# Date 2008-01-16 Time 05:59:43 PST -0800 (1200491983.46 s)
#phil __OFF__

Command line arguments: "../965.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21174
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 965

-------------------------------------------------------------------------------
  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: (70.9525, 48.1033, 87.6859, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (70.9525, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02057
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0206

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: (70.9525, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02057
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1645 -  4.3227 [2125/2152]  1912   213  10.0%
  bin  2:  4.3227 -  3.4443 [2035/2051]  1832   203  10.0%
  bin  3:  3.4443 -  3.0128 [2025/2044]  1823   202  10.0%
  bin  4:  3.0128 -  2.7391 [1996/2026]  1798   198   9.9%
  bin  5:  2.7391 -  2.5438 [1982/2001]  1783   199  10.0%
  bin  6:  2.5438 -  2.3944 [1972/2008]  1775   197  10.0%
  bin  7:  2.3944 -  2.2749 [1961/1994]  1764   197  10.0%
  bin  8:  2.2749 -  2.1762 [1952/1986]  1756   196  10.0%
  bin  9:  2.1762 -  2.0926 [1937/1965]  1742   195  10.1%
  bin 10:  2.0926 -  2.0206 [1604/2020]  1445   159   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/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: 0.15 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:
        1.64 -     2.30: 9
        2.30 -     2.95: 1584
        2.95 -     3.60: 4393
        3.60 -     4.25: 8970
        4.25 -     4.90: 12681
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.645 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.771 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.100 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.114 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27632 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_965/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 70.9525 48.10325 87.68585 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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4460   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.274876                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.3668 0.3745      6.5441      6.5213|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.4096 0.4211      6.8564      6.8625|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.4443 0.3900      6.7021      6.5999|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.4523 0.4541      6.5359       6.481|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.4891 0.4154      6.3733      6.3796|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.4877 0.4792      6.2699      6.1841|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.4953 0.4353      6.2416      6.1395|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.4935 0.4591      6.1756      6.1659|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.5020 0.5009      6.1007      6.1531|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.5096 0.4528      6.1131       6.033|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.5114 0.4974      6.0412      6.0761|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.5083 0.5373      5.9689      6.0364|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.5079 0.4962      5.8877      5.8595|
| 14:  2.0710 -  2.0206 0.72    912  103 0.4905 0.5351      5.8384      5.7485|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1379   153  0.70  34.33   0.82     0.73      71883.37|
|  2:  4.8209 -  3.8471  1325   149  0.72  33.34   0.88     0.80      97337.81|
|  3:  3.8471 -  3.3669  1309   146  0.64  40.81   0.87     0.78     101544.60|
|  4:  3.3669 -  3.0618  1291   136  0.56  47.03   0.88     0.70      91175.61|
|  5:  3.0618 -  2.8439  1285   145  0.48  53.71   0.87     0.63      72544.66|
|  6:  2.8439 -  2.6772  1278   145  0.46  55.34   0.87     0.60      62205.72|
|  7:  2.6772 -  2.5438  1281   141  0.45  55.89   0.90     0.59      54573.50|
|  8:  2.5438 -  2.4335  1268   142  0.45  55.93   0.90     0.60      51476.76|
|  9:  2.4335 -  2.3402  1270   143  0.44  57.09   0.89     0.61      47484.11|
| 10:  2.3402 -  2.2597  1250   135  0.45  56.19   0.91     0.62      43625.77|
| 11:  2.2597 -  2.1892  1262   146  0.41  59.36   0.91     0.59      42603.69|
| 12:  2.1892 -  2.1268  1260   133  0.36  63.09   0.91     0.53      41911.85|
| 13:  2.1268 -  2.0710  1260   142  0.32  66.34   0.89     0.46      38162.57|
| 14:  2.0710 -  2.0206   912   103  0.31  67.04   0.93     0.40      30254.49|
|alpha:            min =        0.40 max =            0.80 mean =         0.62|
|beta:             min =    30254.49 max =       101544.60 mean =     61470.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.74|
|phase err.(test): min =        0.00 max =           89.93 mean =        52.92|
|-----------------------------------------------------------------------------|

============================== 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 = 12.261788             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.205   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.190774              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.529   (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 |  1.645 -  1.970:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.970 -  2.296:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.296 -  2.621:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.621 -  2.947:     1545 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.947 -  3.272:     1881 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.272 -  3.598:     2512 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.598 -  3.923:     4644 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.923 -  4.249:     4326 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.249 -  4.574:     5740 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     6941 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.645 |       0.192 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4460   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.274876                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4543   r_free= 0.4377   ksol= 0.28   Bsol= 45.63   scale= 0.913   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,4.43,0.99,0.00,0.00,0.00); trace/3= 0.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267890                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.714876             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.810   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.037829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.284   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4543      final r-factor (work) = 0.3558          |
| start r-factor (free) = 0.4377      final r-factor (free) = 0.3870          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.7354 = 10.71 * 0.50 * 6.2659 + 1.00 * 0.1665                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0451 = 10.71 * 0.50 * 6.1438 + 1.00 * 0.1303                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3558      final r-factor (work) = 0.3266          |
| start r-factor (free) = 0.3870      final r-factor (free) = 0.3979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3822 = 1.04 * 1.00 * 6.1438 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3076 = 1.04 * 1.00 * 6.0593 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.64  18.27    None  None   None       |
|    all(noH): 2823   0      0.00    100.64  18.27    None  None   None       |
|    Sol.    : 438    0      0.00    100.64  37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    84.11   14.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.064:  962   |   5:    50.322 -  60.386:   76        |
|      1:    10.064 -  20.129:  918   |   6:    60.386 -  70.450:   50        |
|      2:    20.129 -  30.193:  448   |   7:    70.450 -  80.515:   13        |
|      3:    30.193 -  40.257:  246   |   8:    80.515 -  90.579:    5        |
