# Date 2008-01-16 Time 05:23:31 PST -0800 (1200489811.39 s)
#phil __OFF__

Command line arguments: "../712.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19765
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 712

-------------------------------------------------------------------------------
  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: (70.25, 47.8686, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00068
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0007

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: (70.25, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00068
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2804 [2164/2192]  1947   217  10.0%
  bin  2:  4.2804 -  3.4105 [2058/2077]  1854   204   9.9%
  bin  3:  3.4105 -  2.9832 [2050/2070]  1845   205  10.0%
  bin  4:  2.9832 -  2.7122 [2021/2046]  1820   201   9.9%
  bin  5:  2.7122 -  2.5187 [2014/2033]  1805   209  10.4%
  bin  6:  2.5187 -  2.3708 [1996/2042]  1801   195   9.8%
  bin  7:  2.3708 -  2.2525 [1997/2030]  1801   196   9.8%
  bin  8:  2.2525 -  2.1547 [1988/2024]  1784   204  10.3%
  bin  9:  2.1547 -  2.0720 [1958/1987]  1759   199  10.2%
  bin 10:  2.0720 -  2.0007 [1343/2021]  1214   129   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2151
        3.04 -     3.66: 4601
        3.66 -     4.28: 8827
        4.28 -     4.90: 12270
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.846 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.015 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.111 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.111 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27863 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_712/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 70.25 47.8686 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4259   r_free= 0.4144   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235571                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.3353 0.3409      6.4781      6.4543|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.3589 0.3819      6.7482      6.7869|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.3974 0.3642       6.619      6.5412|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.4142 0.4129      6.4689      6.4026|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.4456 0.3755      6.3245      6.2947|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.4535 0.4612      6.2262      6.1466|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.4527 0.4083      6.1983      6.0937|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.4637 0.4538      6.1474      6.1404|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.4695 0.4341      6.0727      6.1188|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.4945 0.4334      6.0945      6.0447|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.4753 0.4630      6.0028      5.9993|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.4765 0.5423      5.9453      6.0303|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.4984 0.4577      5.8762      5.8141|
| 14:  2.0506 -  2.0007 0.54    698   81 0.4544 0.5245      5.8376      5.7732|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1400   157  0.74  31.05   0.84     0.76      59359.67|
|  2:  4.7738 -  3.8094  1346   151  0.76  30.34   0.92     0.83      82023.21|
|  3:  3.8094 -  3.3338  1325   147  0.69  36.62   0.91     0.83      84151.06|
|  4:  3.3338 -  3.0317  1308   136  0.63  41.54   0.91     0.78      73509.70|
|  5:  3.0317 -  2.8159  1306   150  0.57  46.64   0.92     0.72      57730.94|
|  6:  2.8159 -  2.6508  1297   143  0.53  49.58   0.90     0.69      51441.18|
|  7:  2.6508 -  2.5187  1289   152  0.53  49.65   0.94     0.68      46823.07|
|  8:  2.5187 -  2.4095  1309   136  0.52  50.46   0.92     0.69      44794.56|
|  9:  2.4095 -  2.3171  1277   146  0.51  51.71   0.93     0.71      41260.47|
| 10:  2.3171 -  2.2374  1260   138  0.51  51.66   0.93     0.71      37979.43|
| 11:  2.2374 -  2.1677  1285   147  0.47  54.41   0.93     0.68      37577.63|
| 12:  2.1677 -  2.1059  1282   139  0.41  59.48   0.94     0.59      39039.56|
| 13:  2.1059 -  2.0506  1248   136  0.33  65.45   0.91     0.48      36802.70|
| 14:  2.0506 -  2.0007   698    81  0.29  68.39   0.98     0.36      29607.77|
|alpha:            min =        0.36 max =            0.83 mean =         0.69|
|beta:             min =    29607.77 max =        84151.06 mean =     52622.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.97 mean =        48.16|
|phase err.(test): min =        0.00 max =           89.89 mean =        48.56|
|-----------------------------------------------------------------------------|

============================== 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 = 7.757783              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.971   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.457305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.262   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      182 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1969 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2778 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4555 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4272 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5587 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6683 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.176 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4259   r_free= 0.4144   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235571                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4140   r_free= 0.4018   ksol= 0.29   Bsol= 40.08   scale= 0.941   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.78,4.34,1.53,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.223041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.837400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.569   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.780942              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.031   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4140      final r-factor (work) = 0.3029          |
| start r-factor (free) = 0.4018      final r-factor (free) = 0.3263          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4356 = 6.84 * 0.50 * 6.2221 + 1.00 * 0.1643                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8057 = 6.84 * 0.50 * 6.0546 + 1.00 * 0.1067                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3029      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3263      final r-factor (free) = 0.3412          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7343 = 0.78 * 1.00 * 6.0546 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6459 = 0.78 * 1.00 * 5.9246 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.48   17.66    None  None   None       |
|    all(noH): 2823   0      0.00    95.48   17.66    None  None   None       |
|    Sol.    : 438    0      1.41    95.48   37.80    None  None   None       |
|    Mac.    : 2385   0      0.00    75.59   13.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.549:  933   |   5:    47.742 -  57.291:   94        |
|      1:     9.549 -  19.097: 1010   |   6:    57.291 -  66.839:   48        |
|      2:    19.097 -  28.646:  390   |   7:    66.839 -  76.388:   19        |
|      3:    28.646 -  38.194:  214   |   8:    76.388 -  85.936:    6        |
|      4:    38.194 -  47.742:  106   |   9:    85.936 -  95.485:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2776 r_free = 0.3412             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2774 r_free = 0.3415             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2774   r_free= 0.3415   ksol= 0.29   Bsol= 40.08   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.78,4.34,1.53,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.934048                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2758   r_free= 0.3387   ksol= 0.32   Bsol= 72.68   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,1.91,0.56,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.932044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.041937              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.372495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.606   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2758      final r-factor (work) = 0.2124          |
