# Date 2008-01-16 Time 05:05:52 PST -0800 (1200488752.28 s)
#phil __OFF__

Command line arguments: "../588.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10344
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 588

-------------------------------------------------------------------------------
  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: (69.8988, 47.8686, 86.39, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9676 1.9906
Completeness in resolution range: 0.958554
Completeness with d_max=infinity: 0.955561

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9676
                             d_min =   1.9906

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: (69.8988, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9676 1.9906
Completeness in resolution range: 0.958554
Completeness with d_max=infinity: 0.955561

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9681 -  4.2588 [2150/2178]  1935   215  10.0%
  bin  2:  4.2588 -  3.3933 [2045/2068]  1842   203   9.9%
  bin  3:  3.3933 -  2.9681 [2042/2064]  1837   205  10.0%
  bin  4:  2.9681 -  2.6985 [2011/2030]  1812   199   9.9%
  bin  5:  2.6985 -  2.5060 [2016/2045]  1807   209  10.4%
  bin  6:  2.5060 -  2.3589 [1974/2015]  1785   189   9.6%
  bin  7:  2.3589 -  2.2412 [1984/2020]  1787   197   9.9%
  bin  8:  2.2412 -  2.1439 [1975/2013]  1771   204  10.3%
  bin  9:  2.1439 -  2.0616 [1953/1984]  1757   196  10.0%
  bin 10:  2.0616 -  1.9906 [1439/2019]  1297   142   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 22
        2.42 -     3.04: 2178
        3.04 -     3.66: 4654
        3.66 -     4.28: 8933
        4.28 -     4.90: 12314
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.029 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.095 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.101 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.131 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28096 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_588/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 69.89875 47.8686 86.39 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: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3765   r_free= 0.3621   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.181264                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9681 -  4.7497 0.99   1391  156 0.3172 0.3429      6.4413      6.4641|
|  2:  4.7497 -  3.7901 0.99   1343  149 0.3172 0.3074      6.6698      6.6444|
|  3:  3.7901 -  3.3170 0.99   1317  150 0.3395 0.3118      6.5422      6.4763|
|  4:  3.3170 -  3.0164 0.99   1309  133 0.3536 0.2992      6.3939      6.2415|
|  5:  3.0164 -  2.8017 0.98   1286  147 0.3915 0.3483      6.2753       6.234|
|  6:  2.8017 -  2.6375 0.98   1291  143 0.3987 0.3827      6.1866      6.0465|
|  7:  2.6375 -  2.5060 0.99   1296  153 0.4019 0.3562      6.1643      6.0237|
|  8:  2.5060 -  2.3974 0.99   1283  133 0.4053 0.4276      6.0887      6.1086|
|  9:  2.3974 -  2.3055 0.98   1279  147 0.4209 0.4103      6.0456      6.0502|
| 10:  2.3055 -  2.2262 0.97   1255  141 0.4201 0.4225      6.0342      6.0175|
| 11:  2.2262 -  2.1568 0.98   1272  142 0.4149 0.3496      5.9533      5.9101|
| 12:  2.1568 -  2.0953 0.99   1273  141 0.4273 0.4470      5.9106      5.9795|
| 13:  2.0953 -  2.0403 0.97   1267  133 0.4355 0.3871      5.8322      5.7891|
| 14:  2.0403 -  1.9906 0.61    768   91 0.3996 0.4610      5.7596      5.7386|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9681 -  4.7497  1391   156  0.73  31.15   0.85     0.76      58566.02|
|  2:  4.7497 -  3.7901  1343   149  0.79  27.01   0.94     0.86      65859.98|
|  3:  3.7901 -  3.3170  1317   150  0.76  30.59   0.95     0.90      63180.93|
|  4:  3.3170 -  3.0164  1309   133  0.73  33.20   0.95     0.88      51543.51|
|  5:  3.0164 -  2.8017  1286   147  0.68  37.63   0.94     0.85      42518.28|
|  6:  2.8017 -  2.6375  1291   143  0.66  38.96   0.94     0.83      36227.15|
|  7:  2.6375 -  2.5060  1296   153  0.65  39.92   0.97     0.82      34408.72|
|  8:  2.5060 -  2.3974  1283   133  0.62  42.71   0.96     0.80      34652.48|
|  9:  2.3974 -  2.3055  1279   147  0.58  45.41   0.96     0.80      33759.27|
| 10:  2.3055 -  2.2262  1255   141  0.59  45.11   0.99     0.80      31768.67|
| 11:  2.2262 -  2.1568  1272   142  0.59  45.21   0.98     0.82      29051.42|
| 12:  2.1568 -  2.0953  1273   141  0.57  47.07   1.00     0.81      28620.09|
| 13:  2.0953 -  2.0403  1267   133  0.52  50.30   0.97     0.74      26316.96|
| 14:  2.0403 -  1.9906   768    91  0.48  53.83   1.01     0.64      23457.59|
|alpha:            min =        0.64 max =            0.90 mean =         0.81|
|beta:             min =    23457.59 max =        65859.98 mean =     40776.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           89.98 mean =        40.03|
|phase err.(test): min =        0.00 max =           89.86 mean =        40.30|
|-----------------------------------------------------------------------------|

============================== 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 = 8.575945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.960950              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.737   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      176 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2002 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1853 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2801 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4585 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4348 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5622 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6692 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.178 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    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: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3765   r_free= 0.3621   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.181264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3605   r_free= 0.3445   ksol= 0.30   Bsol= 34.64   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,5.49,-1.78,0.00,-0.00,-0.00); trace/3= 0.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.160810                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.969830              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.736   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.534132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.570   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3605      final r-factor (work) = 0.2373          |
| start r-factor (free) = 0.3445      final r-factor (free) = 0.2601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7195 = 7.97 * 0.50 * 6.1623 + 1.00 * 0.1634                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6601 = 7.97 * 0.50 * 5.9073 + 1.00 * 0.1199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2373      final r-factor (work) = 0.2161          |
| start r-factor (free) = 0.2601      final r-factor (free) = 0.2709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1614 = 0.53 * 1.00 * 5.9073 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0655 = 0.53 * 1.00 * 5.7121 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.73   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    72.73   17.01    None  None   None       |
|    Sol.    : 438    0      4.47    72.73   38.17    None  None   None       |
|    Mac.    : 2385   0      0.00    62.83   13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.273:  585   |   5:    36.365 -  43.638:  129        |
|      1:     7.273 -  14.546: 1090   |   6:    43.638 -  50.911:   95        |
|      2:    14.546 -  21.819:  493   |   7:    50.911 -  58.183:   67        |
|      3:    21.819 -  29.092:  194   |   8:    58.183 -  65.456:   31        |