|      4:    40.257 -  50.322:  104   |   9:    90.579 - 100.643:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3266 r_free = 0.3979             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3265 r_free = 0.3972             target_work(ml) = 6.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3265   r_free= 0.3972   ksol= 0.28   Bsol= 45.63   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,4.43,0.99,0.00,0.00,0.00); trace/3= 0.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.064243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3258   r_free= 0.3959   ksol= 0.28   Bsol= 62.99   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,2.88,0.92,0.00,0.00,0.00); trace/3= 0.91                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.066211                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.144058             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.645  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.609144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.137  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3258      final r-factor (work) = 0.2535          |
| start r-factor (free) = 0.3959      final r-factor (free) = 0.3022          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.9668 = 13.14 * 0.50 * 6.0615 + 1.00 * 0.1303                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3706 = 13.14 * 0.50 * 5.9698 + 1.00 * 0.1367                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2535      final r-factor (work) = 0.2263          |
| start r-factor (free) = 0.3022      final r-factor (free) = 0.2799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6557 = 0.61 * 1.00 * 5.9698 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5391 = 0.61 * 1.00 * 5.7815 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.43   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    95.43   17.70    None  None   None       |
|    Sol.    : 438    0      0.00    95.43   40.88    None  None   None       |
|    Mac.    : 2385   0      0.00    80.75   13.44    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 -   9.544: 1072   |   5:    47.717 -  57.261:   88        |
|      1:     9.544 -  19.087:  914   |   6:    57.261 -  66.804:   63        |
|      2:    19.087 -  28.631:  318   |   7:    66.804 -  76.348:   27        |
|      3:    28.631 -  38.174:  189   |   8:    76.348 -  85.891:   13        |
|      4:    38.174 -  47.717:  137   |   9:    85.891 -  95.435:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2263 r_free = 0.2799             target_work(ml) = 5.753         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2259 r_free = 0.2800             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2259   r_free= 0.2800   ksol= 0.28   Bsol= 62.99   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,2.88,0.92,0.00,0.00,0.00); trace/3= 0.91                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.752048                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2248   r_free= 0.2790   ksol= 0.32   Bsol= 72.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,1.32,0.58,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.749556                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.804775              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.735   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.499591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.219  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2248      final r-factor (work) = 0.1728          |
| start r-factor (free) = 0.2790      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9142 = 5.80 * 0.50 * 5.7806 + 1.00 * 0.1367                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4716 = 5.80 * 0.50 * 5.6434 + 1.00 * 0.0923                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1728      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.2025          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8337 = 0.50 * 1.00 * 5.6434 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7413 = 0.50 * 1.00 * 5.4615 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.84   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    95.84   17.18    None  None   None       |
|    Sol.    : 438    0      3.82    95.84   43.08    None  None   None       |
|    Mac.    : 2385   0      0.00    90.02   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 -   9.584: 1165   |   5:    47.921 -  57.505:   96        |
|      1:     9.584 -  19.168:  947   |   6:    57.505 -  67.089:   76        |
|      2:    19.168 -  28.752:  241   |   7:    67.089 -  76.673:   33        |
|      3:    28.752 -  38.337:  133   |   8:    76.673 -  86.257:   11        |
|      4:    38.337 -  47.921:  115   |   9:    86.257 -  95.841:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1578 r_free = 0.2025             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1578 r_free = 0.2024             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1578   r_free= 0.2024   ksol= 0.32   Bsol= 72.39   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,1.32,0.58,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.432634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1581   r_free= 0.2026   ksol= 0.33   Bsol= 79.69   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,0.32,0.34,0.00,0.00,0.00); trace/3= -0.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.911678              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.513   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.924  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1581      final r-factor (work) = 0.1375          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0465 = 2.91 * 0.50 * 5.4636 + 1.00 * 0.0923                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8934 = 2.91 * 0.50 * 5.3711 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.1836      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7564 = 0.51 * 1.00 * 5.3711 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7214 = 0.51 * 1.00 * 5.3025 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.49  16.83    None  None   None       |
|    all(noH): 2823   0      0.00    100.49  16.83    None  None   None       |
|    Sol.    : 438    0      1.33    100.49  43.44    None  None   None       |
|    Mac.    : 2385   0      0.00    98.20   11.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.049: 1294   |   5:    50.243 -  60.291:   79        |
|      1:    10.049 -  20.097:  912   |   6:    60.291 -  70.340:   76        |
|      2:    20.097 -  30.146:  192   |   7:    70.340 -  80.388:   29        |
|      3:    30.146 -  40.194:  124   |   8:    80.388 -  90.437:    8        |
|      4:    40.194 -  50.243:  102   |   9:    90.437 - 100.485:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1326 r_free = 0.1808             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1808             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1808   ksol= 0.33   Bsol= 79.69   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,0.32,0.34,0.00,0.00,0.00); trace/3= -0.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.288561                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1807   ksol= 0.33   Bsol= 77.26   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,0.07,0.54,0.00,0.00,0.00); trace/3= -0.14                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.288905                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.871397              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.992  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.296254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.737  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1328      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6873 = 2.87 * 0.50 * 5.3029 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6278 = 2.87 * 0.50 * 5.2585 + 1.00 * 0.0782                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5703 = 0.30 * 1.00 * 5.2585 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5602 = 0.30 * 1.00 * 5.2298 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.94   16.15    None  None   None       |
|    all(noH): 2823   0      0.00    99.94   16.15    None  None   None       |
|    Sol.    : 438    0      1.86    99.94   41.23    None  None   None       |
|    Mac.    : 2385   0      0.00    96.22   11.54    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 -   9.995: 1333   |   5:    49.972 -  59.967:   78        |
|      1:     9.995 -  19.989:  899   |   6:    59.967 -  69.961:   57        |
|      2:    19.989 -  29.983:  194   |   7:    69.961 -  79.956:   23        |
|      3:    29.983 -  39.978:  118   |   8:    79.956 -  89.950:    7        |
