# Date 2008-01-16 Time 05:50:25 PST -0800 (1200491425.27 s)
#phil __OFF__

Command line arguments: "../901.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29889
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 901

-------------------------------------------------------------------------------
  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, 46.6953, 88.5498, 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: 3.31, per 1000 atoms: 1.17


================================== 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, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.99283
Completeness in resolution range: 0.947015
Completeness with d_max=infinity: 0.944185

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   1.9928

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, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.99283
Completeness in resolution range: 0.947015
Completeness with d_max=infinity: 0.944185

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.2648 [2171/2196]  1951   220  10.1%
  bin  2:  4.2648 -  3.3975 [2084/2104]  1879   205   9.8%
  bin  3:  3.3975 -  2.9717 [2074/2093]  1866   208  10.0%
  bin  4:  2.9717 -  2.7017 [2027/2057]  1823   204  10.1%
  bin  5:  2.7017 -  2.5089 [2033/2052]  1832   201   9.9%
  bin  6:  2.5089 -  2.3616 [2012/2037]  1809   203  10.1%
  bin  7:  2.3616 -  2.2437 [2025/2053]  1820   205  10.1%
  bin  8:  2.2437 -  2.1463 [1988/2024]  1790   198  10.0%
  bin  9:  2.1463 -  2.0639 [1997/2039]  1803   194   9.7%
  bin 10:  2.0639 -  1.9928 [1178/2030]  1057   121  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 13
        2.39 -     3.02: 1991
        3.02 -     3.64: 4549
        3.64 -     4.27: 8968
        4.27 -     4.90: 12382
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.760 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.849 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.849 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.932 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27898 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_901/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 46.69535 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3964   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.922    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.193453                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7570 0.99   1412  156 0.3282 0.2935      6.4852      6.3544|
|  2:  4.7570 -  3.7951 0.99   1363  153 0.3171 0.3439      6.6459      6.7005|
|  3:  3.7951 -  3.3211 0.99   1325  143 0.3579 0.2952      6.5521       6.464|
|  4:  3.3211 -  3.0200 0.99   1330  152 0.3792 0.3825      6.3999      6.3943|
|  5:  3.0200 -  2.8050 0.99   1311  147 0.4248 0.3925      6.2769      6.2695|
|  6:  2.8050 -  2.6406 0.99   1313  143 0.4014 0.4419      6.1586      6.1414|
|  7:  2.6406 -  2.5089 0.99   1297  144 0.4245 0.4141      6.1477      6.1087|
|  8:  2.5089 -  2.4002 0.98   1294  146 0.4557 0.4331      6.1309       6.128|
|  9:  2.4002 -  2.3081 0.98   1289  138 0.4354 0.4217      6.0427      6.0586|
| 10:  2.3081 -  2.2287 1.00   1278  149 0.4593 0.4457      6.0502      6.0167|
| 11:  2.2287 -  2.1592 0.98   1305  141 0.4609 0.4416        5.99      6.0031|
| 12:  2.1592 -  2.0976 0.98   1268  146 0.4632 0.4116      5.9177       5.928|
| 13:  2.0976 -  2.0426 0.99   1282  139 0.4437 0.4919      5.8077       5.782|
| 14:  2.0426 -  1.9928 0.43    563   62 0.4395 0.4260      5.8123      5.7368|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7570  1412   156  0.79  26.33   0.84     0.81      45163.79|
|  2:  4.7570 -  3.7951  1363   153  0.81  25.50   0.93     0.89      64245.43|
|  3:  3.7951 -  3.3211  1325   143  0.73  32.53   0.94     0.88      67959.76|
|  4:  3.3211 -  3.0200  1330   152  0.67  38.29   0.93     0.81      62458.19|
|  5:  3.0200 -  2.8050  1311   147  0.59  44.93   0.94     0.74      52009.26|
|  6:  2.8050 -  2.6406  1313   143  0.56  47.26   0.93     0.71      48424.47|
|  7:  2.6406 -  2.5089  1297   144  0.55  47.84   0.95     0.71      44436.62|
|  8:  2.5089 -  2.4002  1294   146  0.55  48.23   0.92     0.72      40099.22|
|  9:  2.4002 -  2.3081  1289   138  0.55  47.90   0.96     0.74      36714.06|
| 10:  2.3081 -  2.2287  1278   149  0.53  49.50   0.98     0.73      34184.01|
| 11:  2.2287 -  2.1592  1305   141  0.52  50.69   0.95     0.73      34443.81|
| 12:  2.1592 -  2.0976  1268   146  0.51  51.66   0.96     0.72      31324.19|
| 13:  2.0976 -  2.0426  1282   139  0.49  53.05   0.96     0.72      27616.25|
| 14:  2.0426 -  1.9928   563    62  0.53  49.61   1.00     0.72      22626.66|
|alpha:            min =        0.71 max =            0.89 mean =         0.76|
|beta:             min =    22626.66 max =        67959.76 mean =     44785.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.33|
|phase err.(test): min =        0.00 max =           89.59 mean =        42.90|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.356583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.167327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.947   (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 |  1.760 -  2.074:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.074 -  2.388:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.388 -  2.702:      116 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.702 -  3.016:     1875 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.016 -  3.330:     1842 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.330 -  3.644:     2707 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.644 -  3.958:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.958 -  4.272:     4323 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.272 -  4.586:     5624 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.586 -  4.900:     6758 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| 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  1.760 |       0.188 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3964   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.922    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.193453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3821   r_free= 0.3759   ksol= 0.32   Bsol= 60.84   scale= 0.954   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.87,5.74,-0.00,0.00,0.00); trace/3= 0.24                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.174674                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.983513              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.681   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.592118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.586   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3821      final r-factor (work) = 0.2350          |
| start r-factor (free) = 0.3759      final r-factor (free) = 0.2648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7975 = 7.98 * 0.50 * 6.1709 + 1.00 * 0.1650                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.8081 = 7.98 * 0.50 * 5.9366 + 1.00 * 0.1104                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2350      final r-factor (work) = 0.2160          |
| start r-factor (free) = 0.2648      final r-factor (free) = 0.2698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5217 = 0.59 * 1.00 * 5.9366 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4318 = 0.59 * 1.00 * 5.7012 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.89   16.98    None  None   None       |
|    all(noH): 2823   0      0.00    72.89   16.98    None  None   None       |
|    Sol.    : 438    0      2.84    64.60   38.53    None  None   None       |
|    Mac.    : 2385   0      0.00    72.89   13.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.289:  495   |   5:    36.447 -  43.736:  118        |
|      1:     7.289 -  14.579: 1133   |   6:    43.736 -  51.025:  103        |
|      2:    14.579 -  21.868:  561   |   7:    51.025 -  58.314:   65        |
|      3:    21.868 -  29.157:  215   |   8:    58.314 -  65.604:   14        |