| start r-factor (free) = 0.3387      final r-factor (free) = 0.2601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0417 = 5.04 * 0.50 * 5.9243 + 1.00 * 0.1067                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7716 = 5.04 * 0.50 * 5.8306 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2124      final r-factor (work) = 0.2001          |
| start r-factor (free) = 0.2601      final r-factor (free) = 0.2447          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1888 = 0.37 * 1.00 * 5.8306 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1231 = 0.37 * 1.00 * 5.6705 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.11   17.26    None  None   None       |
|    all(noH): 2823   0      0.00    96.11   17.26    None  None   None       |
|    Sol.    : 438    0      3.06    96.11   38.87    None  None   None       |
|    Mac.    : 2385   0      0.00    76.49   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.611: 1024   |   5:    48.054 -  57.664:   88        |
|      1:     9.611 -  19.222: 1030   |   6:    57.664 -  67.275:   48        |
|      2:    19.222 -  28.832:  301   |   7:    67.275 -  76.886:   18        |
|      3:    28.832 -  38.443:  183   |   8:    76.886 -  86.497:    6        |
|      4:    38.443 -  48.054:  122   |   9:    86.497 -  96.107:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2001 r_free = 0.2447             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1998 r_free = 0.2448             target_work(ml) = 5.650         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1998   r_free= 0.2448   ksol= 0.32   Bsol= 72.68   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,1.91,0.56,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.650471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1997   r_free= 0.2446   ksol= 0.33   Bsol= 72.67   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,0.50,0.19,0.00,0.00,0.00); trace/3= -0.42                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.649859                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.222153              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.838  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.919659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.181  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1997      final r-factor (work) = 0.1488          |
| start r-factor (free) = 0.2446      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8795 = 5.22 * 0.50 * 5.6705 + 1.00 * 0.0733                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5012 = 5.22 * 0.50 * 5.5235 + 1.00 * 0.0790                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1488      final r-factor (work) = 0.1341          |
| start r-factor (free) = 0.1899      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0906 = 0.92 * 1.00 * 5.5235 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9100 = 0.92 * 1.00 * 5.3256 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.20   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.20   17.25    None  None   None       |
|    Sol.    : 438    0      4.43    98.20   42.89    None  None   None       |
|    Mac.    : 2385   0      0.00    92.07   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.820: 1152   |   5:    49.101 -  58.922:   95        |
|      1:     9.820 -  19.641: 1005   |   6:    58.922 -  68.742:   69        |
|      2:    19.641 -  29.461:  222   |   7:    68.742 -  78.562:   39        |
|      3:    29.461 -  39.281:  134   |   8:    78.562 -  88.382:    9        |
|      4:    39.281 -  49.101:   95   |   9:    88.382 -  98.202:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1341 r_free = 0.1821             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1340 r_free = 0.1821             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1821   ksol= 0.33   Bsol= 72.67   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,0.50,0.19,0.00,0.00,0.00); trace/3= -0.42                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.299777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1823   ksol= 0.33   Bsol= 76.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.38,0.07,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301281                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.999632              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.420  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.583183              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.684  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1343      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1823      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4057 = 2.00 * 0.50 * 5.3277 + 1.00 * 0.0790                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3332 = 2.00 * 0.50 * 5.2749 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0884 = 0.58 * 1.00 * 5.2749 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0692 = 0.58 * 1.00 * 5.2424 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.04   16.86    None  None   None       |
|    all(noH): 2823   0      0.00    99.04   16.86    None  None   None       |
|    Sol.    : 438    0      2.15    99.04   42.38    None  None   None       |
|    Mac.    : 2385   0      0.00    95.49   12.18    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 -   9.904: 1221   |   5:    49.519 -  59.423:  102        |
|      1:     9.904 -  19.808:  983   |   6:    59.423 -  69.326:   56        |
|      2:    19.808 -  29.711:  192   |   7:    69.326 -  79.230:   30        |
|      3:    29.711 -  39.615:  129   |   8:    79.230 -  89.134:   11        |
|      4:    39.615 -  49.519:   95   |   9:    89.134 -  99.038:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1703             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1704             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1704   ksol= 0.33   Bsol= 76.73   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.38,0.07,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1702   ksol= 0.33   Bsol= 72.57   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-0.43,0.34,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234434                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.484939              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662380              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1948 = 3.48 * 0.50 * 5.2429 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1453 = 3.48 * 0.50 * 5.2034 + 1.00 * 0.0787                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4584 = 0.66 * 1.00 * 5.2034 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4417 = 0.66 * 1.00 * 5.1787 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.66   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    98.66   16.48    None  None   None       |
|    Sol.    : 438    0      1.48    98.66   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    98.13   11.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.866: 1262   |   5:    49.330 -  59.196:   88        |
|      1:     9.866 -  19.732:  951   |   6:    59.196 -  69.062:   57        |
|      2:    19.732 -  29.598:  200   |   7:    69.062 -  78.928:   28        |
|      3:    29.598 -  39.464:  124   |   8:    78.928 -  88.794:    9        |
|      4:    39.464 -  49.330:   98   |   9:    88.794 -  98.660:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1634             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1635             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1635   ksol= 0.33   Bsol= 72.57   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-0.43,0.34,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176421                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.0991 0.1328      5.3965      5.5706|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.0829 0.1020      5.4159      5.5976|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.1041 0.1503      5.4618       5.854|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.1224 0.1655      5.4607      5.6117|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.1407 0.1816      5.3788      5.5708|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.1321 0.2153      5.2705      5.5505|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.1308 0.1689      5.2104      5.3534|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.1213 0.1732      5.1258      5.3807|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.1231 0.1942      5.0647      5.3722|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.1218 0.1678      5.0261      5.1985|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.1191 0.1987      4.9613      5.2987|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.1127 0.1827      4.8897      5.2174|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.1139 0.1775        4.81      5.0506|