|      4:    39.978 -  49.972:  108   |   9:    89.950 -  99.944:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1690             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1227 r_free = 0.1690             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1690   ksol= 0.33   Bsol= 77.26   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,0.07,0.54,0.00,0.00,0.00); trace/3= -0.14                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.223191                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.1037 0.1321       5.429      5.5584|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.0872 0.1101      5.4635      5.6507|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.1105 0.1565      5.5194      5.9026|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.1319 0.1714      5.5297      5.6643|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.1507 0.1888      5.4443      5.6392|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.1450 0.2164      5.3404      5.5635|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.1396 0.1793      5.2665      5.4366|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.1343 0.1910      5.1877      5.4571|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.1309 0.1856      5.1135      5.3291|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.1290 0.1930       5.068      5.3038|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.1268 0.1916      5.0175      5.3232|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.1228 0.1755      4.9404      5.2321|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.1237 0.1840      4.8661      5.0995|
| 14:  2.0710 -  2.0206 0.72    912  103 0.1172 0.1937      4.7508      5.0361|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1379   153  0.94   9.73   0.96     0.93       7934.85|
|  2:  4.8209 -  3.8471  1325   149  0.95   8.50   0.99     0.97       9574.75|
|  3:  3.8471 -  3.3669  1309   146  0.93  11.76   1.01     1.01      11234.10|
|  4:  3.3669 -  3.0618  1291   136  0.91  14.76   1.00     0.97      11696.68|
|  5:  3.0618 -  2.8439  1285   145  0.88  17.77   1.00     0.98      10368.41|
|  6:  2.8439 -  2.6772  1278   145  0.88  18.08   0.97     0.94       8714.63|
|  7:  2.6772 -  2.5438  1281   141  0.89  17.51   0.99     0.96       7627.29|
|  8:  2.5438 -  2.4335  1268   142  0.89  17.01   0.98     0.94       6545.31|
|  9:  2.4335 -  2.3402  1270   143  0.89  17.47   0.99     0.94       5823.09|
| 10:  2.3402 -  2.2597  1250   135  0.89  17.07   0.99     0.95       5266.76|
| 11:  2.2597 -  2.1892  1262   146  0.89  17.23   0.98     0.93       4921.34|
| 12:  2.1892 -  2.1268  1260   133  0.90  16.46   0.99     0.98       4440.29|
| 13:  2.1268 -  2.0710  1260   142  0.90  16.76   0.97     0.95       3751.86|
| 14:  2.0710 -  2.0206   912   103  0.90  16.33   0.95     0.91       3006.16|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3006.16 max =        11696.68 mean =      7329.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.12 mean =        14.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1691   ksol= 0.32   Bsol= 70.05   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,-0.09,0.57,-0.00,0.00,0.00); trace/3= -0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.223124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1691   ksol= 0.32   Bsol= 70.05   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,-0.09,0.57,-0.00,0.00,0.00); trace/3= -0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.223124                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.1033 0.1323      5.4261      5.5564|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.0869 0.1097      5.4605      5.6456|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.1104 0.1563      5.5182      5.9035|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.1321 0.1715       5.531       5.665|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.1510 0.1892       5.446      5.6414|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.1450 0.2163      5.3414      5.5633|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.1397 0.1796      5.2674      5.4377|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.1343 0.1912      5.1884       5.458|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.1308 0.1855       5.114      5.3296|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.1290 0.1935      5.0686      5.3053|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.1268 0.1914      5.0178       5.323|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.1227 0.1757      4.9407      5.2332|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.1238 0.1840      4.8659      5.0992|
| 14:  2.0710 -  2.0206 0.72    912  103 0.1173 0.1935      4.7501       5.035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1379   153  0.94   9.70   0.96     0.93       7899.75|
|  2:  4.8209 -  3.8471  1325   149  0.95   8.45   0.99     0.97       9517.63|
|  3:  3.8471 -  3.3669  1309   146  0.93  11.72   1.01     1.01      11183.94|
|  4:  3.3669 -  3.0618  1291   136  0.91  14.78   1.00     0.97      11723.38|
|  5:  3.0618 -  2.8439  1285   145  0.88  17.78   1.00     0.98      10397.49|
|  6:  2.8439 -  2.6772  1278   145  0.88  18.10   0.97     0.94       8737.79|
|  7:  2.6772 -  2.5438  1281   141  0.89  17.52   0.99     0.96       7639.99|
|  8:  2.5438 -  2.4335  1268   142  0.89  17.03   0.98     0.94       6558.33|
|  9:  2.4335 -  2.3402  1270   143  0.89  17.49   0.99     0.93       5834.86|
| 10:  2.3402 -  2.2597  1250   135  0.89  17.09   0.99     0.94       5277.00|
| 11:  2.2597 -  2.1892  1262   146  0.89  17.24   0.98     0.93       4929.48|
| 12:  2.1892 -  2.1268  1260   133  0.90  16.47   0.99     0.98       4444.98|
| 13:  2.1268 -  2.0710  1260   142  0.90  16.76   0.97     0.95       3749.09|
| 14:  2.0710 -  2.0206   912   103  0.90  16.30   0.95     0.91       2997.22|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2997.22 max =        11723.38 mean =      7328.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.14 mean =        14.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.95   16.15    None  None   None       |
|    all(noH): 2823   0      0.00    99.95   16.15    None  None   None       |
|    Sol.    : 438    0      1.86    99.95   41.23    None  None   None       |
|    Mac.    : 2385   0      0.00    96.22   11.55    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 -   9.997: 1333   |   5:    49.975 -  59.970:   78        |
|      1:     9.997 -  19.992:  899   |   6:    59.970 -  69.964:   57        |
|      2:    19.992 -  29.986:  194   |   7:    69.964 -  79.959:   23        |
|      3:    29.986 -  39.981:  118   |   8:    79.959 -  89.953:    7        |
|      4:    39.981 -  49.975:  108   |   9:    89.953 -  99.947:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.435 - 4.991
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.756 - 4.991

peak=    5.894 closest distance to " O   HOH Z 210 " =    1.312
peak=    5.494 closest distance to " NH2 ARG A  56 " =    2.331
peak=    5.196 closest distance to " CB  GLN A 223 " =    1.360
peak=    4.957 closest distance to " CB  SER A  63 " =    1.233
peak=    4.944 closest distance to " CG  PRO A  54 " =    1.367
peak=    4.683 closest distance to " O   PRO A 198 " =    1.566
peak=    4.671 closest distance to " CA  ALA A  51 " =    1.027
peak=    4.644 closest distance to " O   HOH Z 433 " =    1.700
peak=    4.584 closest distance to " O   HOH Z  49 " =    1.129
peak=    4.583 closest distance to " O   HOH Z 418 " =    2.194
peak=    4.549 closest distance to " CB  GLN A 183 " =    1.263
peak=    4.432 closest distance to " OE1 GLN A  88 " =    0.997
peak=    4.429 closest distance to " O   HOH Z 425 " =    1.645
peak=    4.412 closest distance to " O   HOH Z 134 " =    2.001
peak=    4.408 closest distance to " CB  TRP A 266 " =    1.064
peak=    4.382 closest distance to " O   HOH Z  95 " =    2.055
peak=    4.382 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.377 closest distance to " CB  VAL A 202 " =    1.518
peak=    4.345 closest distance to " O   HOH Z 369 " =    2.031
peak=    4.342 closest distance to " O   HOH Z 214 " =    1.460
peak=    4.339 closest distance to " CD  LYS A 166 " =    1.456
peak=    4.295 closest distance to " O   HOH Z 232 " =    2.412
peak=    4.282 closest distance to " CB  GLU A 128 " =    1.059
peak=    4.261 closest distance to " O   HOH Z  44 " =    2.151
peak=    4.214 closest distance to " CG  PRO A 280 " =    0.789
peak=    4.190 closest distance to " O   HOH Z 234 " =    3.869
peak=    4.181 closest distance to " CB  ARG A 190 " =    1.770
peak=    4.174 closest distance to " CZ  PHE A 218 " =    1.160
peak=    4.173 closest distance to " O   HOH Z 196 " =    1.779
peak=    4.125 closest distance to " O   ALA A 165 " =    1.392
peak=    4.117 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.088 closest distance to " O   HOH Z 423 " =    1.831