|      4:    29.157 -  36.447:  118   |   9:    65.604 -  72.893:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2160 r_free = 0.2698             target_work(ml) = 5.709         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2158 r_free = 0.2696             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2158   r_free= 0.2696   ksol= 0.32   Bsol= 60.84   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.87,5.74,-0.00,0.00,0.00); trace/3= 0.24                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.708351                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2122   r_free= 0.2666   ksol= 0.34   Bsol= 72.73   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.73,1.33,-0.00,0.00,0.00); trace/3= -1.30                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.700182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.593765              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.883   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2122      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2666      final r-factor (free) = 0.2071          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5080 = 2.59 * 0.50 * 5.7041 + 1.00 * 0.1104                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3084 = 2.59 * 0.50 * 5.5906 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1644      final r-factor (work) = 0.1522          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.1991          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7893 = 0.49 * 1.00 * 5.5906 + 1.00 * 0.0513                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6675 = 0.49 * 1.00 * 5.4245 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.55   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    80.55   17.73    None  None   None       |
|    Sol.    : 438    0      4.80    80.55   42.51    None  None   None       |
|    Mac.    : 2385   0      0.00    68.18   13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.055:  595   |   5:    40.274 -  48.329:   78        |
|      1:     8.055 -  16.110: 1290   |   6:    48.329 -  56.384:  102        |
|      2:    16.110 -  24.164:  396   |   7:    56.384 -  64.438:   79        |
|      3:    24.164 -  32.219:  132   |   8:    64.438 -  72.493:   32        |
|      4:    32.219 -  40.274:  109   |   9:    72.493 -  80.548:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1522 r_free = 0.1991             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1520 r_free = 0.1990             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1520   r_free= 0.1990   ksol= 0.34   Bsol= 72.73   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.73,1.33,-0.00,0.00,0.00); trace/3= -1.30                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.405544                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1518   r_free= 0.1985   ksol= 0.34   Bsol= 75.45   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.47,0.26,-0.00,0.00,0.00); trace/3= -1.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.403678                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.317882              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284518              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.205  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1292          |
| start r-factor (free) = 0.1985      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3438 = 2.32 * 0.50 * 5.4237 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2414 = 2.32 * 0.50 * 5.3330 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1292      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5282 = 0.28 * 1.00 * 5.3330 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5039 = 0.28 * 1.00 * 5.2521 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    84.31   17.27    None  None   None       |
|    all(noH): 2823   0      0.98    84.31   17.27    None  None   None       |
|    Sol.    : 438    0      2.48    84.31   41.36    None  None   None       |
|    Mac.    : 2385   0      0.98    73.36   12.84    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:     0.983 -   9.316:  894   |   5:    42.646 -  50.979:   80        |
|      1:     9.316 -  17.649: 1158   |   6:    50.979 -  59.311:   90        |
|      2:    17.649 -  25.981:  280   |   7:    59.311 -  67.644:   49        |
|      3:    25.981 -  34.314:  132   |   8:    67.644 -  75.977:   20        |
|      4:    34.314 -  42.646:  111   |   9:    75.977 -  84.309:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1257 r_free = 0.1695             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1256 r_free = 0.1693             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1693   ksol= 0.34   Bsol= 75.45   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.47,0.26,-0.00,0.00,0.00); trace/3= -1.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.235473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1689   ksol= 0.33   Bsol= 69.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.38,-0.12,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.235056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.839132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.132  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.346488              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.260  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8901 = 1.84 * 0.50 * 5.2518 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8561 = 1.84 * 0.50 * 5.2162 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8168 = 0.35 * 1.00 * 5.2162 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8108 = 0.35 * 1.00 * 5.1988 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.13   17.09    None  None   None       |
|    all(noH): 2823   0      0.00    86.13   17.09    None  None   None       |
|    Sol.    : 438    0      0.00    86.13   40.89    None  None   None       |
|    Mac.    : 2385   0      0.64    75.45   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.613:  762   |   5:    43.066 -  51.679:   83        |
|      1:     8.613 -  17.226: 1274   |   6:    51.679 -  60.292:   86        |
|      2:    17.226 -  25.839:  303   |   7:    60.292 -  68.905:   47        |
|      3:    25.839 -  34.452:  136   |   8:    68.905 -  77.518:   16        |
|      4:    34.452 -  43.066:  110   |   9:    77.518 -  86.131:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1646             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1647             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1647   ksol= 0.33   Bsol= 69.21   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.38,-0.12,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1647   ksol= 0.33   Bsol= 69.21   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.30,-0.23,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.594710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.159  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.346464              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.425  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2044 = 1.59 * 0.50 * 5.1985 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1991 = 1.59 * 0.50 * 5.1966 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2030 = 2.35 * 1.00 * 5.1966 + 1.00 * 0.0094                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1991 = 2.35 * 1.00 * 5.1940 + 1.00 * 0.0117                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.98  17.39    None  None   None       |
|    all(noH): 2823   0      0.00    104.98  17.39    None  None   None       |
|    Sol.    : 438    0      1.37    104.98  42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    92.01   12.77    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 -  10.498: 1222   |   5:    52.491 -  62.990:   90        |
|      1:    10.498 -  20.997: 1000   |   6:    62.990 -  73.488:   45        |
|      2:    20.997 -  31.495:  200   |   7:    73.488 -  83.986:   27        |
|      3:    31.495 -  41.993:  138   |   8:    83.986 -  94.484:    6        |