| 14:  2.0506 -  2.0007 0.54    698   81 0.1107 0.1733      4.7311       4.964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1400   157  0.94   9.49   0.96     0.93       7584.08|
|  2:  4.7738 -  3.8094  1346   151  0.95   8.00   1.00     0.99       8938.68|
|  3:  3.8094 -  3.3338  1325   147  0.94  10.98   1.02     1.02      10171.39|
|  4:  3.3338 -  3.0317  1308   136  0.92  13.91   1.00     0.98      10532.87|
|  5:  3.0317 -  2.8159  1306   150  0.89  16.94   1.00     0.97       9176.00|
|  6:  2.8159 -  2.6508  1297   143  0.89  17.47   0.98     0.95       7968.90|
|  7:  2.6508 -  2.5187  1289   152  0.90  16.36   0.99     0.96       6828.40|
|  8:  2.5187 -  2.4095  1309   136  0.90  15.97   0.98     0.95       5977.49|
|  9:  2.4095 -  2.3171  1277   146  0.90  16.66   0.99     0.94       5372.93|
| 10:  2.3171 -  2.2374  1260   138  0.89  16.96   0.98     0.94       4986.80|
| 11:  2.2374 -  2.1677  1285   147  0.89  16.84   0.97     0.93       4595.37|
| 12:  2.1677 -  2.1059  1282   139  0.91  15.88   1.00     0.99       4115.36|
| 13:  2.1059 -  2.0506  1248   136  0.90  16.47   0.98     0.96       3534.67|
| 14:  2.0506 -  2.0007   698    81  0.90  15.84   0.95     0.90       2912.40|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     2912.40 max =        10532.87 mean =      6784.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.62 mean =        14.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1635   ksol= 0.32   Bsol= 68.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.44,0.43,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176397                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1635   ksol= 0.32   Bsol= 68.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.44,0.43,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.0989 0.1328      5.3948      5.5697|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.0828 0.1019      5.4146       5.596|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.1041 0.1504      5.4616      5.8553|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.1225 0.1658      5.4615      5.6121|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.1408 0.1817      5.3798      5.5716|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.1320 0.2153      5.2707      5.5507|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.1309 0.1692      5.2109      5.3541|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.1213 0.1732      5.1264      5.3813|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.1230 0.1940       5.065       5.372|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.1218 0.1681      5.0263         5.2|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.1191 0.1986      4.9611      5.2978|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.1127 0.1826      4.8896      5.2175|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.1139 0.1775      4.8099      5.0501|
| 14:  2.0506 -  2.0007 0.54    698   81 0.1107 0.1730      4.7308      4.9628|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1400   157  0.94   9.49   0.96     0.93       7574.19|
|  2:  4.7738 -  3.8094  1346   151  0.95   8.00   1.00     0.99       8916.90|
|  3:  3.8094 -  3.3338  1325   147  0.94  10.96   1.02     1.02      10157.16|
|  4:  3.3338 -  3.0317  1308   136  0.92  13.92   1.01     0.99      10549.85|
|  5:  3.0317 -  2.8159  1306   150  0.89  16.95   1.00     0.97       9191.03|
|  6:  2.8159 -  2.6508  1297   143  0.89  17.48   0.98     0.95       7975.70|
|  7:  2.6508 -  2.5187  1289   152  0.90  16.36   0.99     0.97       6835.47|
|  8:  2.5187 -  2.4095  1309   136  0.90  15.98   0.99     0.95       5984.39|
|  9:  2.4095 -  2.3171  1277   146  0.90  16.67   0.99     0.94       5380.88|
| 10:  2.3171 -  2.2374  1260   138  0.89  16.97   0.98     0.94       4988.51|
| 11:  2.2374 -  2.1677  1285   147  0.90  16.84   0.98     0.94       4594.60|
| 12:  2.1677 -  2.1059  1282   139  0.91  15.88   1.00     0.99       4115.33|
| 13:  2.1059 -  2.0506  1248   136  0.90  16.47   0.98     0.97       3532.04|
| 14:  2.0506 -  2.0007   698    81  0.90  15.83   0.95     0.91       2906.46|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2906.46 max =        10549.85 mean =      6785.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.63 mean =        14.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.66   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    98.66   16.48    None  None   None       |
|    Sol.    : 438    0      1.48    98.66   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    98.13   11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.869: 1262   |   5:    49.333 -  59.199:   88        |
|      1:     9.869 -  19.735:  951   |   6:    59.199 -  69.065:   57        |
|      2:    19.735 -  29.601:  200   |   7:    69.065 -  78.931:   28        |
|      3:    29.601 -  39.467:  124   |   8:    78.931 -  88.797:    9        |
|      4:    39.467 -  49.333:   98   |   9:    88.797 -  98.663:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.639 - 5.725
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 315
   mapped sites are within: 0.741 - 5.725

peak=    6.208 closest distance to " O   HOH Z 210 " =    1.312
peak=    5.847 closest distance to " O   HOH Z 113 " =    2.187
peak=    5.331 closest distance to " CB  GLN A 223 " =    1.405
peak=    5.030 closest distance to " CG  PRO A  54 " =    1.335
peak=    4.967 closest distance to " CB  SER A  63 " =    1.163
peak=    4.867 closest distance to " CB  ARG A 190 " =    1.743
peak=    4.830 closest distance to " CB  GLN A 183 " =    1.256
peak=    4.675 closest distance to " O   PRO A 198 " =    1.542
peak=    4.561 closest distance to " O   HOH Z 369 " =    2.217
peak=    4.484 closest distance to " O   HOH Z 403 " =    1.745
peak=    4.466 closest distance to " CD2 TRP A 179 " =    1.297
peak=    4.426 closest distance to " O   HOH Z 234 " =    3.784
peak=    4.401 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.349 closest distance to " CA  ALA A  51 " =    0.960
peak=    4.339 closest distance to " CZ  PHE A 218 " =    1.194
peak=    4.327 closest distance to " O   HOH Z  43 " =    1.979
peak=    4.312 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.312 closest distance to " CB  ARG A 275 " =    0.893
peak=    4.273 closest distance to " O   HOH Z  44 " =    2.252
peak=    4.270 closest distance to " CB  GLU A 277 " =    3.786
peak=    4.241 closest distance to " CG  PRO A  90 " =    1.214
peak=    4.232 closest distance to " CB  GLU A 152 " =    1.125
peak=    4.231 closest distance to " CB  GLU A 128 " =    1.119
peak=    4.193 closest distance to " O   HOH Z 402 " =    1.578
peak=    4.189 closest distance to " O   HOH Z 134 " =    1.544
peak=    4.162 closest distance to " O   HOH Z 189 " =    2.613
peak=    4.154 closest distance to " CD  LYS A 166 " =    1.350
peak=    4.143 closest distance to " CG  PRO A 213 " =    1.193
peak=    4.137 closest distance to " CG  PRO A 280 " =    0.791
peak=    4.135 closest distance to " O   HOH Z 368 " =    2.237
peak=    4.115 closest distance to " O   SER A  87 " =    2.242
peak=    4.104 closest distance to " O   HOH Z 298 " =    1.926
peak=    4.096 closest distance to " CB  ARG A  79 " =    1.423
peak=    4.095 closest distance to " CB  VAL A 202 " =    1.493
peak=    4.090 closest distance to " CD  ARG A 269 " =    1.018
peak=    4.064 closest distance to " CA  ARG A 195 " =    1.223
peak=    4.040 closest distance to " CB  TYR A 169 " =    0.860
peak=    4.035 closest distance to " O   HOH Z 412 " =    3.635
peak=    4.014 closest distance to " O   ALA A 165 " =    1.381