|      4:    29.092 -  36.365:  131   |   9:    65.456 -  72.729:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2161 r_free = 0.2709             target_work(ml) = 5.725         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2158 r_free = 0.2712             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2158   r_free= 0.2712   ksol= 0.30   Bsol= 34.64   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,5.49,-1.78,0.00,-0.00,-0.00); trace/3= 0.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.724083                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2118   r_free= 0.2658   ksol= 0.33   Bsol= 60.91   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,1.15,-1.04,0.00,-0.00,-0.00); trace/3= -0.81                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.709819                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.447240              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.733   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.253601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.316  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2118      final r-factor (work) = 0.1606          |
| start r-factor (free) = 0.2658      final r-factor (free) = 0.1994          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9546 = 3.45 * 0.50 * 5.7056 + 1.00 * 0.1202                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7108 = 3.45 * 0.50 * 5.5972 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1497          |
| start r-factor (free) = 0.1994      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4354 = 0.25 * 1.00 * 5.5972 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3790 = 0.25 * 1.00 * 5.4021 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    75.38   16.74    None  None   None       |
|    all(noH): 2823   0      0.86    75.38   16.74    None  None   None       |
|    Sol.    : 438    0      4.41    75.38   38.99    None  None   None       |
|    Mac.    : 2385   0      0.86    72.84   12.65    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:     0.859 -   8.311:  736   |   5:    38.118 -  45.570:  102        |
|      1:     8.311 -  15.763: 1180   |   6:    45.570 -  53.022:   94        |
|      2:    15.763 -  23.214:  362   |   7:    53.022 -  60.473:   55        |
|      3:    23.214 -  30.666:  135   |   8:    60.473 -  67.925:   36        |
|      4:    30.666 -  38.118:  116   |   9:    67.925 -  75.377:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1497 r_free = 0.1871             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1495 r_free = 0.1872             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1495   r_free= 0.1872   ksol= 0.33   Bsol= 60.91   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,1.15,-1.04,0.00,-0.00,-0.00); trace/3= -0.81                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1863   ksol= 0.33   Bsol= 60.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.29,-0.87,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.372783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.988313              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.971  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651737              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.317  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1863      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4339 = 1.99 * 0.50 * 5.4020 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3223 = 1.99 * 0.50 * 5.2948 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4598 = 0.65 * 1.00 * 5.2948 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4132 = 0.65 * 1.00 * 5.2213 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.13   16.83    None  None   None       |
|    all(noH): 2823   0      0.00    86.13   16.83    None  None   None       |
|    Sol.    : 438    0      3.78    82.48   40.79    None  None   None       |
|    Mac.    : 2385   0      0.00    86.13   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.613:  854   |   5:    43.067 -  51.680:  103        |
|      1:     8.613 -  17.227: 1190   |   6:    51.680 -  60.293:   87        |
|      2:    17.227 -  25.840:  287   |   7:    60.293 -  68.907:   46        |
|      3:    25.840 -  34.453:  130   |   8:    68.907 -  77.520:   18        |
|      4:    34.453 -  43.067:  103   |   9:    77.520 -  86.133:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1661             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1661             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1661   ksol= 0.33   Bsol= 60.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.29,-0.87,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215717                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1660   ksol= 0.33   Bsol= 60.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-0.70,-0.67,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215238                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.126065              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.509  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.015301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.665  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2188 = 3.13 * 0.50 * 5.2209 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1714 = 3.13 * 0.50 * 5.1798 + 1.00 * 0.0753                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2692 = 1.02 * 1.00 * 5.1798 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2404 = 1.02 * 1.00 * 5.1509 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.39   16.69    None  None   None       |
|    all(noH): 2823   0      0.00    98.39   16.69    None  None   None       |
|    Sol.    : 438    0      3.57    85.53   40.90    None  None   None       |
|    Mac.    : 2385   0      0.00    98.39   12.25    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 -   9.839: 1165   |   5:    49.194 -  59.032:   91        |
|      1:     9.839 -  19.678: 1035   |   6:    59.032 -  68.871:   62        |
|      2:    19.678 -  29.516:  197   |   7:    68.871 -  78.710:   16        |
|      3:    29.516 -  39.355:  134   |   8:    78.710 -  88.549:    9        |
|      4:    39.355 -  49.194:  111   |   9:    88.549 -  98.387:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1601             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1602             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1602   ksol= 0.33   Bsol= 60.14   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-0.70,-0.67,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1598   ksol= 0.33   Bsol= 60.14   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.67,-0.39,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.150629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.464085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.151  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.496981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8466 = 1.46 * 0.50 * 5.1518 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8352 = 1.46 * 0.50 * 5.1656 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5779 = 0.50 * 1.00 * 5.1656 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5804 = 0.50 * 1.00 * 5.1716 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.74   16.34    None  None   None       |
|    all(noH): 2823   0      0.00    99.74   16.34    None  None   None       |
|    Sol.    : 438    0      4.57    86.94   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    99.74   12.00    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 -   9.974: 1247   |   5:    49.868 -  59.842:   87        |
|      1:     9.974 -  19.947:  971   |   6:    59.842 -  69.816:   49        |
|      2:    19.947 -  29.921:  202   |   7:    69.816 -  79.789:   12        |
|      3:    29.921 -  39.895:  126   |   8:    79.789 -  89.763:    7        |
|      4:    39.895 -  49.868:  119   |   9:    89.763 -  99.737:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1607             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1609             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1609   ksol= 0.33   Bsol= 60.14   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.67,-0.39,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.171152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9681 -  4.7497 0.99   1391  156 0.0980 0.1246      5.3734      5.5283|
|  2:  4.7497 -  3.7901 0.99   1343  149 0.0861 0.1047      5.4299      5.6211|
|  3:  3.7901 -  3.3170 0.99   1317  150 0.1049 0.1504      5.4691      5.8376|
|  4:  3.3170 -  3.0164 0.99   1309  133 0.1267 0.1635      5.4775      5.6309|
|  5:  3.0164 -  2.8017 0.98   1286  147 0.1374 0.1738      5.3646      5.5417|
|  6:  2.8017 -  2.6375 0.98   1291  143 0.1345 0.2083      5.2774      5.5118|