|      4:    41.993 -  52.491:   91   |   9:    94.484 - 104.983:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1664             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1665             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1665   ksol= 0.33   Bsol= 69.21   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.30,-0.23,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199372                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7570 0.99   1412  156 0.0977 0.1301      5.3876      5.5561|
|  2:  4.7570 -  3.7951 0.99   1363  153 0.0870 0.1145      5.4497      5.6402|
|  3:  3.7951 -  3.3211 0.99   1325  143 0.1104 0.1550      5.5095      5.8533|
|  4:  3.3211 -  3.0200 0.99   1330  152 0.1274 0.1756      5.4889      5.6577|
|  5:  3.0200 -  2.8050 0.99   1311  147 0.1412 0.1787      5.3758      5.6104|
|  6:  2.8050 -  2.6406 0.99   1313  143 0.1294 0.2107      5.2641      5.5602|
|  7:  2.6406 -  2.5089 0.99   1297  144 0.1363 0.1637      5.2345      5.3505|
|  8:  2.5089 -  2.4002 0.98   1294  146 0.1237 0.1677      5.1331      5.3687|
|  9:  2.4002 -  2.3081 0.98   1289  138 0.1274 0.2015      5.1011      5.3957|
| 10:  2.3081 -  2.2287 1.00   1278  149 0.1230 0.1754       5.015      5.2509|
| 11:  2.2287 -  2.1592 0.98   1305  141 0.1205 0.1868      5.0004      5.3124|
| 12:  2.1592 -  2.0976 0.98   1268  146 0.1229 0.1911      4.9478      5.2661|
| 13:  2.0976 -  2.0426 0.99   1282  139 0.1180 0.1832      4.8418      5.0787|
| 14:  2.0426 -  1.9928 0.43    563   62 0.0995 0.1680      4.7025      4.9684|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7570  1412   156  0.94   9.05   0.96     0.93       7158.47|
|  2:  4.7570 -  3.7951  1363   153  0.95   8.09   1.00     0.99       9259.10|
|  3:  3.7951 -  3.3211  1325   143  0.93  11.68   1.02     1.01      10909.89|
|  4:  3.3211 -  3.0200  1330   152  0.91  14.70   1.00     0.98      11057.34|
|  5:  3.0200 -  2.8050  1311   147  0.89  16.70   0.99     0.97       9214.55|
|  6:  2.8050 -  2.6406  1313   143  0.89  17.33   0.97     0.94       7937.68|
|  7:  2.6406 -  2.5089  1297   144  0.90  16.71   0.98     0.95       7118.31|
|  8:  2.5089 -  2.4002  1294   146  0.90  16.73   0.98     0.95       6144.95|
|  9:  2.4002 -  2.3081  1289   138  0.90  16.83   0.98     0.94       5741.49|
| 10:  2.3081 -  2.2287  1278   149  0.90  16.61   0.98     0.94       4895.80|
| 11:  2.2287 -  2.1592  1305   141  0.89  17.17   0.96     0.91       4785.66|
| 12:  2.1592 -  2.0976  1268   146  0.90  17.05   0.99     0.98       4589.13|
| 13:  2.0976 -  2.0426  1282   139  0.89  17.87   0.97     0.95       3891.81|
| 14:  2.0426 -  1.9928   563    62  0.92  14.56   0.94     0.91       2833.49|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2833.49 max =        11057.34 mean =      7026.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.02|
|phase err.(test): min =        0.00 max =           89.14 mean =        14.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1664   ksol= 0.32   Bsol= 69.21   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.06,-0.05,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1664   ksol= 0.32   Bsol= 69.21   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.06,-0.05,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199359                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7570 0.99   1412  156 0.0976 0.1300      5.3864      5.5575|
|  2:  4.7570 -  3.7951 0.99   1363  153 0.0871 0.1146      5.4506      5.6406|
|  3:  3.7951 -  3.3211 0.99   1325  143 0.1104 0.1550      5.5097      5.8537|
|  4:  3.3211 -  3.0200 0.99   1330  152 0.1273 0.1756      5.4888      5.6577|
|  5:  3.0200 -  2.8050 0.99   1311  147 0.1411 0.1786      5.3755      5.6097|
|  6:  2.8050 -  2.6406 0.99   1313  143 0.1294 0.2108      5.2641      5.5606|
|  7:  2.6406 -  2.5089 0.99   1297  144 0.1363 0.1637      5.2345      5.3508|
|  8:  2.5089 -  2.4002 0.98   1294  146 0.1237 0.1676      5.1332      5.3683|
|  9:  2.4002 -  2.3081 0.98   1289  138 0.1274 0.2016      5.1011      5.3961|
| 10:  2.3081 -  2.2287 1.00   1278  149 0.1229 0.1752      5.0151      5.2499|
| 11:  2.2287 -  2.1592 0.98   1305  141 0.1205 0.1866      5.0004      5.3119|
| 12:  2.1592 -  2.0976 0.98   1268  146 0.1229 0.1911      4.9476      5.2661|
| 13:  2.0976 -  2.0426 0.99   1282  139 0.1180 0.1834      4.8419      5.0785|
| 14:  2.0426 -  1.9928 0.43    563   62 0.0996 0.1680      4.7033      4.9691|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7570  1412   156  0.94   9.07   0.96     0.93       7160.38|
|  2:  4.7570 -  3.7951  1363   153  0.95   8.09   1.00     0.99       9270.75|
|  3:  3.7951 -  3.3211  1325   143  0.93  11.69   1.02     1.02      10919.02|
|  4:  3.3211 -  3.0200  1330   152  0.91  14.70   1.01     0.98      11057.51|
|  5:  3.0200 -  2.8050  1311   147  0.89  16.70   1.00     0.98       9214.04|
|  6:  2.8050 -  2.6406  1313   143  0.89  17.33   0.98     0.95       7934.97|
|  7:  2.6406 -  2.5089  1297   144  0.90  16.71   0.99     0.96       7117.62|
|  8:  2.5089 -  2.4002  1294   146  0.90  16.73   0.99     0.96       6145.44|
|  9:  2.4002 -  2.3081  1289   138  0.90  16.83   0.99     0.95       5743.62|
| 10:  2.3081 -  2.2287  1278   149  0.90  16.61   0.99     0.95       4892.28|
| 11:  2.2287 -  2.1592  1305   141  0.89  17.16   0.97     0.92       4780.79|
| 12:  2.1592 -  2.0976  1268   146  0.90  17.05   1.00     0.99       4585.19|
| 13:  2.0976 -  2.0426  1282   139  0.89  17.87   0.98     0.96       3892.88|
| 14:  2.0426 -  1.9928   563    62  0.92  14.59   0.96     0.92       2837.24|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2837.24 max =        11057.51 mean =      7027.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.03|
|phase err.(test): min =        0.00 max =           89.15 mean =        14.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.99  17.39    None  None   None       |
|    all(noH): 2823   0      0.00    104.99  17.39    None  None   None       |
|    Sol.    : 438    0      1.37    104.99  42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    92.01   12.77    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 -  10.501: 1222   |   5:    52.494 -  62.993:   90        |
|      1:    10.501 -  21.000: 1000   |   6:    62.993 -  73.491:   45        |
|      2:    21.000 -  31.498:  200   |   7:    73.491 -  83.989:   27        |
|      3:    31.498 -  41.996:  138   |   8:    83.989 -  94.487:    6        |
|      4:    41.996 -  52.494:   91   |   9:    94.487 - 104.986:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.492 - 5.495
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 295
   mapped sites are within: 0.702 - 5.495

peak=    5.311 closest distance to " NE2 GLN A  11 " =    1.097
peak=    5.278 closest distance to " CB  GLN A 223 " =    1.478
peak=    5.277 closest distance to " CG  PRO A 280 " =    0.991
peak=    5.214 closest distance to " CZ  PHE A 218 " =    1.097
peak=    5.110 closest distance to " NH2 ARG A  56 " =    2.124
peak=    5.085 closest distance to " CG  PRO A  54 " =    1.362
peak=    4.812 closest distance to " CG  PRO A 198 " =    1.239
peak=    4.772 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.732 closest distance to " O   HOH Z 298 " =    2.061
peak=    4.723 closest distance to " CB  PRO A  54 " =    1.042
peak=    4.666 closest distance to " O   HOH Z 144 " =    1.953
peak=    4.607 closest distance to " O   HOH Z 369 " =    2.157
peak=    4.536 closest distance to " O   HOH Z 232 " =    2.346
peak=    4.527 closest distance to " CB  ARG A 190 " =    1.614
peak=    4.519 closest distance to " O   HOH Z 188 " =    2.783
peak=    4.493 closest distance to " CD  ARG A 159 " =    0.774
peak=    4.464 closest distance to " CB  ASN A 148 " =    1.495
peak=    4.439 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.402 closest distance to " CB  ARG A  79 " =    1.455
peak=    4.402 closest distance to " CG2 VAL A 257 " =    0.871
peak=    4.378 closest distance to " CA  TYR A  30 " =    0.969
