# Date 2008-01-16 Time 05:24:50 PST -0800 (1200489890.36 s)
#phil __OFF__

Command line arguments: "../724.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22420
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 724

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 48.1033, 88.1178, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00074
Completeness in resolution range: 0.945096
Completeness with d_max=infinity: 0.942187

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0007

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00074
Completeness in resolution range: 0.945096
Completeness with d_max=infinity: 0.942187

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2806 [2188/2216]  1965   223  10.2%
  bin  2:  4.2806 -  3.4106 [2071/2094]  1868   203   9.8%
  bin  3:  3.4106 -  2.9833 [2072/2094]  1864   208  10.0%
  bin  4:  2.9833 -  2.7123 [2044/2063]  1840   204  10.0%
  bin  5:  2.7123 -  2.5188 [2023/2052]  1816   207  10.2%
  bin  6:  2.5188 -  2.3709 [2013/2054]  1815   198   9.8%
  bin  7:  2.3709 -  2.2526 [2010/2047]  1814   196   9.8%
  bin  8:  2.2526 -  2.1548 [2007/2043]  1802   205  10.2%
  bin  9:  2.1548 -  2.0721 [2013/2045]  1817   196   9.7%
  bin 10:  2.0721 -  2.0007 [1148/2019]  1029   119  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/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:
        1.66 -     2.31: 14
        2.31 -     2.95: 1623
        2.95 -     3.60: 4425
        3.60 -     4.25: 8989
        4.25 -     4.90: 12680
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.658 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.926 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.926 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.957 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27726 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_724/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/model_refine_001.geo

CPU time processing inputs: 8.89


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 48.10325 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4692   r_free= 0.4592   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.283559                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7742 0.99   1411  157 0.3763 0.3723      6.5637      6.5459|
|  2:  4.7742 -  3.8095 0.99   1369  152 0.4207 0.4494      6.8658      6.8965|
|  3:  3.8095 -  3.3339 0.99   1333  150 0.4532 0.4149      6.6995      6.6245|
|  4:  3.3339 -  3.0318 0.99   1319  139 0.4621 0.4451      6.5277      6.4744|
|  5:  3.0318 -  2.8160 0.99   1308  148 0.4955 0.4302      6.3681      6.4004|
|  6:  2.8160 -  2.6509 0.98   1308  149 0.5023 0.4911      6.2716      6.1465|
|  7:  2.6509 -  2.5188 0.99   1305  150 0.4879 0.4572      6.2393       6.171|
|  8:  2.5188 -  2.4096 0.99   1318  139 0.5048 0.5053      6.1737       6.161|
|  9:  2.4096 -  2.3172 0.98   1290  145 0.5008 0.4878      6.1024      6.1703|
| 10:  2.3172 -  2.2375 0.98   1295  142 0.5130 0.4606      6.0967      6.0577|
| 11:  2.2375 -  2.1678 0.98   1286  144 0.5162 0.5201      6.0261      6.0403|
| 12:  2.1678 -  2.1060 0.99   1283  142 0.5093 0.5712       5.959      6.0108|
| 13:  2.1060 -  2.0507 0.97   1278  136 0.5162 0.5013      5.8843      5.8276|
| 14:  2.0507 -  2.0007 0.41    527   66 0.4813 0.5065      5.8508      5.7571|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7742  1411   157  0.70  34.62   0.81     0.73      72865.66|
|  2:  4.7742 -  3.8095  1369   152  0.70  35.45   0.88     0.78     106808.58|
|  3:  3.8095 -  3.3339  1333   150  0.61  43.32   0.87     0.76     110576.08|
|  4:  3.3339 -  3.0318  1319   139  0.52  49.91   0.88     0.68      96444.74|
|  5:  3.0318 -  2.8160  1308   148  0.46  54.89   0.87     0.62      73694.80|
|  6:  2.8160 -  2.6509  1308   149  0.42  58.29   0.86     0.57      64812.41|
|  7:  2.6509 -  2.5188  1305   150  0.42  58.19   0.91     0.55      58904.03|
|  8:  2.5188 -  2.4096  1318   139  0.40  59.73   0.89     0.55      54898.19|
|  9:  2.4096 -  2.3172  1290   145  0.40  60.09   0.89     0.57      51156.55|
| 10:  2.3172 -  2.2375  1295   142  0.41  59.07   0.91     0.59      45729.76|
| 11:  2.2375 -  2.1678  1286   144  0.36  63.19   0.90     0.54      45733.67|
| 12:  2.1678 -  2.1060  1283   142  0.30  67.52   0.90     0.45      44970.88|
| 13:  2.1060 -  2.0507  1278   136  0.25  71.16   0.88     0.38      40473.07|
| 14:  2.0507 -  2.0007   527    66  0.31  66.98   0.99     0.39      29104.95|
|alpha:            min =        0.38 max =            0.78 mean =         0.59|
|beta:             min =    29104.95 max =       110576.08 mean =     65957.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.12|
|phase err.(test): min =        0.00 max =           89.99 mean =        55.51|
|-----------------------------------------------------------------------------|

============================== 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 = 13.617623             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.455   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.396257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.461   (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 |  1.658 -  1.982:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.982 -  2.306:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.306 -  2.630:       43 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.630 -  2.955:     1580 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.955 -  3.279:     1877 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.279 -  3.603:     2548 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.603 -  3.927:     4662 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.927 -  4.252:     4327 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.252 -  4.576:     5737 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     6943 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.658 |       0.218 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4692   r_free= 0.4592   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.283559                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4587   r_free= 0.4477   ksol= 0.28   Bsol= 39.96   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.98,4.22,2.52,0.00,0.00,0.00); trace/3= 0.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.276653                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.479640             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.179843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.034   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4587      final r-factor (work) = 0.3664          |
| start r-factor (free) = 0.4477      final r-factor (free) = 0.3975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.1745 = 11.48 * 0.50 * 6.2731 + 1.00 * 0.1679                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4943 = 11.48 * 0.50 * 6.1593 + 1.00 * 0.1411                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3664      final r-factor (work) = 0.3368          |
| start r-factor (free) = 0.3975      final r-factor (free) = 0.4081          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2729 = 1.18 * 1.00 * 6.1593 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1924 = 1.18 * 1.00 * 6.0787 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.82  18.83    None  None   None       |
|    all(noH): 2823   0      0.00    105.82  18.83    None  None   None       |
