8784e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8784e-01
   1_xyz:   1.260  0.011  0.078 15.517  0.006  4.107   9.2012e-02
   1_adp:   1.260  0.011  0.078 15.517  0.006  4.107   9.2012e-02
   1_occ:   1.260  0.011  0.078 15.517  0.006  4.107   9.2012e-02
   2_bss:   1.260  0.011  0.078 15.517  0.006  4.107   9.2012e-02
   2_xyz:   1.002  0.006  0.069 14.513  0.004  4.108   5.6603e-02
   2_adp:   1.002  0.006  0.069 14.513  0.004  4.108   5.6603e-02
   2_occ:   1.002  0.006  0.069 14.513  0.004  4.108   5.6603e-02
   3_bss:   1.002  0.006  0.069 14.513  0.004  4.108   5.6603e-02
   3_xyz:   0.938  0.005  0.068 14.569  0.004  4.108   5.2329e-02
   3_adp:   0.938  0.005  0.068 14.569  0.004  4.108   5.2329e-02
   3_occ:   0.938  0.005  0.068 14.569  0.004  4.108   5.2329e-02
   4_bss:   0.938  0.005  0.068 14.569  0.004  4.108   5.2329e-02
   4_xyz:   1.138  0.008  0.079 15.046  0.005  4.108   7.1849e-02
   4_adp:   1.138  0.008  0.079 15.046  0.005  4.108   7.1849e-02
   4_occ:   1.138  0.008  0.079 15.046  0.005  4.108   7.1849e-02
   5_bss:   1.138  0.008  0.079 15.046  0.005  4.108   7.1849e-02
   5_xyz:   0.992  0.006  0.072 14.630  0.004  4.108   5.7436e-02
   5_adp:   0.992  0.006  0.072 14.630  0.004  4.108   5.7436e-02
   5_occ:   0.992  0.006  0.072 14.630  0.004  4.108   5.7436e-02
   5_bss:   0.992  0.006  0.072 14.630  0.004  4.108   5.7436e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.422   2.3954e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.422   2.3954e-01
   1_xyz:   8.138  0.090  0.276 86.357  0.038  2.130   1.0313e-01
   1_adp:   8.138  0.090  0.276 86.357  0.038  2.130   1.0313e-01
   1_occ:   8.138  0.090  0.276 86.357  0.038  2.130   1.0313e-01
   2_bss:   8.138  0.090  0.276 86.357  0.038  2.130   1.0313e-01
   2_xyz:   6.556  0.039  0.246 82.653  0.043  2.367   4.6744e-02
   2_adp:   6.556  0.039  0.246 82.653  0.043  2.367   4.6744e-02
   2_occ:   6.556  0.039  0.246 82.653  0.043  2.367   4.6744e-02
   3_bss:   6.556  0.039  0.246 82.653  0.043  2.367   4.6744e-02
   3_xyz:   6.705  0.036  0.219 84.315  0.039  2.396   3.5010e-02
   3_adp:   6.705  0.036  0.219 84.315  0.039  2.396   3.5010e-02
   3_occ:   6.705  0.036  0.219 84.315  0.039  2.396   3.5010e-02
   4_bss:   6.705  0.036  0.219 84.315  0.039  2.396   3.5010e-02
   4_xyz:   7.424  0.046  0.252 82.002  0.042  2.238   5.6682e-02
   4_adp:   7.424  0.046  0.252 82.002  0.042  2.238   5.6682e-02
   4_occ:   7.424  0.046  0.252 82.002  0.042  2.238   5.6682e-02
   5_bss:   7.424  0.046  0.252 82.002  0.042  2.238   5.6682e-02
   5_xyz:   6.877  0.045  0.240 82.649  0.042  2.348   3.8716e-02
   5_adp:   6.877  0.045  0.240 82.649  0.042  2.348   3.8716e-02
   5_occ:   6.877  0.045  0.240 82.649  0.042  2.348   3.8716e-02
   5_bss:   6.877  0.045  0.240 82.649  0.042  2.348   3.8716e-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:  90.71   0.00  17.99  90.71   0.00  13.80  79.74   7.12  40.78
   1_occ:  90.71   0.00  17.99  90.71   0.00  13.80  79.74   7.12  40.78
   2_bss:  90.71   0.00  17.99  90.71   0.00  13.80  79.74   7.12  40.78
   2_xyz:  90.71   0.00  17.99  90.71   0.00  13.80  79.74   7.12  40.78
   2_adp:  90.66   0.00  17.89  90.66   0.00  13.76  79.17   7.01  40.35