peak=    4.321 closest distance to " CZ3 TRP A 266 " =    1.123
peak=    4.306 closest distance to " O   HOH Z 287 " =    1.917
peak=    4.302 closest distance to " CA  ARG A 195 " =    1.284
peak=    4.268 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.250 closest distance to " CB  SER A  63 " =    1.235
peak=    4.230 closest distance to " CE  LYS A  76 " =    0.894
peak=    4.216 closest distance to " O   HOH Z  78 " =    1.624
peak=    4.195 closest distance to " O   HOH Z 406 " =    1.757
peak=    4.159 closest distance to " O   HOH Z 126 " =    2.010
peak=    4.154 closest distance to " CD2 TRP A 179 " =    1.303
peak=    4.150 closest distance to " CB  GLU A 128 " =    0.935
peak=    4.112 closest distance to " CB  LEU A 228 " =    1.113
peak=    4.110 closest distance to " CG  PRO A 243 " =    1.070
peak=    4.080 closest distance to " CB  SER A 210 " =    0.823
peak=    4.068 closest distance to " O   HOH Z  53 " =    2.494
peak=    4.067 closest distance to " NH1AARG A 145 " =    1.327
peak=    4.063 closest distance to " CB  GLU A 277 " =    3.799
peak=    4.047 closest distance to " CG  LEU A 167 " =    1.253
peak=    4.038 closest distance to " O   HOH Z 427 " =    2.988
peak=    4.036 closest distance to " O   HOH Z 214 " =    2.465
peak=    4.035 closest distance to " CD  ARG A 269 " =    0.960
peak=    4.027 closest distance to " CB  ASN A  39 " =    0.934
peak=    4.021 closest distance to " CB  TRP A 266 " =    1.049
peak=    4.019 closest distance to " CA  ALA A  51 " =    0.963
peak=    4.005 closest distance to " CB  VAL A 265 " =    1.251
peak=    3.976 closest distance to " CB  ASP A 124 " =    0.828
peak=    3.973 closest distance to " CB  ASN A 142 " =    1.004
peak=    3.964 closest distance to " ND2 ASN A 187 " =    1.475
peak=    3.961 closest distance to " CE1 PHE A  38 " =    1.220
peak=    3.956 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.929 closest distance to " CA  SER A  87 " =    0.993
peak=    3.929 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.925 closest distance to " O  BHOH Z  74 " =    1.239
peak=    3.919 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.904 closest distance to " O   HOH Z 353 " =    2.589
peak=    3.901 closest distance to " CA  VAL A 125 " =    1.174
peak=    3.900 closest distance to " O   PRO A 198 " =    1.559
peak=    3.892 closest distance to " O   THR A 220 " =    1.234
peak=    3.889 closest distance to " CB  TYR A 169 " =    0.741
peak=    3.885 closest distance to " CB  ALA A 104 " =    0.733
peak=    3.882 closest distance to " O   HOH Z 133 " =    2.703
peak=    3.863 closest distance to " CD1 LEU A 300 " =    1.104
peak=    3.848 closest distance to " CB  PRO A  90 " =    1.129
peak=    3.826 closest distance to " O   HOH Z 303 " =    2.198
peak=    3.786 closest distance to " NZ  LYS A 117 " =    3.149
peak=    3.777 closest distance to " NE2 HIS A 207 " =    1.117
peak=    3.776 closest distance to " O   HOH Z   9 " =    1.920
peak=    3.775 closest distance to " CA  THR A 264 " =    0.905
peak=    3.772 closest distance to " O   ASN A  74 " =    1.394
peak=    3.759 closest distance to " O   HOH Z 265 " =    2.064
peak=    3.756 closest distance to " O   THR A 251 " =    1.141
peak=    3.756 closest distance to " O   HOH Z  21 " =    1.754
peak=    3.751 closest distance to " O   TYR A 116 " =    1.302
peak=    3.749 closest distance to " CD  ARG A  66 " =    2.325
peak=    3.741 closest distance to " O   HOH Z 180 " =    2.214
peak=    3.719 closest distance to " O   HOH Z 316 " =    3.114
peak=    3.713 closest distance to " O   HOH Z 411 " =    3.942
peak=    3.712 closest distance to " O   HOH Z 313 " =    2.021
peak=    3.707 closest distance to " O   HOH Z 234 " =    3.855
peak=    3.703 closest distance to " O   HOH Z 285 " =    2.187
peak=    3.693 closest distance to " CA  ASN A 127 " =    1.120
peak=    3.691 closest distance to " O   HOH Z  57 " =    2.106
peak=    3.671 closest distance to " CD BLYS A 290 " =    0.957
peak=    3.669 closest distance to " CB  SER A 212 " =    1.195
peak=    3.667 closest distance to " O   HOH Z 158 " =    3.104
peak=    3.654 closest distance to " CA  ARG A  36 " =    1.087
peak=    3.654 closest distance to " CB  MET A  40 " =    0.782
peak=    3.653 closest distance to " O   HOH Z  88 " =    4.020
peak=    3.652 closest distance to " O   HOH Z 394 " =    4.041
peak=    3.646 closest distance to " CG2AVAL A 121 " =    2.510
peak=    3.637 closest distance to " O   THR A 182 " =    1.427
peak=    3.634 closest distance to " O   HOH Z   1 " =    2.052
peak=    3.632 closest distance to " O   HOH Z 126 " =    1.559
peak=    3.623 closest distance to " O   HOH Z 126 " =    1.951
peak=    3.618 closest distance to " CA  ARG A 102 " =    1.156
peak=    3.617 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.615 closest distance to " CG2 THR A 221 " =    1.012
peak=    3.595 closest distance to " CA  ALA A 160 " =    1.048
peak=    3.593 closest distance to " O   HOH Z 359 " =    1.550
peak=    3.588 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.583 closest distance to " CA  ALA A 154 " =    1.063
peak=    3.578 closest distance to " CB  TYR A 116 " =    0.811
peak=    3.561 closest distance to " CG  GLU A  37 " =    0.915
peak=    3.554 closest distance to " O   HOH Z 280 " =    2.954
peak=    3.554 closest distance to " CA  ILE A 234 " =    1.033
peak=    3.546 closest distance to " CG  PHE A 204 " =    0.858
peak=    3.542 closest distance to " O   HOH Z 294 " =    1.596
peak=    3.541 closest distance to " CA  ASP A 162 " =    1.016
peak=    3.540 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.535 closest distance to " CD  LYS A 166 " =    1.302
peak=    3.530 closest distance to " O   HOH Z 368 " =    3.644
peak=    3.530 closest distance to " O   HOH Z  43 " =    1.905
peak=    3.523 closest distance to " O   HOH Z 423 " =    1.482
peak=    3.518 closest distance to " O   HOH Z 272 " =    1.781
peak=    3.516 closest distance to " N   PHE A 130 " =    1.198
peak=    3.516 closest distance to " O   HOH Z 346 " =    1.728
peak=    3.515 closest distance to " CB  SER A 216 " =    0.979
peak=    3.514 closest distance to " CB  ASN A 110 " =    1.136
peak=    3.514 closest distance to " CB  MET A  47 " =    1.003
peak=    3.513 closest distance to " CD  ARG A  66 " =    2.229
peak=    3.512 closest distance to " CB  ASP A 140 " =    1.103
peak=    3.512 closest distance to " CA  ASP A 124 " =    0.774
peak=    3.512 closest distance to " CA  ALA A 158 " =    1.239
peak=    3.509 closest distance to " OG  SER A  62 " =    2.976
peak=    3.507 closest distance to " CB  ASN A 187 " =    1.148
peak=    3.503 closest distance to " O   HOH Z 128 " =    2.375
peak=    3.502 closest distance to " OE1 GLN A  55 " =    1.484
peak=    3.501 closest distance to " O   HOH Z 261 " =    1.784
peak=    3.494 closest distance to " O   HOH Z 368 " =    2.052
peak=    3.492 closest distance to " CA  MET A 105 " =    1.031
peak=    3.492 closest distance to " O   PHE A 192 " =    1.368
peak=    3.478 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.478 closest distance to " CB  ARG A 138 " =    0.997
peak=    3.477 closest distance to " O   HOH Z 250 " =    1.389
peak=    3.476 closest distance to " ND2 ASN A 249 " =    1.901
peak=    3.474 closest distance to " O   HOH Z 251 " =    1.664
peak=    3.469 closest distance to " O   HOH Z  10 " =    1.792
peak=    3.466 closest distance to " OD1 ASN A  69 " =    2.632
peak=    3.460 closest distance to " CG  ARG A 138 " =    1.250
peak=    3.458 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.451 closest distance to " O   HOH Z 148 " =    3.543
peak=    3.448 closest distance to " CB  GLU A  37 " =    0.929
peak=    3.448 closest distance to " O   HOH Z 185 " =    1.863
peak=    3.444 closest distance to " CE  LYS A  48 " =    1.148
peak=    3.439 closest distance to " CA  ASN A 215 " =    1.127
peak=    3.438 closest distance to " O   HOH Z 106 " =    4.179
peak=    3.436 closest distance to " O   ASN A  74 " =    2.051
peak=    3.435 closest distance to " NE2 GLN A  73 " =    3.999
peak=    3.433 closest distance to " O   SER A  87 " =    2.353