|    Sol.    : 438    0      0.00    105.82  37.55    None  None   None       |
|    Mac.    : 2385   0      0.00    84.78   15.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.582:  964   |   5:    52.911 -  63.494:   67        |
|      1:    10.582 -  21.165:  941   |   6:    63.494 -  74.076:   39        |
|      2:    21.165 -  31.747:  468   |   7:    74.076 -  84.658:   14        |
|      3:    31.747 -  42.329:  213   |   8:    84.658 -  95.241:    5        |
|      4:    42.329 -  52.911:  111   |   9:    95.241 - 105.823:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3368 r_free = 0.4081             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3365 r_free = 0.4071             target_work(ml) = 6.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3365   r_free= 0.4071   ksol= 0.28   Bsol= 39.96   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.98,4.22,2.52,0.00,0.00,0.00); trace/3= 0.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.082043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3351   r_free= 0.4048   ksol= 0.30   Bsol= 52.61   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,2.49,1.51,0.00,0.00,0.00); trace/3= 0.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.083980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.536586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.572   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.566959              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.225  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3351      final r-factor (work) = 0.2892          |
| start r-factor (free) = 0.4048      final r-factor (free) = 0.3560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0169 = 6.54 * 0.50 * 6.0814 + 1.00 * 0.1411                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7777 = 6.54 * 0.50 * 6.0288 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2892      final r-factor (work) = 0.2824          |
| start r-factor (free) = 0.3560      final r-factor (free) = 0.3496          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4385 = 0.57 * 1.00 * 6.0288 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3946 = 0.57 * 1.00 * 5.9638 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.05  17.98    None  None   None       |
|    all(noH): 2823   0      0.00    107.05  17.98    None  None   None       |
|    Sol.    : 438    0      0.00    107.05  36.54    None  None   None       |
|    Mac.    : 2385   0      0.00    83.46   14.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.705: 1050   |   5:    53.526 -  64.231:   59        |
|      1:    10.705 -  21.411:  955   |   6:    64.231 -  74.937:   27        |
|      2:    21.411 -  32.116:  432   |   7:    74.937 -  85.642:   11        |
|      3:    32.116 -  42.821:  181   |   8:    85.642 -  96.347:    3        |
|      4:    42.821 -  53.526:  104   |   9:    96.347 - 107.052:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2824 r_free = 0.3496             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2823 r_free = 0.3497             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2823   r_free= 0.3497   ksol= 0.30   Bsol= 52.61   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,2.49,1.51,0.00,0.00,0.00); trace/3= 0.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.958893                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2825   r_free= 0.3495   ksol= 0.31   Bsol= 64.79   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,2.02,1.04,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.959786                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.707727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.073   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.396159              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.594  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2825      final r-factor (work) = 0.2239          |
| start r-factor (free) = 0.3495      final r-factor (free) = 0.2795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0580 = 7.71 * 0.50 * 5.9640 + 1.00 * 0.0737                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6872 = 7.71 * 0.50 * 5.8665 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2239      final r-factor (work) = 0.2041          |
| start r-factor (free) = 0.2795      final r-factor (free) = 0.2646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2041 = 1.40 * 1.00 * 5.8665 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9767 = 1.40 * 1.00 * 5.7004 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.43  18.55    None  None   None       |
|    all(noH): 2823   0      0.00    111.43  18.55    None  None   None       |
|    Sol.    : 438    0      2.00    111.43  44.84    None  None   None       |
|    Mac.    : 2385   0      0.00    102.00  13.73    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 -  11.143: 1299   |   5:    55.716 -  66.859:   79        |
|      1:    11.143 -  22.287:  824   |   6:    66.859 -  78.003:   57        |
|      2:    22.287 -  33.430:  244   |   7:    78.003 -  89.146:   28        |
|      3:    33.430 -  44.573:  166   |   8:    89.146 - 100.289:    7        |
|      4:    44.573 -  55.716:  114   |   9:   100.289 - 111.432:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2041 r_free = 0.2646             target_work(ml) = 5.676         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2039 r_free = 0.2646             target_work(ml) = 5.676         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2039   r_free= 0.2646   ksol= 0.31   Bsol= 64.79   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,2.02,1.04,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.675584                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2039   r_free= 0.2640   ksol= 0.33   Bsol= 82.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.92,0.66,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.675338                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.014442              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.369  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352069              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.538  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2039      final r-factor (work) = 0.1719          |
| start r-factor (free) = 0.2640      final r-factor (free) = 0.2201          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6719 = 3.01 * 0.50 * 5.7016 + 1.00 * 0.0784                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5058 = 3.01 * 0.50 * 5.6047 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1719      final r-factor (work) = 0.1634          |
| start r-factor (free) = 0.2201      final r-factor (free) = 0.2075          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9912 = 0.35 * 1.00 * 5.6047 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9466 = 0.35 * 1.00 * 5.4919 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.35  17.44    None  None   None       |
|    all(noH): 2823   0      0.00    107.35  17.44    None  None   None       |
|    Sol.    : 438    0      3.84    107.35  44.01    None  None   None       |
|    Mac.    : 2385   0      0.00    98.92   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.735: 1354   |   5:    53.675 -  64.410:   77        |
|      1:    10.735 -  21.470:  844   |   6:    64.410 -  75.145:   55        |