|  7:  2.6375 -  2.5060 0.99   1296  153 0.1249 0.1679      5.1832      5.3871|
|  8:  2.5060 -  2.3974 0.99   1283  133 0.1227 0.1823      5.1221      5.3759|
|  9:  2.3974 -  2.3055 0.98   1279  147 0.1199 0.1921      5.0533      5.3622|
| 10:  2.3055 -  2.2262 0.97   1255  141 0.1186 0.1740       5.015      5.2041|
| 11:  2.2262 -  2.1568 0.98   1272  142 0.1214 0.1804      4.9615      5.2668|
| 12:  2.1568 -  2.0953 0.99   1273  141 0.1142 0.1720      4.8854      5.1667|
| 13:  2.0953 -  2.0403 0.97   1267  133 0.1150 0.1699      4.8154      5.0608|
| 14:  2.0403 -  1.9906 0.61    768   91 0.1128 0.1887      4.7375      5.0188|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9681 -  4.7497  1391   156  0.94   9.05   0.97     0.94       6922.72|
|  2:  4.7497 -  3.7901  1343   149  0.95   8.05   1.00     0.99       8804.06|
|  3:  3.7901 -  3.3170  1317   150  0.94  10.97   1.02     1.01      10216.54|
|  4:  3.3170 -  3.0164  1309   133  0.92  14.03   1.00     0.98      10576.64|
|  5:  3.0164 -  2.8017  1286   147  0.90  16.45   0.99     0.97       8879.17|
|  6:  2.8017 -  2.6375  1291   143  0.89  17.10   0.98     0.95       7837.32|
|  7:  2.6375 -  2.5060  1296   153  0.90  15.81   0.99     0.96       6445.76|
|  8:  2.5060 -  2.3974  1283   133  0.90  15.96   0.99     0.95       5964.45|
|  9:  2.3974 -  2.3055  1279   147  0.90  16.31   0.99     0.94       5246.35|
| 10:  2.3055 -  2.2262  1255   141  0.90  16.42   0.98     0.94       4885.62|
| 11:  2.2262 -  2.1568  1272   142  0.90  16.20   0.98     0.94       4421.75|
| 12:  2.1568 -  2.0953  1273   141  0.91  15.48   0.99     0.97       3946.07|
| 13:  2.0953 -  2.0403  1267   133  0.90  16.37   0.98     0.97       3534.54|
| 14:  2.0403 -  1.9906   768    91  0.90  15.93   0.95     0.91       2919.06|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2919.06 max =        10576.64 mean =      6608.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.47|
|phase err.(test): min =        0.00 max =           89.61 mean =        13.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1608   ksol= 0.32   Bsol= 57.93   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.60,-0.22,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.171248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1608   ksol= 0.32   Bsol= 57.93   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.60,-0.22,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.171248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9681 -  4.7497 0.99   1391  156 0.0979 0.1246       5.373      5.5281|
|  2:  4.7497 -  3.7901 0.99   1343  149 0.0860 0.1046      5.4291      5.6202|
|  3:  3.7901 -  3.3170 0.99   1317  150 0.1049 0.1504      5.4688      5.8376|
|  4:  3.3170 -  3.0164 0.99   1309  133 0.1268 0.1637      5.4778       5.631|
|  5:  3.0164 -  2.8017 0.98   1286  147 0.1375 0.1738       5.365      5.5417|
|  6:  2.8017 -  2.6375 0.98   1291  143 0.1345 0.2081      5.2775      5.5116|
|  7:  2.6375 -  2.5060 0.99   1296  153 0.1249 0.1680      5.1834      5.3873|
|  8:  2.5060 -  2.3974 0.99   1283  133 0.1226 0.1825      5.1226      5.3766|
|  9:  2.3974 -  2.3055 0.98   1279  147 0.1199 0.1920      5.0536       5.362|
| 10:  2.3055 -  2.2262 0.97   1255  141 0.1187 0.1742      5.0155      5.2054|
| 11:  2.2262 -  2.1568 0.98   1272  142 0.1215 0.1804      4.9618      5.2668|
| 12:  2.1568 -  2.0953 0.99   1273  141 0.1142 0.1722      4.8855      5.1677|
| 13:  2.0953 -  2.0403 0.97   1267  133 0.1150 0.1699      4.8156      5.0606|
| 14:  2.0403 -  1.9906 0.61    768   91 0.1128 0.1887      4.7376      5.0184|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9681 -  4.7497  1391   156  0.94   9.05   0.97     0.94       6913.16|
|  2:  4.7497 -  3.7901  1343   149  0.95   8.05   1.01     0.99       8790.60|
|  3:  3.7901 -  3.3170  1317   150  0.94  10.96   1.02     1.02      10204.03|
|  4:  3.3170 -  3.0164  1309   133  0.92  14.03   1.01     0.98      10580.95|
|  5:  3.0164 -  2.8017  1286   147  0.90  16.45   1.00     0.97       8876.14|
|  6:  2.8017 -  2.6375  1291   143  0.89  17.10   0.98     0.95       7836.78|
|  7:  2.6375 -  2.5060  1296   153  0.90  15.81   0.99     0.96       6449.45|
|  8:  2.5060 -  2.3974  1283   133  0.90  15.98   0.99     0.96       5971.23|
|  9:  2.3974 -  2.3055  1279   147  0.90  16.32   1.00     0.95       5254.13|
| 10:  2.3055 -  2.2262  1255   141  0.90  16.44   0.99     0.95       4890.60|
| 11:  2.2262 -  2.1568  1272   142  0.90  16.21   0.99     0.95       4426.14|
| 12:  2.1568 -  2.0953  1273   141  0.91  15.48   1.00     0.98       3949.01|
| 13:  2.0953 -  2.0403  1267   133  0.90  16.37   0.99     0.98       3534.64|
| 14:  2.0403 -  1.9906   768    91  0.90  15.92   0.96     0.91       2917.12|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     2917.12 max =        10580.95 mean =      6607.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.48|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.040)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.74   16.35    None  None   None       |
|    all(noH): 2823   0      0.00    99.74   16.35    None  None   None       |
|    Sol.    : 438    0      4.57    86.95   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    99.74   12.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.977: 1247   |   5:    49.871 -  59.845:   87        |
|      1:     9.977 -  19.950:  971   |   6:    59.845 -  69.819:   49        |
|      2:    19.950 -  29.924:  202   |   7:    69.819 -  79.792:   12        |
|      3:    29.924 -  39.898:  126   |   8:    79.792 -  89.766:    7        |
|      4:    39.898 -  49.871:  119   |   9:    89.766 -  99.740:    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)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.627 - 4.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 322
   mapped sites are within: 0.740 - 4.777

peak=    5.641 closest distance to " NH2 ARG A  56 " =    2.352
peak=    5.530 closest distance to " CB  GLN A 223 " =    1.383
peak=    5.142 closest distance to " CB  SER A  63 " =    1.175
peak=    4.968 closest distance to " CG  PRO A 280 " =    0.800
peak=    4.941 closest distance to " O   HOH Z 210 " =    1.067
peak=    4.939 closest distance to " CG  PRO A  90 " =    1.221
peak=    4.932 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.919 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.887 closest distance to " O   HOH Z 403 " =    1.728
peak=    4.862 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.839 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.822 closest distance to " C   PRO A 198 " =    1.506
peak=    4.790 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.717 closest distance to " CB  ARG A 190 " =    1.742
peak=    4.608 closest distance to " O   HOH Z  15 " =    2.270
peak=    4.579 closest distance to " O   HOH Z 402 " =    1.557
peak=    4.538 closest distance to " O   HOH Z  43 " =    2.206
peak=    4.507 closest distance to " O   HOH Z 234 " =    3.786
peak=    4.451 closest distance to " CD  ARG A 269 " =    1.050
peak=    4.419 closest distance to " O   HOH Z 189 " =    2.314
peak=    4.388 closest distance to " CB  GLU A 128 " =    1.165
peak=    4.360 closest distance to " O   HOH Z 298 " =    1.892
peak=    4.338 closest distance to " O   HOH Z 134 " =    1.561
peak=    4.300 closest distance to " CG1 ILE A  33 " =    1.295
peak=    4.280 closest distance to " CB  ARG A  79 " =    1.295
peak=    4.255 closest distance to " O   HOH Z 209 " =    2.338
peak=    4.252 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.251 closest distance to " O   HOH Z  44 " =    2.010
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.135
peak=    4.241 closest distance to " NH2 ARG A 156 " =    1.190
peak=    4.225 closest distance to " NZ  LYS A 117 " =    3.227
peak=    4.183 closest distance to " CA  ARG A  36 " =    1.067
peak=    4.171 closest distance to " O   SER A  87 " =    2.195
peak=    4.171 closest distance to " O   HOH Z  40 " =    1.859
peak=    4.160 closest distance to " O   HOH Z  97 " =    2.016
peak=    4.155 closest distance to " O   HOH Z 369 " =    2.258
peak=    4.113 closest distance to " CZ  PHE A 218 " =    1.073
peak=    4.107 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.093 closest distance to " O   HOH Z 368 " =    2.042
peak=    4.082 closest distance to " CB  TYR A 169 " =    0.793