peak=    4.079 closest distance to " CD1 LEU A 300 " =    1.126
peak=    4.073 closest distance to " O   HOH Z 403 " =    1.842
peak=    4.071 closest distance to " CB  PRO A  54 " =    0.890
peak=    4.066 closest distance to " CB  ARG A 275 " =    0.869
peak=    4.056 closest distance to " CA  ALA A 160 " =    1.042
peak=    4.048 closest distance to " CD  ARG A  66 " =    2.627
peak=    4.044 closest distance to " O   HOH Z  43 " =    1.942
peak=    4.037 closest distance to " CA  ILE A 106 " =    0.832
peak=    4.018 closest distance to " CD  ARG A 269 " =    1.004
peak=    4.018 closest distance to " O   HOH Z 133 " =    2.421
peak=    4.015 closest distance to " O   HOH Z 412 " =    3.472
peak=    3.973 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.960 closest distance to " CZ3 TRP A 266 " =    1.112
peak=    3.946 closest distance to " CA  ALA A 295 " =    1.071
peak=    3.938 closest distance to " CG1 ILE A  33 " =    1.226
peak=    3.936 closest distance to " CG  PRO A 198 " =    1.190
peak=    3.929 closest distance to " OD1 ASN A 217 " =    1.631
peak=    3.924 closest distance to " CB  ARG A  79 " =    1.413
peak=    3.901 closest distance to " CG1 VAL A 153 " =    1.093
peak=    3.900 closest distance to " O   HOH Z 258 " =    2.104
peak=    3.892 closest distance to " CA  ARG A 195 " =    1.134
peak=    3.884 closest distance to " CB  LEU A 228 " =    1.129
peak=    3.876 closest distance to " O   HOH Z  30 " =    1.632
peak=    3.875 closest distance to " CB  GLU A 277 " =    3.816
peak=    3.874 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.859 closest distance to " O   HOH Z 189 " =    2.784
peak=    3.853 closest distance to " CB  ASP A 140 " =    0.893
peak=    3.841 closest distance to " CB  TYR A 169 " =    0.809
peak=    3.837 closest distance to " CB  GLU A 152 " =    1.113
peak=    3.826 closest distance to " O   HOH Z  15 " =    2.118
peak=    3.818 closest distance to " O   HOH Z  54 " =    1.297
peak=    3.808 closest distance to " OG BSER A 164 " =    2.224
peak=    3.803 closest distance to " OE1 GLN A  11 " =    2.164
peak=    3.803 closest distance to " NH2 ARG A 156 " =    1.191
peak=    3.796 closest distance to " O   HOH Z 368 " =    2.300
peak=    3.796 closest distance to " O   HOH Z   7 " =    1.181
peak=    3.784 closest distance to " CB  ASN A 148 " =    1.429
peak=    3.780 closest distance to " O   SER A  87 " =    2.292
peak=    3.776 closest distance to " CB  ASP A 124 " =    0.762
peak=    3.774 closest distance to " CZ  PHE A  38 " =    1.226
peak=    3.762 closest distance to " CB  ASN A 142 " =    1.085
peak=    3.761 closest distance to " O   HOH Z 357 " =    2.283
peak=    3.760 closest distance to " ND2 ASN A 187 " =    1.421
peak=    3.759 closest distance to " O   HOH Z 126 " =    1.660
peak=    3.756 closest distance to " O   HOH Z 285 " =    2.965
peak=    3.751 closest distance to " O   HOH Z 154 " =    1.617
peak=    3.747 closest distance to " O   HOH Z 132 " =    2.894
peak=    3.745 closest distance to " O   HOH Z 415 " =    1.501
peak=    3.739 closest distance to " O   HOH Z 437 " =    1.774
peak=    3.737 closest distance to " CA  ALA A 100 " =    1.115
peak=    3.735 closest distance to " O   HOH Z 154 " =    2.371
peak=    3.734 closest distance to " O   HOH Z 261 " =    2.055
peak=    3.727 closest distance to " O   HOH Z 281 " =    4.979
peak=    3.725 closest distance to " O   HOH Z 346 " =    1.552
peak=    3.724 closest distance to " CG2BVAL A  41 " =    0.875
peak=    3.722 closest distance to " O   HOH Z 415 " =    1.339
peak=    3.720 closest distance to " O   HOH Z  20 " =    1.861
peak=    3.719 closest distance to " CB  GLN A  88 " =    1.127
peak=    3.713 closest distance to " O   HOH Z 406 " =    1.664
peak=    3.705 closest distance to " O   HOH Z 298 " =    2.018
peak=    3.700 closest distance to " CG2 VAL A 197 " =    1.196
peak=    3.693 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.689 closest distance to " O   HOH Z 377 " =    1.355
peak=    3.675 closest distance to " CD1 LEU A  96 " =    0.825
peak=    3.675 closest distance to " O   ASN A  74 " =    1.605
peak=    3.669 closest distance to " CA  ASP A 191 " =    1.005
peak=    3.669 closest distance to " O   HOH Z  48 " =    1.893
peak=    3.665 closest distance to " O   HOH Z 265 " =    1.898
peak=    3.661 closest distance to " O   HOH Z  40 " =    1.883
peak=    3.654 closest distance to " O   HOH Z 139 " =    1.280
peak=    3.642 closest distance to " CA  ASP A 162 " =    1.164
peak=    3.640 closest distance to " O   HOH Z 435 " =    2.822
peak=    3.638 closest distance to " NH1AARG A 145 " =    1.277
peak=    3.633 closest distance to " O   TYR A 116 " =    1.397
peak=    3.633 closest distance to " CG AARG A 275 " =    1.125
peak=    3.631 closest distance to " CD2 LEU A 297 " =    0.998
peak=    3.630 closest distance to " O   HOH Z 374 " =    2.904
peak=    3.628 closest distance to " O   HOH Z 362 " =    3.068
peak=    3.628 closest distance to " O   HOH Z 394 " =    1.735
peak=    3.624 closest distance to " O   HOH Z 117 " =    2.133
peak=    3.620 closest distance to " CB  SER A  62 " =    0.869
peak=    3.618 closest distance to " NE2 GLN A  77 " =    3.332
peak=    3.616 closest distance to " O   HOH Z  61 " =    1.622
peak=    3.610 closest distance to " CB  SER A 141 " =    1.114
peak=    3.606 closest distance to " CD2 TRP A 179 " =    1.313
peak=    3.602 closest distance to " CA  SER A  12 " =    1.611
peak=    3.599 closest distance to " O   HOH Z 389 " =    2.075
peak=    3.592 closest distance to " CA  PRO A  54 " =    1.159
peak=    3.590 closest distance to " OD2 ASP A 298 " =    3.794
peak=    3.589 closest distance to " O   HOH Z 336 " =    1.938
peak=    3.588 closest distance to " CB  GLU A  46 " =    0.993
peak=    3.580 closest distance to " CG  PRO A 243 " =    1.132
peak=    3.579 closest distance to " CA  GLU A  46 " =    0.858
peak=    3.573 closest distance to " O   HOH Z 271 " =    2.504
peak=    3.567 closest distance to " O   HOH Z 316 " =    3.185
peak=    3.566 closest distance to " O   HOH Z  63 " =    1.507
peak=    3.562 closest distance to " O   HOH Z 248 " =    1.772
peak=    3.557 closest distance to " O   HOH Z 417 " =    3.175
peak=    3.556 closest distance to " NE2 HIS A 115 " =    1.074
peak=    3.556 closest distance to " CA  GLY A 196 " =    1.033
peak=    3.554 closest distance to " O   HOH Z 303 " =    2.384
peak=    3.552 closest distance to " O   HOH Z 214 " =    2.471
peak=    3.549 closest distance to " O   HOH Z 156 " =    2.653
peak=    3.545 closest distance to " CB  ASN A 285 " =    0.827
peak=    3.544 closest distance to " CG  GLN A  11 " =    1.244
peak=    3.542 closest distance to " O   HOH Z 193 " =    2.331
peak=    3.541 closest distance to " O   ASN A 209 " =    1.256
peak=    3.537 closest distance to " O   HOH Z  80 " =    2.094
peak=    3.533 closest distance to " CB  LEU A  83 " =    0.860
peak=    3.533 closest distance to " O   HOH Z 380 " =    1.819
peak=    3.533 closest distance to " CZ3 TRP A  85 " =    0.914
peak=    3.527 closest distance to " N   ASN A  39 " =    1.374
peak=    3.519 closest distance to " CA  ARG A  36 " =    1.104
peak=    3.518 closest distance to " O   HOH Z 422 " =    1.033
peak=    3.513 closest distance to " N   GLY A  98 " =    1.128
peak=    3.513 closest distance to " CA  SER A  87 " =    1.009
peak=    3.510 closest distance to " CA  ALA A  21 " =    1.311
peak=    3.507 closest distance to " O   HOH Z 294 " =    1.568
peak=    3.505 closest distance to " O   HOH Z  44 " =    1.839
peak=    3.502 closest distance to " OD1 ASN A  69 " =    2.444
peak=    3.500 closest distance to " N   CYS A 260 " =    0.770
peak=    3.492 closest distance to " O   THR A 251 " =    1.187
peak=    3.491 closest distance to " CA  TYR A 116 " =    1.381
peak=    3.489 closest distance to " O   HOH Z 203 " =    1.783
peak=    3.482 closest distance to " CD  ARG A 159 " =    0.885
peak=    3.477 closest distance to " O   HOH Z 126 " =    2.207
peak=    3.473 closest distance to " NE1 TRP A  92 " =    1.732
peak=    3.472 closest distance to " CD  ARG A 195 " =    0.983
peak=    3.471 closest distance to " CD  PRO A  54 " =    0.973
peak=    3.468 closest distance to " O   HOH Z 234 " =    1.967
peak=    3.467 closest distance to " CA  GLU A 152 " =    0.916
peak=    3.459 closest distance to " O   HOH Z 284 " =    3.025
peak=    3.459 closest distance to " CB  GLU A  37 " =    0.880
peak=    3.459 closest distance to " CB  SER A   3 " =    1.497
peak=    3.454 closest distance to " CG2 THR A 221 " =    1.009