|      2:    21.470 -  32.205:  211   |   7:    75.145 -  85.880:   26        |
|      3:    32.205 -  42.940:  125   |   8:    85.880 -  96.615:    9        |
|      4:    42.940 -  53.675:  117   |   9:    96.615 - 107.350:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1634 r_free = 0.2075             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1633 r_free = 0.2074             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1633   r_free= 0.2074   ksol= 0.33   Bsol= 82.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.92,0.66,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.465024                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1637   r_free= 0.2072   ksol= 0.34   Bsol= 84.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,0.21,0.50,0.00,0.00,0.00); trace/3= -0.26                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.466862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.940113              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.976  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451179              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.277  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1637      final r-factor (work) = 0.1393          |
| start r-factor (free) = 0.2072      final r-factor (free) = 0.1851          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1338 = 2.94 * 0.50 * 5.4934 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9991 = 2.94 * 0.50 * 5.3941 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1393      final r-factor (work) = 0.1343          |
| start r-factor (free) = 0.1851      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4467 = 0.45 * 1.00 * 5.3941 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4096 = 0.45 * 1.00 * 5.3122 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.53  16.98    None  None   None       |
|    all(noH): 2823   0      0.00    107.53  16.98    None  None   None       |
|    Sol.    : 438    0      0.00    107.53  43.87    None  None   None       |
|    Mac.    : 2385   0      0.00    97.68   12.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.753: 1422   |   5:    53.765 -  64.518:   81        |
|      1:    10.753 -  21.506:  836   |   6:    64.518 -  75.271:   51        |
|      2:    21.506 -  32.259:  172   |   7:    75.271 -  86.024:   29        |
|      3:    32.259 -  43.012:  113   |   8:    86.024 -  96.777:    7        |
|      4:    43.012 -  53.765:  107   |   9:    96.777 - 107.530:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1343 r_free = 0.1829             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1341 r_free = 0.1829             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1341   r_free= 0.1829   ksol= 0.34   Bsol= 84.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,0.21,0.50,0.00,0.00,0.00); trace/3= -0.26                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301836                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7742 0.99   1411  157 0.1036 0.1402      5.4415      5.6341|
|  2:  4.7742 -  3.8095 0.99   1369  152 0.0940 0.1128      5.5128        5.68|
|  3:  3.8095 -  3.3339 0.99   1333  150 0.1241 0.1764      5.6139      5.9895|
|  4:  3.3339 -  3.0318 0.99   1319  139 0.1434 0.1873      5.5764      5.7333|
|  5:  3.0318 -  2.8160 0.99   1308  148 0.1663 0.1780      5.5079       5.608|
|  6:  2.8160 -  2.6509 0.98   1308  149 0.1561 0.2476      5.3922       5.628|
|  7:  2.6509 -  2.5188 0.99   1305  150 0.1534 0.1932      5.3451      5.5297|
|  8:  2.5188 -  2.4096 0.99   1318  139 0.1472 0.2089      5.2768      5.4834|
|  9:  2.4096 -  2.3172 0.98   1290  145 0.1513 0.2370       5.213      5.5358|
| 10:  2.3172 -  2.2375 0.98   1295  142 0.1420 0.1864      5.1497      5.2821|
| 11:  2.2375 -  2.1678 0.98   1286  144 0.1401 0.2169      5.0772      5.4114|
| 12:  2.1678 -  2.1060 0.99   1283  142 0.1360 0.1945      5.0035      5.2873|
| 13:  2.1060 -  2.0507 0.97   1278  136 0.1395 0.1864      4.9352      5.0879|
| 14:  2.0507 -  2.0007 0.41    527   66 0.1350 0.2048      4.8774      5.1198|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7742  1411   157  0.93   9.99   0.96     0.92       8068.11|
|  2:  4.7742 -  3.8095  1369   152  0.94   9.30   1.00     0.98      10632.30|
|  3:  3.8095 -  3.3339  1333   150  0.92  13.28   1.02     1.01      13248.56|
|  4:  3.3339 -  3.0318  1319   139  0.90  16.19   1.00     0.98      13062.42|
|  5:  3.0318 -  2.8160  1308   148  0.87  19.04   1.00     0.97      11431.93|
|  6:  2.8160 -  2.6509  1308   149  0.87  19.71   0.97     0.95       9800.03|
|  7:  2.6509 -  2.5188  1305   150  0.88  18.87   1.00     0.97       8876.10|
|  8:  2.5188 -  2.4096  1318   139  0.87  19.48   0.99     0.94       8087.84|
|  9:  2.4096 -  2.3172  1290   145  0.87  19.70   0.99     0.92       6971.79|
| 10:  2.3172 -  2.2375  1295   142  0.87  19.86   0.98     0.93       6464.49|
| 11:  2.2375 -  2.1678  1286   144  0.88  19.11   0.98     0.93       5689.00|
| 12:  2.1678 -  2.1060  1283   142  0.89  18.01   0.99     0.98       4936.56|
| 13:  2.1060 -  2.0507  1278   136  0.88  18.57   0.97     0.95       4283.42|
| 14:  2.0507 -  2.0007   527    66  0.88  18.70   0.94     0.89       3770.88|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3770.88 max =        13248.56 mean =      8469.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.79 mean =        16.97|
|phase err.(test): min =        0.00 max =           89.48 mean =        16.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1827   ksol= 0.33   Bsol= 79.11   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-0.06,0.65,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302905                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1827   ksol= 0.33   Bsol= 79.11   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-0.06,0.65,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302905                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7742 0.99   1411  157 0.1058 0.1406      5.4533      5.6298|
|  2:  4.7742 -  3.8095 0.99   1369  152 0.0945 0.1112      5.5147      5.6753|
|  3:  3.8095 -  3.3339 0.99   1333  150 0.1243 0.1751      5.6127      5.9877|
|  4:  3.3339 -  3.0318 0.99   1319  139 0.1438 0.1878      5.5778      5.7339|
|  5:  3.0318 -  2.8160 0.99   1308  148 0.1665 0.1778      5.5091      5.6082|
|  6:  2.8160 -  2.6509 0.98   1308  149 0.1558 0.2472      5.3918      5.6264|
|  7:  2.6509 -  2.5188 0.99   1305  150 0.1533 0.1934      5.3451        5.53|
|  8:  2.5188 -  2.4096 0.99   1318  139 0.1471 0.2091      5.2769      5.4843|
|  9:  2.4096 -  2.3172 0.98   1290  145 0.1512 0.2375      5.2131      5.5362|
| 10:  2.3172 -  2.2375 0.98   1295  142 0.1419 0.1873      5.1497      5.2832|
| 11:  2.2375 -  2.1678 0.98   1286  144 0.1399 0.2168      5.0764      5.4104|
| 12:  2.1678 -  2.1060 0.99   1283  142 0.1361 0.1953      5.0032      5.2892|
| 13:  2.1060 -  2.0507 0.97   1278  136 0.1398 0.1849       4.935      5.0852|
| 14:  2.0507 -  2.0007 0.41    527   66 0.1348 0.2038      4.8776      5.1176|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7742  1411   157  0.93  10.05   0.95     0.92       8020.64|
|  2:  4.7742 -  3.8095  1369   152  0.94   9.25   1.00     0.99      10513.13|
|  3:  3.8095 -  3.3339  1333   150  0.92  13.19   1.02     1.02      13104.83|
