# Date 2008-01-16 Time 04:31:36 PST -0800 (1200486696.39 s)
#phil __OFF__

Command line arguments: "../349.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25586
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 349

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.97086
Completeness in resolution range: 0.925931
Completeness with d_max=infinity: 0.923139

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9941
                             d_min =   1.9709

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.97086
Completeness in resolution range: 0.925931
Completeness with d_max=infinity: 0.923139

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9945 -  4.2175 [2222/2250]  1998   224  10.1%
  bin  2:  4.2175 -  3.3600 [2126/2149]  1910   216  10.2%
  bin  3:  3.3600 -  2.9389 [2097/2122]  1892   205   9.8%
  bin  4:  2.9389 -  2.6718 [2090/2106]  1878   212  10.1%
  bin  5:  2.6718 -  2.4812 [2055/2099]  1846   209  10.2%
  bin  6:  2.4812 -  2.3355 [2072/2100]  1869   203   9.8%
  bin  7:  2.3355 -  2.2190 [2044/2080]  1845   199   9.7%
  bin  8:  2.2190 -  2.1226 [2058/2100]  1850   208  10.1%
  bin  9:  2.1226 -  2.0411 [2019/2066]  1818   201  10.0%
  bin 10:  2.0411 -  1.9709 [ 806/2084]   724    82  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 11
        2.18 -     2.86: 1144
        2.86 -     3.54: 4398
        3.54 -     4.22: 9123
        4.22 -     4.90: 13426
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.499 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.614 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.750 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.815 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28097 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_349/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 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: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4557   r_free= 0.4469   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.263261                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.7042 0.99   1443  159 0.3538 0.3734      6.5254      6.5458|
|  2:  4.7042 -  3.7531 0.99   1395  155 0.3915 0.4012      6.7806      6.8003|
|  3:  3.7531 -  3.2844 0.99   1353  149 0.4335 0.4026      6.6482      6.5935|
|  4:  3.2844 -  2.9867 0.99   1358  148 0.4424 0.4190      6.4676      6.4391|
|  5:  2.9867 -  2.7741 0.98   1323  153 0.4872 0.4437      6.3459      6.3504|
|  6:  2.7741 -  2.6114 0.99   1359  147 0.4847 0.5120      6.2553      6.1614|
|  7:  2.6114 -  2.4812 0.98   1293  155 0.4816 0.4344      6.2068      6.1219|
|  8:  2.4812 -  2.3737 0.99   1344  134 0.5121 0.4710       6.165      6.1392|
|  9:  2.3737 -  2.2826 0.99   1339  151 0.5040 0.4715      6.1026      6.1583|
| 10:  2.2826 -  2.2041 0.98   1319  146 0.5085 0.4854      6.0822      6.0727|
| 11:  2.2041 -  2.1354 0.97   1278  151 0.5244 0.5117      6.0229      6.0205|
| 12:  2.1354 -  2.0745 0.99   1327  146 0.5028 0.5317      5.9332      5.9621|
| 13:  2.0745 -  2.0200 0.88   1196  127 0.5194 0.5718      5.8635      5.8396|
| 14:  2.0200 -  1.9709 0.23    303   38 0.4857 0.4407      5.8856      5.7276|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.7042  1443   159  0.71  33.73   0.83     0.73      68272.20|
|  2:  4.7042 -  3.7531  1395   155  0.72  33.24   0.92     0.81      95253.52|
|  3:  3.7531 -  3.2844  1353   149  0.64  40.82   0.89     0.81      98941.44|
|  4:  3.2844 -  2.9867  1358   148  0.56  47.12   0.91     0.74      85542.91|
|  5:  2.9867 -  2.7741  1323   153  0.49  52.56   0.88     0.68      68858.61|
|  6:  2.7741 -  2.6114  1359   147  0.48  54.05   0.90     0.64      59083.49|
|  7:  2.6114 -  2.4812  1293   155  0.47  54.70   0.93     0.63      54465.41|
|  8:  2.4812 -  2.3737  1344   134  0.45  56.02   0.90     0.62      49255.80|
|  9:  2.3737 -  2.2826  1339   151  0.44  56.49   0.90     0.64      47057.03|
| 10:  2.2826 -  2.2041  1319   146  0.43  57.33   0.92     0.62      42977.15|
| 11:  2.2041 -  2.1354  1278   151  0.37  62.57   0.92     0.57      44812.30|
| 12:  2.1354 -  2.0745  1327   146  0.30  67.51   0.92     0.48      44371.77|
| 13:  2.0745 -  2.0200  1196   127  0.26  70.80   0.91     0.42      40352.63|
| 14:  2.0200 -  1.9709   303    38  0.33  65.28   0.99     0.43      30160.82|
|alpha:            min =        0.42 max =            0.81 mean =         0.64|
|beta:             min =    30160.82 max =        98941.44 mean =     61412.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.67|
|phase err.(test): min =        0.00 max =           90.00 mean =        52.83|
|-----------------------------------------------------------------------------|

============================== 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 = 7.804018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.799299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.850   (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 |  1.499 -  1.839:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.839 -  2.179:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.179 -  2.519:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.519 -  2.859:     1112 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.859 -  3.199:     1925 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.199 -  3.539:     2473 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.539 -  3.880:     4622 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.880 -  4.220:     4501 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.220 -  4.560:     6098 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.560 -  4.900:     7328 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.499 |       0.370 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4557   r_free= 0.4469   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.263261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4480   r_free= 0.4371   ksol= 0.30   Bsol= 29.78   scale= 0.939   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,3.73,1.31,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.256418                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.763157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.689   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.990795              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.532   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4480      final r-factor (work) = 0.3376          |
| start r-factor (free) = 0.4371      final r-factor (free) = 0.3610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3283 = 6.76 * 0.50 * 6.2550 + 1.00 * 0.1765                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8083 = 6.76 * 0.50 * 6.1195 + 1.00 * 0.1148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3376      final r-factor (work) = 0.3059          |
| start r-factor (free) = 0.3610      final r-factor (free) = 0.3710          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0690 = 0.99 * 1.00 * 6.1195 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9731 = 0.99 * 1.00 * 6.0038 + 1.00 * 0.0246                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.21   18.75    None  None   None       |
|    all(noH): 2823   0      0.00    82.21   18.75    None  None   None       |
|    Sol.    : 438    0      0.00    82.21   37.49    None  None   None       |
|    Mac.    : 2385   0      0.00    71.77   15.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.221:  691   |   5:    41.106 -  49.327:  125        |
|      1:     8.221 -  16.442:  869   |   6:    49.327 -  57.548:   77        |
|      2:    16.442 -  24.663:  513   |   7:    57.548 -  65.769:   40        |
|      3:    24.663 -  32.885:  304   |   8:    65.769 -  73.990:   12        |
|      4:    32.885 -  41.106:  189   |   9:    73.990 -  82.211:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3059 r_free = 0.3710             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3056 r_free = 0.3708             target_work(ml) = 6.010         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3056   r_free= 0.3708   ksol= 0.30   Bsol= 29.78   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,3.73,1.31,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.010488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3047   r_free= 0.3680   ksol= 0.32   Bsol= 56.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,1.61,0.30,0.00,0.00,0.00); trace/3= -0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.009287                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.003028              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.990   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3047      final r-factor (work) = 0.2293          |