peak=    4.013 closest distance to " O   HOH Z 133 " =    2.726
peak=    4.004 closest distance to " O   HOH Z  15 " =    2.253
peak=    4.000 closest distance to " O   HOH Z 423 " =    1.862
peak=    3.992 closest distance to " CA  ARG A  36 " =    1.098
peak=    3.982 closest distance to " OG BSER A 164 " =    2.270
peak=    3.977 closest distance to " O   HOH Z  49 " =    0.921
peak=    3.967 closest distance to " CB  TRP A 266 " =    1.022
peak=    3.959 closest distance to " O   HOH Z  40 " =    1.918
peak=    3.931 closest distance to " O   HOH Z 425 " =    1.403
peak=    3.919 closest distance to " O   HOH Z  63 " =    2.035
peak=    3.908 closest distance to " CB  PRO A  54 " =    0.900
peak=    3.904 closest distance to " NH2 ARG A 156 " =    1.214
peak=    3.895 closest distance to " O   ASN A  74 " =    1.790
peak=    3.894 closest distance to " O   HOH Z  97 " =    2.037
peak=    3.888 closest distance to " O   HOH Z 433 " =    1.535
peak=    3.866 closest distance to " CA  ALA A 295 " =    1.089
peak=    3.865 closest distance to " O   HOH Z 280 " =    2.978
peak=    3.861 closest distance to " O   HOH Z 261 " =    1.948
peak=    3.850 closest distance to " O   HOH Z 285 " =    2.676
peak=    3.846 closest distance to " CG  ARG A  66 " =    2.595
peak=    3.843 closest distance to " NE2 GLN A  77 " =    3.329
peak=    3.810 closest distance to " O   HOH Z 362 " =    3.433
peak=    3.807 closest distance to " O   HOH Z 406 " =    1.569
peak=    3.800 closest distance to " NE2 GLN A  11 " =    1.130
peak=    3.799 closest distance to " O   HOH Z 336 " =    1.880
peak=    3.795 closest distance to " CB  ASP A 140 " =    0.977
peak=    3.794 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.779 closest distance to " O   HOH Z  80 " =    1.844
peak=    3.766 closest distance to " O   HOH Z 346 " =    1.518
peak=    3.753 closest distance to " CB  GLU A  46 " =    1.014
peak=    3.752 closest distance to " ND2 ASN A 187 " =    1.516
peak=    3.748 closest distance to " O   HOH Z 147 " =    1.798
peak=    3.745 closest distance to " O   HOH Z 214 " =    2.823
peak=    3.744 closest distance to " N   HIS A 108 " =    1.890
peak=    3.740 closest distance to " O   HOH Z 417 " =    3.068
peak=    3.733 closest distance to " CG  PRO A 243 " =    1.090
peak=    3.730 closest distance to " CG1 ILE A  33 " =    1.167
peak=    3.726 closest distance to " CB  ASN A 148 " =    1.433
peak=    3.719 closest distance to " CD2 LEU A 297 " =    0.986
peak=    3.716 closest distance to " O   HOH Z 258 " =    2.104
peak=    3.713 closest distance to " O   HOH Z 128 " =    2.126
peak=    3.710 closest distance to " NH1AARG A 145 " =    1.355
peak=    3.708 closest distance to " CZ3 TRP A 266 " =    1.100
peak=    3.699 closest distance to " O   HOH Z 271 " =    2.727
peak=    3.694 closest distance to " O   HOH Z 383 " =    2.236
peak=    3.694 closest distance to " O   HOH Z 418 " =    1.524
peak=    3.693 closest distance to " O   HOH Z 174 " =    2.331
peak=    3.689 closest distance to " CE  LYS A  76 " =    0.825
peak=    3.688 closest distance to " CA  ILE A 106 " =    0.822
peak=    3.678 closest distance to " O   HOH Z  21 " =    1.835
peak=    3.678 closest distance to " O   HOH Z  44 " =    1.830
peak=    3.672 closest distance to " O   HOH Z 427 " =    3.115
peak=    3.672 closest distance to " O   HOH Z 299 " =    4.418
peak=    3.666 closest distance to " OD1 ASN A 217 " =    1.788
peak=    3.663 closest distance to " OE1 GLN A  55 " =    1.559
peak=    3.662 closest distance to " N   CYS A 260 " =    0.829
peak=    3.658 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.650 closest distance to " CB  LEU A 228 " =    1.089
peak=    3.648 closest distance to " O   HOH Z 389 " =    2.030
peak=    3.647 closest distance to " O   HOH Z  19 " =    1.635
peak=    3.646 closest distance to " O   HOH Z  20 " =    1.558
peak=    3.646 closest distance to " O   HOH Z 203 " =    1.821
peak=    3.645 closest distance to " OD1 ASN A  69 " =    2.534
peak=    3.634 closest distance to " OH  TYR A 116 " =    1.183
peak=    3.626 closest distance to " O   HOH Z 291 " =    1.454
peak=    3.620 closest distance to " O   HOH Z 287 " =    1.934
peak=    3.620 closest distance to " CB  ARG A  79 " =    0.943
peak=    3.618 closest distance to " NZ  LYS A  48 " =    1.250
peak=    3.618 closest distance to " CG  PRO A 198 " =    1.149
peak=    3.616 closest distance to " O   HOH Z 374 " =    2.861
peak=    3.614 closest distance to " O   HOH Z 303 " =    2.329
peak=    3.611 closest distance to " N   ASN A  39 " =    1.340
peak=    3.609 closest distance to " O   HOH Z 345 " =    1.650
peak=    3.603 closest distance to " OG BSER A 134 " =    2.877
peak=    3.601 closest distance to " OD2 ASP A 298 " =    3.865
peak=    3.598 closest distance to " O   HOH Z 316 " =    3.095
peak=    3.595 closest distance to " O   HOH Z 353 " =    2.749
peak=    3.593 closest distance to " CA  PRO A  54 " =    1.373
peak=    3.591 closest distance to " CB  SER A 141 " =    1.011
peak=    3.590 closest distance to " O   HOH Z 285 " =    1.710
peak=    3.584 closest distance to " O   HOH Z 357 " =    2.212
peak=    3.583 closest distance to " CD1 LEU A 300 " =    1.153
peak=    3.582 closest distance to " CA  ALA A 160 " =    0.930
peak=    3.580 closest distance to " O   HOH Z 265 " =    2.014
peak=    3.571 closest distance to " O   HOH Z 214 " =    1.298
peak=    3.570 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.569 closest distance to " CD  PRO A  54 " =    1.013
peak=    3.569 closest distance to " O  BHOH Z 338 " =    2.130
peak=    3.566 closest distance to " CZ  PHE A  38 " =    1.232
peak=    3.564 closest distance to " CA  VAL A 125 " =    1.262
peak=    3.559 closest distance to " CA  ASP A 162 " =    1.115
peak=    3.558 closest distance to " CG2 THR A 221 " =    1.100
peak=    3.554 closest distance to " CB  ASN A 142 " =    1.175
peak=    3.551 closest distance to " O   HOH Z  68 " =    2.017
peak=    3.551 closest distance to " O   HOH Z 294 " =    1.499
peak=    3.548 closest distance to " O   HOH Z  30 " =    1.119
peak=    3.548 closest distance to " CB  TRP A 179 " =    1.377
peak=    3.542 closest distance to " OE1 GLN A  11 " =    2.091
peak=    3.542 closest distance to " CD1 LEU A  96 " =    0.766
peak=    3.539 closest distance to " CB  ALA A 291 " =    1.220
peak=    3.538 closest distance to " CB  LEU A  83 " =    0.865
peak=    3.538 closest distance to " O   HOH Z 279 " =    2.231
peak=    3.534 closest distance to " CA  GLU A  46 " =    0.929
peak=    3.531 closest distance to " O   HOH Z 248 " =    1.547
peak=    3.530 closest distance to " CA  ALA A  21 " =    1.323
peak=    3.529 closest distance to " O   HOH Z 435 " =    2.878
peak=    3.521 closest distance to " CG2 VAL A 197 " =    1.165
peak=    3.519 closest distance to " O   HOH Z 126 " =    2.073
peak=    3.512 closest distance to " O   HOH Z 250 " =    1.548
peak=    3.510 closest distance to " O   HOH Z  59 " =    2.508
peak=    3.507 closest distance to " CE1 TYR A 186 " =    1.216
peak=    3.506 closest distance to " O   HOH Z 327 " =    1.606
peak=    3.503 closest distance to " CA  TYR A 116 " =    1.272
peak=    3.501 closest distance to " O   HOH Z  78 " =    1.615
peak=    3.501 closest distance to " CB  THR A  52 " =    0.842
peak=    3.501 closest distance to " CG  MET A 185 " =    1.110
peak=    3.498 closest distance to " CA  ASP A 191 " =    0.972
peak=    3.494 closest distance to " O   HOH Z 156 " =    2.619
peak=    3.494 closest distance to " O   ASP A 124 " =    1.344
peak=    3.493 closest distance to " CB  SER A  62 " =    0.873
peak=    3.490 closest distance to " CB  ASN A 285 " =    0.936
peak=    3.489 closest distance to " O   ALA A 158 " =    1.155
peak=    3.483 closest distance to " C   TYR A 214 " =    1.548
peak=    3.475 closest distance to " NZ  LYS A 117 " =    3.080
peak=    3.474 closest distance to " O   HOH Z 142 " =    1.532
peak=    3.471 closest distance to " O   HOH Z 102 " =    1.240
peak=    3.468 closest distance to " CG AARG A 275 " =    1.179
peak=    3.443 closest distance to " CB  GLN A  88 " =    1.165
peak=    3.440 closest distance to " O   TYR A 116 " =    1.454
peak=    3.440 closest distance to " O   HOH Z 180 " =    2.205
peak=    3.440 closest distance to " O   HOH Z 393 " =    3.282