peak=    4.075 closest distance to " O   HOH Z  59 " =    2.439
peak=    4.062 closest distance to " CD2 TRP A 179 " =    1.357
peak=    4.050 closest distance to " O   HOH Z 265 " =    2.081
peak=    4.035 closest distance to " CB  GLU A 277 " =    3.662
peak=    4.021 closest distance to " CA  ARG A 195 " =    1.208
peak=    4.021 closest distance to " O   HOH Z 132 " =    2.622
peak=    4.021 closest distance to " NH2BARG A 145 " =    2.151
peak=    4.000 closest distance to " O   HOH Z 352 " =    1.901
peak=    3.991 closest distance to " CA  ASN A 176 " =    1.162
peak=    3.985 closest distance to " CB  SER A 141 " =    1.058
peak=    3.968 closest distance to " CB  LEU A 228 " =    1.123
peak=    3.958 closest distance to " OD1 ASN A  69 " =    2.539
peak=    3.957 closest distance to " CA  ALA A  51 " =    0.958
peak=    3.956 closest distance to " O   HOH Z 423 " =    1.889
peak=    3.951 closest distance to " CA  ALA A  21 " =    1.314
peak=    3.922 closest distance to " O   HOH Z 389 " =    2.024
peak=    3.900 closest distance to " CG  ARG A  66 " =    2.673
peak=    3.888 closest distance to " O   HOH Z 316 " =    3.031
peak=    3.883 closest distance to " CB  SER A  62 " =    0.857
peak=    3.874 closest distance to " CD2 LEU A 297 " =    0.868
peak=    3.868 closest distance to " O   HOH Z 102 " =    1.281
peak=    3.865 closest distance to " CB  ALA A 291 " =    1.267
peak=    3.863 closest distance to " O   HOH Z  63 " =    1.891
peak=    3.862 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.837 closest distance to " O   HOH Z  80 " =    1.774
peak=    3.834 closest distance to " C   ILE A 106 " =    1.897
peak=    3.816 closest distance to " CB  ASN A 148 " =    1.342
peak=    3.810 closest distance to " O   HOH Z 412 " =    3.591
peak=    3.808 closest distance to " CB  SER A   3 " =    1.294
peak=    3.807 closest distance to " CB  TRP A 179 " =    1.327
peak=    3.807 closest distance to " O   HOH Z 357 " =    2.082
peak=    3.805 closest distance to " O   HOH Z 418 " =    1.453
peak=    3.803 closest distance to " CG2 ILE A 120 " =    1.094
peak=    3.796 closest distance to " O   HOH Z 362 " =    3.585
peak=    3.795 closest distance to " O   HOH Z 247 " =    1.446
peak=    3.794 closest distance to " O   HOH Z  67 " =    2.035
peak=    3.792 closest distance to " N   ASN A  39 " =    1.285
peak=    3.779 closest distance to " CB  ASN A  39 " =    0.847
peak=    3.774 closest distance to " CG2BVAL A  41 " =    0.854
peak=    3.772 closest distance to " CG AARG A 275 " =    1.141
peak=    3.766 closest distance to " O   HOH Z  78 " =    1.678
peak=    3.761 closest distance to " O   HOH Z 433 " =    1.474
peak=    3.750 closest distance to " O   HOH Z 374 " =    2.714
peak=    3.749 closest distance to " CB  ASP A 140 " =    0.927
peak=    3.736 closest distance to " O   HOH Z 284 " =    2.911
peak=    3.735 closest distance to " O   HOH Z 250 " =    1.411
peak=    3.727 closest distance to " O   ASN A  74 " =    1.475
peak=    3.727 closest distance to " O   THR A 251 " =    1.177
peak=    3.717 closest distance to " O   HOH Z 261 " =    1.749
peak=    3.712 closest distance to " O   HOH Z 126 " =    1.969
peak=    3.707 closest distance to " O   HOH Z 272 " =    1.898
peak=    3.693 closest distance to " O   HOH Z 245 " =    1.359
peak=    3.692 closest distance to " O   HOH Z 142 " =    1.515
peak=    3.690 closest distance to " O   HOH Z 291 " =    1.539
peak=    3.689 closest distance to " CA  ALA A 160 " =    0.898
peak=    3.688 closest distance to " O   HOH Z  20 " =    1.426
peak=    3.688 closest distance to " O   HOH Z 185 " =    1.715
peak=    3.674 closest distance to " CD1 LEU A 300 " =    1.174
peak=    3.668 closest distance to " ND2 ASN A 187 " =    1.554
peak=    3.658 closest distance to " CZ  PHE A  38 " =    1.275
peak=    3.656 closest distance to " O   HOH Z 371 " =    3.137
peak=    3.656 closest distance to " O   HOH Z 147 " =    1.848
peak=    3.655 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.650 closest distance to " O   HOH Z 346 " =    1.593
peak=    3.650 closest distance to " O   HOH Z  66 " =    2.122
peak=    3.644 closest distance to " O   HOH Z 163 " =    1.580
peak=    3.642 closest distance to " O   HOH Z 279 " =    2.151
peak=    3.640 closest distance to " CD  LYS A 166 " =    1.355
peak=    3.637 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.632 closest distance to " O   THR A 220 " =    1.062
peak=    3.631 closest distance to " C   GLY A  80 " =    1.160
peak=    3.628 closest distance to " CA  ASP A 191 " =    0.842
peak=    3.628 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.619 closest distance to " O   HOH Z 402 " =    2.879
peak=    3.609 closest distance to " O   HOH Z 380 " =    1.767
peak=    3.606 closest distance to " NE2 GLN A  77 " =    3.334
peak=    3.605 closest distance to " CZ3 TRP A 266 " =    1.069
peak=    3.603 closest distance to " O   HOH Z 426 " =    1.522
peak=    3.603 closest distance to " O   HOH Z 132 " =    2.748
peak=    3.599 closest distance to " CG  GLN A  11 " =    1.213
peak=    3.597 closest distance to " OG BSER A 164 " =    2.333
peak=    3.596 closest distance to " CA  ASP A 162 " =    1.155
peak=    3.595 closest distance to " CG  ARG A  66 " =    0.984
peak=    3.593 closest distance to " O   HOH Z 345 " =    1.652
peak=    3.589 closest distance to " CD1 LEU A  96 " =    0.755
peak=    3.587 closest distance to " CG1BVAL A  72 " =    1.817
peak=    3.586 closest distance to " O   HOH Z 403 " =    1.502
peak=    3.579 closest distance to " O   HOH Z  21 " =    1.829
peak=    3.579 closest distance to " O   HOH Z 421 " =    1.930
peak=    3.579 closest distance to " CB  PRO A 198 " =    1.091
peak=    3.576 closest distance to " O   TRP A 274 " =    1.913
peak=    3.575 closest distance to " N   ASP A 132 " =    1.217
peak=    3.571 closest distance to " CB  VAL A 202 " =    1.492
peak=    3.563 closest distance to " CB  MET A  40 " =    0.834
peak=    3.557 closest distance to " O   HOH Z 158 " =    3.002
peak=    3.556 closest distance to " CB  LEU A  83 " =    0.814
peak=    3.551 closest distance to " OG1 THR A 294 " =    2.373
peak=    3.543 closest distance to " O   HOH Z 287 " =    1.829
peak=    3.540 closest distance to " O   HOH Z 437 " =    1.479
peak=    3.533 closest distance to " O   HOH Z 227 " =    1.695
peak=    3.532 closest distance to " O   HOH Z 258 " =    2.225
peak=    3.527 closest distance to " CG  GLN A  58 " =    2.642
peak=    3.524 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.521 closest distance to " CD  ARG A 159 " =    0.810
peak=    3.516 closest distance to " CE  LYS A  76 " =    0.817
peak=    3.513 closest distance to " CG2 VAL A 257 " =    0.844
peak=    3.507 closest distance to " O   HOH Z 173 " =    2.281
peak=    3.506 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.505 closest distance to " O   HOH Z 344 " =    3.121
peak=    3.494 closest distance to " O   HOH Z 214 " =    2.406
peak=    3.490 closest distance to " CG2 ILE A  20 " =    1.346
peak=    3.485 closest distance to " O   HOH Z 406 " =    1.544
peak=    3.484 closest distance to " O   HOH Z 193 " =    1.787
peak=    3.482 closest distance to " CA  VAL A 125 " =    1.270
peak=    3.480 closest distance to " CA  ASN A 215 " =    1.060
peak=    3.479 closest distance to " OD2 ASP A 298 " =    3.960
peak=    3.478 closest distance to " O   ALA A 165 " =    1.370
peak=    3.477 closest distance to " O   HOH Z 124 " =    2.054
peak=    3.474 closest distance to " O   HOH Z 180 " =    2.335
peak=    3.473 closest distance to " N   ILE A  33 " =    1.088
peak=    3.472 closest distance to " O   HOH Z 271 " =    2.720
peak=    3.471 closest distance to " CB  ALA A 248 " =    1.264
peak=    3.470 closest distance to " O   HOH Z  54 " =    1.674
peak=    3.462 closest distance to " O   HOH Z 386 " =    2.285
peak=    3.460 closest distance to " CB  ASN A 285 " =    0.952
peak=    3.456 closest distance to " CA  ALA A 295 " =    1.109
peak=    3.455 closest distance to " CA  VAL A  41 " =    0.859
peak=    3.455 closest distance to " NZ  LYS A 166 " =    3.054
peak=    3.451 closest distance to " NH1AARG A 145 " =    1.258
peak=    3.450 closest distance to " NZ  LYS A  48 " =    1.218
peak=    3.444 closest distance to " CA  GLU A 152 " =    0.864
peak=    3.442 closest distance to " NE2 GLN A  11 " =    0.959
peak=    3.441 closest distance to " CA  ASP A 191 " =    1.083