peak=    3.426 closest distance to " O   HOH Z 172 " =    3.325
peak=    3.423 closest distance to " CB  LEU A  83 " =    0.712
peak=    3.420 closest distance to " O   HOH Z 167 " =    1.725
peak=    3.420 closest distance to " O   HOH Z  90 " =    2.297
peak=    3.419 closest distance to " OG BSER A 134 " =    2.833
peak=    3.414 closest distance to " O   HOH Z 248 " =    1.656
peak=    3.414 closest distance to " O   HOH Z 371 " =    2.915
peak=    3.404 closest distance to " CA  ILE A 263 " =    1.140
peak=    3.400 closest distance to " CA  GLN A  94 " =    0.793
peak=    3.399 closest distance to " OE2 GLU A  53 " =    1.176
peak=    3.396 closest distance to " CB  ALA A 114 " =    0.789
peak=    3.394 closest distance to " O   HOH Z 365 " =    2.866
peak=    3.388 closest distance to " O   ALA A 165 " =    1.588
peak=    3.387 closest distance to " N   ASN A  39 " =    1.333
peak=    3.383 closest distance to " O   HOH Z 171 " =    4.185
peak=    3.376 closest distance to " N   ASN A 127 " =    1.287
peak=    3.375 closest distance to " CB  ALA A  43 " =    0.795
peak=    3.374 closest distance to " CB  TYR A 169 " =    0.702
peak=    3.373 closest distance to " CB  GLN A  89 " =    1.296
peak=    3.372 closest distance to " OG1 THR A 279 " =    1.413
peak=    3.370 closest distance to " CD1 LEU A  96 " =    0.748
peak=    3.367 closest distance to " CB  ILE A 120 " =    1.257
peak=    3.364 closest distance to " O   HOH Z 183 " =    1.474
peak=    3.358 closest distance to " CG2 THR A  29 " =    1.371
peak=    3.358 closest distance to " O   HOH Z 421 " =    2.271
peak=    3.357 closest distance to " CB  ALA A 291 " =    1.083
peak=    3.356 closest distance to " NH1 ARG A 138 " =    1.033
peak=    3.352 closest distance to " N   HIS A 108 " =    1.911
peak=    3.349 closest distance to " O   HOH Z 213 " =    2.791
peak=    3.347 closest distance to " CE1 TYR A 186 " =    1.381
peak=    3.346 closest distance to " CB  ASN A 215 " =    1.193
peak=    3.338 closest distance to " O   HOH Z 392 " =    2.892
peak=    3.337 closest distance to " CB  THR A  31 " =    1.566
peak=    3.337 closest distance to " O   HOH Z 425 " =    1.289
peak=    3.329 closest distance to " CA  MET A  40 " =    1.264
peak=    3.323 closest distance to " O   HOH Z  80 " =    1.625
peak=    3.323 closest distance to " CB  THR A  82 " =    1.330
peak=    3.323 closest distance to " CA  THR A 221 " =    1.097
peak=    3.322 closest distance to " N   SER A 271 " =    0.999
peak=    3.317 closest distance to " OD2 ASP A 286 " =    3.286
peak=    3.316 closest distance to " CG2 ILE A 151 " =    0.976
peak=    3.311 closest distance to " O   HOH Z 325 " =    2.422
peak=    3.308 closest distance to " CG1 VAL A 153 " =    0.998
peak=    3.305 closest distance to " CG  GLN A 144 " =    0.858
peak=    3.303 closest distance to " CB  SER A   3 " =    1.400
peak=    3.294 closest distance to " CA  PRO A 280 " =    1.250
peak=    3.286 closest distance to " O   HOH Z  59 " =    1.810
peak=    3.283 closest distance to " O   HOH Z 391 " =    2.927
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.158
peak=    3.283 closest distance to " CB  GLN A  88 " =    1.264
peak=    3.282 closest distance to " CB  PHE A 204 " =    0.793
peak=    3.277 closest distance to " CB  ALA A   1 " =    4.719
peak=    3.274 closest distance to " O   HOH Z 152 " =    2.347
peak=    3.271 closest distance to " N   ARG A 156 " =    1.357
peak=    3.268 closest distance to " O   HOH Z  61 " =    1.684
peak=    3.267 closest distance to " O   HOH Z  88 " =    3.093
peak=    3.262 closest distance to " N   TYR A 116 " =    1.525
peak=    3.260 closest distance to " CA  ALA A 233 " =    1.395
peak=    3.259 closest distance to " CA  ARG A 156 " =    1.152
peak=    3.258 closest distance to " O   ASP A 191 " =    1.486
peak=    3.256 closest distance to " O   HOH Z 193 " =    2.018
peak=    3.255 closest distance to " O   HOH Z 409 " =    2.709
peak=    3.253 closest distance to " CE3 TRP A  85 " =    0.980
peak=    3.250 closest distance to " O   HOH Z 116 " =    3.246
peak=    3.246 closest distance to " O   HOH Z 211 " =    0.951
peak=    3.245 closest distance to " O   HOH Z 218 " =    4.623
peak=    3.244 closest distance to " OD1 ASP A 171 " =    1.237
peak=    3.243 closest distance to " O   PHE A  61 " =    1.311
peak=    3.242 closest distance to " O   HOH Z 273 " =    2.833
peak=    3.242 closest distance to " CA  ASN A 217 " =    1.269
peak=    3.241 closest distance to " CB  ARG A 102 " =    0.828
peak=    3.240 closest distance to " O   HOH Z 352 " =    1.864
peak=    3.233 closest distance to " CG2 ILE A 120 " =    1.222
peak=    3.233 closest distance to " O   HOH Z 302 " =    1.954
peak=    3.231 closest distance to " O   HOH Z  94 " =    2.432
peak=    3.229 closest distance to " O   HOH Z 116 " =    1.832
peak=    3.226 closest distance to " O   HOH Z 305 " =    3.683
peak=    3.225 closest distance to " OG  SER A 135 " =    1.228
peak=    3.223 closest distance to " OG BSER A 164 " =    2.373
peak=    3.223 closest distance to " CB  GLU A 152 " =    1.207
peak=    3.220 closest distance to " CA  GLU A  46 " =    0.838
peak=    3.220 closest distance to " NE  ARG A  79 " =    1.067
peak=    3.219 closest distance to " CB  SER A  97 " =    0.901
peak=    3.210 closest distance to " CG AARG A 275 " =    1.189
peak=    3.209 closest distance to " OE2 GLU A  44 " =    1.123
peak=    3.207 closest distance to " CB  SER A 273 " =    0.876
peak=    3.205 closest distance to " O   SER A 164 " =    1.524
peak=    3.202 closest distance to " NH2AARG A 275 " =    3.690
peak=    3.201 closest distance to " O   THR A 294 " =    1.105
peak=    3.198 closest distance to " CA  ALA A 100 " =    1.060
peak=    3.197 closest distance to " CD1AILE A 234 " =    0.997
peak=    3.189 closest distance to " CA  SER A  95 " =    0.972
peak=    3.188 closest distance to " CG  MET A 185 " =    1.203
peak=    3.187 closest distance to " O   HOH Z   2 " =    1.444
peak=    3.182 closest distance to " CG2 ILE A 239 " =    0.749
peak=    3.178 closest distance to " O   HOH Z 426 " =    1.881
peak=    3.175 closest distance to " O   HOH Z 147 " =    1.805
peak=    3.175 closest distance to " N   TYR A  15 " =    0.749
peak=    3.173 closest distance to " CH2 TRP A  70 " =    0.887
peak=    3.166 closest distance to " CB  LEU A  96 " =    1.383
peak=    3.166 closest distance to " O   GLN A 278 " =    1.414
peak=    3.165 closest distance to " OE2 GLU A  53 " =    1.875
peak=    3.164 closest distance to " OG1 THR A  82 " =    0.847
peak=    3.164 closest distance to " N   ARG A  66 " =    1.402
peak=    3.163 closest distance to " O   HOH Z 344 " =    3.168
peak=    3.163 closest distance to " CG2 ILE A  20 " =    1.447
peak=    3.162 closest distance to " ND2BASN A 224 " =    0.880
peak=    3.160 closest distance to " O   HOH Z   9 " =    1.351
peak=    3.152 closest distance to " CB  ALA A 299 " =    0.992
peak=    3.152 closest distance to " CE3 TRP A 150 " =    1.090
peak=    3.151 closest distance to " CB  ASN A 173 " =    1.129
peak=    3.145 closest distance to " CG1 ILE A 151 " =    1.045
peak=    3.144 closest distance to " CD1 ILE A 199 " =    1.003
peak=    3.143 closest distance to " O   HOH Z 193 " =    1.770
peak=    3.139 closest distance to " N   GLU A 152 " =    1.464
peak=    3.131 closest distance to " O   HOH Z  28 " =    1.865
peak=    3.129 closest distance to " O   HOH Z 124 " =    2.063
peak=    3.124 closest distance to " CD  ARG A 219 " =    1.103
peak=    3.122 closest distance to " CG1 ILE A  33 " =    1.272
peak=    3.117 closest distance to " CB  PRO A 243 " =    1.483
peak=    3.113 closest distance to " CG  GLN A  11 " =    1.627
peak=    3.111 closest distance to " OG  SER A 245 " =    1.781
peak=    3.105 closest distance to " CA  ILE A 106 " =    0.831
peak=    3.105 closest distance to " CB  PHE A  16 " =    1.244
peak=    3.105 closest distance to " O   HOH Z 227 " =    1.887
peak=    3.103 closest distance to " O   HOH Z  62 " =    1.950
peak=    3.100 closest distance to " O   HOH Z 261 " =    1.609