| start r-factor (free) = 0.3680      final r-factor (free) = 0.2792          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1353 = 6.00 * 0.50 * 6.0038 + 1.00 * 0.1148                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8108 = 6.00 * 0.50 * 5.9043 + 1.00 * 0.0890                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2293      final r-factor (work) = 0.2125          |
| start r-factor (free) = 0.2792      final r-factor (free) = 0.2648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1113 = 0.35 * 1.00 * 5.9043 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0650 = 0.35 * 1.00 * 5.7302 + 1.00 * 0.0352                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.65   18.07    None  None   None       |
|    all(noH): 2823   0      0.00    90.65   18.07    None  None   None       |
|    Sol.    : 438    0      4.46    81.08   38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    90.65   14.40    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 -   9.065:  767   |   5:    45.325 -  54.390:  118        |
|      1:     9.065 -  18.130: 1112   |   6:    54.390 -  63.455:   47        |
|      2:    18.130 -  27.195:  380   |   7:    63.455 -  72.520:   19        |
|      3:    27.195 -  36.260:  230   |   8:    72.520 -  81.585:    5        |
|      4:    36.260 -  45.325:  144   |   9:    81.585 -  90.650:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2125 r_free = 0.2648             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2123 r_free = 0.2647             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2123   r_free= 0.2647   ksol= 0.32   Bsol= 56.45   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,1.61,0.30,0.00,0.00,0.00); trace/3= -0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.703854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2116   r_free= 0.2641   ksol= 0.32   Bsol= 63.96   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-0.20,-0.47,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.703164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.102329              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.309   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.388559              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.011   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2116      final r-factor (work) = 0.1563          |
| start r-factor (free) = 0.2641      final r-factor (free) = 0.1990          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5789 = 6.10 * 0.50 * 5.7322 + 1.00 * 0.0890                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1120 = 6.10 * 0.50 * 5.5825 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1563      final r-factor (work) = 0.1391          |
| start r-factor (free) = 0.1990      final r-factor (free) = 0.1845          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1844 = 0.39 * 1.00 * 5.5825 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0958 = 0.39 * 1.00 * 5.3683 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.87   17.80    None  None   None       |
|    all(noH): 2823   0      0.00    80.87   17.80    None  None   None       |
|    Sol.    : 438    0      5.43    80.87   41.69    None  None   None       |
|    Mac.    : 2385   0      0.00    79.32   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.087:  581   |   5:    40.435 -  48.522:   99        |
|      1:     8.087 -  16.174: 1310   |   6:    48.522 -  56.608:   90        |
|      2:    16.174 -  24.261:  380   |   7:    56.608 -  64.695:   65        |
|      3:    24.261 -  32.348:  146   |   8:    64.695 -  72.782:   36        |
|      4:    32.348 -  40.435:  105   |   9:    72.782 -  80.869:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1391 r_free = 0.1845             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1390 r_free = 0.1845             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1845   ksol= 0.32   Bsol= 63.96   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-0.20,-0.47,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1391   r_free= 0.1845   ksol= 0.33   Bsol= 67.54   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.32,-0.86,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.646477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.246  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1391      final r-factor (work) = 0.1309          |
| start r-factor (free) = 0.1845      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5015 = 1.65 * 0.50 * 5.3722 + 1.00 * 0.0789                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4197 = 1.65 * 0.50 * 5.3045 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6674 = 0.31 * 1.00 * 5.3045 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6566 = 0.31 * 1.00 * 5.2706 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    82.48   17.58    None  None   None       |
|    all(noH): 2823   0      1.17    82.48   17.58    None  None   None       |
|    Sol.    : 438    0      5.85    81.83   41.42    None  None   None       |
|    Mac.    : 2385   0      1.17    82.48   13.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.168 -   9.299:  850   |   5:    41.823 -  49.954:   99        |
|      1:     9.299 -  17.430: 1178   |   6:    49.954 -  58.085:   84        |
|      2:    17.430 -  25.561:  286   |   7:    58.085 -  66.216:   56        |
|      3:    25.561 -  33.692:  127   |   8:    66.216 -  74.347:   28        |
|      4:    33.692 -  41.823:  106   |   9:    74.347 -  82.478:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1727             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1287 r_free = 0.1727             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1727   ksol= 0.33   Bsol= 67.54   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.32,-0.86,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.263282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1728   ksol= 0.33   Bsol= 63.97   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-1.65,-0.90,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.263217                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.707508              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.766  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.812  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1878 = 2.71 * 0.50 * 5.2705 + 1.00 * 0.0529                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1452 = 2.71 * 0.50 * 5.2264 + 1.00 * 0.0699                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5464 = 0.49 * 1.00 * 5.2264 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5304 = 0.49 * 1.00 * 5.1928 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    90.24   17.40    None  None   None       |
|    all(noH): 2823   0      1.19    90.24   17.40    None  None   None       |
|    Sol.    : 438    0      5.53    88.81   41.33    None  None   None       |
|    Mac.    : 2385   0      1.19    90.24   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.186 -  10.092: 1045   |   5:    45.715 -  54.620:   90        |
|      1:    10.092 -  18.997: 1093   |   6:    54.620 -  63.526:   76        |
|      2:    18.997 -  27.903:  227   |   7:    63.526 -  72.432:   46        |
|      3:    27.903 -  36.809:  125   |   8:    72.432 -  81.337:   10        |
|      4:    36.809 -  45.715:  107   |   9:    81.337 -  90.243:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1634             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1634             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1634   ksol= 0.33   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-1.65,-0.90,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.189686                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.7042 0.99   1443  159 0.0992 0.1300      5.3973      5.5748|