   2_occ:  90.66   0.00  17.89  90.66   0.00  13.76  79.17   7.01  40.35
   3_bss:  90.66   0.00  17.89  90.66   0.00  13.76  79.17   7.01  40.35
   3_xyz:  90.66   0.00  17.89  90.66   0.00  13.76  79.17   7.01  40.35
   3_adp:  94.17   1.81  17.64  94.17   1.81  13.47  82.69   6.28  40.36
   3_occ:  94.17   1.81  17.64  94.17   1.81  13.47  82.69   6.28  40.36
   4_bss:  94.17   1.81  17.64  94.17   1.81  13.47  82.69   6.28  40.36
   4_xyz:  94.17   1.81  17.64  94.17   1.81  13.47  82.69   6.28  40.36
   4_adp:  92.97   2.15  17.22  92.97   2.15  13.22  82.28   5.93  39.04
   4_occ:  92.97   2.15  17.22  92.97   2.15  13.22  82.28   5.93  39.04
   5_bss:  92.97   2.15  17.22  92.97   2.15  13.22  82.28   5.93  39.04
   5_xyz:  92.97   2.15  17.22  92.97   2.15  13.22  82.28   5.93  39.04
   5_adp:  92.91   1.73  17.11  92.91   1.73  13.11  81.86   5.91  38.92
   5_occ:  92.91   1.73  17.11  92.91   1.73  13.11  81.86   5.91  38.92
   5_bss:  92.85   1.67  17.05  92.85   1.67  13.05  81.80   5.84  38.85
------------------------------------------------------------------------
 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:    1.593    0.018    0.389
   1_adp:    1.593    0.018    0.389
   1_occ:    1.593    0.018    0.389
   2_bss:    1.593    0.018    0.389
   2_xyz:    1.291    0.050    0.460
   2_adp:    1.291    0.050    0.460
   2_occ:    1.291    0.050    0.460
   3_bss:    1.291    0.050    0.460
   3_xyz:    1.366    0.036    0.492
   3_adp:    1.366    0.036    0.492
   3_occ:    1.366    0.036    0.492
   4_bss:    1.366    0.036    0.492
   4_xyz:    1.292    0.084    0.514
   4_adp:    1.292    0.084    0.514
   4_occ:    1.292    0.084    0.514
   5_bss:    1.292    0.084    0.514
   5_xyz:    1.415    0.073    0.517
   5_adp:    1.415    0.073    0.517
   5_occ:    1.415    0.073    0.517
   5_bss:    1.415    0.073    0.517
------------------------------------------------------------------------

CPU time actual refinement: 338.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/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_309/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_309/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.79 
  Macro-tasks:
    bulk solvent and scale       = 41.48  
    individual site refinement   = 134.83 
    weights calculation          = 29.45  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.48 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 108.89 
    alpha_beta                      = 8.62   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.19 
    fmodel                         = 7.26   
    r_factors                      = 0.23   
    phase_errors                   = 11.06  
    foms                           = 0.17   
    TOTAL for micro-tasks          = 255.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.812 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    650 calls, 108.53 s
gradients_fft:          595 calls, 103.06 s

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

# Date 2008-01-16 Time 04:31:42 PST -0800 (1200486702.49 s)
Start R-work = 0.3888, R-free = 0.3850 (no bulk solvent and anisotropic scale)
Final R-work = 0.1344, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.3781, R-free = 0.3724
Final R-work = 0.1069, R-free = 0.1547