|  4:  3.3339 -  3.0318  1319   139  0.90  16.18   1.00     0.98      13062.81|
|  5:  3.0318 -  2.8160  1308   148  0.87  19.04   1.00     0.97      11439.70|
|  6:  2.8160 -  2.6509  1308   149  0.87  19.68   0.98     0.95       9798.63|
|  7:  2.6509 -  2.5188  1305   150  0.88  18.88   1.00     0.97       8878.83|
|  8:  2.5188 -  2.4096  1318   139  0.87  19.49   0.99     0.94       8099.52|
|  9:  2.4096 -  2.3172  1290   145  0.87  19.71   0.99     0.92       6981.22|
| 10:  2.3172 -  2.2375  1295   142  0.87  19.87   0.98     0.93       6469.60|
| 11:  2.2375 -  2.1678  1286   144  0.88  19.12   0.98     0.93       5697.05|
| 12:  2.1678 -  2.1060  1283   142  0.89  17.99   0.99     0.98       4931.65|
| 13:  2.1060 -  2.0507  1278   136  0.88  18.55   0.97     0.95       4271.25|
| 14:  2.0507 -  2.0007   527    66  0.88  18.66   0.95     0.89       3754.72|
|alpha:            min =        0.89 max =            1.02 mean =         0.96|
|beta:             min =     3754.72 max =        13104.83 mean =      8447.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        16.96|
|phase err.(test): min =        0.00 max =           89.88 mean =        16.21|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.53  16.98    None  None   None       |
|    all(noH): 2823   0      0.00    107.53  16.98    None  None   None       |
|    Sol.    : 438    0      0.00    107.53  43.88    None  None   None       |
|    Mac.    : 2385   0      0.00    97.69   12.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.756: 1422   |   5:    53.768 -  64.521:   81        |
|      1:    10.756 -  21.509:  836   |   6:    64.521 -  75.274:   51        |
|      2:    21.509 -  32.262:  172   |   7:    75.274 -  86.027:   29        |
|      3:    32.262 -  43.015:  113   |   8:    86.027 -  96.780:    7        |
|      4:    43.015 -  53.768:  107   |   9:    96.780 - 107.533:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.455 - 5.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 345
   mapped sites are within: 0.760 - 5.691

peak=    6.477 closest distance to " O   GLN A  11 " =    1.129
peak=    6.309 closest distance to " O  BHOH Z  74 " =    1.141
peak=    5.991 closest distance to " O   HOH Z 203 " =    1.020
peak=    5.700 closest distance to " O   HOH Z 210 " =    1.519
peak=    5.457 closest distance to " O   HOH Z  54 " =    1.396
peak=    5.213 closest distance to " O   HOH Z 248 " =    1.594
peak=    5.189 closest distance to " OD1 ASN A 301 " =    1.073
peak=    5.088 closest distance to " O   HOH Z 117 " =    1.348
peak=    4.966 closest distance to " O   HOH Z  65 " =    1.143
peak=    4.888 closest distance to " CB  SER A  63 " =    1.258
peak=    4.864 closest distance to " CD2 TRP A 179 " =    1.275
peak=    4.856 closest distance to " O   HOH Z 403 " =    2.031
peak=    4.815 closest distance to " O   HOH Z 113 " =    2.031
peak=    4.741 closest distance to " O   HOH Z  69 " =    1.396
peak=    4.656 closest distance to " O   HOH Z  49 " =    1.450
peak=    4.579 closest distance to " CG  PRO A  54 " =    1.362
peak=    4.573 closest distance to " CB  GLN A 223 " =    1.460
peak=    4.519 closest distance to " CG  PRO A 280 " =    0.899
peak=    4.474 closest distance to " O   HOH Z 261 " =    2.381
peak=    4.448 closest distance to " NH2 ARG A 156 " =    1.188
peak=    4.436 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.409 closest distance to " O   HOH Z 412 " =    3.343
peak=    4.357 closest distance to " OD1 ASN A  69 " =    0.837
peak=    4.328 closest distance to " N   SER A 164 " =    0.984
peak=    4.311 closest distance to " O   PRO A 198 " =    1.583
peak=    4.306 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.297 closest distance to " CG  ARG A  66 " =    2.774
peak=    4.283 closest distance to " CB  TRP A 179 " =    1.335
peak=    4.256 closest distance to " CE1 HIS A 115 " =    1.160
peak=    4.244 closest distance to " O   HOH Z 431 " =    1.224
peak=    4.242 closest distance to " CZ3 TRP A 266 " =    1.101
peak=    4.233 closest distance to " CA  GLN A  11 " =    1.231
peak=    4.232 closest distance to " NE2 GLN A  11 " =    1.212
peak=    4.220 closest distance to " O   HOH Z 394 " =    1.822
peak=    4.190 closest distance to " O   HOH Z 426 " =    1.168
peak=    4.179 closest distance to " CG1AVAL A 121 " =    0.829
peak=    4.173 closest distance to " CB  ASN A  39 " =    0.810
peak=    4.158 closest distance to " O   HOH Z 425 " =    1.623
peak=    4.155 closest distance to " O   HOH Z  80 " =    2.083
peak=    4.147 closest distance to " CB  ARG A 275 " =    0.812
peak=    4.141 closest distance to " O   HOH Z 176 " =    1.824
peak=    4.136 closest distance to " CG  PRO A  90 " =    1.330
peak=    4.135 closest distance to " CB  ASN A  45 " =    1.123
peak=    4.131 closest distance to " O   HOH Z 141 " =    1.732
peak=    4.129 closest distance to " O   HOH Z 214 " =    1.736
peak=    4.099 closest distance to " CA  ARG A 195 " =    1.122
peak=    4.081 closest distance to " O   HOH Z 422 " =    1.059
peak=    4.073 closest distance to " CZ  PHE A  38 " =    1.139
peak=    4.062 closest distance to " O   HOH Z 139 " =    1.331
peak=    4.059 closest distance to " CZ  PHE A 218 " =    1.144
peak=    4.055 closest distance to " CB  SER A  62 " =    0.875
peak=    4.045 closest distance to " CG AARG A 275 " =    1.170
peak=    4.044 closest distance to " O   HOH Z 149 " =    2.291
peak=    4.032 closest distance to " CG  GLN A  77 " =    0.829
peak=    4.018 closest distance to " CG2BVAL A  41 " =    0.886
peak=    3.978 closest distance to " O   HOH Z 147 " =    1.496
peak=    3.962 closest distance to " CB  ASN A 285 " =    0.866
peak=    3.956 closest distance to " NE2 GLN A  77 " =    3.136
peak=    3.941 closest distance to " O   ALA A 165 " =    1.383
peak=    3.939 closest distance to " O   HOH Z 433 " =    1.782
peak=    3.939 closest distance to " CD  LYS A 166 " =    1.528
peak=    3.925 closest distance to " CG  PRO A 243 " =    1.158
peak=    3.923 closest distance to " O   HOH Z 102 " =    1.371
peak=    3.910 closest distance to " O   SER A  87 " =    2.262
peak=    3.888 closest distance to " CA  ARG A  36 " =    1.062
peak=    3.874 closest distance to " CG1 ILE A 120 " =    1.145
peak=    3.868 closest distance to " CA  ALA A 100 " =    1.168
peak=    3.860 closest distance to " CB  ARG A 190 " =    1.857
peak=    3.839 closest distance to " OE1 GLN A  11 " =    2.417
peak=    3.836 closest distance to " O   HOH Z 134 " =    1.922
peak=    3.835 closest distance to " CB  ASN A 148 " =    1.504
peak=    3.835 closest distance to " CB  GLU A 128 " =    1.059
peak=    3.831 closest distance to " O   HOH Z 298 " =    1.985
peak=    3.827 closest distance to " O   HOH Z 234 " =    3.842
peak=    3.825 closest distance to " O   HOH Z 128 " =    1.401
peak=    3.825 closest distance to " O   HOH Z  63 " =    1.671
peak=    3.820 closest distance to " CB  TYR A 169 " =    0.814
peak=    3.816 closest distance to " O   HOH Z  48 " =    2.131
peak=    3.801 closest distance to " O   HOH Z  43 " =    2.178
peak=    3.801 closest distance to " O   HOH Z 406 " =    1.692
peak=    3.799 closest distance to " O   HOH Z 346 " =    1.695
peak=    3.797 closest distance to " CB  PRO A  54 " =    0.923
peak=    3.786 closest distance to " O   HOH Z  35 " =    2.018
peak=    3.773 closest distance to " O   HOH Z 394 " =    4.089
peak=    3.772 closest distance to " CG2 VAL A 197 " =    1.215