|  2:  4.7042 -  3.7531 0.99   1395  155 0.0837 0.1052      5.4242      5.6149|
|  3:  3.7531 -  3.2844 0.99   1353  149 0.1101 0.1510      5.4878       5.833|
|  4:  3.2844 -  2.9867 0.99   1358  148 0.1307 0.1741      5.4842      5.6557|
|  5:  2.9867 -  2.7741 0.98   1323  153 0.1410 0.1763      5.3844      5.5432|
|  6:  2.7741 -  2.6114 0.99   1359  147 0.1350 0.2205      5.2797      5.5562|
|  7:  2.6114 -  2.4812 0.98   1293  155 0.1331 0.1742      5.2252      5.4097|
|  8:  2.4812 -  2.3737 0.99   1344  134 0.1249 0.1736      5.1444       5.313|
|  9:  2.3737 -  2.2826 0.99   1339  151 0.1234 0.1922      5.0645      5.3838|
| 10:  2.2826 -  2.2041 0.98   1319  146 0.1192 0.1759      4.9962      5.1904|
| 11:  2.2041 -  2.1354 0.97   1278  151 0.1208 0.1836       4.934      5.2742|
| 12:  2.1354 -  2.0745 0.99   1327  146 0.1153 0.1582      4.8685      5.0728|
| 13:  2.0745 -  2.0200 0.88   1196  127 0.1157 0.1898      4.7907      5.0681|
| 14:  2.0200 -  1.9709 0.23    303   38 0.1028 0.1691      4.7209      4.9448|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.7042  1443   159  0.94   9.46   0.97     0.94       7517.38|
|  2:  4.7042 -  3.7531  1395   155  0.95   8.13   1.01     0.99       9039.53|
|  3:  3.7531 -  3.2844  1353   149  0.93  11.60   1.02     1.01      10602.05|
|  4:  3.2844 -  2.9867  1358   148  0.91  14.90   1.01     0.99      10990.61|
|  5:  2.9867 -  2.7741  1323   153  0.89  17.19   0.99     0.97       9425.66|
|  6:  2.7741 -  2.6114  1359   147  0.88  17.90   0.98     0.95       8158.75|
|  7:  2.6114 -  2.4812  1293   155  0.89  16.90   0.98     0.95       7050.35|
|  8:  2.4812 -  2.3737  1344   134  0.89  17.02   0.99     0.95       6346.06|
|  9:  2.3737 -  2.2826  1339   151  0.90  16.80   0.99     0.94       5370.04|
| 10:  2.2826 -  2.2041  1319   146  0.89  16.63   0.98     0.94       4797.08|
| 11:  2.2041 -  2.1354  1278   151  0.90  16.58   0.98     0.95       4300.05|
| 12:  2.1354 -  2.0745  1327   146  0.91  15.97   0.99     0.98       3898.57|
| 13:  2.0745 -  2.0200  1196   127  0.90  16.87   0.98     0.96       3403.97|
| 14:  2.0200 -  1.9709   303    38  0.91  15.33   0.95     0.91       2873.38|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2873.38 max =        10990.61 mean =      6980.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.99|
|phase err.(test): min =        0.00 max =           89.16 mean =        14.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1631   ksol= 0.32   Bsol= 61.32   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-1.61,-0.73,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188902                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1631   ksol= 0.32   Bsol= 61.32   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-1.61,-0.73,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188902                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.7042 0.99   1443  159 0.0989 0.1288      5.3834      5.5554|
|  2:  4.7042 -  3.7531 0.99   1395  155 0.0846 0.1049      5.4242      5.6188|
|  3:  3.7531 -  3.2844 0.99   1353  149 0.1105 0.1505        5.49      5.8309|
|  4:  3.2844 -  2.9867 0.99   1358  148 0.1310 0.1750       5.486      5.6588|
|  5:  2.9867 -  2.7741 0.98   1323  153 0.1410 0.1765      5.3843      5.5436|
|  6:  2.7741 -  2.6114 0.99   1359  147 0.1349 0.2206      5.2799      5.5561|
|  7:  2.6114 -  2.4812 0.98   1293  155 0.1330 0.1744       5.226      5.4104|
|  8:  2.4812 -  2.3737 0.99   1344  134 0.1247 0.1737      5.1444      5.3143|
|  9:  2.3737 -  2.2826 0.99   1339  151 0.1232 0.1924      5.0644      5.3843|
| 10:  2.2826 -  2.2041 0.98   1319  146 0.1190 0.1759       4.996      5.1908|
| 11:  2.2041 -  2.1354 0.97   1278  151 0.1207 0.1832      4.9337       5.273|
| 12:  2.1354 -  2.0745 0.99   1327  146 0.1153 0.1584      4.8683      5.0732|
| 13:  2.0745 -  2.0200 0.88   1196  127 0.1157 0.1897      4.7909      5.0666|
| 14:  2.0200 -  1.9709 0.23    303   38 0.1027 0.1693      4.7227      4.9466|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.7042  1443   159  0.94   9.26   0.97     0.94       7121.96|
|  2:  4.7042 -  3.7531  1395   155  0.95   8.07   1.01     0.99       8881.35|
|  3:  3.7531 -  3.2844  1353   149  0.93  11.61   1.02     1.02      10628.15|
|  4:  3.2844 -  2.9867  1358   148  0.91  14.91   1.01     0.99      11022.62|
|  5:  2.9867 -  2.7741  1323   153  0.89  17.21   1.00     0.97       9433.43|
|  6:  2.7741 -  2.6114  1359   147  0.88  17.90   0.98     0.96       8163.12|
|  7:  2.6114 -  2.4812  1293   155  0.89  16.92   0.99     0.95       7071.71|
|  8:  2.4812 -  2.3737  1344   134  0.89  17.03   1.00     0.96       6353.81|
|  9:  2.3737 -  2.2826  1339   151  0.90  16.82   0.99     0.94       5380.00|
| 10:  2.2826 -  2.2041  1319   146  0.89  16.64   0.99     0.95       4797.88|
| 11:  2.2041 -  2.1354  1278   151  0.90  16.58   0.98     0.95       4297.80|
| 12:  2.1354 -  2.0745  1327   146  0.91  15.97   1.00     0.99       3898.39|
| 13:  2.0745 -  2.0200  1196   127  0.90  16.87   0.98     0.97       3401.90|
| 14:  2.0200 -  1.9709   303    38  0.91  15.36   0.96     0.91       2875.68|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     2875.68 max =        11022.62 mean =      6943.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.98|
|phase err.(test): min =        0.00 max =           89.47 mean =        14.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    90.20   17.36    None  None   None       |
|    all(noH): 2823   0      1.14    90.20   17.36    None  None   None       |
|    Sol.    : 438    0      5.49    88.77   41.29    None  None   None       |
|    Mac.    : 2385   0      1.14    90.20   12.96    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:     1.145 -  10.050: 1045   |   5:    45.673 -  54.579:   90        |
|      1:    10.050 -  18.956: 1093   |   6:    54.579 -  63.484:   76        |
|      2:    18.956 -  27.862:  227   |   7:    63.484 -  72.390:   46        |
|      3:    27.862 -  36.767:  125   |   8:    72.390 -  81.296:   10        |
|      4:    36.767 -  45.673:  107   |   9:    81.296 -  90.201:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.705 - 5.395
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 304
   mapped sites are within: 0.705 - 5.395

peak=   12.113 closest distance to " O  BHOH Z  74 " =    1.487
peak=    5.908 closest distance to " O   HOH Z 210 " =    1.279
peak=    5.514 closest distance to " O   HOH Z 113 " =    2.048
peak=    5.278 closest distance to " O   HOH Z  49 " =    1.402
peak=    4.958 closest distance to " O   HOH Z 403 " =    1.914
peak=    4.883 closest distance to " CG  PRO A  54 " =    1.305
peak=    4.773 closest distance to " O   HOH Z 248 " =    1.474
peak=    4.768 closest distance to " CB  SER A  63 " =    1.080
peak=    4.739 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.648 closest distance to " CA  TYR A  30 " =    0.917
peak=    4.629 closest distance to " O   HOH Z  43 " =    2.469
peak=    4.616 closest distance to " CB  ARG A 190 " =    1.770
peak=    4.578 closest distance to " O   HOH Z  40 " =    1.924
peak=    4.536 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.534 closest distance to " CD2 TRP A 179 " =    1.343
peak=    4.532 closest distance to " CB  GLN A 223 " =    1.382
peak=    4.505 closest distance to " CG  PRO A  90 " =    1.212
peak=    4.459 closest distance to " O   HOH Z 369 " =    2.241
peak=    4.352 closest distance to " O   HOH Z 423 " =    1.886
peak=    4.351 closest distance to " O   HOH Z 209 " =    2.307
peak=    4.336 closest distance to " O   HOH Z 232 " =    2.294
peak=    4.311 closest distance to " O   HOH Z 402 " =    1.550
peak=    4.305 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.281 closest distance to " CG  PRO A 280 " =    0.732
peak=    4.280 closest distance to " O   HOH Z  63 " =    1.954
peak=    4.257 closest distance to " CB  GLU A 277 " =    3.710
peak=    4.233 closest distance to " CG  PRO A 213 " =    1.244
peak=    4.204 closest distance to " O   HOH Z 130 " =    2.727
peak=    4.175 closest distance to " O   HOH Z 234 " =    3.677
peak=    4.172 closest distance to " O   HOH Z  44 " =    2.148
peak=    4.168 closest distance to " O   SER A  87 " =    2.246
peak=    4.155 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.147 closest distance to " CB  SER A 141 " =    1.074