peak=    3.452 closest distance to " CB  ALA A  71 " =    1.298
peak=    3.442 closest distance to " CA  GLN A  88 " =    1.372
peak=    3.440 closest distance to " O   HOH Z 383 " =    2.152
peak=    3.440 closest distance to " O   HOH Z 128 " =    2.316
peak=    3.437 closest distance to " CA  ASN A 217 " =    1.343
peak=    3.435 closest distance to " CB  MET A  40 " =    0.875
peak=    3.435 closest distance to " N   ASN A 127 " =    1.251
peak=    3.432 closest distance to " CB  ALA A 291 " =    1.151
peak=    3.432 closest distance to " O   HOH Z 301 " =    1.524
peak=    3.428 closest distance to " O   HOH Z  78 " =    2.226
peak=    3.424 closest distance to " O   HOH Z 245 " =    1.317
peak=    3.413 closest distance to " OG  SER A 276 " =    1.530
peak=    3.411 closest distance to " O   HOH Z 174 " =    2.169
peak=    3.407 closest distance to " NE2 GLN A  11 " =    1.205
peak=    3.402 closest distance to " O   HOH Z  88 " =    1.712
peak=    3.399 closest distance to " CB  ALA A  43 " =    0.933
peak=    3.398 closest distance to " NZ  LYS A  48 " =    1.347
peak=    3.393 closest distance to " O   HOH Z 327 " =    1.693
peak=    3.393 closest distance to " CA  LEU A  83 " =    1.452
peak=    3.391 closest distance to " O   HOH Z 135 " =    2.063
peak=    3.389 closest distance to " O   HOH Z 164 " =    3.498
peak=    3.387 closest distance to " CB  PRO A  90 " =    1.316
peak=    3.387 closest distance to " CA  VAL A 125 " =    1.156
peak=    3.384 closest distance to " CB  PRO A 198 " =    0.980
peak=    3.382 closest distance to " O   HOH Z 146 " =    1.680
peak=    3.382 closest distance to " O   HOH Z 285 " =    1.820
peak=    3.380 closest distance to " OH  TYR A 169 " =    0.886
peak=    3.380 closest distance to " O   HOH Z 432 " =    1.901
peak=    3.375 closest distance to " N   ILE A  33 " =    1.014
peak=    3.373 closest distance to " CG  GLU A  37 " =    0.965
peak=    3.370 closest distance to " O   HOH Z 193 " =    1.776
peak=    3.369 closest distance to " CA  ASP A 124 " =    0.788
peak=    3.367 closest distance to " O   HOH Z  68 " =    2.007
peak=    3.364 closest distance to " O   HOH Z 244 " =    1.721
peak=    3.362 closest distance to " O   HOH Z 374 " =    3.545
peak=    3.360 closest distance to " O   HOH Z 250 " =    1.393
peak=    3.359 closest distance to " CG  LEU A 167 " =    1.029
peak=    3.358 closest distance to " CB  THR A  52 " =    0.895
peak=    3.358 closest distance to " CB  PHE A 283 " =    0.756
peak=    3.353 closest distance to " O   ASP A 124 " =    1.163
peak=    3.352 closest distance to " O   HOH Z 345 " =    1.727
peak=    3.348 closest distance to " CA  ASN A 249 " =    1.366
peak=    3.348 closest distance to " CB  ILE A 120 " =    1.470
peak=    3.345 closest distance to " CE1 TYR A 186 " =    1.219
peak=    3.341 closest distance to " ND2 ASN A 249 " =    0.882
peak=    3.340 closest distance to " CB  GLN A 103 " =    0.908
peak=    3.332 closest distance to " N   TYR A 116 " =    1.517
peak=    3.323 closest distance to " O   HOH Z 150 " =    2.002
peak=    3.323 closest distance to " O   HOH Z 139 " =    4.991
peak=    3.315 closest distance to " O   HOH Z 200 " =    1.558
peak=    3.311 closest distance to " O   HOH Z  21 " =    1.819
peak=    3.310 closest distance to " NE AARG A 275 " =    1.248
peak=    3.306 closest distance to " CG  ARG A 138 " =    1.146
peak=    3.305 closest distance to " O   ASN A  74 " =    1.795
peak=    3.299 closest distance to " CB  PRO A 243 " =    1.393
peak=    3.297 closest distance to " OG BSER A 134 " =    2.852
peak=    3.295 closest distance to " O   ASP A 200 " =    1.703
peak=    3.295 closest distance to " CB  ARG A 156 " =    1.004
peak=    3.292 closest distance to " CA  VAL A  41 " =    0.813
peak=    3.291 closest distance to " CZ  PHE A 192 " =    0.995
peak=    3.287 closest distance to " O   HOH Z 175 " =    3.739
peak=    3.287 closest distance to " OE1 GLN A  58 " =    3.496
peak=    3.285 closest distance to " CG2 ILE A  20 " =    1.462
peak=    3.279 closest distance to " CD1 LEU A 228 " =    1.698
peak=    3.278 closest distance to " CA  SER A  32 " =    1.687
peak=    3.278 closest distance to " O   HOH Z  76 " =    1.292
peak=    3.277 closest distance to " O   PRO A 213 " =    1.650
peak=    3.276 closest distance to " CA  TRP A  92 " =    0.929
peak=    3.273 closest distance to " N   THR A  52 " =    1.107
peak=    3.271 closest distance to " O   HOH Z 394 " =    4.052
peak=    3.270 closest distance to " O   HOH Z  90 " =    3.461
peak=    3.270 closest distance to " CD ALYS A 290 " =    1.059
peak=    3.269 closest distance to " CD  ARG A  66 " =    2.411
peak=    3.264 closest distance to " CB  MET A  47 " =    0.950
peak=    3.264 closest distance to " CG1 ILE A  49 " =    1.661
peak=    3.263 closest distance to " CB  PHE A 204 " =    0.883
peak=    3.262 closest distance to " N   SER A 164 " =    1.003
peak=    3.261 closest distance to " O   ALA A 158 " =    1.219
peak=    3.261 closest distance to " CA  ALA A 154 " =    1.013
peak=    3.256 closest distance to " O   HOH Z 128 " =    1.850
peak=    3.256 closest distance to " CG2 VAL A 126 " =    0.879
peak=    3.256 closest distance to " C   ILE A 106 " =    1.870
peak=    3.246 closest distance to " O   THR A 220 " =    1.052
peak=    3.241 closest distance to " O   HOH Z 199 " =    1.670
peak=    3.239 closest distance to " CA  ALA A 233 " =    1.677
peak=    3.237 closest distance to " O   HOH Z  32 " =    2.164
peak=    3.234 closest distance to " O   HOH Z 147 " =    1.581
peak=    3.233 closest distance to " O   HOH Z 185 " =    1.747
peak=    3.232 closest distance to " O   HOH Z 298 " =    2.456
peak=    3.226 closest distance to " O   HOH Z 180 " =    2.201
peak=    3.225 closest distance to " O   HOH Z  19 " =    1.680
peak=    3.223 closest distance to " O   HOH Z 343 " =    2.227
peak=    3.217 closest distance to " O   HOH Z 313 " =    1.765
peak=    3.212 closest distance to " O   HOH Z 427 " =    3.163
peak=    3.212 closest distance to " O   HOH Z 125 " =    3.889
peak=    3.212 closest distance to " O   HOH Z 193 " =    1.859
peak=    3.211 closest distance to " CG  GLN A  89 " =    1.562
peak=    3.210 closest distance to " O   HOH Z 371 " =    2.686
peak=    3.208 closest distance to " O   HOH Z 134 " =    2.368
peak=    3.207 closest distance to " CB  TYR A 247 " =    0.962
peak=    3.204 closest distance to " OG  SER A 245 " =    1.607
peak=    3.203 closest distance to " O   HOH Z 196 " =    3.790
peak=    3.200 closest distance to " O   PHE A 155 " =    1.110
peak=    3.194 closest distance to " O   HOH Z 251 " =    1.636
peak=    3.187 closest distance to " O   HOH Z 368 " =    4.667
peak=    3.187 closest distance to " OD2 ASP A 200 " =    1.287
peak=    3.185 closest distance to " CA  ARG A 102 " =    1.161
peak=    3.184 closest distance to " O  BHOH Z 338 " =    2.276
peak=    3.183 closest distance to " O   GLY A  91 " =    1.204
peak=    3.181 closest distance to " CA  THR A 221 " =    1.687
peak=    3.181 closest distance to " CA  ARG A  66 " =    0.968
peak=    3.181 closest distance to " O   HOH Z  54 " =    1.410
peak=    3.178 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.178 closest distance to " O   HOH Z 395 " =    1.443
peak=    3.176 closest distance to " O   HOH Z 305 " =    3.681
peak=    3.175 closest distance to " CD2 LEU A 255 " =    1.385
peak=    3.175 closest distance to " O   PHE A  61 " =    1.391
peak=    3.173 closest distance to " OG  SER A  22 " =    2.804
peak=    3.172 closest distance to " CG1 ILE A  20 " =    1.187
peak=    3.171 closest distance to " O   HOH Z 286 " =    2.074
peak=    3.169 closest distance to " CB  ALA A   9 " =    1.583
peak=    3.166 closest distance to " NH2BARG A 145 " =    1.998
peak=    3.163 closest distance to " CG  MET A 185 " =    1.059
peak=    3.161 closest distance to " O   HOH Z 247 " =    1.519
peak=    3.159 closest distance to " CG2 THR A 220 " =    0.761
peak=    3.157 closest distance to " CA  ALA A 158 " =    1.228
peak=    3.154 closest distance to " CA  THR A 182 " =    1.217
peak=    3.153 closest distance to " CB  TYR A 116 " =    1.196
peak=    3.148 closest distance to " CB  SER A 210 " =    0.902
peak=    3.147 closest distance to " O   HOH Z 142 " =    1.464
peak=    3.142 closest distance to " OH  TYR A  30 " =    1.539
peak=    3.126 closest distance to " O   HOH Z 387 " =    2.912
peak=    3.126 closest distance to " CG  GLN A  58 " =    2.731
peak=    3.125 closest distance to " CB  ASN A 187 " =    1.157
peak=    3.124 closest distance to " CB  GLN A 240 " =    1.567
peak=    3.123 closest distance to " OH  TYR A 116 " =    1.317