peak=    3.771 closest distance to " O   HOH Z 415 " =    1.161
peak=    3.765 closest distance to " CB  GLU A  46 " =    1.046
peak=    3.764 closest distance to " CB  MET A 105 " =    1.069
peak=    3.750 closest distance to " CD  ARG A 195 " =    1.001
peak=    3.747 closest distance to " N   THR A  52 " =    1.140
peak=    3.746 closest distance to " OE1 GLU A   2 " =    1.347
peak=    3.741 closest distance to " CB  THR A  52 " =    0.855
peak=    3.732 closest distance to " O   HOH Z 389 " =    2.159
peak=    3.721 closest distance to " NH1AARG A 145 " =    1.298
peak=    3.720 closest distance to " O   HOH Z  44 " =    1.994
peak=    3.717 closest distance to " O   HOH Z 369 " =    1.932
peak=    3.713 closest distance to " CB  ALA A   1 " =    0.924
peak=    3.712 closest distance to " O   HOH Z 358 " =    1.332
peak=    3.711 closest distance to " O  BHOH Z 338 " =    1.077
peak=    3.705 closest distance to " O   HOH Z 196 " =    1.533
peak=    3.696 closest distance to " CB  MET A  40 " =    0.994
peak=    3.686 closest distance to " CD  ARG A  36 " =    1.008
peak=    3.681 closest distance to " O   THR A 251 " =    1.220
peak=    3.680 closest distance to " OE1 GLN A  88 " =    0.885
peak=    3.667 closest distance to " O   HOH Z  88 " =    3.393
peak=    3.660 closest distance to " O   HOH Z 132 " =    3.133
peak=    3.651 closest distance to " CG  PRO A 198 " =    1.120
peak=    3.651 closest distance to " O   HOH Z 154 " =    2.326
peak=    3.634 closest distance to " O   HOH Z 404 " =    1.683
peak=    3.632 closest distance to " O   HOH Z 377 " =    1.363
peak=    3.629 closest distance to " O   HOH Z 146 " =    1.742
peak=    3.629 closest distance to " O   HOH Z 362 " =    3.230
peak=    3.621 closest distance to " CB  VAL A 202 " =    1.465
peak=    3.607 closest distance to " ND2 ASN A  69 " =    1.296
peak=    3.605 closest distance to " O   HOH Z 189 " =    2.952
peak=    3.596 closest distance to " O   HOH Z 250 " =    2.452
peak=    3.595 closest distance to " CA  THR A 246 " =    1.000
peak=    3.588 closest distance to " CB  GLU A 152 " =    1.135
peak=    3.588 closest distance to " CB  GLN A  88 " =    1.189
peak=    3.588 closest distance to " O   HOH Z 265 " =    1.960
peak=    3.581 closest distance to " CA  ASN A 249 " =    1.332
peak=    3.569 closest distance to " O   HOH Z 284 " =    2.919
peak=    3.569 closest distance to " CA  VAL A 125 " =    1.303
peak=    3.565 closest distance to " O   HOH Z  20 " =    1.807
peak=    3.562 closest distance to " O   HOH Z  40 " =    1.912
peak=    3.558 closest distance to " O   HOH Z 124 " =    1.085
peak=    3.558 closest distance to " CA  ASN A 217 " =    1.323
peak=    3.549 closest distance to " CG2 THR A 221 " =    1.040
peak=    3.547 closest distance to " O   HOH Z 199 " =    1.533
peak=    3.541 closest distance to " O   HOH Z  48 " =    1.943
peak=    3.534 closest distance to " CB  GLU A 277 " =    3.819
peak=    3.531 closest distance to " CA  SER A  12 " =    1.501
peak=    3.530 closest distance to " O   HOH Z 316 " =    3.019
peak=    3.530 closest distance to " O   HOH Z   9 " =    1.149
peak=    3.529 closest distance to " O   HOH Z 301 " =    1.510
peak=    3.521 closest distance to " CE1 TYR A 186 " =    1.351
peak=    3.520 closest distance to " O   HOH Z 298 " =    2.206
peak=    3.519 closest distance to " O   HOH Z  53 " =    1.193
peak=    3.515 closest distance to " O   HOH Z 146 " =    1.287
peak=    3.511 closest distance to " CA  TYR A 116 " =    1.389
peak=    3.510 closest distance to " O   HOH Z 417 " =    2.981
peak=    3.505 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.503 closest distance to " CG  GLN A  58 " =    1.130
peak=    3.503 closest distance to " O   HOH Z 418 " =    1.934
peak=    3.501 closest distance to " CA  ASP A 191 " =    1.241
peak=    3.500 closest distance to " O   HOH Z 437 " =    1.826
peak=    3.497 closest distance to " CD2 TYR A  68 " =    0.843
peak=    3.485 closest distance to " O   HOH Z  67 " =    1.078
peak=    3.478 closest distance to " CD1 LEU A  96 " =    0.760
peak=    3.474 closest distance to " CB  GLU A  37 " =    0.916
peak=    3.473 closest distance to " O   HOH Z   6 " =    1.234
peak=    3.467 closest distance to " O   HOH Z 246 " =    1.511
peak=    3.465 closest distance to " CA  ALA A  51 " =    0.961
peak=    3.459 closest distance to " O   HOH Z 133 " =    2.854
peak=    3.457 closest distance to " CA  GLU A 152 " =    0.935
peak=    3.457 closest distance to " O   HOH Z 209 " =    2.094
peak=    3.456 closest distance to " CB  ARG A  79 " =    1.248
peak=    3.455 closest distance to " O   HOH Z 401 " =    1.231
peak=    3.451 closest distance to " NH2BARG A 145 " =    1.935
peak=    3.449 closest distance to " O   HOH Z 368 " =    2.176
peak=    3.449 closest distance to " ND2 ASN A 249 " =    0.888
peak=    3.440 closest distance to " O   HOH Z 126 " =    1.616
peak=    3.439 closest distance to " CE3 TRP A 274 " =    3.591
peak=    3.436 closest distance to " O   HOH Z  15 " =    2.231
peak=    3.433 closest distance to " O   HOH Z  27 " =    1.105
peak=    3.426 closest distance to " CA  GLY A 196 " =    0.956
peak=    3.423 closest distance to " ND2 ASN A 187 " =    1.565
peak=    3.423 closest distance to " O   HOH Z 428 " =    1.061
peak=    3.417 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.416 closest distance to " O   ASP A 200 " =    1.625
peak=    3.416 closest distance to " CB  PRO A  90 " =    1.190
peak=    3.415 closest distance to " ND2 ASN A 301 " =    0.921
peak=    3.410 closest distance to " O   HOH Z   7 " =    1.451
peak=    3.407 closest distance to " O   ASP A 124 " =    1.325
peak=    3.407 closest distance to " CB  ALA A 248 " =    1.280
peak=    3.406 closest distance to " O   THR A 220 " =    1.179
peak=    3.406 closest distance to " OH  TYR A  68 " =    0.996
peak=    3.406 closest distance to " O   HOH Z 415 " =    1.670
peak=    3.405 closest distance to " O   HOH Z 435 " =    2.800
peak=    3.404 closest distance to " CB  LEU A  83 " =    0.799
peak=    3.403 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.402 closest distance to " O   HOH Z  90 " =    3.645
peak=    3.401 closest distance to " CB  TYR A 116 " =    1.215
peak=    3.400 closest distance to " CA  ALA A 160 " =    0.985
peak=    3.398 closest distance to " CB  ASP A 124 " =    0.832
peak=    3.398 closest distance to " O   HOH Z  76 " =    1.169
peak=    3.397 closest distance to " O   HOH Z 395 " =    1.431
peak=    3.397 closest distance to " O   HOH Z 430 " =    5.691
peak=    3.395 closest distance to " O   HOH Z 295 " =    1.047
peak=    3.393 closest distance to " CB  PHE A 283 " =    0.908
peak=    3.384 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.379 closest distance to " OG  SER A  62 " =    2.878
peak=    3.379 closest distance to " CB  SER A 141 " =    1.062
peak=    3.377 closest distance to " CB  ASN A 187 " =    1.263
peak=    3.377 closest distance to " CG2 THR A  29 " =    1.431
peak=    3.377 closest distance to " OE1 GLN A  58 " =    3.522
peak=    3.376 closest distance to " N   TYR A 116 " =    1.705
peak=    3.368 closest distance to " O   HOH Z 200 " =    1.645
peak=    3.365 closest distance to " O   HOH Z 139 " =    4.805
peak=    3.359 closest distance to " CA  ILE A 106 " =    0.788
peak=    3.351 closest distance to " O   HOH Z 251 " =    1.564
peak=    3.350 closest distance to " N   GLY A 262 " =    1.249