peak=    3.434 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.430 closest distance to " OE1 GLU A   2 " =    1.996
peak=    3.427 closest distance to " O   HOH Z 214 " =    1.372
peak=    3.426 closest distance to " CG2 THR A 221 " =    1.096
peak=    3.422 closest distance to " CE1 TYR A 186 " =    1.239
peak=    3.418 closest distance to " CD  PRO A  54 " =    0.967
peak=    3.416 closest distance to " CA  SER A  87 " =    1.034
peak=    3.412 closest distance to " N   GLY A  98 " =    1.136
peak=    3.412 closest distance to " O   HOH Z 427 " =    3.028
peak=    3.410 closest distance to " O   HOH Z 345 " =    2.956
peak=    3.409 closest distance to " O   HOH Z 365 " =    2.795
peak=    3.404 closest distance to " CB  ARG A 269 " =    0.825
peak=    3.400 closest distance to " CB  SER A 273 " =    0.850
peak=    3.400 closest distance to " CA  THR A 221 " =    0.914
peak=    3.400 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.399 closest distance to " OE1 GLN A  11 " =    1.912
peak=    3.392 closest distance to " O   HOH Z 109 " =    2.388
peak=    3.390 closest distance to " CG2 VAL A  78 " =    0.943
peak=    3.388 closest distance to " CB  MET A  47 " =    0.909
peak=    3.383 closest distance to " O   HOH Z 427 " =    2.894
peak=    3.380 closest distance to " O   HOH Z 303 " =    2.220
peak=    3.379 closest distance to " O   HOH Z 336 " =    1.714
peak=    3.378 closest distance to " CB  VAL A 265 " =    1.205
peak=    3.376 closest distance to " OG  SER A 245 " =    1.600
peak=    3.362 closest distance to " O   HOH Z 435 " =    2.913
peak=    3.361 closest distance to " CA  ASP A 140 " =    1.246
peak=    3.355 closest distance to " CE1 HIS A 108 " =    1.149
peak=    3.354 closest distance to " CG2 THR A 220 " =    0.777
peak=    3.353 closest distance to " CB  ASN A 142 " =    1.216
peak=    3.352 closest distance to " OD2 ASP A 286 " =    2.833
peak=    3.352 closest distance to " N   CYS A 260 " =    0.779
peak=    3.351 closest distance to " O   HOH Z 299 " =    4.507
peak=    3.349 closest distance to " O   HOH Z 150 " =    1.543
peak=    3.346 closest distance to " O   ASP A 124 " =    1.343
peak=    3.343 closest distance to " CG1 VAL A 153 " =    1.010
peak=    3.340 closest distance to " O   HOH Z 419 " =    1.556
peak=    3.339 closest distance to " O   HOH Z 393 " =    3.265
peak=    3.332 closest distance to " O   HOH Z  78 " =    1.869
peak=    3.328 closest distance to " O   HOH Z 383 " =    2.117
peak=    3.317 closest distance to " O   HOH Z  89 " =    2.175
peak=    3.315 closest distance to " OG BSER A 134 " =    2.810
peak=    3.314 closest distance to " O   HOH Z 295 " =    1.547
peak=    3.309 closest distance to " O   HOH Z  19 " =    1.554
peak=    3.309 closest distance to " O   HOH Z 261 " =    1.887
peak=    3.306 closest distance to " OG BSER A 258 " =    3.238
peak=    3.304 closest distance to " O   HOH Z 148 " =    3.313
peak=    3.302 closest distance to " CB  GLN A  89 " =    1.265
peak=    3.299 closest distance to " NZ  LYS A 117 " =    1.689
peak=    3.288 closest distance to " CG  ARG A 219 " =    1.245
peak=    3.286 closest distance to " CB  ASN A 187 " =    1.288
peak=    3.282 closest distance to " CA  LEU A  83 " =    1.242
peak=    3.279 closest distance to " O   HOH Z 250 " =    1.705
peak=    3.277 closest distance to " CD1 LEU A 222 " =    0.743
peak=    3.273 closest distance to " O   HOH Z 298 " =    2.397
peak=    3.272 closest distance to " CA  TYR A 116 " =    1.376
peak=    3.272 closest distance to " CG  GLN A 205 " =    1.193
peak=    3.269 closest distance to " O   ALA A 158 " =    1.180
peak=    3.269 closest distance to " O   TYR A 116 " =    1.443
peak=    3.267 closest distance to " O   HOH Z 130 " =    2.278
peak=    3.266 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.265 closest distance to " O   HOH Z  35 " =    2.244
peak=    3.264 closest distance to " O   HOH Z 417 " =    2.930
peak=    3.264 closest distance to " OG  SER A  62 " =    2.857
peak=    3.252 closest distance to " OD1 ASP A 238 " =    0.901
peak=    3.251 closest distance to " CB  ASN A 215 " =    1.183
peak=    3.248 closest distance to " CD  ARG A 139 " =    1.284
peak=    3.246 closest distance to " O   HOH Z 422 " =    2.527
peak=    3.243 closest distance to " CA  GLY A 241 " =    0.922
peak=    3.239 closest distance to " CA  GLN A  88 " =    1.277
peak=    3.225 closest distance to " O   HOH Z  63 " =    2.307
peak=    3.224 closest distance to " CA  ALA A  84 " =    1.149
peak=    3.222 closest distance to " O   SER A  26 " =    1.623
peak=    3.221 closest distance to " CE  LYS A 119 " =    1.101
peak=    3.220 closest distance to " O   HOH Z 409 " =    3.203
peak=    3.218 closest distance to " O   HOH Z 361 " =    2.513
peak=    3.213 closest distance to " CA  MET A 105 " =    1.074
peak=    3.212 closest distance to " O   HOH Z 281 " =    4.777
peak=    3.211 closest distance to " CD1 ILE A 199 " =    1.088
peak=    3.210 closest distance to " O   HOH Z 234 " =    1.870
peak=    3.207 closest distance to " N   ARG A 156 " =    1.463
peak=    3.206 closest distance to " CG  MET A 185 " =    1.106
peak=    3.202 closest distance to " O   HOH Z 171 " =    1.869
peak=    3.200 closest distance to " OH  TYR A 116 " =    1.119
peak=    3.198 closest distance to " CB  PHE A  16 " =    1.012
peak=    3.197 closest distance to " CA  ALA A 248 " =    1.200
peak=    3.195 closest distance to " O   HOH Z 353 " =    2.798
peak=    3.193 closest distance to " CA  SER A  32 " =    1.603
peak=    3.192 closest distance to " CA  PRO A  90 " =    0.919
peak=    3.189 closest distance to " O   HOH Z 282 " =    2.115
peak=    3.188 closest distance to " CA  ILE A 106 " =    0.791
peak=    3.186 closest distance to " O   HOH Z 421 " =    2.578
peak=    3.186 closest distance to " N   TRP A 150 " =    1.039
peak=    3.181 closest distance to " ND1 HIS A  81 " =    1.595
peak=    3.177 closest distance to " O   HOH Z 248 " =    1.793
peak=    3.177 closest distance to " O   HOH Z  49 " =    1.916
peak=    3.175 closest distance to " OE1 GLN A  58 " =    3.495
peak=    3.174 closest distance to " CB  MET A 105 " =    1.053
peak=    3.173 closest distance to " O   HOH Z 394 " =    1.651
peak=    3.173 closest distance to " O   HOH Z 334 " =    1.461
peak=    3.173 closest distance to " CB  ALA A  71 " =    1.314
peak=    3.172 closest distance to " CB  TYR A 116 " =    0.951
peak=    3.169 closest distance to " CB  PRO A 243 " =    1.295
peak=    3.167 closest distance to " ND2 ASN A 249 " =    0.896
peak=    3.158 closest distance to " CB  SER A  26 " =    1.753
peak=    3.158 closest distance to " CB  TYR A 169 " =    0.921
peak=    3.158 closest distance to " CD  ARG A  66 " =    2.714
peak=    3.156 closest distance to " CB  HIS A 108 " =    0.773
peak=    3.154 closest distance to " O   HOH Z 425 " =    1.332
peak=    3.152 closest distance to " CB  THR A  52 " =    0.909
peak=    3.149 closest distance to " CB  ILE A 120 " =    1.308
peak=    3.143 closest distance to " CA  TRP A  85 " =    1.100
peak=    3.140 closest distance to " O   HOH Z  19 " =    1.504
peak=    3.138 closest distance to " O   HOH Z 432 " =    1.675
peak=    3.135 closest distance to " CB  GLN A 103 " =    0.867
peak=    3.133 closest distance to " O   HOH Z  46 " =    1.394
peak=    3.126 closest distance to " O   HOH Z 207 " =    1.554
peak=    3.123 closest distance to " C   TYR A 214 " =    1.562
peak=    3.119 closest distance to " CA  THR A 221 " =    1.426
peak=    3.117 closest distance to " CA  ALA A 100 " =    1.155
peak=    3.114 closest distance to " O   HOH Z 156 " =    2.637
peak=    3.112 closest distance to " NH2AARG A 275 " =    3.593
peak=    3.110 closest distance to " CB  PHE A 204 " =    0.909
peak=    3.104 closest distance to " O   HOH Z 327 " =    1.678
peak=    3.098 closest distance to " NE2 HIS A 115 " =    0.992
peak=    3.097 closest distance to " O   HOH Z 261 " =    2.248
peak=    3.095 closest distance to " CB  ALA A 100 " =    1.291
peak=    3.094 closest distance to " O   HOH Z  88 " =    1.655
peak=    3.093 closest distance to " O  BHOH Z  74 " =    1.351
peak=    3.091 closest distance to " CD1 LEU A 228 " =    1.625
peak=    3.090 closest distance to " O   HOH Z 294 " =    1.550
peak=    3.085 closest distance to " CA  ALA A 291 " =    0.787
peak=    3.084 closest distance to " O   HOH Z 417 " =    2.232