peak=    4.145 closest distance to " CA  ALA A  51 " =    0.940
peak=    4.140 closest distance to " O   HOH Z 346 " =    1.602
peak=    4.134 closest distance to " O   HOH Z  65 " =    1.005
peak=    4.133 closest distance to " CD  LYS A 166 " =    1.456
peak=    4.133 closest distance to " O   HOH Z 368 " =    2.039
peak=    4.132 closest distance to " O   HOH Z 406 " =    1.560
peak=    4.126 closest distance to " O   HOH Z 214 " =    1.383
peak=    4.100 closest distance to " O   PRO A 198 " =    1.495
peak=    4.064 closest distance to " CB  ARG A  79 " =    1.596
peak=    4.033 closest distance to " CG1 ILE A  33 " =    1.198
peak=    4.012 closest distance to " O   HOH Z 298 " =    1.777
peak=    4.009 closest distance to " O   HOH Z  59 " =    2.299
peak=    4.005 closest distance to " CA  ARG A  36 " =    1.078
peak=    3.995 closest distance to " O   HOH Z 362 " =    3.536
peak=    3.944 closest distance to " O   HOH Z 389 " =    1.923
peak=    3.937 closest distance to " O   HOH Z 189 " =    2.837
peak=    3.933 closest distance to " CD  ARG A 269 " =    1.006
peak=    3.932 closest distance to " O   HOH Z 365 " =    2.619
peak=    3.921 closest distance to " CB  SER A  26 " =    1.772
peak=    3.917 closest distance to " O   HOH Z 134 " =    1.577
peak=    3.910 closest distance to " O   HOH Z 265 " =    1.946
peak=    3.910 closest distance to " O   HOH Z 412 " =    3.599
peak=    3.907 closest distance to " O   HOH Z 433 " =    1.541
peak=    3.895 closest distance to " O   HOH Z 261 " =    2.235
peak=    3.887 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.881 closest distance to " CB  TYR A 169 " =    0.792
peak=    3.879 closest distance to " O   HOH Z 117 " =    2.011
peak=    3.869 closest distance to " O   HOH Z 102 " =    1.423
peak=    3.868 closest distance to " CG  PRO A 243 " =    1.095
peak=    3.868 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.866 closest distance to " CB  ASN A 285 " =    0.956
peak=    3.861 closest distance to " CZ  PHE A 218 " =    1.118
peak=    3.856 closest distance to " CG1BVAL A  72 " =    1.913
peak=    3.856 closest distance to " O   HOH Z 345 " =    1.732
peak=    3.853 closest distance to " N   ASN A  39 " =    1.252
peak=    3.849 closest distance to " O   HOH Z 124 " =    1.154
peak=    3.846 closest distance to " O   HOH Z 414 " =    1.646
peak=    3.843 closest distance to " CB  TRP A 179 " =    1.306
peak=    3.822 closest distance to " O   HOH Z 380 " =    1.882
peak=    3.817 closest distance to " NH2BARG A 145 " =    2.060
peak=    3.801 closest distance to " CD  PRO A  54 " =    0.899
peak=    3.800 closest distance to " O   HOH Z 394 " =    1.577
peak=    3.799 closest distance to " O   HOH Z 128 " =    1.560
peak=    3.793 closest distance to " O   HOH Z 251 " =    1.642
peak=    3.789 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.781 closest distance to " O   HOH Z 142 " =    1.518
peak=    3.774 closest distance to " O   HOH Z 126 " =    1.926
peak=    3.771 closest distance to " CG2BVAL A  41 " =    0.889
peak=    3.770 closest distance to " CG  PRO A 198 " =    1.286
peak=    3.766 closest distance to " N   CYS A 260 " =    0.878
peak=    3.762 closest distance to " O   HOH Z 132 " =    2.703
peak=    3.762 closest distance to " O   ALA A 165 " =    1.362
peak=    3.761 closest distance to " CZ3 TRP A 266 " =    1.068
peak=    3.758 closest distance to " CZ  PHE A  38 " =    1.242
peak=    3.752 closest distance to " CG  GLN A  11 " =    1.336
peak=    3.744 closest distance to " O   HOH Z 422 " =    2.733
peak=    3.742 closest distance to " O   HOH Z 203 " =    1.815
peak=    3.738 closest distance to " O   HOH Z  80 " =    1.858
peak=    3.735 closest distance to " OE1 GLN A  55 " =    1.607
peak=    3.735 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.732 closest distance to " O   HOH Z 285 " =    2.763
peak=    3.726 closest distance to " NE2 GLN A  11 " =    1.165
peak=    3.717 closest distance to " OH  TYR A 116 " =    1.176
peak=    3.701 closest distance to " CD  LYS A  76 " =    1.891
peak=    3.700 closest distance to " O   ASP A 124 " =    1.788
peak=    3.699 closest distance to " CA  ALA A 295 " =    1.038
peak=    3.693 closest distance to " O   HOH Z 291 " =    1.455
peak=    3.688 closest distance to " O   HOH Z 146 " =    2.196
peak=    3.688 closest distance to " NH2 ARG A 156 " =    1.201
peak=    3.686 closest distance to " O   HOH Z  15 " =    2.158
peak=    3.683 closest distance to " O   HOH Z 132 " =    2.676
peak=    3.683 closest distance to " O   HOH Z 193 " =    1.635
peak=    3.680 closest distance to " O   HOH Z 214 " =    3.059
peak=    3.673 closest distance to " O   HOH Z 250 " =    1.408
peak=    3.668 closest distance to " O   HOH Z 336 " =    1.898
peak=    3.659 closest distance to " CB  ASN A 148 " =    1.446
peak=    3.641 closest distance to " CB  VAL A 202 " =    1.447
peak=    3.627 closest distance to " O   HOH Z 258 " =    2.165
peak=    3.625 closest distance to " O   HOH Z 280 " =    3.012
peak=    3.624 closest distance to " O   HOH Z 227 " =    1.664
peak=    3.622 closest distance to " O   HOH Z 128 " =    2.249
peak=    3.613 closest distance to " NZ  LYS A 117 " =    2.975
peak=    3.611 closest distance to " O   HOH Z 316 " =    3.015
peak=    3.610 closest distance to " CB  SER A  62 " =    0.871
peak=    3.604 closest distance to " O   HOH Z 421 " =    2.038
peak=    3.600 closest distance to " O   HOH Z 417 " =    2.801
peak=    3.597 closest distance to " O   HOH Z  68 " =    1.850
peak=    3.584 closest distance to " O   HOH Z 154 " =    1.503
peak=    3.583 closest distance to " O   HOH Z 404 " =    1.562
peak=    3.577 closest distance to " CB  GLU A 128 " =    1.131
peak=    3.574 closest distance to " CD1 LEU A  96 " =    0.768
peak=    3.570 closest distance to " O   HOH Z  61 " =    1.562
peak=    3.560 closest distance to " CG2 ILE A  20 " =    1.401
peak=    3.556 closest distance to " NH1AARG A 145 " =    1.355
peak=    3.556 closest distance to " O   HOH Z 189 " =    2.486
peak=    3.555 closest distance to " O   HOH Z 425 " =    1.353
peak=    3.552 closest distance to " O   HOH Z 427 " =    2.868
peak=    3.545 closest distance to " CA  ALA A 160 " =    0.894
peak=    3.543 closest distance to " CB  THR A  52 " =    0.792
peak=    3.541 closest distance to " CA  ASN A 176 " =    1.599
peak=    3.538 closest distance to " O   HOH Z 185 " =    1.780
peak=    3.532 closest distance to " CG2 VAL A 197 " =    1.144
peak=    3.531 closest distance to " CG2 ILE A 120 " =    1.206
peak=    3.527 closest distance to " OG BSER A 164 " =    2.238
peak=    3.527 closest distance to " CG1 ILE A  20 " =    1.254
peak=    3.520 closest distance to " CB  SER A   3 " =    1.330
peak=    3.517 closest distance to " O   HOH Z 128 " =    1.967
peak=    3.516 closest distance to " OE1 GLN A  11 " =    2.016
peak=    3.509 closest distance to " O   HOH Z 117 " =    1.100
peak=    3.509 closest distance to " O   HOH Z  20 " =    1.387
peak=    3.508 closest distance to " CG  GLU A  37 " =    0.954
peak=    3.507 closest distance to " CB  ARG A  79 " =    0.954
peak=    3.501 closest distance to " O   HOH Z  78 " =    1.679
peak=    3.500 closest distance to " O   HOH Z 246 " =    1.398
peak=    3.498 closest distance to " O   HOH Z 359 " =    1.625
peak=    3.498 closest distance to " CD2 LEU A 297 " =    0.973
peak=    3.496 closest distance to " CB  ASN A 142 " =    1.173
peak=    3.486 closest distance to " O   HOH Z  21 " =    1.815
peak=    3.485 closest distance to " CA  TYR A 116 " =    1.329
peak=    3.483 closest distance to " O   HOH Z 427 " =    3.129
peak=    3.483 closest distance to " O   HOH Z 193 " =    1.914
peak=    3.461 closest distance to " CA  VAL A 125 " =    1.234
peak=    3.459 closest distance to " CD  ARG A 159 " =    0.832
peak=    3.458 closest distance to " CA  ALA A 100 " =    1.017
peak=    3.450 closest distance to " O   HOH Z 163 " =    1.492
peak=    3.447 closest distance to " CB  ASP A 124 " =    0.705
peak=    3.440 closest distance to " O   HOH Z  39 " =    1.186
peak=    3.434 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.430 closest distance to " O   HOH Z 287 " =    1.838
peak=    3.428 closest distance to " CB  LEU A  83 " =    0.805
peak=    3.426 closest distance to " O   HOH Z 299 " =    4.325