peak=    3.343 closest distance to " O   HOH Z  88 " =    1.803
peak=    3.334 closest distance to " CB  ASN A 142 " =    1.250
peak=    3.333 closest distance to " N   ASN A 252 " =    1.257
peak=    3.330 closest distance to " CG  GLU A  37 " =    0.962
peak=    3.329 closest distance to " O   HOH Z  68 " =    1.814
peak=    3.328 closest distance to " CA  ARG A 139 " =    1.372
peak=    3.326 closest distance to " O   HOH Z 343 " =    2.544
peak=    3.321 closest distance to " NH2AARG A 145 " =    1.089
peak=    3.320 closest distance to " OG BSER A  99 " =    2.849
peak=    3.320 closest distance to " CA  ASP A 191 " =    0.908
peak=    3.319 closest distance to " NH2 ARG A  56 " =    1.032
peak=    3.317 closest distance to " CA  VAL A  41 " =    0.868
peak=    3.317 closest distance to " O   HOH Z 177 " =    1.459
peak=    3.316 closest distance to " O   HOH Z 234 " =    1.835
peak=    3.311 closest distance to " NH1 ARG A  14 " =    1.232
peak=    3.310 closest distance to " O   HOH Z 299 " =    4.212
peak=    3.306 closest distance to " CB  MET A  47 " =    0.934
peak=    3.305 closest distance to " CB  ARG A 219 " =    1.381
peak=    3.304 closest distance to " O   HOH Z 336 " =    1.917
peak=    3.304 closest distance to " CB  PHE A  16 " =    1.282
peak=    3.302 closest distance to " CG2 THR A  42 " =    0.810
peak=    3.301 closest distance to " CA  LEU A  83 " =    1.299
peak=    3.301 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.299 closest distance to " O   HOH Z 116 " =    1.303
peak=    3.295 closest distance to " O   ASN A 217 " =    1.689
peak=    3.293 closest distance to " CB  ARG A  79 " =    0.908
peak=    3.289 closest distance to " O   HOH Z  88 " =    2.644
peak=    3.286 closest distance to " CG  ARG A 138 " =    1.475
peak=    3.285 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.284 closest distance to " CE  LYS A  76 " =    0.826
peak=    3.283 closest distance to " ND2 ASN A  45 " =    1.470
peak=    3.281 closest distance to " CG2AVAL A 121 " =    1.941
peak=    3.276 closest distance to " O   HOH Z 403 " =    1.292
peak=    3.275 closest distance to " N   GLU A  44 " =    1.472
peak=    3.274 closest distance to " CG1 VAL A 153 " =    1.093
peak=    3.273 closest distance to " O   SER A 141 " =    1.342
peak=    3.271 closest distance to " CZ3 TRP A  85 " =    0.870
peak=    3.270 closest distance to " O   HOH Z 250 " =    1.267
peak=    3.266 closest distance to " CG2 THR A 220 " =    0.789
peak=    3.266 closest distance to " OG BSER A 164 " =    2.124
peak=    3.263 closest distance to " O   GLY A  91 " =    1.123
peak=    3.263 closest distance to " NH1 ARG A  36 " =    1.254
peak=    3.261 closest distance to " O   HOH Z 359 " =    1.522
peak=    3.259 closest distance to " CA  CYS A 260 " =    1.505
peak=    3.258 closest distance to " NZ  LYS A 117 " =    2.953
peak=    3.257 closest distance to " CB  ALA A 256 " =    1.537
peak=    3.256 closest distance to " O   HOH Z 281 " =    2.539
peak=    3.255 closest distance to " O   HOH Z 213 " =    1.601
peak=    3.249 closest distance to " O   HOH Z  21 " =    1.826
peak=    3.243 closest distance to " O   HOH Z 287 " =    2.373
peak=    3.243 closest distance to " O   HOH Z  47 " =    2.680
peak=    3.242 closest distance to " CA  SER A  87 " =    0.955
peak=    3.237 closest distance to " O   HOH Z 272 " =    1.261
peak=    3.232 closest distance to " O  BHOH Z 338 " =    2.156
peak=    3.232 closest distance to " CE1 TYR A  30 " =    0.957
peak=    3.232 closest distance to " CB  ALA A  71 " =    1.301
peak=    3.230 closest distance to " CA  GLY A 267 " =    1.086
peak=    3.224 closest distance to " NH1BARG A 102 " =    1.006
peak=    3.224 closest distance to " CB  ALA A  43 " =    1.017
peak=    3.223 closest distance to " N   ASN A  39 " =    1.285
peak=    3.222 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.221 closest distance to " CB  PRO A  54 " =    1.306
peak=    3.219 closest distance to " CD  LYS A  76 " =    1.925
peak=    3.218 closest distance to " O   HOH Z 193 " =    1.878
peak=    3.218 closest distance to " CB  VAL A 265 " =    1.242
peak=    3.216 closest distance to " CD  ARG A 159 " =    0.846
peak=    3.213 closest distance to " O   VAL A  72 " =    1.256
peak=    3.213 closest distance to " CA  ALA A 248 " =    1.260
peak=    3.204 closest distance to " OG  SER A 245 " =    1.562
peak=    3.204 closest distance to " O   HOH Z 195 " =    1.387
peak=    3.199 closest distance to " O   HOH Z 421 " =    1.890
peak=    3.199 closest distance to " OE1 GLN A  58 " =    0.966
peak=    3.197 closest distance to " O   HOH Z 364 " =    2.109
peak=    3.194 closest distance to " N   ALA A  10 " =    1.697
peak=    3.193 closest distance to " O   HOH Z 435 " =    1.935
peak=    3.193 closest distance to " O   HOH Z 432 " =    1.680
peak=    3.192 closest distance to " CA  ASP A 162 " =    1.141
peak=    3.192 closest distance to " O   ARG A 275 " =    0.812
peak=    3.189 closest distance to " NH1 ARG A 269 " =    0.773
peak=    3.188 closest distance to " C   TYR A 214 " =    1.542
peak=    3.188 closest distance to " CG2 ILE A  20 " =    1.318
peak=    3.183 closest distance to " O   HOH Z 144 " =    1.520
peak=    3.181 closest distance to " OH  TYR A 116 " =    1.294
peak=    3.178 closest distance to " CB  ARG A 156 " =    1.072
peak=    3.177 closest distance to " O   HOH Z 383 " =    2.151
peak=    3.177 closest distance to " O   HOH Z 219 " =    2.247
peak=    3.177 closest distance to " O   HOH Z 420 " =    5.319
peak=    3.174 closest distance to " CB  ALA A 114 " =    0.791
peak=    3.170 closest distance to " O   HOH Z 131 " =    2.534
peak=    3.169 closest distance to " CB  GLN A 194 " =    0.949
peak=    3.166 closest distance to " CB  SER A 210 " =    1.011
peak=    3.162 closest distance to " O   HOH Z  22 " =    2.297
peak=    3.162 closest distance to " CB  LEU A 281 " =    0.872
peak=    3.157 closest distance to " O   HOH Z 313 " =    2.028
peak=    3.156 closest distance to " CG2 VAL A 126 " =    0.978
peak=    3.153 closest distance to " O   HOH Z 423 " =    1.826
peak=    3.152 closest distance to " N   TYR A 247 " =    1.275
peak=    3.151 closest distance to " CB  SER A  26 " =    0.825
peak=    3.150 closest distance to " O   HOH Z  59 " =    1.947
peak=    3.145 closest distance to " O   HOH Z 344 " =    3.309
peak=    3.143 closest distance to " O   HOH Z  26 " =    1.056
peak=    3.141 closest distance to " CB  LEU A   5 " =    1.183
peak=    3.140 closest distance to " O   HOH Z 213 " =    2.702
peak=    3.139 closest distance to " CG2 ILE A 234 " =    1.347
peak=    3.128 closest distance to " O   HOH Z 134 " =    2.348
peak=    3.125 closest distance to " N   ILE A  33 " =    0.968
peak=    3.121 closest distance to " CD  ARG A  24 " =    1.234
peak=    3.120 closest distance to " O   HOH Z 240 " =    2.487
peak=    3.120 closest distance to " C   ILE A 106 " =    1.853
peak=    3.117 closest distance to " CA  ASN A 176 " =    1.299
peak=    3.117 closest distance to " ND1 HIS A  81 " =    1.352
peak=    3.117 closest distance to " CB  PRO A 198 " =    1.133
peak=    3.114 closest distance to " CG1 ILE A  20 " =    1.290
peak=    3.112 closest distance to " CA  GLN A 223 " =    0.818
peak=    3.105 closest distance to " O   HOH Z  39 " =    1.319
peak=    3.104 closest distance to " OE1 GLN A 223 " =    2.373
peak=    3.104 closest distance to " N   ALA A 292 " =    0.992
peak=    3.102 closest distance to " CB  ALA A 100 " =    1.287