peak=    3.122 closest distance to " CA  GLN A  11 " =    1.001
peak=    3.113 closest distance to " CB  ALA A 248 " =    1.049
peak=    3.112 closest distance to " O   HOH Z 421 " =    1.830
peak=    3.109 closest distance to " CA  LYS A 166 " =    1.419
peak=    3.108 closest distance to " O   HOH Z 148 " =    3.307
peak=    3.108 closest distance to " O   HOH Z 163 " =    1.661
peak=    3.107 closest distance to " CA  THR A 264 " =    0.847
peak=    3.105 closest distance to " O   HOH Z 353 " =    2.815
peak=    3.093 closest distance to " CA  LYS A 117 " =    1.289
peak=    3.083 closest distance to " CA  ALA A  84 " =    1.280
peak=    3.077 closest distance to " O   HOH Z 141 " =    1.661
peak=    3.073 closest distance to " CA  SER A  26 " =    0.970
peak=    3.065 closest distance to " NH1 ARG A  14 " =    1.053
peak=    3.063 closest distance to " CB  LEU A   5 " =    1.192
peak=    3.044 closest distance to " CG2 ILE A 234 " =    0.936
peak=    3.035 closest distance to " O   HOH Z 409 " =    3.001
peak=    3.027 closest distance to " O   THR A 182 " =    1.466
peak=    3.019 closest distance to " NH2AARG A 275 " =    3.441
peak=    3.017 closest distance to " CB  ASN A 148 " =    2.020
peak=    3.007 closest distance to " CB  ARG A  79 " =    0.871

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.443 - 5.828
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 223
   mapped sites are within: 0.715 - 5.828

peak=   -4.760 closest distance to " CD  GLN A  58 " =    0.869
peak=   -4.623 closest distance to " CD  GLN A 223 " =    1.398
peak=   -4.476 closest distance to " CD  GLN A  88 " =    1.036
peak=   -4.417 closest distance to " CG1 VAL A 250 " =    2.727
peak=   -4.394 closest distance to " CD1 PHE A  59 " =    2.044
peak=   -4.384 closest distance to " O   HOH Z 411 " =    5.551
peak=   -4.370 closest distance to " CG1 VAL A 112 " =    2.598
peak=   -4.249 closest distance to " CB  PRO A 243 " =    2.792
peak=   -4.204 closest distance to " O   HOH Z 150 " =    0.715
peak=   -4.182 closest distance to " OXT GLY A 302 " =    3.074
peak=   -4.137 closest distance to " CD  ARG A 156 " =    2.134
peak=   -4.106 closest distance to " CB  ALA A  10 " =    2.161
peak=   -4.100 closest distance to " CD  ARG A  14 " =    3.437
peak=   -4.077 closest distance to " O   HOH Z   5 " =    1.578
peak=   -4.036 closest distance to " O   HOH Z 377 " =    0.907
peak=   -4.027 closest distance to " C   SER A 206 " =    1.327
peak=   -4.020 closest distance to " CG  ARG A 269 " =    2.392
peak=   -4.015 closest distance to " CE2 PHE A  61 " =    2.654
peak=   -3.977 closest distance to " CD1 PHE A 130 " =    2.390
peak=   -3.970 closest distance to " O   HOH Z  19 " =    2.214
peak=   -3.964 closest distance to " O   HOH Z 407 " =    0.820
peak=   -3.945 closest distance to " O   HOH Z 166 " =    2.317
peak=   -3.936 closest distance to " O   HOH Z 283 " =    2.226
peak=   -3.936 closest distance to " O   HOH Z 128 " =    2.613
peak=   -3.913 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.882 closest distance to " CD2 TYR A 293 " =    1.817
peak=   -3.874 closest distance to " OD1 ASN A 148 " =    1.409
peak=   -3.867 closest distance to " CZ3 TRP A 179 " =    1.204
peak=   -3.864 closest distance to " C   ASN A 285 " =    2.459
peak=   -3.855 closest distance to " O   HOH Z   6 " =    1.312
peak=   -3.850 closest distance to " CD1 LEU A 101 " =    2.533
peak=   -3.848 closest distance to " CB  ALA A 161 " =    2.617
peak=   -3.838 closest distance to " O   HOH Z 234 " =    4.412
peak=   -3.832 closest distance to " O   PRO A 198 " =    1.337
peak=   -3.820 closest distance to " CB  ALA A 291 " =    2.465
peak=   -3.798 closest distance to " O   VAL A  67 " =    2.776
peak=   -3.795 closest distance to " O   HOH Z 166 " =    1.662
peak=   -3.786 closest distance to " CE2 TYR A  30 " =    2.701
peak=   -3.784 closest distance to " O   HOH Z  58 " =    1.035
peak=   -3.769 closest distance to " OG  SER A  97 " =    2.262
peak=   -3.744 closest distance to " O   HOH Z 348 " =    2.359
peak=   -3.741 closest distance to " NE2 GLN A 223 " =    1.061
peak=   -3.714 closest distance to " ND2 ASN A  45 " =    2.034
peak=   -3.664 closest distance to " OG BSER A 210 " =    1.397
peak=   -3.662 closest distance to " O   HOH Z 185 " =    2.604
peak=   -3.658 closest distance to " CG  GLN A  11 " =    1.412
peak=   -3.656 closest distance to " CA  GLY A 241 " =    2.370
peak=   -3.653 closest distance to " C   HIS A 108 " =    1.074
peak=   -3.650 closest distance to " CD2 PHE A  61 " =    2.076
peak=   -3.636 closest distance to " ND2 ASN A  45 " =    1.102
peak=   -3.635 closest distance to " O   HOH Z 252 " =    3.717
peak=   -3.623 closest distance to " OD1 ASP A 191 " =    1.453
peak=   -3.611 closest distance to " NE2 GLN A 194 " =    1.972
peak=   -3.604 closest distance to " ND2 ASN A 249 " =    2.350
peak=   -3.581 closest distance to " CG2 ILE A  20 " =    3.030
peak=   -3.573 closest distance to " O   HOH Z 155 " =    1.853
peak=   -3.570 closest distance to " CG  MET A 105 " =    0.904
peak=   -3.568 closest distance to " CA  GLY A 203 " =    2.467
peak=   -3.563 closest distance to " O   HOH Z 120 " =    4.271
peak=   -3.551 closest distance to " OE1 GLN A 223 " =    2.394
peak=   -3.547 closest distance to " O   SER A 210 " =    1.766
peak=   -3.536 closest distance to " NH2 ARG A 159 " =    2.402
peak=   -3.534 closest distance to " O   HOH Z  49 " =    1.061
peak=   -3.529 closest distance to " CB  SER A 146 " =    2.188
peak=   -3.526 closest distance to " O   ALA A  34 " =    2.547
peak=   -3.526 closest distance to " O   HOH Z  37 " =    1.798
peak=   -3.504 closest distance to " CB  PHE A  16 " =    2.538
peak=   -3.501 closest distance to " C   ALA A 158 " =    1.377
peak=   -3.499 closest distance to " O   HOH Z 113 " =    2.496
peak=   -3.497 closest distance to " O   HOH Z 197 " =    2.160
peak=   -3.495 closest distance to " O   HOH Z 149 " =    1.917
peak=   -3.492 closest distance to " CG2 ILE A  49 " =    2.705
peak=   -3.490 closest distance to " CB  ALA A  43 " =    2.643
peak=   -3.489 closest distance to " O   SER A 276 " =    1.880
peak=   -3.489 closest distance to " O   HOH Z 418 " =    1.338
peak=   -3.479 closest distance to " C   ARG A  79 " =    2.738
peak=   -3.479 closest distance to " O   HOH Z 275 " =    1.651
peak=   -3.477 closest distance to " O   HOH Z  52 " =    1.668
peak=   -3.466 closest distance to " OD2 ASP A 171 " =    2.377
peak=   -3.459 closest distance to " O   HOH Z 351 " =    1.646
peak=   -3.446 closest distance to " O   HOH Z   7 " =    1.535
peak=   -3.446 closest distance to " CA  SER A  62 " =    2.525
peak=   -3.433 closest distance to " O   HOH Z 109 " =    3.299
peak=   -3.432 closest distance to " CG1AVAL A 121 " =    1.515
peak=   -3.429 closest distance to " ND2BASN A 224 " =    1.926
peak=   -3.427 closest distance to " O   HOH Z  90 " =    3.476
peak=   -3.421 closest distance to " O   HOH Z 136 " =    2.281
peak=   -3.416 closest distance to " O   HOH Z 290 " =    1.180
peak=   -3.410 closest distance to " C   LEU A 143 " =    1.238
peak=   -3.407 closest distance to " O   ALA A  10 " =    1.849
peak=   -3.404 closest distance to " O   HOH Z 394 " =    1.628
peak=   -3.404 closest distance to " CD  GLN A  73 " =    0.751
peak=   -3.401 closest distance to " NE2 GLN A 103 " =    1.818
peak=   -3.397 closest distance to " O   HOH Z 111 " =    1.445
peak=   -3.396 closest distance to " N   ALA A 226 " =    2.070
peak=   -3.394 closest distance to " O   HOH Z 308 " =    1.556
peak=   -3.391 closest distance to " CA  GLY A 241 " =    3.211
peak=   -3.386 closest distance to " CD1 LEU A  25 " =    2.507
peak=   -3.378 closest distance to " CB  PHE A 192 " =    2.014
peak=   -3.378 closest distance to " O   HOH Z   7 " =    1.187
peak=   -3.378 closest distance to " O   HOH Z 200 " =    1.188
peak=   -3.377 closest distance to " OH  TYR A 247 " =    2.294
peak=   -3.375 closest distance to " O   HOH Z 298 " =    2.774
peak=   -3.374 closest distance to " O   HOH Z 392 " =    1.407
peak=   -3.374 closest distance to " O   HOH Z 264 " =    1.869
peak=   -3.372 closest distance to " O   HOH Z 210 " =    0.719
peak=   -3.370 closest distance to " O   HOH Z 377 " =    2.092
peak=   -3.370 closest distance to " O   HOH Z 371 " =    1.347
peak=   -3.368 closest distance to " CG  GLU A 277 " =    1.227
peak=   -3.361 closest distance to " CE3 TRP A 150 " =    2.160
peak=   -3.359 closest distance to " CZ  PHE A  38 " =    2.545
peak=   -3.358 closest distance to " O   VAL A 189 " =    2.559
peak=   -3.352 closest distance to " O   HOH Z 139 " =    3.353