peak=    3.424 closest distance to " NE2 GLN A  77 " =    3.210
peak=    3.422 closest distance to " O   HOH Z 393 " =    3.249
peak=    3.420 closest distance to " CA  ILE A 106 " =    0.822
peak=    3.418 closest distance to " CA  ASP A 162 " =    1.140
peak=    3.416 closest distance to " O   HOH Z 245 " =    1.338
peak=    3.413 closest distance to " CA  SER A  87 " =    1.083
peak=    3.410 closest distance to " CB  GLU A  46 " =    1.048
peak=    3.410 closest distance to " O   HOH Z 126 " =    1.574
peak=    3.400 closest distance to " O   HOH Z 357 " =    2.131
peak=    3.392 closest distance to " O   HOH Z 272 " =    1.877
peak=    3.391 closest distance to " CB  ALA A 248 " =    1.351
peak=    3.390 closest distance to " CG  MET A 185 " =    1.068
peak=    3.389 closest distance to " CG2AVAL A 121 " =    2.156
peak=    3.388 closest distance to " O   HOH Z 271 " =    2.638
peak=    3.385 closest distance to " O   HOH Z  85 " =    1.652
peak=    3.383 closest distance to " CB  THR A  31 " =    1.533
peak=    3.382 closest distance to " O   HOH Z 279 " =    2.116
peak=    3.381 closest distance to " O   HOH Z 353 " =    2.785
peak=    3.381 closest distance to " OE1 GLN A 223 " =    2.247
peak=    3.375 closest distance to " O   HOH Z  48 " =    1.721
peak=    3.373 closest distance to " CD  ARG A 195 " =    0.971
peak=    3.372 closest distance to " ND2 ASN A 249 " =    0.923
peak=    3.370 closest distance to " O   HOH Z 298 " =    4.226
peak=    3.368 closest distance to " CG AARG A 275 " =    1.231
peak=    3.366 closest distance to " N   HIS A 108 " =    1.830
peak=    3.365 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.364 closest distance to " O   HOH Z 313 " =    1.931
peak=    3.363 closest distance to " CB  PHE A  16 " =    1.088
peak=    3.357 closest distance to " CE  LYS A 119 " =    1.163
peak=    3.353 closest distance to " O   HOH Z 124 " =    2.092
peak=    3.353 closest distance to " O   HOH Z 193 " =    1.756
peak=    3.352 closest distance to " O   TYR A 116 " =    1.459
peak=    3.332 closest distance to " CB  ALA A 100 " =    1.305
peak=    3.330 closest distance to " O   HOH Z 383 " =    2.085
peak=    3.326 closest distance to " NZ  LYS A  48 " =    1.226
peak=    3.325 closest distance to " O   HOH Z 303 " =    2.344
peak=    3.321 closest distance to " CB  GLN A  88 " =    1.086
peak=    3.315 closest distance to " CG  GLN A  58 " =    1.000
peak=    3.311 closest distance to " O   HOH Z 298 " =    2.287
peak=    3.308 closest distance to " CB  ALA A 291 " =    1.261
peak=    3.305 closest distance to " O   HOH Z 158 " =    2.956
peak=    3.301 closest distance to " CA  SER A  32 " =    1.637
peak=    3.299 closest distance to " O   HOH Z 200 " =    2.945
peak=    3.298 closest distance to " O   HOH Z 130 " =    2.573
peak=    3.293 closest distance to " O   ALA A 158 " =    1.123
peak=    3.288 closest distance to " OG BSER A 134 " =    2.872
peak=    3.286 closest distance to " CA  ALA A 158 " =    1.296
peak=    3.285 closest distance to " CD  LYS A 119 " =    1.927
peak=    3.278 closest distance to " O   HOH Z 371 " =    3.058
peak=    3.274 closest distance to " O   HOH Z 327 " =    1.668
peak=    3.274 closest distance to " O   HOH Z 219 " =    1.937
peak=    3.271 closest distance to " O   HOH Z 213 " =    1.709
peak=    3.267 closest distance to " O   HOH Z  83 " =    1.592
peak=    3.265 closest distance to " OG BSER A 212 " =    2.658
peak=    3.264 closest distance to " CG  ARG A 138 " =    1.225
peak=    3.261 closest distance to " O   HOH Z 213 " =    2.273
peak=    3.259 closest distance to " O   HOH Z 199 " =    1.653
peak=    3.259 closest distance to " CD2 TYR A 186 " =    1.004
peak=    3.257 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.253 closest distance to " CB  PHE A 204 " =    0.727
peak=    3.251 closest distance to " O   THR A 220 " =    1.089
peak=    3.246 closest distance to " CB  PRO A  90 " =    1.132
peak=    3.244 closest distance to " OG  SER A 245 " =    1.548
peak=    3.243 closest distance to " O   HOH Z  63 " =    2.048
peak=    3.241 closest distance to " O   HOH Z 325 " =    2.082
peak=    3.237 closest distance to " O   LEU A 228 " =    1.841
peak=    3.236 closest distance to " CG2 THR A  29 " =    1.273
peak=    3.233 closest distance to " O   HOH Z 173 " =    2.206
peak=    3.232 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.230 closest distance to " O   HOH Z 409 " =    3.368
peak=    3.229 closest distance to " CG1 ILE A  49 " =    1.593
peak=    3.229 closest distance to " CG2 THR A 220 " =    0.752
peak=    3.217 closest distance to " CG2 ILE A 234 " =    1.141
peak=    3.217 closest distance to " O   HOH Z 358 " =    2.108
peak=    3.215 closest distance to " CZ3 TRP A  85 " =    0.929
peak=    3.213 closest distance to " CG2 THR A 221 " =    1.186
peak=    3.211 closest distance to " O   HOH Z 435 " =    2.964
peak=    3.208 closest distance to " CB  PRO A 198 " =    1.030
peak=    3.207 closest distance to " NH2AARG A 275 " =    3.552
peak=    3.206 closest distance to " CB  LEU A 228 " =    1.090
peak=    3.205 closest distance to " N   TYR A 247 " =    1.318
peak=    3.204 closest distance to " O   HOH Z  35 " =    2.211
peak=    3.199 closest distance to " CD  ARG A  66 " =    2.728
peak=    3.198 closest distance to " CA  GLU A 152 " =    0.850
peak=    3.195 closest distance to " CA  ALA A  21 " =    1.327
peak=    3.188 closest distance to " CD1 ILE A 199 " =    1.143
peak=    3.187 closest distance to " O   HOH Z 394 " =    3.777
peak=    3.186 closest distance to " O   HOH Z 130 " =    2.266
peak=    3.185 closest distance to " CB  ALA A   9 " =    1.632
peak=    3.182 closest distance to " O  BHOH Z 338 " =    2.165
peak=    3.182 closest distance to " CA  GLU A  46 " =    0.884
peak=    3.182 closest distance to " CA  LYS A 117 " =    1.271
peak=    3.181 closest distance to " O   HOH Z 109 " =    1.624
peak=    3.179 closest distance to " O   HOH Z 299 " =    4.169
peak=    3.178 closest distance to " O   HOH Z 139 " =    4.732
peak=    3.177 closest distance to " O   HOH Z  80 " =    1.956
peak=    3.174 closest distance to " N   ASP A 162 " =    1.218
peak=    3.172 closest distance to " CG1 VAL A 153 " =    1.059
peak=    3.171 closest distance to " CA  ALA A 227 " =    1.334
peak=    3.163 closest distance to " O   HOH Z   9 " =    2.317
peak=    3.160 closest distance to " O   HOH Z 420 " =    5.395
peak=    3.158 closest distance to " N   TYR A 116 " =    1.628
peak=    3.157 closest distance to " O   HOH Z 426 " =    1.359
peak=    3.146 closest distance to " O   HOH Z 366 " =    2.543
peak=    3.142 closest distance to " CA  MET A 105 " =    1.059
peak=    3.142 closest distance to " O   HOH Z 358 " =    1.277
peak=    3.141 closest distance to " CB  LEU A   5 " =    1.151
peak=    3.140 closest distance to " CB  MET A 105 " =    1.067
peak=    3.140 closest distance to " CB  PRO A 243 " =    1.316
peak=    3.136 closest distance to " O   GLY A  91 " =    1.282
peak=    3.134 closest distance to " CE1 HIS A  81 " =    1.589
peak=    3.133 closest distance to " CD  ARG A 139 " =    1.268
peak=    3.132 closest distance to " CA  GLY A 241 " =    0.942
peak=    3.132 closest distance to " O   ASN A 284 " =    1.734
peak=    3.127 closest distance to " O   HOH Z 240 " =    2.310
peak=    3.120 closest distance to " CD1 LEU A 300 " =    1.055
peak=    3.117 closest distance to " CA  ALA A  84 " =    1.155
peak=    3.116 closest distance to " CD  GLN A 194 " =    1.578
peak=    3.116 closest distance to " OE1 GLU A   2 " =    1.799
peak=    3.111 closest distance to " O   HOH Z 240 " =    2.938
peak=    3.108 closest distance to " O   HOH Z  88 " =    3.269
peak=    3.105 closest distance to " CD1 LEU A 228 " =    1.614
peak=    3.103 closest distance to " O   ASP A 200 " =    1.643
peak=    3.096 closest distance to " OD2 ASP A 298 " =    3.704
peak=    3.086 closest distance to " CB  ASN A 148 " =    2.003
peak=    3.082 closest distance to " OD1 ASN A  69 " =    2.343
peak=    3.080 closest distance to " CB  MET A  47 " =    1.052
peak=    3.077 closest distance to " O   HOH Z  19 " =    1.505
peak=    3.076 closest distance to " CB  GLN A 103 " =    0.854
peak=    3.075 closest distance to " O   HOH Z 435 " =    1.714
peak=    3.072 closest distance to " CB  PHE A 204 " =    0.756