peak=    3.099 closest distance to " N   ALA A 256 " =    1.277
peak=    3.093 closest distance to " CB  ALA A 248 " =    1.007
peak=    3.086 closest distance to " CA  LYS A 290 " =    1.242
peak=    3.082 closest distance to " CG2BVAL A  41 " =    0.901
peak=    3.082 closest distance to " CB  ALA A 180 " =    1.223
peak=    3.080 closest distance to " CD  GLU A 236 " =    1.072
peak=    3.077 closest distance to " O   HOH Z 430 " =    5.495
peak=    3.076 closest distance to " C   ALA A 299 " =    0.964
peak=    3.074 closest distance to " O   HOH Z 271 " =    2.621
peak=    3.056 closest distance to " O   HOH Z 120 " =    3.419
peak=    3.034 closest distance to " CG BARG A 102 " =    1.927
peak=    3.024 closest distance to " CB  SER A  62 " =    0.790
peak=    3.000 closest distance to " OG BSER A 134 " =    3.142

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.761 - 5.763
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 204
   mapped sites are within: 0.761 - 5.763

peak=   -4.694 closest distance to " CD  ARG A  14 " =    3.489
peak=   -4.608 closest distance to " O   HOH Z 377 " =    2.037
peak=   -4.349 closest distance to " O   PRO A 198 " =    1.273
peak=   -4.330 closest distance to " OG BSER A 134 " =    1.373
peak=   -4.272 closest distance to " CG2 ILE A  49 " =    2.796
peak=   -4.223 closest distance to " O   HOH Z 231 " =    2.287
peak=   -4.216 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -4.209 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.059 closest distance to " CD2 TYR A 293 " =    1.867
peak=   -4.017 closest distance to " CB  PRO A 243 " =    2.719
peak=   -3.975 closest distance to " N   ALA A  43 " =    2.602
peak=   -3.967 closest distance to " CG1 VAL A 250 " =    2.663
peak=   -3.950 closest distance to " CD  GLN A  58 " =    0.992
peak=   -3.915 closest distance to " CE2 TYR A  30 " =    2.716
peak=   -3.885 closest distance to " CG  GLN A 223 " =    2.249
peak=   -3.883 closest distance to " O   HOH Z 394 " =    1.561
peak=   -3.872 closest distance to " CZ3 TRP A 179 " =    1.197
peak=   -3.855 closest distance to " CB  ALA A  43 " =    2.654
peak=   -3.852 closest distance to " O   HOH Z  73 " =    2.210
peak=   -3.839 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.812 closest distance to " O   HOH Z 411 " =    5.658
peak=   -3.809 closest distance to " O   HOH Z 351 " =    1.427
peak=   -3.797 closest distance to " CG1 VAL A 112 " =    3.039
peak=   -3.791 closest distance to " CE  MET A 105 " =    2.403
peak=   -3.780 closest distance to " O   ALA A  10 " =    1.705
peak=   -3.780 closest distance to " O   TYR A 247 " =    2.867
peak=   -3.777 closest distance to " CG  ARG A 269 " =    2.487
peak=   -3.771 closest distance to " OG  SER A  97 " =    2.289
peak=   -3.770 closest distance to " O   HOH Z 295 " =    1.739
peak=   -3.770 closest distance to " CE BMET A  47 " =    1.386
peak=   -3.760 closest distance to " O   HOH Z  38 " =    1.559
peak=   -3.724 closest distance to " O   HOH Z 198 " =    1.831
peak=   -3.714 closest distance to " O   HOH Z 196 " =    2.194
peak=   -3.700 closest distance to " O   HOH Z 407 " =    3.227
peak=   -3.691 closest distance to " OD1 ASP A 171 " =    1.587
peak=   -3.680 closest distance to " CA  ASP A  27 " =    2.500
peak=   -3.675 closest distance to " CE2 PHE A  61 " =    2.692
peak=   -3.671 closest distance to " CA  GLY A 241 " =    2.323
peak=   -3.670 closest distance to " CB  GLN A  11 " =    1.711
peak=   -3.651 closest distance to " CE3 TRP A 150 " =    2.228
peak=   -3.648 closest distance to " CD2 PHE A  61 " =    2.141
peak=   -3.648 closest distance to " O   HOH Z  51 " =    1.629
peak=   -3.647 closest distance to " O   HOH Z 211 " =    0.857
peak=   -3.641 closest distance to " CA  VAL A  67 " =    3.020
peak=   -3.640 closest distance to " CB  HIS A  86 " =    1.143
peak=   -3.637 closest distance to " OD1 ASN A 148 " =    1.369
peak=   -3.630 closest distance to " O   VAL A  67 " =    2.715
peak=   -3.624 closest distance to " ND2 ASN A 249 " =    2.400
peak=   -3.619 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -3.617 closest distance to " O   PRO A 163 " =    2.040
peak=   -3.616 closest distance to " CG  PRO A 198 " =    1.869
peak=   -3.605 closest distance to " O   HOH Z 111 " =    1.676
peak=   -3.604 closest distance to " O   HOH Z 102 " =    1.561
peak=   -3.592 closest distance to " CB  ALA A   7 " =    2.197
peak=   -3.590 closest distance to " CB  ASN A  39 " =    2.297
peak=   -3.589 closest distance to " O   HOH Z 359 " =    3.095
peak=   -3.584 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.579 closest distance to " O   PHE A 218 " =    1.408
peak=   -3.568 closest distance to " OE1 GLN A  88 " =    1.074
peak=   -3.555 closest distance to " NH2AARG A 275 " =    5.569
peak=   -3.554 closest distance to " CA  GLY A 241 " =    3.361
peak=   -3.541 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.535 closest distance to " CB  ASP A 286 " =    2.149
peak=   -3.528 closest distance to " N   THR A  52 " =    1.711
peak=   -3.524 closest distance to " O   HOH Z 185 " =    2.304
peak=   -3.513 closest distance to " O   HOH Z  52 " =    1.441
peak=   -3.507 closest distance to " O   GLY A  17 " =    1.186
peak=   -3.500 closest distance to " OXT GLY A 302 " =    3.135
peak=   -3.497 closest distance to " O   TYR A 186 " =    1.704
peak=   -3.492 closest distance to " O   HOH Z 191 " =    5.763
peak=   -3.492 closest distance to " CE2 TYR A 116 " =    3.217
peak=   -3.487 closest distance to " O   HOH Z  10 " =    1.467
peak=   -3.483 closest distance to " CD2 HIS A 207 " =    2.194
peak=   -3.482 closest distance to " O   HOH Z 216 " =    1.180
peak=   -3.481 closest distance to " O   HOH Z 128 " =    2.652
peak=   -3.481 closest distance to " O   HOH Z   9 " =    1.775
peak=   -3.480 closest distance to " CB  ALA A 100 " =    2.262
peak=   -3.471 closest distance to " O   HOH Z 133 " =    1.283
peak=   -3.469 closest distance to " CB  TRP A  85 " =    2.577
peak=   -3.463 closest distance to " OH  TYR A 172 " =    1.844
peak=   -3.458 closest distance to " O   HOH Z  64 " =    1.492
peak=   -3.458 closest distance to " C   ASN A 285 " =    2.433
peak=   -3.457 closest distance to " CG  MET A 105 " =    0.998
peak=   -3.452 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.447 closest distance to " CB  PHE A 192 " =    2.117
peak=   -3.440 closest distance to " O   HOH Z 281 " =    2.621
peak=   -3.439 closest distance to " O   HOH Z 372 " =    2.440
peak=   -3.429 closest distance to " O   HOH Z 290 " =    1.228
peak=   -3.423 closest distance to " O   HOH Z 345 " =    2.232
peak=   -3.421 closest distance to " CG2 THR A 178 " =    2.336
peak=   -3.416 closest distance to " CB  ALA A   9 " =    2.458
peak=   -3.414 closest distance to " O   HOH Z 247 " =    1.995
peak=   -3.409 closest distance to " CD1 LEU A 101 " =    2.368
peak=   -3.401 closest distance to " O   HOH Z 103 " =    1.832
peak=   -3.401 closest distance to " O   HOH Z 292 " =    1.769
peak=   -3.399 closest distance to " CG  PRO A 243 " =    1.793
peak=   -3.394 closest distance to " O   GLU A 152 " =    1.389
peak=   -3.393 closest distance to " CD  ARG A  79 " =    1.146
peak=   -3.389 closest distance to " O   HOH Z 174 " =    2.643
peak=   -3.385 closest distance to " O   HOH Z 118 " =    1.442
peak=   -3.383 closest distance to " CB  ALA A 129 " =    2.427
peak=   -3.376 closest distance to " CA  GLY A 133 " =    2.251
peak=   -3.366 closest distance to " CG1 VAL A 125 " =    1.845
peak=   -3.364 closest distance to " O   HOH Z 275 " =    1.814
peak=   -3.362 closest distance to " ND2 ASN A  45 " =    1.179
peak=   -3.352 closest distance to " N   THR A 157 " =    1.584
peak=   -3.352 closest distance to " O   HOH Z 275 " =    1.563
peak=   -3.350 closest distance to " CG2 ILE A 263 " =    2.350
peak=   -3.343 closest distance to " O   HOH Z 252 " =    4.032
peak=   -3.341 closest distance to " O   HOH Z 174 " =    3.909
peak=   -3.341 closest distance to " O   ALA A 180 " =    1.350
peak=   -3.338 closest distance to " O   HOH Z 166 " =    1.953