peak=   -3.350 closest distance to " CG2 VAL A 189 " =    2.187
peak=   -3.339 closest distance to " CA  TYR A  68 " =    2.991
peak=   -3.337 closest distance to " N   ARG A 275 " =    1.292
peak=   -3.332 closest distance to " CG  GLU A  53 " =    1.602
peak=   -3.331 closest distance to " O   LEU A 101 " =    2.098
peak=   -3.331 closest distance to " N   THR A 157 " =    1.733
peak=   -3.325 closest distance to " CZ  TYR A 169 " =    1.879
peak=   -3.324 closest distance to " O   HOH Z 109 " =    3.535
peak=   -3.322 closest distance to " O   HOH Z  70 " =    2.256
peak=   -3.313 closest distance to " NH2 ARG A  66 " =    1.836
peak=   -3.299 closest distance to " O   HOH Z 236 " =    1.648
peak=   -3.293 closest distance to " O   HOH Z 198 " =    1.462
peak=   -3.293 closest distance to " O   HOH Z 301 " =    2.394
peak=   -3.288 closest distance to " O   HOH Z  40 " =    3.199
peak=   -3.287 closest distance to " ND2 ASN A  69 " =    1.542
peak=   -3.287 closest distance to " OG1 THR A  82 " =    1.530
peak=   -3.286 closest distance to " O   HOH Z 403 " =    0.992
peak=   -3.286 closest distance to " SD  MET A 105 " =    2.514
peak=   -3.281 closest distance to " O   HOH Z 193 " =    2.092
peak=   -3.277 closest distance to " CD2 PHE A 225 " =    1.331
peak=   -3.271 closest distance to " O   SER A 135 " =    1.815
peak=   -3.269 closest distance to " O   HOH Z 117 " =    4.625
peak=   -3.263 closest distance to " CG  ASP A 231 " =    0.833
peak=   -3.262 closest distance to " CD1 LEU A   5 " =    2.588
peak=   -3.261 closest distance to " C   THR A 279 " =    1.035
peak=   -3.259 closest distance to " O   GLY A 262 " =    2.462
peak=   -3.257 closest distance to " O   PRO A 163 " =    2.160
peak=   -3.254 closest distance to " O   ASP A 171 " =    1.030
peak=   -3.253 closest distance to " CA  LYS A 166 " =    2.223
peak=   -3.252 closest distance to " O   HOH Z 318 " =    1.459
peak=   -3.252 closest distance to " O   SER A 271 " =    2.193
peak=   -3.252 closest distance to " CA  VAL A 197 " =    0.990
peak=   -3.251 closest distance to " O   PHE A 218 " =    1.419
peak=   -3.250 closest distance to " O   HOH Z  91 " =    2.277
peak=   -3.249 closest distance to " NE  ARG A  66 " =    4.408
peak=   -3.248 closest distance to " O   HOH Z 422 " =    1.302
peak=   -3.246 closest distance to " O   HOH Z 198 " =    2.379
peak=   -3.242 closest distance to " O   HOH Z 177 " =    1.965
peak=   -3.241 closest distance to " O   HOH Z 388 " =    1.890
peak=   -3.240 closest distance to " NE2 GLN A  58 " =    2.682
peak=   -3.235 closest distance to " OG  SER A  26 " =    1.182
peak=   -3.232 closest distance to " O   HOH Z 171 " =    2.389
peak=   -3.232 closest distance to " N   ALA A  43 " =    2.714
peak=   -3.231 closest distance to " CB  TRP A  85 " =    2.524
peak=   -3.231 closest distance to " CB  ALA A 131 " =    2.390
peak=   -3.226 closest distance to " CG2 ILE A 263 " =    2.259
peak=   -3.225 closest distance to " N   SER A 276 " =    1.534
peak=   -3.224 closest distance to " O   HOH Z 292 " =    4.755
peak=   -3.217 closest distance to " O   HOH Z 165 " =    1.855
peak=   -3.213 closest distance to " OD2 ASP A 171 " =    1.903
peak=   -3.210 closest distance to " CH2 TRP A 177 " =    2.044
peak=   -3.210 closest distance to " CG  ASP A 132 " =    2.415
peak=   -3.209 closest distance to " O   HOH Z  60 " =    1.517
peak=   -3.200 closest distance to " CD  ARG A 139 " =    1.457
peak=   -3.199 closest distance to " O   HOH Z 396 " =    1.827
peak=   -3.197 closest distance to " O   HOH Z 184 " =    1.620
peak=   -3.194 closest distance to " OD1 ASN A 173 " =    1.417
peak=   -3.193 closest distance to " CG  PRO A 163 " =    2.030
peak=   -3.191 closest distance to " O   GLY A  17 " =    1.229
peak=   -3.187 closest distance to " OD1 ASP A 171 " =    1.513
peak=   -3.186 closest distance to " O   HOH Z 384 " =    2.131
peak=   -3.185 closest distance to " O   HOH Z 114 " =    3.933
peak=   -3.183 closest distance to " CD1 TRP A 179 " =    0.965
peak=   -3.180 closest distance to " CD1 ILE A 109 " =    2.985
peak=   -3.179 closest distance to " O   HOH Z 259 " =    2.111
peak=   -3.178 closest distance to " O   HOH Z 251 " =    5.042
peak=   -3.176 closest distance to " CG  PRO A 243 " =    1.732
peak=   -3.176 closest distance to " N   ALA A 242 " =    1.823
peak=   -3.174 closest distance to " O   HOH Z 413 " =    4.971
peak=   -3.170 closest distance to " O   HOH Z 154 " =    1.394
peak=   -3.170 closest distance to " OG  SER A  63 " =    1.144
peak=   -3.168 closest distance to " C   VAL A 265 " =    0.876
peak=   -3.167 closest distance to " CD2 PHE A  59 " =    2.491
peak=   -3.161 closest distance to " O   HOH Z  71 " =    2.003
peak=   -3.156 closest distance to " O   HOH Z 367 " =    3.712
peak=   -3.155 closest distance to " CD  ARG A 139 " =    1.041
peak=   -3.155 closest distance to " CD1 ILE A 263 " =    1.954
peak=   -3.153 closest distance to " OE2 GLU A  53 " =    1.232
peak=   -3.149 closest distance to " CH2 TRP A 150 " =    1.197
peak=   -3.143 closest distance to " O   HOH Z 325 " =    1.980
peak=   -3.136 closest distance to " CB  SER A 210 " =    1.046
peak=   -3.133 closest distance to " O   GLN A 240 " =    2.625
peak=   -3.133 closest distance to " O   HOH Z  88 " =    2.497
peak=   -3.132 closest distance to " O   HOH Z 326 " =    5.035
peak=   -3.125 closest distance to " CZ  TYR A  68 " =    1.162
peak=   -3.122 closest distance to " CG2BVAL A  41 " =    2.107
peak=   -3.122 closest distance to " O   HOH Z 174 " =    3.652
peak=   -3.119 closest distance to " CG2BVAL A  41 " =    1.516
peak=   -3.114 closest distance to " OD1 ASN A 301 " =    1.976
peak=   -3.109 closest distance to " O   HOH Z 108 " =    2.211
peak=   -3.108 closest distance to " CG  TRP A 266 " =    1.952
peak=   -3.098 closest distance to " CG  PHE A 283 " =    2.686
peak=   -3.096 closest distance to " OE2 GLU A 277 " =    2.918
peak=   -3.094 closest distance to " O   SER A  95 " =    1.897
peak=   -3.081 closest distance to " O   HOH Z 196 " =    1.893
peak=   -3.080 closest distance to " CG1 VAL A  78 " =    2.621
peak=   -3.076 closest distance to " CD  LYS A 289 " =    2.328
peak=   -3.073 closest distance to " CG1 VAL A 112 " =    2.890
peak=   -3.067 closest distance to " O   HOH Z 191 " =    5.828
peak=   -3.063 closest distance to " O   HOH Z 210 " =    1.239
peak=   -3.039 closest distance to " O   HOH Z 288 " =    1.655
peak=   -3.037 closest distance to " O   HOH Z 219 " =    4.405
peak=   -3.034 closest distance to " O   HOH Z 422 " =    1.541
peak=   -3.033 closest distance to " O   HOH Z 336 " =    5.447
peak=   -3.023 closest distance to " O   HOH Z 198 " =    1.378
peak=   -3.023 closest distance to " O   HOH Z 414 " =    1.749
peak=   -3.015 closest distance to " O   HOH Z 210 " =    1.008

================= 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    :  0.4625 0.4460   6.274876e+00   6.246382e+00
   1_bss:  0.4543 0.4377   6.267890e+00   6.235933e+00
   1_xyz:  0.3558 0.3870   6.110561e+00   6.154463e+00
   1_adp:  0.3266 0.3979   6.065041e+00   6.166308e+00
   1_occ:  0.3265 0.3972   6.064243e+00   6.165622e+00
   2_bss:  0.3258 0.3959   6.066211e+00   6.166727e+00
   2_xyz:  0.2535 0.3022   5.834590e+00   5.973441e+00
   2_adp:  0.2263 0.2799   5.752897e+00   5.917521e+00
   2_occ:  0.2259 0.2800   5.752048e+00   5.917295e+00
   3_bss:  0.2248 0.2790   5.749556e+00   5.914110e+00
   3_xyz:  0.1728 0.2149   5.504109e+00   5.693348e+00
   3_adp:  0.1578 0.2025   5.433347e+00   5.632747e+00
   3_occ:  0.1578 0.2024   5.432634e+00   5.632177e+00
   4_bss:  0.1581 0.2026   5.433141e+00   5.631570e+00
   4_xyz:  0.1375 0.1836   5.319533e+00   5.537348e+00
   4_adp:  0.1326 0.1808   5.288951e+00   5.511259e+00
   4_occ:  0.1326 0.1808   5.288561e+00   5.511183e+00
   5_bss:  0.1328 0.1807   5.288905e+00   5.510674e+00
   5_xyz:  0.1236 0.1716   5.232354e+00   5.465869e+00
   5_adp:  0.1228 0.1690   5.223538e+00   5.453960e+00
   5_occ:  0.1227 0.1690   5.223191e+00   5.453993e+00
   5_bss:  0.1227 0.1691   5.223124e+00   5.453965e+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:  0.279  45.633  -2.918   4.427   0.987   0.000   0.000   0.000
   1_xyz:  0.279  45.633  -2.918   4.427   0.987   0.000   0.000   0.000
   1_adp:  0.279  45.633  -2.918   4.427   0.987   0.000   0.000   0.000
   1_occ:  0.279  45.633  -2.918   4.427   0.987   0.000   0.000   0.000
   2_bss:  0.279  62.986  -1.071   2.882   0.925   0.000   0.000   0.000
   2_xyz:  0.279  62.986  -1.071   2.882   0.925   0.000   0.000   0.000
   2_adp:  0.279  62.986  -1.071   2.882   0.925   0.000   0.000   0.000
   2_occ:  0.279  62.986  -1.071   2.882   0.925   0.000   0.000   0.000