peak=    3.439 closest distance to " CG2BVAL A  41 " =    0.893
peak=    3.434 closest distance to " O   HOH Z  47 " =    2.431
peak=    3.426 closest distance to " NH2AARG A 275 " =    3.408
peak=    3.420 closest distance to " CA  GLU A 152 " =    0.887
peak=    3.419 closest distance to " O   HOH Z 199 " =    1.661
peak=    3.416 closest distance to " O   HOH Z 189 " =    2.822
peak=    3.415 closest distance to " O   HOH Z 365 " =    2.759
peak=    3.414 closest distance to " CB  PRO A  90 " =    1.177
peak=    3.412 closest distance to " O   HOH Z 421 " =    1.851
peak=    3.406 closest distance to " O   HOH Z 245 " =    1.301
peak=    3.405 closest distance to " CA  SER A  32 " =    1.651
peak=    3.405 closest distance to " CG2 THR A  29 " =    1.388
peak=    3.404 closest distance to " O   HOH Z 193 " =    2.283
peak=    3.401 closest distance to " O   HOH Z 158 " =    3.106
peak=    3.400 closest distance to " O   ASP A 191 " =    1.504
peak=    3.392 closest distance to " O   HOH Z 125 " =    3.834
peak=    3.385 closest distance to " O   HOH Z 176 " =    1.548
peak=    3.383 closest distance to " O   HOH Z 359 " =    1.530
peak=    3.379 closest distance to " O   HOH Z 130 " =    2.234
peak=    3.378 closest distance to " CB  ALA A 100 " =    1.270
peak=    3.377 closest distance to " CG2 ILE A 120 " =    1.130
peak=    3.377 closest distance to " O   HOH Z 422 " =    2.599
peak=    3.373 closest distance to " O   HOH Z 305 " =    3.708
peak=    3.372 closest distance to " O   HOH Z 298 " =    2.434
peak=    3.364 closest distance to " O   HOH Z 126 " =    1.583
peak=    3.362 closest distance to " O   HOH Z 251 " =    1.593
peak=    3.358 closest distance to " O   HOH Z 371 " =    3.072
peak=    3.356 closest distance to " CD  ARG A 195 " =    0.914
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.788
peak=    3.344 closest distance to " O   THR A 220 " =    1.192
peak=    3.343 closest distance to " O   HOH Z  48 " =    1.720
peak=    3.341 closest distance to " CB  ALA A 248 " =    1.328
peak=    3.339 closest distance to " OG  SER A 245 " =    1.610
peak=    3.339 closest distance to " CA  ASN A 217 " =    1.273
peak=    3.338 closest distance to " CB  ASP A 298 " =    1.182
peak=    3.338 closest distance to " CB  SER A   3 " =    1.421
peak=    3.337 closest distance to " CB  TYR A 116 " =    1.028
peak=    3.336 closest distance to " CB  GLN A  89 " =    1.290
peak=    3.335 closest distance to " O   HOH Z 325 " =    2.197
peak=    3.334 closest distance to " CG  ARG A 219 " =    1.210
peak=    3.331 closest distance to " CG1 VAL A 153 " =    1.093
peak=    3.330 closest distance to " O   HOH Z 380 " =    1.798
peak=    3.330 closest distance to " CA  GLY A 241 " =    0.894
peak=    3.327 closest distance to " CA  LYS A 117 " =    1.240
peak=    3.325 closest distance to " O   HOH Z 250 " =    1.316
peak=    3.324 closest distance to " O   HOH Z 185 " =    1.721
peak=    3.319 closest distance to " O   HOH Z 361 " =    2.599
peak=    3.317 closest distance to " CG2AVAL A  72 " =    1.906
peak=    3.315 closest distance to " OG  SER A  22 " =    2.783
peak=    3.310 closest distance to " CA  ALA A 233 " =    1.789
peak=    3.304 closest distance to " CG  GLN A  11 " =    1.324
peak=    3.300 closest distance to " OE1 GLU A   2 " =    1.814
peak=    3.298 closest distance to " CD2 TYR A 186 " =    1.013
peak=    3.297 closest distance to " O   HOH Z  88 " =    1.745
peak=    3.287 closest distance to " O   HOH Z 281 " =    4.965
peak=    3.286 closest distance to " CB  MET A  40 " =    0.974
peak=    3.283 closest distance to " O   HOH Z   1 " =    2.758
peak=    3.283 closest distance to " O   HOH Z 109 " =    2.603
peak=    3.276 closest distance to " OE1 GLN A  58 " =    3.653
peak=    3.274 closest distance to " CG2 ILE A  20 " =    1.361
peak=    3.273 closest distance to " CA  ALA A 100 " =    0.984
peak=    3.269 closest distance to " CB  ALA A   9 " =    1.628
peak=    3.269 closest distance to " NE2 HIS A 115 " =    1.018
peak=    3.268 closest distance to " CA  LEU A  83 " =    1.302
peak=    3.268 closest distance to " CA  ASN A 215 " =    1.093
peak=    3.262 closest distance to " CB  ASN A 187 " =    1.194
peak=    3.260 closest distance to " O   HOH Z 411 " =    1.720
peak=    3.257 closest distance to " CG  LEU A 167 " =    1.120
peak=    3.256 closest distance to " CA  SER A  87 " =    1.054
peak=    3.256 closest distance to " CZ3 TRP A  85 " =    0.982
peak=    3.253 closest distance to " CB  ALA A 248 " =    0.951
peak=    3.248 closest distance to " O   HOH Z 196 " =    1.229
peak=    3.247 closest distance to " O   HOH Z 132 " =    2.789
peak=    3.247 closest distance to " O   HOH Z 163 " =    1.614
peak=    3.246 closest distance to " CA  ASN A 252 " =    2.130
peak=    3.245 closest distance to " O   HOH Z 392 " =    2.496
peak=    3.245 closest distance to " O   HOH Z 420 " =    5.725
peak=    3.245 closest distance to " CB  MET A 105 " =    1.095
peak=    3.242 closest distance to " CG  GLU A  37 " =    0.920
peak=    3.242 closest distance to " CA  LYS A 166 " =    1.321
peak=    3.241 closest distance to " CG2 ILE A 234 " =    1.029
peak=    3.238 closest distance to " CA  MET A 188 " =    0.996
peak=    3.227 closest distance to " O   HOH Z 313 " =    1.877
peak=    3.222 closest distance to " CB  ASN A 127 " =    0.884
peak=    3.207 closest distance to " CB  PHE A 283 " =    0.741
peak=    3.205 closest distance to " CA  SER A  12 " =    1.561
peak=    3.201 closest distance to " O   HOH Z 282 " =    2.056
peak=    3.200 closest distance to " O   THR A 251 " =    1.159
peak=    3.199 closest distance to " O   HOH Z 381 " =    1.921
peak=    3.198 closest distance to " CB  GLN A 103 " =    0.870
peak=    3.197 closest distance to " O   HOH Z 173 " =    2.194
peak=    3.197 closest distance to " CB  PHE A 204 " =    0.838
peak=    3.195 closest distance to " ND2 ASN A 249 " =    0.899
peak=    3.195 closest distance to " CB  ALA A  71 " =    1.338
peak=    3.193 closest distance to " CB  VAL A 265 " =    1.245
peak=    3.192 closest distance to " CD  ARG A 159 " =    0.858
peak=    3.191 closest distance to " CB  PHE A 204 " =    0.938
peak=    3.187 closest distance to " CB  MET A  47 " =    0.985
peak=    3.184 closest distance to " OG  SER A  62 " =    2.913
peak=    3.184 closest distance to " N   GLU A  44 " =    2.266
peak=    3.179 closest distance to " CA  MET A 105 " =    1.066
peak=    3.179 closest distance to " N   TYR A 116 " =    1.627
peak=    3.177 closest distance to " CA  LEU A 101 " =    1.860
peak=    3.177 closest distance to " O   HOH Z 344 " =    3.176
peak=    3.170 closest distance to " CG  GLN A  58 " =    2.746
peak=    3.164 closest distance to " CB  ALA A  43 " =    0.819
peak=    3.162 closest distance to " O   HOH Z 355 " =    1.754
peak=    3.162 closest distance to " N   ASN A 127 " =    1.271
peak=    3.156 closest distance to " CG  ARG A 138 " =    1.157
peak=    3.156 closest distance to " O   HOH Z  97 " =    2.326
peak=    3.152 closest distance to " O   HOH Z 128 " =    2.287
peak=    3.151 closest distance to " N   GLY A  98 " =    1.175
peak=    3.150 closest distance to " CB  SER A  97 " =    0.816
peak=    3.142 closest distance to " N   ALA A 158 " =    1.496
peak=    3.141 closest distance to " CA  ALA A 154 " =    0.992
peak=    3.132 closest distance to " CG1 ILE A  49 " =    1.622
peak=    3.130 closest distance to " O   HOH Z 394 " =    1.669
peak=    3.125 closest distance to " O   HOH Z 162 " =    1.602
peak=    3.124 closest distance to " CD  ARG A  66 " =    2.499
peak=    3.124 closest distance to " O   HOH Z 148 " =    3.344
peak=    3.122 closest distance to " CA  ALA A 291 " =    0.777
peak=    3.117 closest distance to " O   HOH Z 216 " =    5.295
peak=    3.114 closest distance to " CA  ALA A 158 " =    1.279
peak=    3.113 closest distance to " O   LEU A 228 " =    1.988
peak=    3.111 closest distance to " CE1 PHE A 218 " =    1.165
peak=    3.110 closest distance to " CA  ASN A 249 " =    1.375
peak=    3.109 closest distance to " CE3 TRP A 150 " =    1.077
peak=    3.109 closest distance to " O   HOH Z 150 " =    1.494
peak=    3.107 closest distance to " CD1 LEU A 228 " =    1.552
peak=    3.099 closest distance to " O   HOH Z 141 " =    1.633
peak=    3.097 closest distance to " O   HOH Z 394 " =    3.874
peak=    3.096 closest distance to " CG2 THR A 220 " =    0.754