peak=   -3.337 closest distance to " N   GLN A 223 " =    0.954
peak=   -3.334 closest distance to " ND2 ASN A  60 " =    4.136
peak=   -3.329 closest distance to " O   HOH Z 389 " =    2.173
peak=   -3.328 closest distance to " O   VAL A 189 " =    1.611
peak=   -3.327 closest distance to " O   HOH Z 357 " =    2.267
peak=   -3.321 closest distance to " O   HOH Z 412 " =    4.444
peak=   -3.318 closest distance to " CG1BVAL A  41 " =    2.821
peak=   -3.317 closest distance to " ND2 ASN A 187 " =    1.610
peak=   -3.315 closest distance to " O   HOH Z  71 " =    2.538
peak=   -3.313 closest distance to " N   THR A 264 " =    1.282
peak=   -3.307 closest distance to " O   HOH Z 348 " =    2.123
peak=   -3.301 closest distance to " O   HOH Z 313 " =    1.873
peak=   -3.297 closest distance to " O   HOH Z  65 " =    1.327
peak=   -3.294 closest distance to " O   HOH Z 326 " =    5.076
peak=   -3.290 closest distance to " O   HOH Z 171 " =    2.143
peak=   -3.290 closest distance to " CD2 LEU A 143 " =    2.572
peak=   -3.289 closest distance to " O   HOH Z 298 " =    2.514
peak=   -3.286 closest distance to " O   ILE A 106 " =    2.014
peak=   -3.281 closest distance to " OD1 ASP A 191 " =    1.697
peak=   -3.274 closest distance to " O   HOH Z  11 " =    1.669
peak=   -3.274 closest distance to " O   HOH Z 193 " =    1.253
peak=   -3.272 closest distance to " OH  TYR A 247 " =    2.199
peak=   -3.272 closest distance to " CZ  PHE A 155 " =    1.251
peak=   -3.271 closest distance to " ND2 ASN A  45 " =    2.070
peak=   -3.271 closest distance to " O   HOH Z 368 " =    1.746
peak=   -3.265 closest distance to " O   HOH Z 134 " =    3.241
peak=   -3.260 closest distance to " CD1 LEU A 255 " =    2.975
peak=   -3.253 closest distance to " CD1 TRP A  70 " =    1.148
peak=   -3.253 closest distance to " O   HOH Z  60 " =    1.423
peak=   -3.248 closest distance to " CZ  PHE A  38 " =    1.131
peak=   -3.247 closest distance to " OG1 THR A  82 " =    1.361
peak=   -3.247 closest distance to " CD1 LEU A   5 " =    2.501
peak=   -3.245 closest distance to " CG2 VAL A 189 " =    2.050
peak=   -3.242 closest distance to " O   HOH Z 421 " =    3.083
peak=   -3.241 closest distance to " N   ASN A  60 " =    1.278
peak=   -3.240 closest distance to " O   ALA A 180 " =    1.104
peak=   -3.237 closest distance to " NE2 GLN A 194 " =    1.914
peak=   -3.235 closest distance to " CZ  PHE A  59 " =    1.788
peak=   -3.235 closest distance to " CB  ALA A 291 " =    2.284
peak=   -3.234 closest distance to " O   HOH Z 429 " =    1.950
peak=   -3.234 closest distance to " SG BCYS A 201 " =    1.001
peak=   -3.230 closest distance to " CG  LEU A  83 " =    1.977
peak=   -3.228 closest distance to " O   HOH Z 365 " =    1.448
peak=   -3.227 closest distance to " CA  SER A 135 " =    1.231
peak=   -3.224 closest distance to " CD2 LEU A 222 " =    2.194
peak=   -3.222 closest distance to " CD  GLU A 236 " =    1.151
peak=   -3.216 closest distance to " C   LEU A 143 " =    1.221
peak=   -3.208 closest distance to " CE1 TYR A 247 " =    2.691
peak=   -3.204 closest distance to " O   HOH Z   6 " =    1.445
peak=   -3.195 closest distance to " C   LEU A 222 " =    0.761
peak=   -3.193 closest distance to " O   HOH Z 176 " =    0.767
peak=   -3.189 closest distance to " CB  ALA A  10 " =    2.247
peak=   -3.188 closest distance to " CB  SER A 245 " =    2.313
peak=   -3.187 closest distance to " O   ALA A  34 " =    2.429
peak=   -3.187 closest distance to " O   TRP A  70 " =    1.544
peak=   -3.187 closest distance to " NZ  LYS A 166 " =    1.196
peak=   -3.179 closest distance to " CG  GLU A 277 " =    1.265
peak=   -3.179 closest distance to " CA  HIS A 207 " =    1.023
peak=   -3.178 closest distance to " CB  PRO A  54 " =    2.602
peak=   -3.173 closest distance to " NE2 GLN A 240 " =    1.653
peak=   -3.169 closest distance to " O   SER A 135 " =    1.440
peak=   -3.167 closest distance to " CG1AVAL A  41 " =    2.817
peak=   -3.166 closest distance to " O   HOH Z 357 " =    2.136
peak=   -3.161 closest distance to " O   HOH Z 350 " =    2.166
peak=   -3.157 closest distance to " O   ARG A 145 " =    1.531
peak=   -3.154 closest distance to " C   ALA A 158 " =    1.654
peak=   -3.153 closest distance to " O   HOH Z 364 " =    1.530
peak=   -3.151 closest distance to " O   SER A 210 " =    1.830
peak=   -3.149 closest distance to " CB  ALA A 291 " =    1.971
peak=   -3.148 closest distance to " N   ALA A 248 " =    1.589
peak=   -3.145 closest distance to " CG  TRP A 266 " =    1.770
peak=   -3.139 closest distance to " O   ARG A  24 " =    1.758
peak=   -3.139 closest distance to " OD1AASN A 224 " =    1.820
peak=   -3.139 closest distance to " O   HOH Z 365 " =    1.778
peak=   -3.133 closest distance to " CD1 LEU A 228 " =    2.384
peak=   -3.133 closest distance to " O   SER A 276 " =    1.866
peak=   -3.130 closest distance to " CA  GLY A 133 " =    2.047
peak=   -3.128 closest distance to " O   HOH Z 191 " =    3.255
peak=   -3.122 closest distance to " OD2 ASP A 191 " =    1.478
peak=   -3.113 closest distance to " OG BSER A 134 " =    1.907
peak=   -3.108 closest distance to " O   ARG A  56 " =    1.793
peak=   -3.106 closest distance to " CE1 PHE A  38 " =    2.781
peak=   -3.103 closest distance to " O   GLN A 240 " =    2.508
peak=   -3.094 closest distance to " O   HOH Z 131 " =    4.051
peak=   -3.091 closest distance to " CG  GLN A  88 " =    0.841
peak=   -3.084 closest distance to " O   HOH Z 340 " =    1.883
peak=   -3.083 closest distance to " O   HOH Z 154 " =    1.980
peak=   -3.080 closest distance to " CD1 ILE A 199 " =    2.662
peak=   -3.068 closest distance to " C   SER A 206 " =    1.421
peak=   -3.067 closest distance to " ND2 ASN A  45 " =    1.542
peak=   -3.033 closest distance to " CB  PRO A 163 " =    2.476
peak=   -3.023 closest distance to " CA  GLY A 241 " =    2.896

================= 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    :  0.3964 0.3858   6.193453e+00   6.171925e+00
   1_bss:  0.3821 0.3759   6.174674e+00   6.152338e+00
   1_xyz:  0.2350 0.2648   5.757184e+00   5.845089e+00
   1_adp:  0.2160 0.2698   5.709044e+00   5.865793e+00
   1_occ:  0.2158 0.2696   5.708351e+00   5.866335e+00
   2_bss:  0.2122 0.2666   5.700182e+00   5.861171e+00
   2_xyz:  0.1644 0.2071   5.462590e+00   5.643378e+00
   2_adp:  0.1522 0.1991   5.406098e+00   5.605910e+00
   2_occ:  0.1520 0.1990   5.405544e+00   5.605709e+00
   3_bss:  0.1518 0.1985   5.403678e+00   5.604017e+00
   3_xyz:  0.1292 0.1747   5.264200e+00   5.486248e+00
   3_adp:  0.1257 0.1695   5.235970e+00   5.455885e+00
   3_occ:  0.1256 0.1693   5.235473e+00   5.455616e+00
   4_bss:  0.1257 0.1689   5.235056e+00   5.453825e+00
   4_xyz:  0.1203 0.1646   5.202681e+00   5.430055e+00
   4_adp:  0.1193 0.1646   5.198749e+00   5.429580e+00
   4_occ:  0.1192 0.1647   5.198874e+00   5.430177e+00
   5_bss:  0.1192 0.1647   5.198854e+00   5.430252e+00
   5_xyz:  0.1185 0.1648   5.198998e+00   5.434038e+00
   5_adp:  0.1177 0.1664   5.199043e+00   5.440814e+00
   5_occ:  0.1177 0.1665   5.199372e+00   5.441386e+00
   5_bss:  0.1176 0.1664   5.199359e+00   5.441457e+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:  0.317  60.843  -2.151  -2.869   5.743  -0.000   0.000   0.000
   1_xyz:  0.317  60.843  -2.151  -2.869   5.743  -0.000   0.000   0.000
   1_adp:  0.317  60.843  -2.151  -2.869   5.743  -0.000   0.000   0.000
   1_occ:  0.317  60.843  -2.151  -2.869   5.743  -0.000   0.000   0.000
   2_bss:  0.336  72.730  -2.488  -2.734   1.328  -0.000   0.000   0.000
   2_xyz:  0.336  72.730  -2.488  -2.734   1.328  -0.000   0.000   0.000
   2_adp:  0.336  72.730  -2.488  -2.734   1.328  -0.000   0.000   0.000
   2_occ:  0.336  72.730  -2.488  -2.734   1.328  -0.000   0.000   0.000
   3_bss:  0.336  75.449  -2.461  -2.475   0.257  -0.000   0.000   0.000
   3_xyz:  0.336  75.449  -2.461  -2.475   0.257  -0.000   0.000   0.000
   3_adp:  0.336  75.449  -2.461  -2.475   0.257  -0.000   0.000   0.000
   3_occ:  0.336  75.449  -2.461  -2.475   0.257  -0.000   0.000   0.000
   4_bss:  0.330  69.207  -2.318  -2.382  -0.120  -0.000  -0.000  -0.000