peak=    3.084 closest distance to " NH1 ARG A  14 " =    1.233
peak=    3.081 closest distance to " CG  GLU A  37 " =    0.874
peak=    3.076 closest distance to " N   ARG A 190 " =    0.966
peak=    3.075 closest distance to " O   HOH Z 414 " =    1.703
peak=    3.071 closest distance to " CB  ASN A 148 " =    2.023
peak=    3.066 closest distance to " CB  SER A 216 " =    0.840
peak=    3.065 closest distance to " CB  LYS A 289 " =    1.009
peak=    3.061 closest distance to " O   HOH Z 329 " =    3.859
peak=    3.059 closest distance to " C   ALA A 299 " =    0.940
peak=    3.054 closest distance to " CD  LYS A 119 " =    1.764
peak=    3.053 closest distance to " O   HOH Z 162 " =    1.708
peak=    3.050 closest distance to " O   HOH Z 301 " =    1.990

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.841 - 5.977
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 218
   mapped sites are within: 0.841 - 5.977

peak=   -4.809 closest distance to " O   HOH Z 266 " =    4.875
peak=   -4.398 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.354 closest distance to " C   HIS A 108 " =    1.079
peak=   -4.346 closest distance to " OXT GLY A 302 " =    2.864
peak=   -4.314 closest distance to " CD  GLN A  58 " =    1.024
peak=   -4.136 closest distance to " O   PRO A 163 " =    2.076
peak=   -4.110 closest distance to " O   GLY A 136 " =    2.377
peak=   -4.045 closest distance to " O   HOH Z   5 " =    1.629
peak=   -4.030 closest distance to " O   HOH Z 165 " =    1.948
peak=   -4.007 closest distance to " O   HOH Z 166 " =    1.791
peak=   -3.995 closest distance to " CD1 LEU A 101 " =    2.498
peak=   -3.978 closest distance to " O   VAL A  67 " =    2.697
peak=   -3.963 closest distance to " CB  PHE A 208 " =    2.301
peak=   -3.961 closest distance to " O   HOH Z 210 " =    0.883
peak=   -3.952 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.951 closest distance to " CE2 TYR A  30 " =    2.687
peak=   -3.938 closest distance to " O   HOH Z  13 " =    1.695
peak=   -3.927 closest distance to " O   ALA A  34 " =    2.396
peak=   -3.907 closest distance to " O   HOH Z 196 " =    2.080
peak=   -3.905 closest distance to " CB  PRO A 243 " =    2.711
peak=   -3.888 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.884 closest distance to " O   PRO A 198 " =    1.307
peak=   -3.883 closest distance to " CH2 TRP A 179 " =    1.251
peak=   -3.852 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.850 closest distance to " CD1 LEU A  25 " =    2.453
peak=   -3.843 closest distance to " CD2 LEU A 237 " =    2.705
peak=   -3.815 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.796 closest distance to " CD  ARG A  14 " =    3.393
peak=   -3.794 closest distance to " CG2 ILE A  49 " =    2.742
peak=   -3.787 closest distance to " CD  GLN A 223 " =    1.329
peak=   -3.774 closest distance to " OE1 GLN A 223 " =    2.173
peak=   -3.770 closest distance to " C   THR A 279 " =    1.115
peak=   -3.744 closest distance to " O   HOH Z 407 " =    3.333
peak=   -3.724 closest distance to " CG  ASP A 132 " =    2.417
peak=   -3.722 closest distance to " O   HOH Z 292 " =    4.568
peak=   -3.719 closest distance to " CA  VAL A  67 " =    2.992
peak=   -3.710 closest distance to " CG  PRO A 243 " =    1.716
peak=   -3.702 closest distance to " ND2 ASN A  45 " =    1.068
peak=   -3.697 closest distance to " CG2 ILE A 263 " =    2.281
peak=   -3.689 closest distance to " O   HOH Z 283 " =    2.110
peak=   -3.687 closest distance to " O   HOH Z  71 " =    1.758
peak=   -3.680 closest distance to " OD1 ASN A 148 " =    1.484
peak=   -3.679 closest distance to " ND2 ASN A 187 " =    1.610
peak=   -3.672 closest distance to " CB  PHE A 192 " =    1.949
peak=   -3.669 closest distance to " CG  GLU A  53 " =    1.424
peak=   -3.669 closest distance to " O   SER A 210 " =    1.893
peak=   -3.659 closest distance to " CG1 VAL A 112 " =    2.576
peak=   -3.658 closest distance to " CD1 PHE A  59 " =    1.964
peak=   -3.653 closest distance to " O   HOH Z 372 " =    2.399
peak=   -3.644 closest distance to " C   SER A 206 " =    1.598
peak=   -3.642 closest distance to " O   PHE A 218 " =    1.501
peak=   -3.639 closest distance to " O   HOH Z 353 " =    2.271
peak=   -3.639 closest distance to " N   ALA A  43 " =    2.673
peak=   -3.638 closest distance to " CA  SER A 276 " =    1.532
peak=   -3.634 closest distance to " CG  ASP A 231 " =    0.841
peak=   -3.626 closest distance to " CB  ALA A  10 " =    2.188
peak=   -3.616 closest distance to " O   ILE A 109 " =    2.622
peak=   -3.590 closest distance to " ND2 ASN A  45 " =    1.784
peak=   -3.584 closest distance to " O   TRP A  92 " =    1.896
peak=   -3.582 closest distance to " CZ  TYR A 169 " =    1.818
peak=   -3.577 closest distance to " OG BSER A 134 " =    1.297
peak=   -3.571 closest distance to " CD  ARG A 195 " =    5.077
peak=   -3.557 closest distance to " OG  SER A   3 " =    1.740
peak=   -3.546 closest distance to " OD1 ASP A 191 " =    1.569
peak=   -3.545 closest distance to " O   HOH Z 234 " =    4.207
peak=   -3.530 closest distance to " CG  GLN A  58 " =    1.011
peak=   -3.526 closest distance to " O   HOH Z 185 " =    2.465
peak=   -3.522 closest distance to " O   HOH Z 377 " =    1.365
peak=   -3.521 closest distance to " O   HOH Z 150 " =    2.303
peak=   -3.520 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.518 closest distance to " NH2 ARG A  66 " =    1.885
peak=   -3.517 closest distance to " O   HOH Z 377 " =    2.048
peak=   -3.514 closest distance to " CG  ARG A 269 " =    2.310
peak=   -3.481 closest distance to " O   HOH Z  52 " =    1.617
peak=   -3.466 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.463 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.462 closest distance to " OG BSER A 210 " =    2.220
peak=   -3.462 closest distance to " O   HOH Z 150 " =    1.926
peak=   -3.460 closest distance to " CB  ALA A 248 " =    2.032
peak=   -3.450 closest distance to " CD  LYS A 289 " =    2.430
peak=   -3.444 closest distance to " CE3 TRP A 150 " =    2.220
peak=   -3.443 closest distance to " C   ASN A 285 " =    2.306
peak=   -3.441 closest distance to " CA  GLY A 133 " =    2.412
peak=   -3.434 closest distance to " CE2 PHE A  61 " =    2.592
peak=   -3.432 closest distance to " O   HOH Z 111 " =    1.614
peak=   -3.430 closest distance to " CD2 LEU A 300 " =    2.794
peak=   -3.428 closest distance to " N   ALA A 248 " =    1.842
peak=   -3.421 closest distance to " CG1 VAL A  78 " =    2.708
peak=   -3.416 closest distance to " NE2 GLN A 194 " =    1.919
peak=   -3.415 closest distance to " N   THR A  52 " =    1.658
peak=   -3.410 closest distance to " CB  ALA A 248 " =    2.219
peak=   -3.409 closest distance to " O   HOH Z 114 " =    3.440
peak=   -3.408 closest distance to " N   ALA A 226 " =    1.997
peak=   -3.402 closest distance to " CD1 TRP A 179 " =    1.102
peak=   -3.400 closest distance to " O   HOH Z  11 " =    2.058
peak=   -3.396 closest distance to " O   HOH Z 290 " =    1.085
peak=   -3.381 closest distance to " C   LEU A 143 " =    1.092
peak=   -3.376 closest distance to " O   HOH Z 418 " =    1.381
peak=   -3.372 closest distance to " O   HOH Z 171 " =    2.180
peak=   -3.369 closest distance to " O   HOH Z   6 " =    1.617
peak=   -3.367 closest distance to " O   GLY A  80 " =    2.549
peak=   -3.366 closest distance to " O   HOH Z 252 " =    4.110
peak=   -3.366 closest distance to " OE2 GLU A   2 " =    1.565
peak=   -3.362 closest distance to " CG2 VAL A 189 " =    2.261
peak=   -3.358 closest distance to " O   HOH Z 311 " =    3.684
peak=   -3.358 closest distance to " O   HOH Z 368 " =    1.862
peak=   -3.350 closest distance to " CB  ALA A 291 " =    2.400
peak=   -3.348 closest distance to " O   HOH Z 414 " =    1.625
peak=   -3.339 closest distance to " O   HOH Z 264 " =    1.798
peak=   -3.339 closest distance to " CG  ARG A 219 " =    2.491
peak=   -3.338 closest distance to " CB  TYR A  15 " =    2.279
peak=   -3.335 closest distance to " CG  LEU A  83 " =    2.067
peak=   -3.329 closest distance to " O   HOH Z 198 " =    2.103
peak=   -3.328 closest distance to " NE2 GLN A 103 " =    1.806
peak=   -3.326 closest distance to " O   HOH Z 422 " =    1.505
peak=   -3.325 closest distance to " O   VAL A 189 " =    2.574
peak=   -3.325 closest distance to " O   HOH Z 150 " =    1.115
peak=   -3.324 closest distance to " O   HOH Z 102 " =    1.585