peak=    3.066 closest distance to " O   HOH Z 305 " =    3.613
peak=    3.063 closest distance to " O   HOH Z 361 " =    3.822
peak=    3.061 closest distance to " O   HOH Z  85 " =    1.563
peak=    3.055 closest distance to " CA  ASP A 191 " =    1.007
peak=    3.052 closest distance to " CD  PRO A 213 " =    1.393
peak=    3.039 closest distance to " OG  SER A  62 " =    2.796
peak=    3.037 closest distance to " CB  LYS A 289 " =    1.092

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.776 - 5.574
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 222
   mapped sites are within: 0.776 - 5.574

peak=   -4.560 closest distance to " O   HOH Z 266 " =    5.351
peak=   -4.523 closest distance to " CD  GLN A  58 " =    0.979
peak=   -4.459 closest distance to " SG  CYS A 254 " =    3.450
peak=   -4.390 closest distance to " O   VAL A  67 " =    2.888
peak=   -4.319 closest distance to " CD2 LEU A 237 " =    2.621
peak=   -4.271 closest distance to " CG2 ILE A  49 " =    2.766
peak=   -4.253 closest distance to " O   HOH Z 422 " =    1.248
peak=   -4.238 closest distance to " CD  GLN A 223 " =    1.329
peak=   -4.229 closest distance to " CA  VAL A  67 " =    3.016
peak=   -4.190 closest distance to " O   HOH Z 377 " =    2.078
peak=   -4.168 closest distance to " CD  ARG A 156 " =    2.053
peak=   -4.125 closest distance to " O   HOH Z 166 " =    1.575
peak=   -4.088 closest distance to " O   PRO A 198 " =    1.364
peak=   -4.066 closest distance to " CD1 PHE A  59 " =    2.073
peak=   -4.053 closest distance to " CD1 LEU A 101 " =    2.378
peak=   -4.013 closest distance to " CB  PRO A 243 " =    2.731
peak=   -4.011 closest distance to " C   HIS A 108 " =    1.072
peak=   -3.970 closest distance to " OXT GLY A 302 " =    2.941
peak=   -3.921 closest distance to " O   ALA A  34 " =    2.342
peak=   -3.918 closest distance to " CE2 TYR A  30 " =    2.795
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    1.971
peak=   -3.889 closest distance to " NE2 GLN A 223 " =    1.126
peak=   -3.865 closest distance to " O   HOH Z 290 " =    1.055
peak=   -3.850 closest distance to " O   HOH Z 150 " =    1.067
peak=   -3.842 closest distance to " C   THR A 279 " =    1.110
peak=   -3.829 closest distance to " CD2 TYR A 293 " =    1.920
peak=   -3.826 closest distance to " CD1 LEU A  25 " =    2.516
peak=   -3.801 closest distance to " CH2 TRP A 179 " =    1.263
peak=   -3.788 closest distance to " O   HOH Z   5 " =    1.656
peak=   -3.782 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.780 closest distance to " O   HOH Z 210 " =    0.806
peak=   -3.774 closest distance to " O   HOH Z 165 " =    1.890
peak=   -3.746 closest distance to " CE2 PHE A  61 " =    2.681
peak=   -3.745 closest distance to " OG  SER A  97 " =    2.241
peak=   -3.731 closest distance to " CE3 TRP A 150 " =    2.317
peak=   -3.713 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.711 closest distance to " OD1 ASP A 171 " =    1.578
peak=   -3.697 closest distance to " CB  TRP A  85 " =    2.503
peak=   -3.683 closest distance to " CG  GLN A  11 " =    1.473
peak=   -3.682 closest distance to " CG  GLU A  53 " =    1.514
peak=   -3.676 closest distance to " CZ  TYR A 169 " =    1.843
peak=   -3.674 closest distance to " O   HOH Z 366 " =    1.576
peak=   -3.672 closest distance to " O   HOH Z 196 " =    2.009
peak=   -3.671 closest distance to " O   HOH Z 394 " =    1.627
peak=   -3.668 closest distance to " CA  GLY A 241 " =    2.382
peak=   -3.650 closest distance to " CB  ALA A 161 " =    2.590
peak=   -3.647 closest distance to " O   SER A 210 " =    1.856
peak=   -3.637 closest distance to " CG  ASP A 132 " =    2.307
peak=   -3.631 closest distance to " CA  GLY A 241 " =    3.203
peak=   -3.624 closest distance to " CD1 ILE A 106 " =    2.193
peak=   -3.620 closest distance to " O   HOH Z 374 " =    2.012
peak=   -3.607 closest distance to " O   HOH Z  13 " =    1.731
peak=   -3.583 closest distance to " O   PRO A 163 " =    2.060
peak=   -3.578 closest distance to " OG BSER A 134 " =    1.321
peak=   -3.573 closest distance to " O   TRP A  92 " =    1.966
peak=   -3.569 closest distance to " O   HOH Z 154 " =    1.600
peak=   -3.563 closest distance to " O   PHE A 218 " =    1.502
peak=   -3.552 closest distance to " O   HOH Z 185 " =    2.521
peak=   -3.542 closest distance to " O   HOH Z 193 " =    1.420
peak=   -3.540 closest distance to " OD1 ASN A 148 " =    1.449
peak=   -3.537 closest distance to " CG  GLN A 103 " =    2.470
peak=   -3.536 closest distance to " O   HOH Z 157 " =    3.553
peak=   -3.535 closest distance to " CB  ALA A 184 " =    2.337
peak=   -3.534 closest distance to " CD1 ILE A 151 " =    2.433
peak=   -3.520 closest distance to " ND2BASN A 224 " =    1.821
peak=   -3.519 closest distance to " NE2 GLN A  88 " =    1.011
peak=   -3.511 closest distance to " CD2 PHE A  61 " =    2.133
peak=   -3.510 closest distance to " CD1 ILE A 109 " =    2.901
peak=   -3.505 closest distance to " CB  ALA A  43 " =    2.500
peak=   -3.500 closest distance to " O   HOH Z  56 " =    1.102
peak=   -3.496 closest distance to " NH2 ARG A  66 " =    1.079
peak=   -3.493 closest distance to " O   ALA A  10 " =    1.900
peak=   -3.491 closest distance to " O   HOH Z 392 " =    1.429
peak=   -3.487 closest distance to " CH2 TRP A 150 " =    1.151
peak=   -3.485 closest distance to " CE BMET A  47 " =    1.751
peak=   -3.478 closest distance to " CG  PHE A 283 " =    2.578
peak=   -3.477 closest distance to " CG1 VAL A 112 " =    2.624
peak=   -3.474 closest distance to " O   HOH Z 418 " =    1.199
peak=   -3.471 closest distance to " O   HOH Z 114 " =    3.505
peak=   -3.470 closest distance to " CG  PRO A 243 " =    1.668
peak=   -3.470 closest distance to " O   HOH Z 150 " =    1.896
peak=   -3.468 closest distance to " CB  ALA A 248 " =    2.240
peak=   -3.465 closest distance to " O   HOH Z 198 " =    1.455
peak=   -3.464 closest distance to " O   HOH Z 351 " =    1.553
peak=   -3.462 closest distance to " CB  PHE A 192 " =    2.113
peak=   -3.460 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.453 closest distance to " O   HOH Z 215 " =    4.088
peak=   -3.441 closest distance to " O   HOH Z   6 " =    1.749
peak=   -3.431 closest distance to " CB  SER A 210 " =    1.172
peak=   -3.430 closest distance to " O   HOH Z  15 " =    1.537
peak=   -3.426 closest distance to " CD  PRO A 243 " =    2.065
peak=   -3.420 closest distance to " N   SER A 276 " =    1.522
peak=   -3.412 closest distance to " O   HOH Z 423 " =    2.353
peak=   -3.409 closest distance to " O   SER A 276 " =    1.697
peak=   -3.409 closest distance to " O   GLY A  80 " =    2.562
peak=   -3.406 closest distance to " CG1AVAL A  41 " =    2.643
peak=   -3.405 closest distance to " CB  ALA A 291 " =    2.420
peak=   -3.397 closest distance to " O   HOH Z 252 " =    3.832
peak=   -3.392 closest distance to " O   HOH Z  65 " =    0.776
peak=   -3.391 closest distance to " OD1 ASP A 191 " =    1.554
peak=   -3.387 closest distance to " O   VAL A 174 " =    2.088
peak=   -3.383 closest distance to " CG1 VAL A 265 " =    2.510
peak=   -3.383 closest distance to " O   ALA A  34 " =    2.100
peak=   -3.382 closest distance to " CG  MET A 105 " =    0.979
peak=   -3.382 closest distance to " ND2 ASN A 249 " =    2.253
peak=   -3.381 closest distance to " CG  LEU A  83 " =    2.093
peak=   -3.379 closest distance to " O   HOH Z 364 " =    5.456
peak=   -3.379 closest distance to " CA  SER A  62 " =    2.699
peak=   -3.367 closest distance to " CD  ARG A 195 " =    5.197
peak=   -3.366 closest distance to " CD  LYS A 289 " =    2.348
peak=   -3.361 closest distance to " C   ASN A 285 " =    2.239
peak=   -3.358 closest distance to " O   HOH Z 264 " =    1.706
peak=   -3.353 closest distance to " NH2 ARG A  56 " =    2.109
peak=   -3.353 closest distance to " O   HOH Z 283 " =    2.282
peak=   -3.350 closest distance to " CA  GLY A 241 " =    2.902
peak=   -3.346 closest distance to " C   SER A 206 " =    1.507
peak=   -3.343 closest distance to " O   HOH Z 234 " =    4.113
peak=   -3.342 closest distance to " O   HOH Z  37 " =    1.896
peak=   -3.336 closest distance to " CB  PRO A 163 " =    2.572
peak=   -3.334 closest distance to " O   SER A 271 " =    2.042
peak=   -3.334 closest distance to " NE2 GLN A 103 " =    1.720
peak=   -3.332 closest distance to " CG1 VAL A  78 " =    2.602