peak=    3.102 closest distance to " CE3 TRP A  85 " =    1.180
peak=    3.101 closest distance to " O   HOH Z 193 " =    2.051
peak=    3.100 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.098 closest distance to " CG  LYS A  76 " =    1.151
peak=    3.096 closest distance to " CA  ALA A 158 " =    1.491
peak=    3.090 closest distance to " CB  LEU A 222 " =    1.355
peak=    3.088 closest distance to " CA  GLY A 229 " =    0.850
peak=    3.088 closest distance to " O   THR A 182 " =    1.446
peak=    3.086 closest distance to " CB  ALA A 114 " =    1.130
peak=    3.084 closest distance to " CG  PHE A 204 " =    0.925
peak=    3.075 closest distance to " O   HOH Z 428 " =    2.122
peak=    3.075 closest distance to " OD2 ASP A 298 " =    3.436
peak=    3.074 closest distance to " O   HOH Z 427 " =    3.333
peak=    3.071 closest distance to " CE1 HIS A  81 " =    1.493
peak=    3.066 closest distance to " O   HOH Z 156 " =    2.714
peak=    3.065 closest distance to " CB  ASP A 140 " =    0.822
peak=    3.064 closest distance to " ND1 HIS A 115 " =    3.035
peak=    3.055 closest distance to " CB  ASN A  39 " =    1.328
peak=    3.054 closest distance to " O   HOH Z  73 " =    2.114
peak=    3.046 closest distance to " CA  PRO A  90 " =    1.028
peak=    3.046 closest distance to " O   HOH Z  47 " =    1.278

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.540 - 5.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 228
   mapped sites are within: 0.757 - 5.746

peak=   -4.985 closest distance to " O   HOH Z 203 " =    0.790
peak=   -4.611 closest distance to " CD  GLN A  58 " =    0.871
peak=   -4.581 closest distance to " O   HOH Z 411 " =    5.512
peak=   -4.494 closest distance to " CD  GLN A 223 " =    1.388
peak=   -4.354 closest distance to " CD1 PHE A  59 " =    2.044
peak=   -4.326 closest distance to " O   GLN A  11 " =    0.894
peak=   -4.314 closest distance to " O   PRO A 198 " =    1.342
peak=   -4.310 closest distance to " O   HOH Z 418 " =    1.199
peak=   -4.266 closest distance to " O   HOH Z 166 " =    1.369
peak=   -4.165 closest distance to " CD  ARG A  14 " =    3.354
peak=   -4.093 closest distance to " CE2 PHE A  61 " =    2.834
peak=   -4.092 closest distance to " CD  GLN A  58 " =    0.953
peak=   -4.070 closest distance to " OD1 ASN A 301 " =    0.843
peak=   -4.047 closest distance to " O   HOH Z 407 " =    0.951
peak=   -4.043 closest distance to " O   HOH Z   7 " =    1.064
peak=   -3.970 closest distance to " CG  PRO A 243 " =    1.671
peak=   -3.964 closest distance to " O   HOH Z 211 " =    1.160
peak=   -3.955 closest distance to " N   ALA A  43 " =    2.681
peak=   -3.949 closest distance to " CG  ARG A 269 " =    2.371
peak=   -3.949 closest distance to " CD2 LEU A 237 " =    2.546
peak=   -3.943 closest distance to " OE1 GLN A  88 " =    1.100
peak=   -3.920 closest distance to " O   VAL A  67 " =    2.842
peak=   -3.918 closest distance to " CG2 ILE A  49 " =    2.683
peak=   -3.880 closest distance to " O   HOH Z 133 " =    1.639
peak=   -3.813 closest distance to " O   ASP A 171 " =    0.976
peak=   -3.780 closest distance to " SD  MET A 105 " =    2.404
peak=   -3.780 closest distance to " O   SER A 206 " =    1.254
peak=   -3.776 closest distance to " CB  ALA A  43 " =    2.788
peak=   -3.760 closest distance to " O   HOH Z 250 " =    1.924
peak=   -3.739 closest distance to " CD2 PHE A  61 " =    2.109
peak=   -3.735 closest distance to " CG  GLN A  11 " =    1.300
peak=   -3.733 closest distance to " O   HOH Z 155 " =    1.681
peak=   -3.731 closest distance to " CB  PRO A 243 " =    2.875
peak=   -3.730 closest distance to " CG2 ILE A  20 " =    2.764
peak=   -3.725 closest distance to " C   VAL A 265 " =    0.867
peak=   -3.718 closest distance to " O   HOH Z 331 " =    1.138
peak=   -3.718 closest distance to " O   HOH Z  67 " =    1.442
peak=   -3.713 closest distance to " O   HOH Z 221 " =    1.008
peak=   -3.710 closest distance to " CE3 TRP A 150 " =    2.212
peak=   -3.702 closest distance to " O   HOH Z   5 " =    1.753
peak=   -3.701 closest distance to " CD1 LEU A 101 " =    2.502
peak=   -3.694 closest distance to " CD  GLN A  88 " =    0.973
peak=   -3.691 closest distance to " C   GLY A 133 " =    1.257
peak=   -3.691 closest distance to " C   ASN A 285 " =    2.351
peak=   -3.677 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.650 closest distance to " O   HOH Z 392 " =    1.171
peak=   -3.646 closest distance to " CG2 VAL A 202 " =    2.208
peak=   -3.643 closest distance to " O   HOH Z 109 " =    3.510
peak=   -3.619 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.619 closest distance to " OD2 ASP A 171 " =    1.871
peak=   -3.618 closest distance to " CD  GLN A 223 " =    0.984
peak=   -3.611 closest distance to " O   HOH Z 196 " =    1.774
peak=   -3.601 closest distance to " O   HOH Z  90 " =    3.571
peak=   -3.595 closest distance to " NE2 GLN A 194 " =    2.103
peak=   -3.592 closest distance to " O   VAL A 189 " =    2.570
peak=   -3.585 closest distance to " O   HOH Z 166 " =    2.356
peak=   -3.576 closest distance to " O   HOH Z 422 " =    1.420
peak=   -3.575 closest distance to " OD2 ASP A 298 " =    1.015
peak=   -3.574 closest distance to " CG2 THR A 182 " =    2.349
peak=   -3.570 closest distance to " O   HOH Z  65 " =    1.914
peak=   -3.568 closest distance to " CD1 LEU A 167 " =    2.102
peak=   -3.568 closest distance to " CA  GLU A 277 " =    1.121
peak=   -3.567 closest distance to " O   SER A 210 " =    1.730
peak=   -3.567 closest distance to " O   HOH Z 234 " =    4.389
peak=   -3.565 closest distance to " O   HOH Z  56 " =    1.611
peak=   -3.563 closest distance to " O   HOH Z  15 " =    1.536
peak=   -3.557 closest distance to " N   ARG A 275 " =    1.144
peak=   -3.551 closest distance to " CD2 TYR A  30 " =    2.787
peak=   -3.547 closest distance to " O   HOH Z 174 " =    1.905
peak=   -3.546 closest distance to " CZ  TYR A 169 " =    1.924
peak=   -3.545 closest distance to " O   HOH Z 368 " =    2.041
peak=   -3.539 closest distance to " O   HOH Z 377 " =    0.763
peak=   -3.536 closest distance to " O   HOH Z 407 " =    3.711
peak=   -3.532 closest distance to " OD1 ASN A 148 " =    1.371
peak=   -3.517 closest distance to " O   PRO A 163 " =    2.171
peak=   -3.508 closest distance to " CA  GLY A 203 " =    2.309
peak=   -3.506 closest distance to " CG  LEU A 281 " =    2.077
peak=   -3.502 closest distance to " OXT GLY A 302 " =    3.034
peak=   -3.501 closest distance to " O   HOH Z  40 " =    2.898
peak=   -3.498 closest distance to " O   HOH Z 114 " =    1.102
peak=   -3.497 closest distance to " O   ARG A 275 " =    1.849
peak=   -3.496 closest distance to " CG  LEU A  83 " =    2.069
peak=   -3.495 closest distance to " NH2 ARG A  79 " =    1.843
peak=   -3.492 closest distance to " O   HOH Z  35 " =    1.242
peak=   -3.485 closest distance to " ND2 ASN A  45 " =    1.842
peak=   -3.481 closest distance to " O   HOH Z   6 " =    1.291
peak=   -3.480 closest distance to " SD  MET A  93 " =    1.624
peak=   -3.468 closest distance to " CG  GLU A  53 " =    1.499
peak=   -3.463 closest distance to " CA  TYR A  68 " =    2.784
peak=   -3.461 closest distance to " N   ALA A 226 " =    2.121
peak=   -3.460 closest distance to " O   ALA A  34 " =    2.461
peak=   -3.458 closest distance to " CA  PRO A 280 " =    1.029
peak=   -3.455 closest distance to " CD1 ILE A 109 " =    2.814