peak=   -3.323 closest distance to " C   ALA A 158 " =    1.370
peak=   -3.321 closest distance to " CB  GLN A  11 " =    1.748
peak=   -3.313 closest distance to " O   GLY A 196 " =    1.088
peak=   -3.312 closest distance to " NE1 TRP A 266 " =    2.426
peak=   -3.310 closest distance to " CA  GLY A 241 " =    2.326
peak=   -3.308 closest distance to " OD1 ASP A 171 " =    1.549
peak=   -3.305 closest distance to " NH2 ARG A  66 " =    5.761
peak=   -3.303 closest distance to " CZ  PHE A 155 " =    1.196
peak=   -3.301 closest distance to " OG  SER A  62 " =    1.614
peak=   -3.296 closest distance to " OD2 ASP A 171 " =    1.854
peak=   -3.293 closest distance to " CD2 TYR A 293 " =    1.911
peak=   -3.292 closest distance to " NH2 ARG A  66 " =    5.634
peak=   -3.292 closest distance to " NH2 ARG A  79 " =    1.669
peak=   -3.290 closest distance to " O   HOH Z  19 " =    2.198
peak=   -3.278 closest distance to " OG BSER A 134 " =    1.951
peak=   -3.275 closest distance to " ND2 ASN A  69 " =    1.551
peak=   -3.274 closest distance to " O   ALA A 160 " =    1.532
peak=   -3.272 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.268 closest distance to " OG BSER A 210 " =    1.348
peak=   -3.264 closest distance to " O   GLN A  11 " =    1.290
peak=   -3.264 closest distance to " O   SER A 276 " =    1.717
peak=   -3.261 closest distance to " CB  ALA A 131 " =    2.377
peak=   -3.261 closest distance to " CG  GLU A 277 " =    1.221
peak=   -3.260 closest distance to " O   ALA A   1 " =    2.011
peak=   -3.257 closest distance to " CB  ASP A 162 " =    2.576
peak=   -3.253 closest distance to " CG  ASP A  50 " =    2.272
peak=   -3.253 closest distance to " ND2 ASN A 249 " =    2.210
peak=   -3.252 closest distance to " CD2 LEU A 237 " =    2.784
peak=   -3.251 closest distance to " O   HOH Z 166 " =    1.931
peak=   -3.251 closest distance to " CD1 TYR A 247 " =    2.388
peak=   -3.234 closest distance to " O   HOH Z 191 " =    5.977
peak=   -3.234 closest distance to " CD2 PHE A 225 " =    1.319
peak=   -3.232 closest distance to " O   HOH Z 426 " =    1.706
peak=   -3.232 closest distance to " O   SER A  95 " =    1.751
peak=   -3.225 closest distance to " NH2 ARG A 159 " =    2.278
peak=   -3.222 closest distance to " OD2 ASP A 171 " =    2.478
peak=   -3.217 closest distance to " O   HOH Z 126 " =    1.984
peak=   -3.216 closest distance to " CD1 LEU A 228 " =    2.255
peak=   -3.208 closest distance to " CD  GLN A 223 " =    0.995
peak=   -3.204 closest distance to " CE  LYS A 119 " =    2.159
peak=   -3.204 closest distance to " CE  MET A 105 " =    2.108
peak=   -3.201 closest distance to " O   HOH Z 136 " =    1.996
peak=   -3.197 closest distance to " CD  ARG A  79 " =    1.198
peak=   -3.197 closest distance to " O   HOH Z 145 " =    2.184
peak=   -3.197 closest distance to " CG1AVAL A  41 " =    2.600
peak=   -3.197 closest distance to " O   HOH Z 128 " =    2.515
peak=   -3.194 closest distance to " O   HOH Z 222 " =    1.307
peak=   -3.193 closest distance to " O   HOH Z 298 " =    2.742
peak=   -3.193 closest distance to " O  BHOH Z 338 " =    1.195
peak=   -3.189 closest distance to " O   HOH Z  38 " =    1.673
peak=   -3.189 closest distance to " CD  GLU A 236 " =    1.083
peak=   -3.187 closest distance to " CG1 VAL A 112 " =    2.915
peak=   -3.185 closest distance to " O   HOH Z  56 " =    1.294
peak=   -3.184 closest distance to " NH2 ARG A  66 " =    3.751
peak=   -3.183 closest distance to " O   ALA A 161 " =    1.549
peak=   -3.182 closest distance to " CZ3 TRP A 274 " =    2.477
peak=   -3.181 closest distance to " CG1 VAL A 112 " =    2.876
peak=   -3.180 closest distance to " CD1 ILE A 106 " =    2.195
peak=   -3.176 closest distance to " O   HOH Z 396 " =    1.824
peak=   -3.175 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.175 closest distance to " CH2 TRP A 150 " =    1.111
peak=   -3.172 closest distance to " O   HOH Z 200 " =    1.394
peak=   -3.168 closest distance to " N   GLN A  58 " =    1.586
peak=   -3.163 closest distance to " NH1 ARG A 195 " =    2.293
peak=   -3.159 closest distance to " CZ  PHE A  38 " =    1.960
peak=   -3.152 closest distance to " CA  GLY A 241 " =    3.146
peak=   -3.148 closest distance to " O   SER A   3 " =    1.131
peak=   -3.146 closest distance to " NE2 GLN A  88 " =    1.770
peak=   -3.145 closest distance to " CD  GLN A  88 " =    1.079
peak=   -3.143 closest distance to " OG  SER A  63 " =    1.237
peak=   -3.139 closest distance to " CG  TRP A 266 " =    1.970
peak=   -3.138 closest distance to " O   HOH Z 174 " =    3.651
peak=   -3.137 closest distance to " O   ASN A 187 " =    1.587
peak=   -3.135 closest distance to " N   SER A 134 " =    1.204
peak=   -3.132 closest distance to " C   GLU A  46 " =    0.957
peak=   -3.131 closest distance to " CB  SER A 210 " =    1.132
peak=   -3.130 closest distance to " O   HOH Z  41 " =    2.262
peak=   -3.130 closest distance to " O   HOH Z 392 " =    1.452
peak=   -3.126 closest distance to " CB  PRO A 163 " =    2.627
peak=   -3.125 closest distance to " O   HOH Z  37 " =    1.794
peak=   -3.125 closest distance to " CB  PHE A  16 " =    2.557
peak=   -3.124 closest distance to " CB  SER A 146 " =    2.170
peak=   -3.123 closest distance to " O   GLU A 152 " =    1.461
peak=   -3.123 closest distance to " NH1 ARG A 195 " =    2.598
peak=   -3.118 closest distance to " O   HOH Z 134 " =    2.424
peak=   -3.116 closest distance to " O   HOH Z 384 " =    2.102
peak=   -3.111 closest distance to " O   TYR A 186 " =    1.683
peak=   -3.110 closest distance to " CB  TRP A  85 " =    2.428
peak=   -3.109 closest distance to " CA  VAL A 197 " =    0.981
peak=   -3.100 closest distance to " O   HOH Z 301 " =    2.343
peak=   -3.083 closest distance to " C   ALA A 242 " =    1.987
peak=   -3.082 closest distance to " O   HOH Z  91 " =    2.179
peak=   -3.079 closest distance to " CG2BVAL A  41 " =    1.583
peak=   -3.072 closest distance to " CG2AVAL A  41 " =    2.880
peak=   -3.068 closest distance to " O   HOH Z 389 " =    1.694
peak=   -3.066 closest distance to " N   VAL A 189 " =    1.710
peak=   -3.064 closest distance to " CD2 PHE A  61 " =    2.051
peak=   -3.059 closest distance to " CB  ALA A   9 " =    2.629
peak=   -3.059 closest distance to " CB  ASP A 286 " =    1.954
peak=   -3.044 closest distance to " O   HOH Z 193 " =    1.814

================= 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    :  0.3765 0.3621   6.181264e+00   6.139597e+00
   1_bss:  0.3605 0.3445   6.160810e+00   6.114946e+00
   1_xyz:  0.2373 0.2601   5.773569e+00   5.861582e+00
   1_adp:  0.2161 0.2709   5.724518e+00   5.888822e+00
   1_occ:  0.2158 0.2712   5.724083e+00   5.888808e+00
   2_bss:  0.2118 0.2658   5.709819e+00   5.875401e+00
   2_xyz:  0.1606 0.1994   5.437178e+00   5.614560e+00
   2_adp:  0.1497 0.1871   5.375559e+00   5.555362e+00
   2_occ:  0.1495 0.1872   5.374783e+00   5.554912e+00
   3_bss:  0.1494 0.1863   5.372783e+00   5.551641e+00
   3_xyz:  0.1273 0.1685   5.240742e+00   5.452422e+00
   3_adp:  0.1228 0.1661   5.215676e+00   5.437359e+00
   3_occ:  0.1228 0.1661   5.215717e+00   5.437492e+00
   4_bss:  0.1227 0.1660   5.215238e+00   5.437300e+00
   4_xyz:  0.1129 0.1601   5.157189e+00   5.401217e+00
   4_adp:  0.1115 0.1601   5.150058e+00   5.398143e+00
   4_occ:  0.1115 0.1602   5.150326e+00   5.398741e+00
   5_bss:  0.1116 0.1598   5.150629e+00   5.397621e+00
   5_xyz:  0.1151 0.1613   5.173001e+00   5.410849e+00
   5_adp:  0.1152 0.1607   5.170981e+00   5.407838e+00
   5_occ:  0.1151 0.1609   5.171152e+00   5.408243e+00
   5_bss:  0.1151 0.1608   5.171248e+00   5.408331e+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:  0.298  34.641  -3.329   5.489  -1.777   0.000  -0.000  -0.000
   1_xyz:  0.298  34.641  -3.329   5.489  -1.777   0.000  -0.000  -0.000
   1_adp:  0.298  34.641  -3.329   5.489  -1.777   0.000  -0.000  -0.000
   1_occ:  0.298  34.641  -3.329   5.489  -1.777   0.000  -0.000  -0.000
   2_bss:  0.325  60.906  -2.551   1.153  -1.045   0.000  -0.000  -0.000
   2_xyz:  0.325  60.906  -2.551   1.153  -1.045   0.000  -0.000  -0.000
   2_adp:  0.325  60.906  -2.551   1.153  -1.045   0.000  -0.000  -0.000
   2_occ:  0.325  60.906  -2.551   1.153  -1.045   0.000  -0.000  -0.000
   3_bss:  0.326  60.136  -2.373  -0.293  -0.866  -0.000  -0.000  -0.000
   3_xyz:  0.326  60.136  -2.373  -0.293  -0.866  -0.000  -0.000  -0.000