peak=    3.091 closest distance to " O   HOH Z 420 " =    2.030
peak=    3.084 closest distance to " OD2 ASP A 298 " =    3.576
peak=    3.080 closest distance to " O   HOH Z 343 " =    2.226
peak=    3.078 closest distance to " CE1 HIS A 108 " =    1.112
peak=    3.077 closest distance to " CB  LEU A   5 " =    1.114
peak=    3.056 closest distance to " O   HOH Z  88 " =    3.362
peak=    3.047 closest distance to " O   TRP A 274 " =    1.845
peak=    3.045 closest distance to " O   HOH Z  78 " =    1.927
peak=    3.043 closest distance to " O   HOH Z 171 " =    3.937

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.802
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 220
   mapped sites are within: 0.777 - 5.802

peak=   -4.793 closest distance to " O   HOH Z 266 " =    5.341
peak=   -4.656 closest distance to " CB  PRO A 243 " =    2.730
peak=   -4.617 closest distance to " CD  GLN A  58 " =    0.950
peak=   -4.516 closest distance to " O   HOH Z  10 " =    1.634
peak=   -4.419 closest distance to " CG1 VAL A 250 " =    2.687
peak=   -4.353 closest distance to " CD1 LEU A 101 " =    2.456
peak=   -4.328 closest distance to " CG1 VAL A 112 " =    2.611
peak=   -4.207 closest distance to " O   VAL A  67 " =    2.770
peak=   -4.189 closest distance to " CD  ARG A  14 " =    3.440
peak=   -4.146 closest distance to " O   HOH Z 196 " =    2.301
peak=   -4.131 closest distance to " CD  ARG A 156 " =    2.118
peak=   -4.130 closest distance to " O   HOH Z 166 " =    1.687
peak=   -4.100 closest distance to " CD1 PHE A  59 " =    2.059
peak=   -4.078 closest distance to " CA  ASP A 298 " =    1.058
peak=   -4.076 closest distance to " OXT GLY A 302 " =    2.993
peak=   -4.072 closest distance to " CG2 ILE A  49 " =    2.730
peak=   -4.060 closest distance to " CD  GLN A 223 " =    1.378
peak=   -4.059 closest distance to " O   HOH Z 283 " =    2.207
peak=   -4.028 closest distance to " CE2 PHE A  61 " =    2.620
peak=   -4.026 closest distance to " N   ALA A  43 " =    2.755
peak=   -4.000 closest distance to " CG2 ILE A  20 " =    3.051
peak=   -3.992 closest distance to " ND2 ASN A  45 " =    1.986
peak=   -3.971 closest distance to " O   HOH Z 231 " =    2.350
peak=   -3.963 closest distance to " O   PRO A 198 " =    1.328
peak=   -3.959 closest distance to " CH2 TRP A 179 " =    1.264
peak=   -3.925 closest distance to " O   HOH Z  13 " =    1.757
peak=   -3.915 closest distance to " O   HOH Z 377 " =    2.093
peak=   -3.896 closest distance to " O   ALA A  34 " =    2.460
peak=   -3.886 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.883 closest distance to " CB  ALA A  10 " =    2.174
peak=   -3.883 closest distance to " CD  GLN A  58 " =    1.110
peak=   -3.874 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.852 closest distance to " CG2 ILE A 263 " =    2.335
peak=   -3.845 closest distance to " O   HOH Z 150 " =    1.060
peak=   -3.844 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.836 closest distance to " O   HOH Z 348 " =    2.342
peak=   -3.829 closest distance to " C   HIS A 108 " =    1.124
peak=   -3.793 closest distance to " O   HOH Z 185 " =    2.491
peak=   -3.786 closest distance to " O   HOH Z 374 " =    1.966
peak=   -3.782 closest distance to " CD1 LEU A  25 " =    2.476
peak=   -3.749 closest distance to " CG2 VAL A 189 " =    2.235
peak=   -3.720 closest distance to " O   HOH Z 394 " =    1.629
peak=   -3.704 closest distance to " O   SER A 210 " =    1.880
peak=   -3.698 closest distance to " C   SER A 206 " =    1.454
peak=   -3.679 closest distance to " CE2 TYR A  30 " =    2.691
peak=   -3.676 closest distance to " O   HOH Z 234 " =    4.333
peak=   -3.673 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.673 closest distance to " C   ASN A 285 " =    2.415
peak=   -3.662 closest distance to " OE1 GLN A 223 " =    2.244
peak=   -3.658 closest distance to " O   HOH Z 290 " =    1.176
peak=   -3.643 closest distance to " CD1 ILE A 151 " =    2.443
peak=   -3.642 closest distance to " O   HOH Z 210 " =    0.882
peak=   -3.637 closest distance to " O   HOH Z 292 " =    4.664
peak=   -3.630 closest distance to " CB  PHE A 192 " =    1.993
peak=   -3.619 closest distance to " O   SER A 276 " =    1.673
peak=   -3.618 closest distance to " O   HOH Z 128 " =    2.689
peak=   -3.616 closest distance to " CB  ALA A 161 " =    2.626
peak=   -3.615 closest distance to " O   PRO A 163 " =    2.146
peak=   -3.613 closest distance to " O   HOH Z 123 " =    2.498
peak=   -3.612 closest distance to " O   HOH Z 264 " =    1.789
peak=   -3.607 closest distance to " CZ  TYR A 169 " =    1.814
peak=   -3.602 closest distance to " O   HOH Z 351 " =    1.544
peak=   -3.601 closest distance to " O   HOH Z  71 " =    2.242
peak=   -3.585 closest distance to " O   HOH Z 197 " =    2.039
peak=   -3.579 closest distance to " ND2 ASN A 187 " =    1.653
peak=   -3.577 closest distance to " O   HOH Z 200 " =    1.280
peak=   -3.576 closest distance to " O   HOH Z   6 " =    1.396
peak=   -3.569 closest distance to " CG1 VAL A  78 " =    2.683
peak=   -3.567 closest distance to " ND2BASN A 224 " =    1.854
peak=   -3.565 closest distance to " O   PHE A 218 " =    1.500
peak=   -3.559 closest distance to " CE BMET A  47 " =    1.810
peak=   -3.537 closest distance to " CB  PHE A  16 " =    2.523
peak=   -3.536 closest distance to " N   SER A 276 " =    1.534
peak=   -3.534 closest distance to " O   HOH Z 171 " =    2.224
peak=   -3.516 closest distance to " OD1 ASN A 249 " =    2.520
peak=   -3.512 closest distance to " CE3 TRP A 150 " =    2.263
peak=   -3.509 closest distance to " NE2 GLN A 223 " =    1.198
peak=   -3.505 closest distance to " CD  ARG A 139 " =    1.544
peak=   -3.504 closest distance to " CD  LYS A 289 " =    2.360
peak=   -3.498 closest distance to " O   HOH Z 372 " =    2.461
peak=   -3.484 closest distance to " CG  GLU A  53 " =    1.574
peak=   -3.482 closest distance to " O   HOH Z 366 " =    1.774
peak=   -3.480 closest distance to " O   HOH Z 236 " =    1.602
peak=   -3.474 closest distance to " O   ALA A   1 " =    1.878
peak=   -3.467 closest distance to " CG  ARG A 269 " =    2.297
peak=   -3.463 closest distance to " ND2 ASN A 249 " =    2.250
peak=   -3.460 closest distance to " O   ALA A  10 " =    1.769
peak=   -3.459 closest distance to " NH2 ARG A 159 " =    2.425
peak=   -3.444 closest distance to " CB  ALA A 291 " =    2.400
peak=   -3.439 closest distance to " O   HOH Z 150 " =    2.083
peak=   -3.437 closest distance to " OG BSER A 210 " =    1.377
peak=   -3.431 closest distance to " O   HOH Z 111 " =    1.676
peak=   -3.426 closest distance to " O   HOH Z 102 " =    1.632
peak=   -3.420 closest distance to " O   HOH Z 377 " =    1.278
peak=   -3.419 closest distance to " CG1 VAL A 112 " =    2.786
peak=   -3.418 closest distance to " CG1AVAL A 121 " =    1.471
peak=   -3.418 closest distance to " O   HOH Z 177 " =    1.940
peak=   -3.412 closest distance to " CD2 PHE A 225 " =    1.304
peak=   -3.409 closest distance to " NE  ARG A  66 " =    4.398
peak=   -3.406 closest distance to " O   HOH Z 109 " =    3.458
peak=   -3.388 closest distance to " O   HOH Z 196 " =    1.940
peak=   -3.387 closest distance to " NH2 ARG A  79 " =    2.144
peak=   -3.383 closest distance to " OG BSER A 134 " =    1.346
peak=   -3.382 closest distance to " O   HOH Z  52 " =    1.628
peak=   -3.382 closest distance to " O   HOH Z 422 " =    1.447
peak=   -3.380 closest distance to " O   HOH Z 252 " =    3.759
peak=   -3.369 closest distance to " O   HOH Z 136 " =    2.130
peak=   -3.369 closest distance to " O   HOH Z  37 " =    1.934
peak=   -3.367 closest distance to " CB  ARG A 219 " =    2.295
peak=   -3.365 closest distance to " CA  GLY A 241 " =    2.371
peak=   -3.362 closest distance to " OH  TYR A 247 " =    2.173
peak=   -3.361 closest distance to " O   VAL A 189 " =    2.634
peak=   -3.360 closest distance to " CA  GLY A 133 " =    2.351
peak=   -3.358 closest distance to " O   HOH Z 165 " =    2.003
peak=   -3.356 closest distance to " O   HOH Z 311 " =    3.790
peak=   -3.355 closest distance to " CD  GLN A  88 " =    0.911
peak=   -3.350 closest distance to " CB  ALA A  43 " =    2.591
peak=   -3.344 closest distance to " C   LEU A 143 " =    1.136
peak=   -3.342 closest distance to " O   HOH Z 198 " =    2.034
peak=   -3.341 closest distance to " N   THR A  52 " =    1.706