   3_bss:  0.321  72.392  -0.914   1.325   0.577   0.000   0.000   0.000
   3_xyz:  0.321  72.392  -0.914   1.325   0.577   0.000   0.000   0.000
   3_adp:  0.321  72.392  -0.914   1.325   0.577   0.000   0.000   0.000
   3_occ:  0.321  72.392  -0.914   1.325   0.577   0.000   0.000   0.000
   4_bss:  0.331  79.688  -1.179   0.322   0.340   0.000   0.000   0.000
   4_xyz:  0.331  79.688  -1.179   0.322   0.340   0.000   0.000   0.000
   4_adp:  0.331  79.688  -1.179   0.322   0.340   0.000   0.000   0.000
   4_occ:  0.331  79.688  -1.179   0.322   0.340   0.000   0.000   0.000
   5_bss:  0.328  77.259  -1.030   0.067   0.541   0.000   0.000   0.000
   5_xyz:  0.328  77.259  -1.030   0.067   0.541   0.000   0.000   0.000
   5_adp:  0.328  77.259  -1.030   0.067   0.541   0.000   0.000   0.000
   5_occ:  0.328  77.259  -1.030   0.067   0.541   0.000   0.000   0.000
   5_bss:  0.319  70.047  -1.009  -0.086   0.565  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.758 0.4871  0.6237    61462.953
   1_bss:  51.884 0.4970  0.6576    58984.868
   1_xyz:  44.047 0.5934  0.7687    43667.440
   1_adp:  44.804 0.5840  0.7480    45248.378
   1_occ:  44.769 0.5845  0.7478    45201.319
   2_bss:  44.628 0.5863  0.7546    45153.328
   2_xyz:  32.264 0.7318  0.9190    24861.735
   2_adp:  29.211 0.7664  0.9268    21180.683
   2_occ:  29.198 0.7666  0.9264    21161.532
   3_bss:  29.014 0.7685  0.9116    20924.688
   3_xyz:  21.439 0.8472  0.9689    12016.163
   3_adp:  19.618 0.8656  0.9669    10663.027
   3_occ:  19.591 0.8658  0.9670    10649.657
   4_bss:  19.545 0.8662  0.9508    10611.062
   4_xyz:  17.277 0.8872  0.9621     8640.605
   4_adp:  16.615 0.8933  0.9546     8259.600
   4_occ:  16.607 0.8934  0.9546     8258.444
   5_bss:  16.591 0.8935  0.9558     8241.045
   5_xyz:  15.612 0.9018  0.9619     7483.941
   5_adp:  15.315 0.9045  0.9554     7327.118
   5_occ:  15.314 0.9045  0.9554     7328.460
   5_bss:  15.315 0.9045  0.9544     7327.132
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6648e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6648e-01
   1_xyz:   1.556  0.013  0.095 15.942  0.006  4.114   1.3033e-01
   1_adp:   1.556  0.013  0.095 15.942  0.006  4.114   1.3033e-01
   1_occ:   1.556  0.013  0.095 15.942  0.006  4.114   1.3033e-01
   2_bss:   1.556  0.013  0.095 15.942  0.006  4.114   1.3033e-01
   2_xyz:   1.549  0.013  0.098 16.006  0.006  4.119   1.3673e-01
   2_adp:   1.549  0.013  0.098 16.006  0.006  4.119   1.3673e-01
   2_occ:   1.549  0.013  0.098 16.006  0.006  4.119   1.3673e-01
   3_bss:   1.549  0.013  0.098 16.006  0.006  4.119   1.3673e-01
   3_xyz:   1.202  0.011  0.078 15.102  0.004  4.115   9.2291e-02
   3_adp:   1.202  0.011  0.078 15.102  0.004  4.115   9.2291e-02
   3_occ:   1.202  0.011  0.078 15.102  0.004  4.115   9.2291e-02
   4_bss:   1.202  0.011  0.078 15.102  0.004  4.115   9.2291e-02
   4_xyz:   1.128  0.010  0.080 14.830  0.004  4.127   7.3925e-02
   4_adp:   1.128  0.010  0.080 14.830  0.004  4.127   7.3925e-02
   4_occ:   1.128  0.010  0.080 14.830  0.004  4.127   7.3925e-02
   5_bss:   1.128  0.010  0.080 14.830  0.004  4.127   7.3925e-02
   5_xyz:   1.134  0.011  0.083 14.895  0.004  4.118   7.8160e-02
   5_adp:   1.134  0.011  0.083 14.895  0.004  4.118   7.8160e-02
   5_occ:   1.134  0.011  0.083 14.895  0.004  4.118   7.8160e-02
   5_bss:   1.134  0.011  0.083 14.895  0.004  4.118   7.8160e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.645   2.4558e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.645   2.4558e-01
   1_xyz:   9.692  0.074  0.325 83.915  0.041  2.094   1.1122e-01
   1_adp:   9.692  0.074  0.325 83.915  0.041  2.094   1.1122e-01
   1_occ:   9.692  0.074  0.325 83.915  0.041  2.094   1.1122e-01
   2_bss:   9.692  0.074  0.325 83.915  0.041  2.094   1.1122e-01
   2_xyz:   9.452  0.071  0.294 83.618  0.042  2.044   1.8719e-01
   2_adp:   9.452  0.071  0.294 83.618  0.042  2.044   1.8719e-01
   2_occ:   9.452  0.071  0.294 83.618  0.042  2.044   1.8719e-01
   3_bss:   9.452  0.071  0.294 83.618  0.042  2.044   1.8719e-01
   3_xyz:   8.207  0.066  0.205 86.706  0.032  2.179   1.8328e-01
   3_adp:   8.207  0.066  0.205 86.706  0.032  2.179   1.8328e-01
   3_occ:   8.207  0.066  0.205 86.706  0.032  2.179   1.8328e-01
   4_bss:   8.207  0.066  0.205 86.706  0.032  2.179   1.8328e-01
   4_xyz:   7.712  0.051  0.240 82.980  0.040  2.238   4.7906e-02
   4_adp:   7.712  0.051  0.240 82.980  0.040  2.238   4.7906e-02
   4_occ:   7.712  0.051  0.240 82.980  0.040  2.238   4.7906e-02
   5_bss:   7.712  0.051  0.240 82.980  0.040  2.238   4.7906e-02
   5_xyz:   8.221  0.052  0.279 82.308  0.035  2.236   5.9206e-02
   5_adp:   8.221  0.052  0.279 82.308  0.035  2.236   5.9206e-02
   5_occ:   8.221  0.052  0.279 82.308  0.035  2.236   5.9206e-02
   5_bss:   8.221  0.052  0.279 82.308  0.035  2.236   5.9206e-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: 100.64   0.00  18.27  84.11   0.00  14.81 100.64   0.00  37.13
   1_occ: 100.64   0.00  18.27  84.11   0.00  14.81 100.64   0.00  37.13
   2_bss: 100.64   0.00  18.27  84.11   0.00  14.81 100.64   0.00  37.13
   2_xyz: 100.64   0.00  18.27  84.11   0.00  14.81 100.64   0.00  37.13
   2_adp:  95.43   0.00  17.70  80.75   0.00  13.44  95.43   0.00  40.88
   2_occ:  95.43   0.00  17.70  80.75   0.00  13.44  95.43   0.00  40.88
   3_bss:  95.43   0.00  17.70  80.75   0.00  13.44  95.43   0.00  40.88
   3_xyz:  95.43   0.00  17.70  80.75   0.00  13.44  95.43   0.00  40.88
   3_adp:  95.84   0.00  17.18  90.02   0.00  12.43  95.84   3.82  43.08
   3_occ:  95.84   0.00  17.18  90.02   0.00  12.43  95.84   3.82  43.08
   4_bss:  95.84   0.00  17.18  90.02   0.00  12.43  95.84   3.82  43.08
   4_xyz:  95.84   0.00  17.18  90.02   0.00  12.43  95.84   3.82  43.08
   4_adp: 100.49   0.00  16.83  98.20   0.00  11.94 100.49   1.33  43.44
   4_occ: 100.49   0.00  16.83  98.20   0.00  11.94 100.49   1.33  43.44
   5_bss: 100.49   0.00  16.83  98.20   0.00  11.94 100.49   1.33  43.44
   5_xyz: 100.49   0.00  16.83  98.20   0.00  11.94 100.49   1.33  43.44
   5_adp:  99.94   0.00  16.15  96.22   0.00  11.54  99.94   1.86  41.23
   5_occ:  99.94   0.00  16.15  96.22   0.00  11.54  99.94   1.86  41.23
   5_bss:  99.95   0.00  16.15  96.22   0.00  11.55  99.95   1.86  41.23
------------------------------------------------------------------------
 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:    1.440    0.015    0.374
   1_adp:    1.440    0.015    0.374
   1_occ:    1.440    0.015    0.374
   2_bss:    1.440    0.015    0.374
   2_xyz:    1.648    0.039    0.664
   2_adp:    1.648    0.039    0.664
   2_occ:    1.648    0.039    0.664
   3_bss:    1.648    0.039    0.664
   3_xyz:    1.590    0.005    0.766
   3_adp:    1.590    0.005    0.766
   3_occ:    1.590    0.005    0.766
   4_bss:    1.590    0.005    0.766
   4_xyz:    1.649    0.092    0.815
   4_adp:    1.649    0.092    0.815
   4_occ:    1.649    0.092    0.815
   5_bss:    1.649    0.092    0.815
   5_xyz:    1.589    0.116    0.841
   5_adp:    1.589    0.116    0.841
   5_occ:    1.589    0.116    0.841
   5_bss:    1.589    0.116    0.841
------------------------------------------------------------------------

CPU time actual refinement: 331.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/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_965/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_965/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.41 
  Macro-tasks:
    bulk solvent and scale       = 48.12  
    individual site refinement   = 130.19 
    weights calculation          = 28.89  
    collect and process          = 6.56   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.87 
  Micro-tasks:
    mask                            = 2.30   
    f_calc                          = 101.17 
    alpha_beta                      = 8.52   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 109.65 
    fmodel                         = 8.01   
    r_factors                      = 0.28   
    phase_errors                   = 10.69  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 242.01 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.738 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    634 calls, 100.74 s
gradients_fft:          579 calls,  96.91 s

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

# Date 2008-01-16 Time 06:05:27 PST -0800 (1200492327.44 s)
Start R-work = 0.4625, R-free = 0.4460 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1830 (no bulk solvent and anisotropic scale)

Start R-work = 0.4543, R-free = 0.4377
Final R-work = 0.1227, R-free = 0.1691