peak=   -3.329 closest distance to " O   HOH Z 285 " =    1.220
peak=   -3.329 closest distance to " OE1 GLN A 223 " =    2.308
peak=   -3.327 closest distance to " OD1 ASN A 301 " =    1.990
peak=   -3.326 closest distance to " O   HOH Z 123 " =    2.426
peak=   -3.319 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.314 closest distance to " O   HOH Z 200 " =    1.251
peak=   -3.313 closest distance to " OD2 ASP A 171 " =    2.403
peak=   -3.311 closest distance to " CB  ALA A  10 " =    2.239
peak=   -3.304 closest distance to " CB  PRO A 213 " =    1.826
peak=   -3.302 closest distance to " ND2 ASN A  69 " =    1.756
peak=   -3.302 closest distance to " OH  TYR A 172 " =    1.876
peak=   -3.301 closest distance to " CD  GLN A  73 " =    0.887
peak=   -3.299 closest distance to " CD2 LEU A 300 " =    2.683
peak=   -3.299 closest distance to " N   ALA A  43 " =    2.783
peak=   -3.297 closest distance to " O   HOH Z 166 " =    1.628
peak=   -3.291 closest distance to " NE2 GLN A  88 " =    1.821
peak=   -3.290 closest distance to " O   HOH Z 149 " =    2.069
peak=   -3.288 closest distance to " O   HOH Z 126 " =    1.807
peak=   -3.285 closest distance to " O   HOH Z 145 " =    2.814
peak=   -3.283 closest distance to " CA  GLY A 133 " =    2.235
peak=   -3.279 closest distance to " O   HOH Z 105 " =    2.224
peak=   -3.279 closest distance to " O   HOH Z  71 " =    2.362
peak=   -3.277 closest distance to " O   HOH Z  52 " =    1.665
peak=   -3.277 closest distance to " NH2 ARG A  79 " =    1.665
peak=   -3.273 closest distance to " O   HOH Z 252 " =    3.734
peak=   -3.269 closest distance to " O   HOH Z 435 " =    2.305
peak=   -3.264 closest distance to " OG BSER A 210 " =    1.353
peak=   -3.259 closest distance to " CZ  PHE A  38 " =    2.294
peak=   -3.259 closest distance to " O   HOH Z 106 " =    1.987
peak=   -3.258 closest distance to " CD  ARG A 139 " =    1.533
peak=   -3.254 closest distance to " N   THR A  52 " =    1.742
peak=   -3.254 closest distance to " O   HOH Z 174 " =    2.231
peak=   -3.252 closest distance to " O   HOH Z 236 " =    1.711
peak=   -3.242 closest distance to " O   HOH Z 109 " =    2.971
peak=   -3.241 closest distance to " O   HOH Z 357 " =    2.205
peak=   -3.240 closest distance to " CG  HIS A  86 " =    1.169
peak=   -3.236 closest distance to " N   ARG A 159 " =    1.721
peak=   -3.236 closest distance to " OG  SER A  26 " =    1.126
peak=   -3.228 closest distance to " O   GLU A 128 " =    1.318
peak=   -3.226 closest distance to " CD2 TYR A 247 " =    2.373
peak=   -3.226 closest distance to " O   HOH Z 198 " =    1.476
peak=   -3.223 closest distance to " O   HOH Z  91 " =    2.198
peak=   -3.223 closest distance to " O   HOH Z 171 " =    2.350
peak=   -3.220 closest distance to " O   GLN A  11 " =    1.340
peak=   -3.218 closest distance to " NE2 GLN A  94 " =    1.833
peak=   -3.214 closest distance to " O   HOH Z 197 " =    2.013
peak=   -3.211 closest distance to " O   ASN A 301 " =    1.310
peak=   -3.204 closest distance to " O   SER A  26 " =    1.578
peak=   -3.201 closest distance to " CB  PHE A  16 " =    2.403
peak=   -3.200 closest distance to " NE  ARG A  66 " =    4.492
peak=   -3.199 closest distance to " CD2 HIS A 207 " =    2.267
peak=   -3.198 closest distance to " O   HOH Z 287 " =    2.012
peak=   -3.198 closest distance to " O   VAL A 189 " =    2.665
peak=   -3.196 closest distance to " O   HOH Z  49 " =    0.859
peak=   -3.194 closest distance to " CZ3 TRP A 274 " =    2.268
peak=   -3.193 closest distance to " O   HOH Z  63 " =    1.149
peak=   -3.193 closest distance to " CA  GLY A 203 " =    2.275
peak=   -3.187 closest distance to " N   ALA A 248 " =    2.502
peak=   -3.183 closest distance to " CG2 THR A  18 " =    2.913
peak=   -3.183 closest distance to " ND2 ASN A  45 " =    1.231
peak=   -3.180 closest distance to " O   ALA A   1 " =    1.981
peak=   -3.177 closest distance to " O   HOH Z 348 " =    2.232
peak=   -3.176 closest distance to " O   HOH Z 174 " =    3.621
peak=   -3.173 closest distance to " CG2 ILE A 263 " =    2.175
peak=   -3.171 closest distance to " CG  ARG A 269 " =    2.232
peak=   -3.170 closest distance to " O   HOH Z 377 " =    1.928
peak=   -3.169 closest distance to " O   HOH Z 148 " =    3.822
peak=   -3.165 closest distance to " O   SER A 273 " =    1.270
peak=   -3.163 closest distance to " O   HOH Z 281 " =    2.398
peak=   -3.162 closest distance to " O   HOH Z 163 " =    5.000
peak=   -3.151 closest distance to " O   ASN A 187 " =    1.648
peak=   -3.150 closest distance to " N   ALA A 248 " =    1.820
peak=   -3.146 closest distance to " NE2 GLN A 278 " =    1.596
peak=   -3.145 closest distance to " O   HOH Z 211 " =    1.491
peak=   -3.144 closest distance to " O   HOH Z  19 " =    2.313
peak=   -3.142 closest distance to " O   SER A   3 " =    1.039
peak=   -3.140 closest distance to " O   HOH Z 135 " =    1.630
peak=   -3.139 closest distance to " OD1 ASN A  39 " =    2.307
peak=   -3.133 closest distance to " O   HOH Z   1 " =    4.386
peak=   -3.132 closest distance to " NH2 ARG A  66 " =    2.080
peak=   -3.126 closest distance to " N   ALA A 226 " =    1.927
peak=   -3.126 closest distance to " OE2 GLU A   2 " =    1.440
peak=   -3.122 closest distance to " SD  MET A 105 " =    2.597
peak=   -3.118 closest distance to " O   HOH Z 251 " =    5.065
peak=   -3.117 closest distance to " O   HOH Z 244 " =    1.362
peak=   -3.108 closest distance to " CA  LYS A 166 " =    2.173
peak=   -3.097 closest distance to " ND2 ASN A 187 " =    1.642
peak=   -3.083 closest distance to " O   HOH Z 139 " =    3.346
peak=   -3.083 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.071 closest distance to " O   HOH Z 166 " =    1.586
peak=   -3.071 closest distance to " C   LEU A 143 " =    1.110
peak=   -3.068 closest distance to " O   HOH Z  78 " =    1.898
peak=   -3.053 closest distance to " OXT GLY A 302 " =    3.274
peak=   -3.048 closest distance to " CB  SER A  62 " =    5.574
peak=   -3.042 closest distance to " CD  GLN A  88 " =    0.904
peak=   -3.034 closest distance to " O   ILE A 263 " =    2.278
peak=   -3.009 closest distance to " O   HOH Z 412 " =    1.975

================= 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    :  0.4557 0.4469   6.263261e+00   6.245279e+00
   1_bss:  0.4480 0.4371   6.256418e+00   6.235939e+00
   1_xyz:  0.3376 0.3610   6.062147e+00   6.111583e+00
   1_adp:  0.3059 0.3710   6.011060e+00   6.130698e+00
   1_occ:  0.3056 0.3708   6.010488e+00   6.130840e+00
   2_bss:  0.3047 0.3680   6.009287e+00   6.129427e+00
   2_xyz:  0.2293 0.2792   5.761105e+00   5.926326e+00
   2_adp:  0.2125 0.2648   5.704338e+00   5.878047e+00
   2_occ:  0.2123 0.2647   5.703854e+00   5.878101e+00
   3_bss:  0.2116 0.2641   5.703164e+00   5.875789e+00
   3_xyz:  0.1563 0.1990   5.423498e+00   5.622436e+00
   3_adp:  0.1391 0.1845   5.330049e+00   5.544948e+00
   3_occ:  0.1390 0.1845   5.329387e+00   5.544353e+00
   4_bss:  0.1391 0.1845   5.330610e+00   5.544164e+00
   4_xyz:  0.1309 0.1747   5.278113e+00   5.492595e+00
   4_adp:  0.1288 0.1727   5.263882e+00   5.477404e+00
   4_occ:  0.1287 0.1727   5.263282e+00   5.476623e+00
   5_bss:  0.1286 0.1728   5.263217e+00   5.476671e+00
   5_xyz:  0.1183 0.1643   5.198517e+00   5.426431e+00
   5_adp:  0.1170 0.1634   5.190180e+00   5.420448e+00
   5_occ:  0.1169 0.1634   5.189686e+00   5.419873e+00
   5_bss:  0.1170 0.1631   5.188902e+00   5.418790e+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:  0.296  29.785  -2.127   3.732   1.312   0.000   0.000   0.000
   1_xyz:  0.296  29.785  -2.127   3.732   1.312   0.000   0.000   0.000
   1_adp:  0.296  29.785  -2.127   3.732   1.312   0.000   0.000   0.000
   1_occ:  0.296  29.785  -2.127   3.732   1.312   0.000   0.000   0.000
   2_bss:  0.317  56.446  -2.156   1.611   0.305   0.000   0.000   0.000
   2_xyz:  0.317  56.446  -2.156   1.611   0.305   0.000   0.000   0.000
   2_adp:  0.317  56.446  -2.156   1.611   0.305   0.000   0.000   0.000
   2_occ:  0.317  56.446  -2.156   1.611   0.305   0.000   0.000   0.000
   3_bss:  0.324  63.961  -2.800  -0.199  -0.467  -0.000  -0.000  -0.000
   3_xyz:  0.324  63.961  -2.800  -0.199  -0.467  -0.000  -0.000  -0.000
   3_adp:  0.324  63.961  -2.800  -0.199  -0.467  -0.000  -0.000  -0.000