peak=   -3.340 closest distance to " O   HOH Z 393 " =    1.440
peak=   -3.339 closest distance to " OD1 ASP A 191 " =    1.566
peak=   -3.331 closest distance to " O   HOH Z 407 " =    3.535
peak=   -3.326 closest distance to " ND2 ASN A  45 " =    1.299
peak=   -3.324 closest distance to " CD1 ILE A 263 " =    1.924
peak=   -3.322 closest distance to " O   HOH Z 106 " =    1.949
peak=   -3.322 closest distance to " CD2 PHE A  61 " =    2.091
peak=   -3.316 closest distance to " CB  ALA A 248 " =    2.245
peak=   -3.312 closest distance to " CG  GLN A  11 " =    1.646
peak=   -3.311 closest distance to " O   HOH Z 211 " =    1.528
peak=   -3.307 closest distance to " O   HOH Z 149 " =    2.092
peak=   -3.305 closest distance to " O   HOH Z 240 " =    3.895
peak=   -3.299 closest distance to " O   HOH Z 378 " =    1.297
peak=   -3.299 closest distance to " O   HOH Z 396 " =    2.057
peak=   -3.296 closest distance to " CA  GLY A 241 " =    3.213
peak=   -3.296 closest distance to " CD2 LEU A 300 " =    2.757
peak=   -3.281 closest distance to " O   HOH Z  19 " =    2.183
peak=   -3.278 closest distance to " O   ASN A 301 " =    1.329
peak=   -3.278 closest distance to " CG  PRO A 243 " =    1.718
peak=   -3.277 closest distance to " OG BSER A 210 " =    2.236
peak=   -3.271 closest distance to " O   HOH Z  78 " =    1.849
peak=   -3.269 closest distance to " CB  ALA A 291 " =    2.173
peak=   -3.268 closest distance to " O   ASN A 187 " =    1.632
peak=   -3.262 closest distance to " O   LEU A 101 " =    2.077
peak=   -3.260 closest distance to " O   HOH Z 256 " =    2.225
peak=   -3.255 closest distance to " O   HOH Z  56 " =    1.855
peak=   -3.252 closest distance to " NE2 GLN A 103 " =    1.779
peak=   -3.249 closest distance to " O   HOH Z 418 " =    1.304
peak=   -3.247 closest distance to " O   HOH Z 409 " =    4.844
peak=   -3.247 closest distance to " O   HOH Z 252 " =    4.088
peak=   -3.244 closest distance to " O   GLN A 240 " =    2.546
peak=   -3.240 closest distance to " O   TRP A  92 " =    1.928
peak=   -3.239 closest distance to " CD1 ILE A 109 " =    2.851
peak=   -3.237 closest distance to " O   HOH Z 351 " =    1.420
peak=   -3.236 closest distance to " O   HOH Z 414 " =    1.529
peak=   -3.236 closest distance to " CG  LEU A  83 " =    2.045
peak=   -3.230 closest distance to " OG BSER A 134 " =    1.949
peak=   -3.230 closest distance to " O   HOH Z 407 " =    1.263
peak=   -3.230 closest distance to " CD  ARG A  79 " =    1.268
peak=   -3.212 closest distance to " O   HOH Z 191 " =    5.802
peak=   -3.207 closest distance to " CB  TRP A  85 " =    2.493
peak=   -3.206 closest distance to " CG  ARG A 219 " =    2.621
peak=   -3.204 closest distance to " O   SER A 271 " =    2.066
peak=   -3.200 closest distance to " OG  SER A  26 " =    1.266
peak=   -3.194 closest distance to " CG2BVAL A  41 " =    1.611
peak=   -3.189 closest distance to " CD  PRO A 213 " =    2.182
peak=   -3.188 closest distance to " CE1 PHE A 218 " =    2.695
peak=   -3.188 closest distance to " O   HOH Z 145 " =    2.806
peak=   -3.185 closest distance to " O   HOH Z  60 " =    1.884
peak=   -3.185 closest distance to " CD  ARG A 195 " =    5.115
peak=   -3.184 closest distance to " O   HOH Z 357 " =    2.125
peak=   -3.180 closest distance to " OD2 ASP A 171 " =    1.879
peak=   -3.177 closest distance to " O   HOH Z 426 " =    1.657
peak=   -3.175 closest distance to " O   TYR A 186 " =    1.759
peak=   -3.170 closest distance to " O   HOH Z 216 " =    1.725
peak=   -3.168 closest distance to " C   ARG A  79 " =    2.701
peak=   -3.166 closest distance to " O   GLY A  75 " =    2.064
peak=   -3.165 closest distance to " CG  ASP A 231 " =    0.841
peak=   -3.160 closest distance to " NH2 ARG A  79 " =    1.662
peak=   -3.160 closest distance to " NE2 GLN A  88 " =    1.069
peak=   -3.159 closest distance to " O   HOH Z 166 " =    1.740
peak=   -3.158 closest distance to " CZ3 TRP A 274 " =    2.397
peak=   -3.155 closest distance to " O   HOH Z 285 " =    1.419
peak=   -3.155 closest distance to " CZ  PHE A  38 " =    2.457
peak=   -3.152 closest distance to " O   HOH Z 292 " =    1.645
peak=   -3.145 closest distance to " CG1 VAL A 125 " =    2.048
peak=   -3.144 closest distance to " N   TYR A  68 " =    2.921
peak=   -3.143 closest distance to " CE  MET A  93 " =    1.705
peak=   -3.142 closest distance to " O   HOH Z  19 " =    0.918
peak=   -3.136 closest distance to " CZ  PHE A  38 " =    1.979
peak=   -3.125 closest distance to " O   HOH Z 126 " =    1.943
peak=   -3.123 closest distance to " CG2AVAL A  41 " =    2.904
peak=   -3.118 closest distance to " O   HOH Z  30 " =    0.777
peak=   -3.117 closest distance to " N   ALA A 226 " =    2.009
peak=   -3.116 closest distance to " OD1 ASP A 171 " =    1.569
peak=   -3.113 closest distance to " CG2 VAL A 202 " =    2.136
peak=   -3.112 closest distance to " CB  ALA A   9 " =    2.494
peak=   -3.112 closest distance to " CB  ASP A 132 " =    2.418
peak=   -3.109 closest distance to " O   HOH Z 275 " =    1.771
peak=   -3.108 closest distance to " OH  TYR A 169 " =    0.970
peak=   -3.108 closest distance to " SD  MET A  40 " =    1.935
peak=   -3.104 closest distance to " ND2 ASN A  60 " =    1.390
peak=   -3.097 closest distance to " NH2 ARG A  66 " =    3.741
peak=   -3.095 closest distance to " OD1 ASN A 301 " =    1.954
peak=   -3.092 closest distance to " O   HOH Z  40 " =    2.411
peak=   -3.091 closest distance to " CA  GLY A 241 " =    2.877
peak=   -3.083 closest distance to " NH2 ARG A  66 " =    2.031
peak=   -3.078 closest distance to " O   PRO A 198 " =    1.341
peak=   -3.076 closest distance to " O   HOH Z   6 " =    1.761
peak=   -3.070 closest distance to " CD2 PHE A  59 " =    2.439
peak=   -3.066 closest distance to " CH2 TRP A 150 " =    1.110
peak=   -3.064 closest distance to " O   ASP A 171 " =    1.042
peak=   -3.060 closest distance to " O   HOH Z 174 " =    2.228
peak=   -3.056 closest distance to " O   HOH Z 114 " =    1.457
peak=   -3.054 closest distance to " O   HOH Z 259 " =    2.066
peak=   -3.053 closest distance to " CA  VAL A 197 " =    0.971
peak=   -3.049 closest distance to " C   GLY A 262 " =    2.160
peak=   -3.017 closest distance to " O   HOH Z 150 " =    1.650

================= 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    :  0.4259 0.4144   6.235571e+00   6.207717e+00
   1_bss:  0.4140 0.4018   6.223041e+00   6.191889e+00
   1_xyz:  0.3029 0.3263   5.983076e+00   6.037930e+00
   1_adp:  0.2776 0.3412   5.934334e+00   6.061371e+00
   1_occ:  0.2774 0.3415   5.934048e+00   6.061603e+00
   2_bss:  0.2758 0.3387   5.932044e+00   6.060063e+00
   2_xyz:  0.2124 0.2601   5.696539e+00   5.856938e+00
   2_adp:  0.2001 0.2447   5.650861e+00   5.812344e+00
   2_occ:  0.1998 0.2448   5.650471e+00   5.813129e+00
   3_bss:  0.1997 0.2446   5.649859e+00   5.812050e+00
   3_xyz:  0.1488 0.1899   5.377095e+00   5.575591e+00
   3_adp:  0.1341 0.1821   5.299942e+00   5.520190e+00
   3_occ:  0.1340 0.1821   5.299777e+00   5.520000e+00
   4_bss:  0.1343 0.1823   5.301281e+00   5.519587e+00
   4_xyz:  0.1262 0.1726   5.250388e+00   5.472543e+00
   4_adp:  0.1244 0.1703   5.234672e+00   5.457006e+00
   4_occ:  0.1243 0.1704   5.234548e+00   5.456787e+00
   5_bss:  0.1242 0.1702   5.234434e+00   5.456701e+00
   5_xyz:  0.1157 0.1644   5.182339e+00   5.422818e+00
   5_adp:  0.1149 0.1634   5.176332e+00   5.417339e+00
   5_occ:  0.1148 0.1635   5.176421e+00   5.417664e+00
   5_bss:  0.1148 0.1635   5.176397e+00   5.417719e+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:  0.289  40.081  -3.782   4.341   1.534   0.000   0.000   0.000
   1_xyz:  0.289  40.081  -3.782   4.341   1.534   0.000   0.000   0.000
   1_adp:  0.289  40.081  -3.782   4.341   1.534   0.000   0.000   0.000
   1_occ:  0.289  40.081  -3.782   4.341   1.534   0.000   0.000   0.000
   2_bss:  0.322  72.679  -2.138   1.907   0.560   0.000   0.000   0.000
   2_xyz:  0.322  72.679  -2.138   1.907   0.560   0.000   0.000   0.000
   2_adp:  0.322  72.679  -2.138   1.907   0.560   0.000   0.000   0.000
   2_occ:  0.322  72.679  -2.138   1.907   0.560   0.000   0.000   0.000
   3_bss:  0.326  72.668  -1.955   0.499   0.191   0.000   0.000   0.000
   3_xyz:  0.326  72.668  -1.955   0.499   0.191   0.000   0.000   0.000
   3_adp:  0.326  72.668  -1.955   0.499   0.191   0.000   0.000   0.000