   4_xyz:  0.330  69.207  -2.318  -2.382  -0.120  -0.000  -0.000  -0.000
   4_adp:  0.330  69.207  -2.318  -2.382  -0.120  -0.000  -0.000  -0.000
   4_occ:  0.330  69.207  -2.318  -2.382  -0.120  -0.000  -0.000  -0.000
   5_bss:  0.330  69.207  -2.230  -2.297  -0.227  -0.000  -0.000  -0.000
   5_xyz:  0.330  69.207  -2.230  -2.297  -0.227  -0.000  -0.000  -0.000
   5_adp:  0.330  69.207  -2.230  -2.297  -0.227  -0.000  -0.000  -0.000
   5_occ:  0.330  69.207  -2.230  -2.297  -0.227  -0.000  -0.000  -0.000
   5_bss:  0.324  69.210  -1.987  -2.063  -0.049  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.290 0.6048  0.7627    44785.671
   1_bss:  42.078 0.6182  0.7887    41877.252
   1_xyz:  26.119 0.8007  0.9727    17934.656
   1_adp:  26.926 0.7915  0.9687    18777.949
   1_occ:  26.967 0.7910  0.9677    18781.853
   2_bss:  26.439 0.7971  0.9266    18516.936
   2_xyz:  19.978 0.8617  0.9675    10988.469
   2_adp:  18.927 0.8720  0.9663    10198.431
   2_occ:  18.923 0.8720  0.9661    10188.483
   3_bss:  18.840 0.8727  0.9580    10129.570
   3_xyz:  16.159 0.8965  0.9707     7787.086
   3_adp:  15.411 0.9033  0.9663     7332.416
   3_occ:  15.408 0.9033  0.9663     7329.319
   4_bss:  15.383 0.9035  0.9648     7291.458
   4_xyz:  14.771 0.9089  0.9688     6884.547
   4_adp:  14.715 0.9096  0.9636     6867.568
   4_occ:  14.733 0.9094  0.9634     6873.853
   5_bss:  14.733 0.9094  0.9642     6874.870
   5_xyz:  14.810 0.9088  0.9638     6948.862
   5_adp:  14.958 0.9076  0.9556     7021.156
   5_occ:  14.967 0.9075  0.9555     7027.002
   5_bss:  14.971 0.9075  0.9628     7027.953
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6495e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6495e-01
   1_xyz:   1.419  0.013  0.089 15.929  0.006  4.118   1.1044e-01
   1_adp:   1.419  0.013  0.089 15.929  0.006  4.118   1.1044e-01
   1_occ:   1.419  0.013  0.089 15.929  0.006  4.118   1.1044e-01
   2_bss:   1.419  0.013  0.089 15.929  0.006  4.118   1.1044e-01
   2_xyz:   1.006  0.007  0.073 14.868  0.003  4.130   5.8044e-02
   2_adp:   1.006  0.007  0.073 14.868  0.003  4.130   5.8044e-02
   2_occ:   1.006  0.007  0.073 14.868  0.003  4.130   5.8044e-02
   3_bss:   1.006  0.007  0.073 14.868  0.003  4.130   5.8044e-02
   3_xyz:   1.010  0.008  0.075 14.711  0.003  4.116   6.0690e-02
   3_adp:   1.010  0.008  0.075 14.711  0.003  4.116   6.0690e-02
   3_occ:   1.010  0.008  0.075 14.711  0.003  4.116   6.0690e-02
   4_bss:   1.010  0.008  0.075 14.711  0.003  4.116   6.0690e-02
   4_xyz:   0.992  0.008  0.075 14.541  0.003  4.121   5.9382e-02
   4_adp:   0.992  0.008  0.075 14.541  0.003  4.121   5.9382e-02
   4_occ:   0.992  0.008  0.075 14.541  0.003  4.121   5.9382e-02
   5_bss:   0.992  0.008  0.075 14.541  0.003  4.121   5.9382e-02
   5_xyz:   0.964  0.007  0.074 14.421  0.003  4.123   5.5589e-02
   5_adp:   0.964  0.007  0.074 14.421  0.003  4.123   5.5589e-02
   5_occ:   0.964  0.007  0.074 14.421  0.003  4.123   5.5589e-02
   5_bss:   0.964  0.007  0.074 14.421  0.003  4.123   5.5589e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.760   2.4367e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.760   2.4367e-01
   1_xyz:   9.710  0.074  0.296 81.572  0.044  2.117   1.0511e-01
   1_adp:   9.710  0.074  0.296 81.572  0.044  2.117   1.0511e-01
   1_occ:   9.710  0.074  0.296 81.572  0.044  2.117   1.0511e-01
   2_bss:   9.710  0.074  0.296 81.572  0.044  2.117   1.0511e-01
   2_xyz:   6.645  0.051  0.256 82.549  0.031  2.289   3.7254e-02
   2_adp:   6.645  0.051  0.256 82.549  0.031  2.289   3.7254e-02
   2_occ:   6.645  0.051  0.256 82.549  0.031  2.289   3.7254e-02
   3_bss:   6.645  0.051  0.256 82.549  0.031  2.289   3.7254e-02
   3_xyz:   7.157  0.055  0.231 83.761  0.028  2.405   5.6897e-02
   3_adp:   7.157  0.055  0.231 83.761  0.028  2.405   5.6897e-02
   3_occ:   7.157  0.055  0.231 83.761  0.028  2.405   5.6897e-02
   4_bss:   7.157  0.055  0.231 83.761  0.028  2.405   5.6897e-02
   4_xyz:   7.318  0.047  0.230 82.070  0.027  2.351   5.7009e-02
   4_adp:   7.318  0.047  0.230 82.070  0.027  2.351   5.7009e-02
   4_occ:   7.318  0.047  0.230 82.070  0.027  2.351   5.7009e-02
   5_bss:   7.318  0.047  0.230 82.070  0.027  2.351   5.7009e-02
   5_xyz:   7.444  0.042  0.228 82.640  0.028  2.437   3.2218e-02
   5_adp:   7.444  0.042  0.228 82.640  0.028  2.437   3.2218e-02
   5_occ:   7.444  0.042  0.228 82.640  0.028  2.437   3.2218e-02
   5_bss:   7.444  0.042  0.228 82.640  0.028  2.437   3.2218e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  72.89   0.00  16.98  72.89   0.00  13.03  64.60   2.84  38.53
   1_occ:  72.89   0.00  16.98  72.89   0.00  13.03  64.60   2.84  38.53
   2_bss:  72.89   0.00  16.98  72.89   0.00  13.03  64.60   2.84  38.53
   2_xyz:  72.89   0.00  16.98  72.89   0.00  13.03  64.60   2.84  38.53
   2_adp:  80.55   0.00  17.73  68.18   0.00  13.18  80.55   4.80  42.51
   2_occ:  80.55   0.00  17.73  68.18   0.00  13.18  80.55   4.80  42.51
   3_bss:  80.55   0.00  17.73  68.18   0.00  13.18  80.55   4.80  42.51
   3_xyz:  80.55   0.00  17.73  68.18   0.00  13.18  80.55   4.80  42.51
   3_adp:  84.31   0.98  17.27  73.36   0.98  12.84  84.31   2.48  41.36
   3_occ:  84.31   0.98  17.27  73.36   0.98  12.84  84.31   2.48  41.36
   4_bss:  84.31   0.98  17.27  73.36   0.98  12.84  84.31   2.48  41.36
   4_xyz:  84.31   0.98  17.27  73.36   0.98  12.84  84.31   2.48  41.36
   4_adp:  86.13   0.00  17.09  75.45   0.64  12.72  86.13   0.00  40.89
   4_occ:  86.13   0.00  17.09  75.45   0.64  12.72  86.13   0.00  40.89
   5_bss:  86.13   0.00  17.09  75.45   0.64  12.72  86.13   0.00  40.89
   5_xyz:  86.13   0.00  17.09  75.45   0.64  12.72  86.13   0.00  40.89
   5_adp: 104.98   0.00  17.39  92.01   0.00  12.77 104.98   1.37  42.56
   5_occ: 104.98   0.00  17.39  92.01   0.00  12.77 104.98   1.37  42.56
   5_bss: 104.99   0.00  17.39  92.01   0.00  12.77 104.99   1.37  42.56
------------------------------------------------------------------------
 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:    1.365    0.029    0.422
   1_adp:    1.365    0.029    0.422
   1_occ:    1.365    0.029    0.422
   2_bss:    1.365    0.029    0.422
   2_xyz:    1.216    0.025    0.461
   2_adp:    1.216    0.025    0.461
   2_occ:    1.216    0.025    0.461
   3_bss:    1.216    0.025    0.461
   3_xyz:    1.168    0.016    0.527
   3_adp:    1.168    0.016    0.527
   3_occ:    1.168    0.016    0.527
   4_bss:    1.168    0.016    0.527
   4_xyz:    1.306    0.029    0.541
   4_adp:    1.306    0.029    0.541
   4_occ:    1.306    0.029    0.541
   5_bss:    1.306    0.029    0.541
   5_xyz:    1.565    0.054    0.553
   5_adp:    1.565    0.054    0.553
   5_occ:    1.565    0.054    0.553
   5_bss:    1.565    0.054    0.553
------------------------------------------------------------------------

CPU time actual refinement: 337.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/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_901/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_901/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.26 
  Macro-tasks:
    bulk solvent and scale       = 45.09  
    individual site refinement   = 141.45 
    weights calculation          = 29.41  
    collect and process          = 6.65   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 222.70 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 104.59 
    alpha_beta                      = 8.53   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 114.85 
    fmodel                         = 7.52   
    r_factors                      = 0.21   
    phase_errors                   = 10.67  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.65 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.715 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    643 calls, 104.19 s
gradients_fft:          588 calls, 100.86 s

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

# Date 2008-01-16 Time 05:56:15 PST -0800 (1200491775.25 s)
Start R-work = 0.3964, R-free = 0.3858 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.3821, R-free = 0.3759
Final R-work = 0.1176, R-free = 0.1664