   3_adp:  0.326  60.136  -2.373  -0.293  -0.866  -0.000  -0.000  -0.000
   3_occ:  0.326  60.136  -2.373  -0.293  -0.866  -0.000  -0.000  -0.000
   4_bss:  0.325  60.136  -2.201  -0.699  -0.668  -0.000  -0.000  -0.000
   4_xyz:  0.325  60.136  -2.201  -0.699  -0.668  -0.000  -0.000  -0.000
   4_adp:  0.325  60.136  -2.201  -0.699  -0.668  -0.000  -0.000  -0.000
   4_occ:  0.325  60.136  -2.201  -0.699  -0.668  -0.000  -0.000  -0.000
   5_bss:  0.325  60.136  -1.894  -0.668  -0.391  -0.000  -0.000  -0.000
   5_xyz:  0.325  60.136  -1.894  -0.668  -0.391  -0.000  -0.000  -0.000
   5_adp:  0.325  60.136  -1.894  -0.668  -0.391  -0.000  -0.000  -0.000
   5_occ:  0.325  60.136  -1.894  -0.668  -0.391  -0.000  -0.000  -0.000
   5_bss:  0.322  57.935  -1.741  -0.603  -0.222  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.059 0.6449  0.8131    40773.524
   1_bss:  38.995 0.6559  0.8254    37119.746
   1_xyz:  27.243 0.7881  0.9499    18494.307
   1_adp:  28.435 0.7740  0.9259    19623.174
   1_occ:  28.452 0.7738  0.9254    19640.830
   2_bss:  27.620 0.7831  0.9121    18825.845
   2_xyz:  19.401 0.8666  0.9741    10096.829
   2_adp:  17.763 0.8827  0.9747     8938.534
   2_occ:  17.748 0.8828  0.9747     8926.280
   3_bss:  17.621 0.8840  0.9646     8838.656
   3_xyz:  15.424 0.9031  0.9742     7178.198
   3_adp:  15.116 0.9059  0.9666     7025.114
   3_occ:  15.119 0.9059  0.9665     7029.065
   4_bss:  15.110 0.9060  0.9668     7026.652
   4_xyz:  14.356 0.9121  0.9709     6516.579
   4_adp:  14.259 0.9130  0.9632     6499.039
   4_occ:  14.270 0.9130  0.9630     6506.198
   5_bss:  14.280 0.9128  0.9699     6491.171
   5_xyz:  14.469 0.9115  0.9687     6627.142
   5_adp:  14.421 0.9118  0.9606     6601.810
   5_occ:  14.425 0.9118  0.9606     6606.869
   5_bss:  14.427 0.9118  0.9652     6606.343
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6336e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6336e-01
   1_xyz:   1.522  0.013  0.090 15.819  0.006  4.118   1.1990e-01
   1_adp:   1.522  0.013  0.090 15.819  0.006  4.118   1.1990e-01
   1_occ:   1.522  0.013  0.090 15.819  0.006  4.118   1.1990e-01
   2_bss:   1.522  0.013  0.090 15.819  0.006  4.118   1.1990e-01
   2_xyz:   1.057  0.007  0.073 14.705  0.004  4.125   6.3404e-02
   2_adp:   1.057  0.007  0.073 14.705  0.004  4.125   6.3404e-02
   2_occ:   1.057  0.007  0.073 14.705  0.004  4.125   6.3404e-02
   3_bss:   1.057  0.007  0.073 14.705  0.004  4.125   6.3404e-02
   3_xyz:   0.990  0.007  0.072 14.741  0.004  4.132   5.8424e-02
   3_adp:   0.990  0.007  0.072 14.741  0.004  4.132   5.8424e-02
   3_occ:   0.990  0.007  0.072 14.741  0.004  4.132   5.8424e-02
   4_bss:   0.990  0.007  0.072 14.741  0.004  4.132   5.8424e-02
   4_xyz:   1.119  0.010  0.083 15.036  0.004  4.117   7.5254e-02
   4_adp:   1.119  0.010  0.083 15.036  0.004  4.117   7.5254e-02
   4_occ:   1.119  0.010  0.083 15.036  0.004  4.117   7.5254e-02
   5_bss:   1.119  0.010  0.083 15.036  0.004  4.117   7.5254e-02
   5_xyz:   0.941  0.006  0.071 14.606  0.004  4.116   5.3814e-02
   5_adp:   0.941  0.006  0.071 14.606  0.004  4.116   5.3814e-02
   5_occ:   0.941  0.006  0.071 14.606  0.004  4.116   5.3814e-02
   5_bss:   0.941  0.006  0.071 14.606  0.004  4.116   5.3814e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4228e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4228e-01
   1_xyz:  10.186  0.081  0.349 87.661  0.031  2.143   1.2603e-01
   1_adp:  10.186  0.081  0.349 87.661  0.031  2.143   1.2603e-01
   1_occ:  10.186  0.081  0.349 87.661  0.031  2.143   1.2603e-01
   2_bss:  10.186  0.081  0.349 87.661  0.031  2.143   1.2603e-01
   2_xyz:   7.302  0.047  0.202 82.630  0.037  2.278   5.9066e-02
   2_adp:   7.302  0.047  0.202 82.630  0.037  2.278   5.9066e-02
   2_occ:   7.302  0.047  0.202 82.630  0.037  2.278   5.9066e-02
   3_bss:   7.302  0.047  0.202 82.630  0.037  2.278   5.9066e-02
   3_xyz:   7.511  0.041  0.230 82.601  0.031  2.372   4.3055e-02
   3_adp:   7.511  0.041  0.230 82.601  0.031  2.372   4.3055e-02
   3_occ:   7.511  0.041  0.230 82.601  0.031  2.372   4.3055e-02
   4_bss:   7.511  0.041  0.230 82.601  0.031  2.372   4.3055e-02
   4_xyz:   8.245  0.050  0.284 82.313  0.035  2.288   5.9507e-02
   4_adp:   8.245  0.050  0.284 82.313  0.035  2.288   5.9507e-02
   4_occ:   8.245  0.050  0.284 82.313  0.035  2.288   5.9507e-02
   5_bss:   8.245  0.050  0.284 82.313  0.035  2.288   5.9507e-02
   5_xyz:   6.959  0.037  0.228 81.454  0.033  2.412   3.0330e-02
   5_adp:   6.959  0.037  0.228 81.454  0.033  2.412   3.0330e-02
   5_occ:   6.959  0.037  0.228 81.454  0.033  2.412   3.0330e-02
   5_bss:   6.959  0.037  0.228 81.454  0.033  2.412   3.0330e-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:  72.73   0.00  17.01  62.83   0.00  13.12  72.73   4.47  38.17
   1_occ:  72.73   0.00  17.01  62.83   0.00  13.12  72.73   4.47  38.17
   2_bss:  72.73   0.00  17.01  62.83   0.00  13.12  72.73   4.47  38.17
   2_xyz:  72.73   0.00  17.01  62.83   0.00  13.12  72.73   4.47  38.17
   2_adp:  75.38   0.86  16.74  72.84   0.86  12.65  75.38   4.41  38.99
   2_occ:  75.38   0.86  16.74  72.84   0.86  12.65  75.38   4.41  38.99
   3_bss:  75.38   0.86  16.74  72.84   0.86  12.65  75.38   4.41  38.99
   3_xyz:  75.38   0.86  16.74  72.84   0.86  12.65  75.38   4.41  38.99
   3_adp:  86.13   0.00  16.83  86.13   0.00  12.43  82.48   3.78  40.79
   3_occ:  86.13   0.00  16.83  86.13   0.00  12.43  82.48   3.78  40.79
   4_bss:  86.13   0.00  16.83  86.13   0.00  12.43  82.48   3.78  40.79
   4_xyz:  86.13   0.00  16.83  86.13   0.00  12.43  82.48   3.78  40.79
   4_adp:  98.39   0.00  16.69  98.39   0.00  12.25  85.53   3.57  40.90
   4_occ:  98.39   0.00  16.69  98.39   0.00  12.25  85.53   3.57  40.90
   5_bss:  98.39   0.00  16.69  98.39   0.00  12.25  85.53   3.57  40.90
   5_xyz:  98.39   0.00  16.69  98.39   0.00  12.25  85.53   3.57  40.90
   5_adp:  99.74   0.00  16.34  99.74   0.00  12.00  86.94   4.57  40.02
   5_occ:  99.74   0.00  16.34  99.74   0.00  12.00  86.94   4.57  40.02
   5_bss:  99.74   0.00  16.35  99.74   0.00  12.00  86.95   4.57  40.02
------------------------------------------------------------------------
 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:    1.376    0.024    0.445
   1_adp:    1.376    0.024    0.445
   1_occ:    1.376    0.024    0.445
   2_bss:    1.376    0.024    0.445
   2_xyz:    1.120    0.048    0.509
   2_adp:    1.120    0.048    0.509
   2_occ:    1.120    0.048    0.509
   3_bss:    1.120    0.048    0.509
   3_xyz:    1.226    0.029    0.574
   3_adp:    1.226    0.029    0.574
   3_occ:    1.226    0.029    0.574
   4_bss:    1.226    0.029    0.574
   4_xyz:    1.281    0.026    0.602
   4_adp:    1.281    0.026    0.602
   4_occ:    1.281    0.026    0.602
   5_bss:    1.281    0.026    0.602
   5_xyz:    1.256    0.038    0.607
   5_adp:    1.256    0.038    0.607
   5_occ:    1.256    0.038    0.607
   5_bss:    1.256    0.038    0.607
------------------------------------------------------------------------

CPU time actual refinement: 329.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/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_588/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_588/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.43 
  Macro-tasks:
    bulk solvent and scale       = 37.82  
    individual site refinement   = 133.45 
    weights calculation          = 29.87  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.86 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 105.70 
    alpha_beta                      = 8.22   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.92 
    fmodel                         = 6.49   
    r_factors                      = 0.24   
    phase_errors                   = 11.05  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 248.88 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.702 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    640 calls, 105.33 s
gradients_fft:          585 calls, 100.86 s

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

# Date 2008-01-16 Time 05:11:35 PST -0800 (1200489095.37 s)
Start R-work = 0.3765, R-free = 0.3621 (no bulk solvent and anisotropic scale)
Final R-work = 0.1337, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.3605, R-free = 0.3445
Final R-work = 0.1151, R-free = 0.1608