   3_occ:  0.326  72.668  -1.955   0.499   0.191   0.000   0.000   0.000
   4_bss:  0.333  76.732  -1.902  -0.377   0.071  -0.000   0.000   0.000
   4_xyz:  0.333  76.732  -1.902  -0.377   0.071  -0.000   0.000   0.000
   4_adp:  0.333  76.732  -1.902  -0.377   0.071  -0.000   0.000   0.000
   4_occ:  0.333  76.732  -1.902  -0.377   0.071  -0.000   0.000   0.000
   5_bss:  0.327  72.573  -1.580  -0.435   0.344  -0.000   0.000   0.000
   5_xyz:  0.327  72.573  -1.580  -0.435   0.344  -0.000   0.000   0.000
   5_adp:  0.327  72.573  -1.580  -0.435   0.344  -0.000   0.000   0.000
   5_occ:  0.327  72.573  -1.580  -0.435   0.344  -0.000   0.000   0.000
   5_bss:  0.321  68.503  -1.415  -0.445   0.435  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.204 0.5438  0.6922    52614.044
   1_bss:  47.060 0.5565  0.7268    49473.966
   1_xyz:  35.566 0.6951  0.8791    30240.957
   1_adp:  36.955 0.6783  0.8533    32480.090
   1_occ:  37.006 0.6777  0.8526    32522.957
   2_bss:  36.487 0.6840  0.8474    32095.866
   2_xyz:  27.029 0.7893  0.9463    18124.276
   2_adp:  25.076 0.8109  0.9475    16207.581
   2_occ:  25.090 0.8107  0.9470    16230.451
   3_bss:  24.985 0.8119  0.9317    16164.840
   3_xyz:  18.291 0.8773  0.9764     9208.215
   3_adp:  17.006 0.8891  0.9706     8311.087
   3_occ:  17.000 0.8892  0.9704     8311.615
   4_bss:  16.983 0.8894  0.9606     8315.976
   4_xyz:  15.882 0.8993  0.9643     7525.635
   4_adp:  15.499 0.9029  0.9571     7352.479
   4_occ:  15.496 0.9029  0.9569     7352.504
   5_bss:  15.495 0.9029  0.9632     7351.212
   5_xyz:  14.826 0.9083  0.9684     6849.760
   5_adp:  14.681 0.9097  0.9607     6780.268
   5_occ:  14.686 0.9097  0.9606     6783.934
   5_bss:  14.689 0.9096  0.9636     6784.533
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6428e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6428e-01
   1_xyz:   1.446  0.011  0.089 15.305  0.006  4.114   1.0670e-01
   1_adp:   1.446  0.011  0.089 15.305  0.006  4.114   1.0670e-01
   1_occ:   1.446  0.011  0.089 15.305  0.006  4.114   1.0670e-01
   2_bss:   1.446  0.011  0.089 15.305  0.006  4.114   1.0670e-01
   2_xyz:   1.180  0.008  0.079 14.325  0.005  4.133   7.2785e-02
   2_adp:   1.180  0.008  0.079 14.325  0.005  4.133   7.2785e-02
   2_occ:   1.180  0.008  0.079 14.325  0.005  4.133   7.2785e-02
   3_bss:   1.180  0.008  0.079 14.325  0.005  4.133   7.2785e-02
   3_xyz:   1.163  0.010  0.080 14.700  0.004  4.134   7.8973e-02
   3_adp:   1.163  0.010  0.080 14.700  0.004  4.134   7.8973e-02
   3_occ:   1.163  0.010  0.080 14.700  0.004  4.134   7.8973e-02
   4_bss:   1.163  0.010  0.080 14.700  0.004  4.134   7.8973e-02
   4_xyz:   1.009  0.008  0.075 14.309  0.004  4.116   5.9180e-02
   4_adp:   1.009  0.008  0.075 14.309  0.004  4.116   5.9180e-02
   4_occ:   1.009  0.008  0.075 14.309  0.004  4.116   5.9180e-02
   5_bss:   1.009  0.008  0.075 14.309  0.004  4.116   5.9180e-02
   5_xyz:   1.142  0.011  0.084 14.662  0.004  4.122   7.8661e-02
   5_adp:   1.142  0.011  0.084 14.662  0.004  4.122   7.8661e-02
   5_occ:   1.142  0.011  0.084 14.662  0.004  4.122   7.8661e-02
   5_bss:   1.142  0.011  0.084 14.662  0.004  4.122   7.8661e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4386e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4386e-01
   1_xyz:   9.117  0.067  0.398 84.690  0.036  2.053   1.0182e-01
   1_adp:   9.117  0.067  0.398 84.690  0.036  2.053   1.0182e-01
   1_occ:   9.117  0.067  0.398 84.690  0.036  2.053   1.0182e-01
   2_bss:   9.117  0.067  0.398 84.690  0.036  2.053   1.0182e-01
   2_xyz:   7.063  0.050  0.274 84.607  0.039  2.314   7.9446e-02
   2_adp:   7.063  0.050  0.274 84.607  0.039  2.314   7.9446e-02
   2_occ:   7.063  0.050  0.274 84.607  0.039  2.314   7.9446e-02
   3_bss:   7.063  0.050  0.274 84.607  0.039  2.314   7.9446e-02
   3_xyz:   8.531  0.065  0.239 82.414  0.033  2.236   6.7477e-02
   3_adp:   8.531  0.065  0.239 82.414  0.033  2.236   6.7477e-02
   3_occ:   8.531  0.065  0.239 82.414  0.033  2.236   6.7477e-02
   4_bss:   8.531  0.065  0.239 82.414  0.033  2.236   6.7477e-02
   4_xyz:   7.238  0.042  0.246 81.955  0.037  2.394   3.7113e-02
   4_adp:   7.238  0.042  0.246 81.955  0.037  2.394   3.7113e-02
   4_occ:   7.238  0.042  0.246 81.955  0.037  2.394   3.7113e-02
   5_bss:   7.238  0.042  0.246 81.955  0.037  2.394   3.7113e-02
   5_xyz:   8.598  0.056  0.305 82.469  0.035  2.323   5.8514e-02
   5_adp:   8.598  0.056  0.305 82.469  0.035  2.323   5.8514e-02
   5_occ:   8.598  0.056  0.305 82.469  0.035  2.323   5.8514e-02
   5_bss:   8.598  0.056  0.305 82.469  0.035  2.323   5.8514e-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:  95.48   0.00  17.66  75.59   0.00  13.96  95.48   1.41  37.80
   1_occ:  95.48   0.00  17.66  75.59   0.00  13.96  95.48   1.41  37.80
   2_bss:  95.48   0.00  17.66  75.59   0.00  13.96  95.48   1.41  37.80
   2_xyz:  95.48   0.00  17.66  75.59   0.00  13.96  95.48   1.41  37.80
   2_adp:  96.11   0.00  17.26  76.49   0.00  13.29  96.11   3.06  38.87
   2_occ:  96.11   0.00  17.26  76.49   0.00  13.29  96.11   3.06  38.87
   3_bss:  96.11   0.00  17.26  76.49   0.00  13.29  96.11   3.06  38.87
   3_xyz:  96.11   0.00  17.26  76.49   0.00  13.29  96.11   3.06  38.87
   3_adp:  98.20   0.00  17.25  92.07   0.00  12.54  98.20   4.43  42.89
   3_occ:  98.20   0.00  17.25  92.07   0.00  12.54  98.20   4.43  42.89
   4_bss:  98.20   0.00  17.25  92.07   0.00  12.54  98.20   4.43  42.89
   4_xyz:  98.20   0.00  17.25  92.07   0.00  12.54  98.20   4.43  42.89
   4_adp:  99.04   0.00  16.86  95.49   0.00  12.18  99.04   2.15  42.38
   4_occ:  99.04   0.00  16.86  95.49   0.00  12.18  99.04   2.15  42.38
   5_bss:  99.04   0.00  16.86  95.49   0.00  12.18  99.04   2.15  42.38
   5_xyz:  99.04   0.00  16.86  95.49   0.00  12.18  99.04   2.15  42.38
   5_adp:  98.66   0.00  16.48  98.13   0.00  11.89  98.66   1.48  41.46
   5_occ:  98.66   0.00  16.48  98.13   0.00  11.89  98.66   1.48  41.46
   5_bss:  98.66   0.00  16.48  98.13   0.00  11.90  98.66   1.48  41.46
------------------------------------------------------------------------
 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:    1.612    0.022    0.356
   1_adp:    1.612    0.022    0.356
   1_occ:    1.612    0.022    0.356
   2_bss:    1.612    0.022    0.356
   2_xyz:    1.218    0.047    0.481
   2_adp:    1.218    0.047    0.481
   2_occ:    1.218    0.047    0.481
   3_bss:    1.218    0.047    0.481
   3_xyz:    1.263    0.088    0.636
   3_adp:    1.263    0.088    0.636
   3_occ:    1.263    0.088    0.636
   4_bss:    1.263    0.088    0.636
   4_xyz:    1.306    0.089    0.660
   4_adp:    1.306    0.089    0.660
   4_occ:    1.306    0.089    0.660
   5_bss:    1.306    0.089    0.660
   5_xyz:    1.289    0.083    0.685
   5_adp:    1.289    0.083    0.685
   5_occ:    1.289    0.083    0.685
   5_bss:    1.289    0.083    0.685
------------------------------------------------------------------------

CPU time actual refinement: 342.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/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_712/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_712/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.84 
  Macro-tasks:
    bulk solvent and scale       = 44.49  
    individual site refinement   = 142.80 
    weights calculation          = 30.31  
    collect and process          = 6.83   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 224.56 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 106.13 
    alpha_beta                      = 8.39   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.69 
    fmodel                         = 7.71   
    r_factors                      = 0.16   
    phase_errors                   = 10.92  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 253.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.771 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    658 calls, 105.50 s
gradients_fft:          603 calls, 102.47 s

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

# Date 2008-01-16 Time 05:29:26 PST -0800 (1200490166.15 s)
Start R-work = 0.4259, R-free = 0.4144 (no bulk solvent and anisotropic scale)
Final R-work = 0.1323, R-free = 0.1781 (no bulk solvent and anisotropic scale)

Start R-work = 0.4140, R-free = 0.4018
Final R-work = 0.1148, R-free = 0.1635