   3_occ:  0.324  63.961  -2.800  -0.199  -0.467  -0.000  -0.000  -0.000
   4_bss:  0.332  67.535  -3.117  -1.323  -0.859  -0.000  -0.000  -0.000
   4_xyz:  0.332  67.535  -3.117  -1.323  -0.859  -0.000  -0.000  -0.000
   4_adp:  0.332  67.535  -3.117  -1.323  -0.859  -0.000  -0.000  -0.000
   4_occ:  0.332  67.535  -3.117  -1.323  -0.859  -0.000  -0.000  -0.000
   5_bss:  0.327  63.975  -3.178  -1.651  -0.895  -0.000  -0.000  -0.000
   5_xyz:  0.327  63.975  -3.178  -1.651  -0.895  -0.000  -0.000  -0.000
   5_adp:  0.327  63.975  -3.178  -1.651  -0.895  -0.000  -0.000  -0.000
   5_occ:  0.327  63.975  -3.178  -1.651  -0.895  -0.000  -0.000  -0.000
   5_bss:  0.323  61.318  -2.962  -1.607  -0.731  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.685 0.4875  0.6443    61405.789
   1_bss:  51.664 0.4988  0.6829    58373.874
   1_xyz:  39.578 0.6481  0.8611    37348.218
   1_adp:  40.985 0.6306  0.8487    39808.727
   1_occ:  41.002 0.6304  0.8473    39789.797
   2_bss:  40.680 0.6342  0.8250    39304.396
   2_xyz:  29.812 0.7586  0.9519    21550.845
   2_adp:  27.391 0.7861  0.9673    19001.555
   2_occ:  27.391 0.7861  0.9669    19001.048
   3_bss:  27.223 0.7879  0.9334    18831.214
   3_xyz:  19.461 0.8661  0.9875    10202.504
   3_adp:  17.612 0.8836  0.9909     8875.647
   3_occ:  17.598 0.8838  0.9911     8868.367
   4_bss:  17.581 0.8839  0.9709     8869.924
   4_xyz:  16.381 0.8949  0.9735     7934.153
   4_adp:  16.040 0.8981  0.9691     7795.016
   4_occ:  16.021 0.8983  0.9692     7782.306
   5_bss:  16.022 0.8983  0.9646     7780.827
   5_xyz:  15.096 0.9059  0.9688     7067.035
   5_adp:  14.954 0.9072  0.9626     6989.622
   5_occ:  14.941 0.9073  0.9627     6979.310
   5_bss:  14.927 0.9074  0.9659     6942.544
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7653e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7653e-01
   1_xyz:   1.514  0.011  0.090 15.124  0.005  4.110   1.1478e-01
   1_adp:   1.514  0.011  0.090 15.124  0.005  4.110   1.1478e-01
   1_occ:   1.514  0.011  0.090 15.124  0.005  4.110   1.1478e-01
   2_bss:   1.514  0.011  0.090 15.124  0.005  4.110   1.1478e-01
   2_xyz:   1.247  0.010  0.080 14.558  0.005  4.109   8.8974e-02
   2_adp:   1.247  0.010  0.080 14.558  0.005  4.109   8.8974e-02
   2_occ:   1.247  0.010  0.080 14.558  0.005  4.109   8.8974e-02
   3_bss:   1.247  0.010  0.080 14.558  0.005  4.109   8.8974e-02
   3_xyz:   1.172  0.010  0.078 14.776  0.004  4.124   7.8904e-02
   3_adp:   1.172  0.010  0.078 14.776  0.004  4.124   7.8904e-02
   3_occ:   1.172  0.010  0.078 14.776  0.004  4.124   7.8904e-02
   4_bss:   1.172  0.010  0.078 14.776  0.004  4.124   7.8904e-02
   4_xyz:   0.938  0.006  0.071 14.291  0.003  4.114   5.2884e-02
   4_adp:   0.938  0.006  0.071 14.291  0.003  4.114   5.2884e-02
   4_occ:   0.938  0.006  0.071 14.291  0.003  4.114   5.2884e-02
   5_bss:   0.938  0.006  0.071 14.291  0.003  4.114   5.2884e-02
   5_xyz:   1.108  0.009  0.080 14.606  0.004  4.120   6.9948e-02
   5_adp:   1.108  0.009  0.080 14.606  0.004  4.120   6.9948e-02
   5_occ:   1.108  0.009  0.080 14.606  0.004  4.120   6.9948e-02
   5_bss:   1.108  0.009  0.080 14.606  0.004  4.120   6.9948e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.499   2.4286e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.499   2.4286e-01
   1_xyz:   8.960  0.067  0.373 83.342  0.026  1.941   9.3465e-02
   1_adp:   8.960  0.067  0.373 83.342  0.026  1.941   9.3465e-02
   1_occ:   8.960  0.067  0.373 83.342  0.026  1.941   9.3465e-02
   2_bss:   8.960  0.067  0.373 83.342  0.026  1.941   9.3465e-02
   2_xyz:   7.823  0.055  0.270 81.088  0.038  2.235   1.8595e-01
   2_adp:   7.823  0.055  0.270 81.088  0.038  2.235   1.8595e-01
   2_occ:   7.823  0.055  0.270 81.088  0.038  2.235   1.8595e-01
   3_bss:   7.823  0.055  0.270 81.088  0.038  2.235   1.8595e-01
   3_xyz:   8.104  0.060  0.243 83.309  0.029  2.163   6.9767e-02
   3_adp:   8.104  0.060  0.243 83.309  0.029  2.163   6.9767e-02
   3_occ:   8.104  0.060  0.243 83.309  0.029  2.163   6.9767e-02
   4_bss:   8.104  0.060  0.243 83.309  0.029  2.163   6.9767e-02
   4_xyz:   6.813  0.032  0.216 81.276  0.032  2.392   3.3878e-02
   4_adp:   6.813  0.032  0.216 81.276  0.032  2.392   3.3878e-02
   4_occ:   6.813  0.032  0.216 81.276  0.032  2.392   3.3878e-02
   5_bss:   6.813  0.032  0.216 81.276  0.032  2.392   3.3878e-02
   5_xyz:   8.392  0.044  0.276 82.583  0.028  2.262   4.8261e-02
   5_adp:   8.392  0.044  0.276 82.583  0.028  2.262   4.8261e-02
   5_occ:   8.392  0.044  0.276 82.583  0.028  2.262   4.8261e-02
   5_bss:   8.392  0.044  0.276 82.583  0.028  2.262   4.8261e-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:  82.21   0.00  18.75  71.77   0.00  15.31  82.21   0.00  37.49
   1_occ:  82.21   0.00  18.75  71.77   0.00  15.31  82.21   0.00  37.49
   2_bss:  82.21   0.00  18.75  71.77   0.00  15.31  82.21   0.00  37.49
   2_xyz:  82.21   0.00  18.75  71.77   0.00  15.31  82.21   0.00  37.49
   2_adp:  90.65   0.00  18.07  90.65   0.00  14.40  81.08   4.46  38.09
   2_occ:  90.65   0.00  18.07  90.65   0.00  14.40  81.08   4.46  38.09
   3_bss:  90.65   0.00  18.07  90.65   0.00  14.40  81.08   4.46  38.09
   3_xyz:  90.65   0.00  18.07  90.65   0.00  14.40  81.08   4.46  38.09
   3_adp:  80.87   0.00  17.80  79.32   0.00  13.42  80.87   5.43  41.69
   3_occ:  80.87   0.00  17.80  79.32   0.00  13.42  80.87   5.43  41.69
   4_bss:  80.87   0.00  17.80  79.32   0.00  13.42  80.87   5.43  41.69
   4_xyz:  80.87   0.00  17.80  79.32   0.00  13.42  80.87   5.43  41.69
   4_adp:  82.48   1.17  17.58  82.48   1.17  13.20  81.83   5.85  41.42
   4_occ:  82.48   1.17  17.58  82.48   1.17  13.20  81.83   5.85  41.42
   5_bss:  82.48   1.17  17.58  82.48   1.17  13.20  81.83   5.85  41.42
   5_xyz:  82.48   1.17  17.58  82.48   1.17  13.20  81.83   5.85  41.42
   5_adp:  90.24   1.19  17.40  90.24   1.19  13.00  88.81   5.53  41.33
   5_occ:  90.24   1.19  17.40  90.24   1.19  13.00  88.81   5.53  41.33
   5_bss:  90.20   1.14  17.36  90.20   1.14  12.96  88.77   5.49  41.29
------------------------------------------------------------------------
 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:    1.889    0.015    0.343
   1_adp:    1.889    0.015    0.343
   1_occ:    1.889    0.015    0.343
   2_bss:    1.889    0.015    0.343
   2_xyz:    1.653    0.027    0.537
   2_adp:    1.653    0.027    0.537
   2_occ:    1.653    0.027    0.537
   3_bss:    1.653    0.027    0.537
   3_xyz:    1.468    0.066    0.692
   3_adp:    1.468    0.066    0.692
   3_occ:    1.468    0.066    0.692
   4_bss:    1.468    0.066    0.692
   4_xyz:    1.414    0.059    0.712
   4_adp:    1.414    0.059    0.712
   4_occ:    1.414    0.059    0.712
   5_bss:    1.414    0.059    0.712
   5_xyz:    1.380    0.078    0.740
   5_adp:    1.380    0.078    0.740
   5_occ:    1.380    0.078    0.740
   5_bss:    1.380    0.078    0.740
------------------------------------------------------------------------

CPU time actual refinement: 350.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/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_349/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_349/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.56 
  Macro-tasks:
    bulk solvent and scale       = 38.90  
    individual site refinement   = 154.35 
    weights calculation          = 29.15  
    collect and process          = 6.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 229.06 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 113.74 
    alpha_beta                      = 8.45   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 124.99 
    fmodel                         = 6.48   
    r_factors                      = 0.18   
    phase_errors                   = 10.79  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 268.46 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.832 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    672 calls, 113.43 s
gradients_fft:          617 calls, 110.21 s

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

# Date 2008-01-16 Time 04:37:41 PST -0800 (1200487061.69 s)
Start R-work = 0.4557, R-free = 0.4469 (no bulk solvent and anisotropic scale)
Final R-work = 0.1404, R-free = 0.1809 (no bulk solvent and anisotropic scale)

Start R-work = 0.4480, R-free = 0.4371
Final R-work = 0.1170, R-free = 0.1631