peak=   -3.452 closest distance to " CD2 TYR A 293 " =    1.889
peak=   -3.448 closest distance to " O   HOH Z  37 " =    1.417
peak=   -3.447 closest distance to " CA  SER A 276 " =    1.491
peak=   -3.443 closest distance to " O   HOH Z 156 " =    3.649
peak=   -3.443 closest distance to " OG  SER A  63 " =    1.151
peak=   -3.442 closest distance to " C   LEU A 222 " =    0.990
peak=   -3.435 closest distance to " CD1 ILE A 106 " =    2.166
peak=   -3.431 closest distance to " NE  ARG A  79 " =    1.248
peak=   -3.427 closest distance to " O   HOH Z  52 " =    1.858
peak=   -3.424 closest distance to " O   HOH Z 155 " =    2.029
peak=   -3.423 closest distance to " ND2 ASN A  60 " =    1.373
peak=   -3.422 closest distance to " O   HOH Z 197 " =    1.837
peak=   -3.414 closest distance to " O   HOH Z 205 " =    0.757
peak=   -3.410 closest distance to " O   SER A 271 " =    2.133
peak=   -3.408 closest distance to " CG2BVAL A  41 " =    1.443
peak=   -3.406 closest distance to " O  BHOH Z  74 " =    1.055
peak=   -3.403 closest distance to " O   HOH Z 134 " =    2.490
peak=   -3.402 closest distance to " CB  SER A 146 " =    2.118
peak=   -3.400 closest distance to " CG  PRO A 280 " =    2.158
peak=   -3.388 closest distance to " NE2 GLN A 223 " =    1.224
peak=   -3.384 closest distance to " CD  ARG A 156 " =    1.978
peak=   -3.382 closest distance to " O   HOH Z 207 " =    1.462
peak=   -3.381 closest distance to " OG BSER A 210 " =    1.217
peak=   -3.374 closest distance to " O   VAL A 174 " =    2.119
peak=   -3.372 closest distance to " O   HOH Z 128 " =    2.563
peak=   -3.371 closest distance to " NE2 GLN A 278 " =    1.798
peak=   -3.369 closest distance to " CD1 ILE A 263 " =    1.994
peak=   -3.366 closest distance to " O   HOH Z 371 " =    1.050
peak=   -3.363 closest distance to " O   HOH Z 424 " =    2.969
peak=   -3.360 closest distance to " O   HOH Z 283 " =    2.531
peak=   -3.357 closest distance to " O   LYS A  76 " =    1.437
peak=   -3.355 closest distance to " O   HOH Z 292 " =    4.726
peak=   -3.355 closest distance to " O   HOH Z 366 " =    1.693
peak=   -3.352 closest distance to " CG  PRO A 163 " =    2.499
peak=   -3.350 closest distance to " O   HOH Z 136 " =    2.552
peak=   -3.347 closest distance to " O   HOH Z 290 " =    0.987
peak=   -3.344 closest distance to " CA  VAL A 197 " =    0.979
peak=   -3.343 closest distance to " O   HOH Z 198 " =    1.431
peak=   -3.342 closest distance to " O   HOH Z  54 " =    1.577
peak=   -3.341 closest distance to " O   HOH Z 171 " =    2.426
peak=   -3.338 closest distance to " O   HOH Z 287 " =    1.680
peak=   -3.336 closest distance to " NH2 ARG A  66 " =    1.918
peak=   -3.333 closest distance to " O   HOH Z 423 " =    1.504
peak=   -3.331 closest distance to " O   HOH Z 191 " =    5.746
peak=   -3.319 closest distance to " O   ILE A 109 " =    2.653
peak=   -3.318 closest distance to " CD2 HIS A 115 " =    1.052
peak=   -3.317 closest distance to " CA  GLY A 241 " =    3.530
peak=   -3.317 closest distance to " CA  GLY A 241 " =    3.061
peak=   -3.309 closest distance to " ND2 ASN A  60 " =    2.088
peak=   -3.306 closest distance to " CZ  ARG A 259 " =    0.879
peak=   -3.302 closest distance to " O   HOH Z 216 " =    1.024
peak=   -3.302 closest distance to " CB  ALA A 131 " =    2.370
peak=   -3.301 closest distance to " CB  ALA A 291 " =    2.483
peak=   -3.301 closest distance to " CG2AVAL A  41 " =    2.839
peak=   -3.300 closest distance to " CZ  ARG A 156 " =    1.696
peak=   -3.299 closest distance to " CD  ARG A  36 " =    0.963
peak=   -3.297 closest distance to " O   SER A 276 " =    1.613
peak=   -3.297 closest distance to " CG2BVAL A 121 " =    1.331
peak=   -3.296 closest distance to " CG  ARG A 259 " =    1.569
peak=   -3.294 closest distance to " O  BHOH Z 338 " =    1.360
peak=   -3.290 closest distance to " CB  PRO A  54 " =    2.588
peak=   -3.282 closest distance to " O   HOH Z 200 " =    1.134
peak=   -3.280 closest distance to " O   HOH Z  19 " =    2.276
peak=   -3.278 closest distance to " O   HOH Z 423 " =    2.668
peak=   -3.271 closest distance to " O   HOH Z 403 " =    1.035
peak=   -3.270 closest distance to " O   PHE A 218 " =    1.411
peak=   -3.266 closest distance to " O   HOH Z 265 " =    1.205
peak=   -3.266 closest distance to " NE2 GLN A  94 " =    1.844
peak=   -3.266 closest distance to " CG1 VAL A 112 " =    2.620
peak=   -3.264 closest distance to " O   HOH Z 326 " =    5.058
peak=   -3.261 closest distance to " O   HOH Z 340 " =    1.553
peak=   -3.260 closest distance to " CZ3 TRP A  70 " =    1.577
peak=   -3.250 closest distance to " NE2 GLN A 103 " =    1.931
peak=   -3.247 closest distance to " CB  ALA A  10 " =    2.189
peak=   -3.247 closest distance to " CG  ARG A 259 " =    2.423
peak=   -3.246 closest distance to " O   HOH Z 165 " =    1.810
peak=   -3.241 closest distance to " O   HOH Z 345 " =    3.126
peak=   -3.235 closest distance to " CD1 PHE A 130 " =    2.404
peak=   -3.234 closest distance to " O   HOH Z 149 " =    1.781
peak=   -3.232 closest distance to " C   THR A 279 " =    1.053
peak=   -3.228 closest distance to " CE  MET A  93 " =    1.856
peak=   -3.226 closest distance to " O   HOH Z 184 " =    1.487
peak=   -3.225 closest distance to " O   HOH Z 336 " =    5.541
peak=   -3.223 closest distance to " OD1 ASP A 171 " =    1.645
peak=   -3.220 closest distance to " O   HOH Z   7 " =    1.303
peak=   -3.217 closest distance to " O   HOH Z  19 " =    0.765
peak=   -3.215 closest distance to " ND2 ASN A  60 " =    2.168
peak=   -3.211 closest distance to " O   HOH Z 259 " =    2.080
peak=   -3.210 closest distance to " CZ  PHE A  38 " =    2.414
peak=   -3.208 closest distance to " CH2 TRP A 150 " =    1.109
peak=   -3.207 closest distance to " CB  ASN A  45 " =    2.150
peak=   -3.201 closest distance to " O   SER A  26 " =    1.494
peak=   -3.190 closest distance to " O   HOH Z 109 " =    1.712
peak=   -3.183 closest distance to " C   ILE A 239 " =    2.235
peak=   -3.179 closest distance to " O   HOH Z 185 " =    2.618
peak=   -3.178 closest distance to " O   HOH Z 109 " =    1.181
peak=   -3.177 closest distance to " O   HOH Z 137 " =    1.317
peak=   -3.177 closest distance to " CD  GLN A  77 " =    1.064
peak=   -3.172 closest distance to " OH  TYR A 247 " =    2.172
peak=   -3.172 closest distance to " OD1 ASN A  39 " =    1.041
peak=   -3.159 closest distance to " O   HOH Z 140 " =    1.867
peak=   -3.157 closest distance to " O   HOH Z  16 " =    1.826
peak=   -3.151 closest distance to " OG BSER A 216 " =    2.318
peak=   -3.150 closest distance to " CD  LYS A 289 " =    2.274
peak=   -3.149 closest distance to " OD1 ASP A 272 " =    1.604
peak=   -3.148 closest distance to " CG  ASN A  45 " =    0.873
peak=   -3.147 closest distance to " CB  ALA A 248 " =    2.281
peak=   -3.143 closest distance to " O   HOH Z 174 " =    3.626
peak=   -3.142 closest distance to " O   HOH Z 435 " =    1.740
peak=   -3.137 closest distance to " O   HOH Z 281 " =    2.351
peak=   -3.136 closest distance to " O   HOH Z  60 " =    1.775
peak=   -3.135 closest distance to " O   SER A 135 " =    1.541
peak=   -3.133 closest distance to " CD2 PHE A 225 " =    1.363
peak=   -3.131 closest distance to " O   HOH Z 151 " =    1.416
peak=   -3.130 closest distance to " O   HOH Z 290 " =    1.259
peak=   -3.130 closest distance to " CA  ASP A  65 " =    1.309
peak=   -3.129 closest distance to " C   ARG A  79 " =    2.757
peak=   -3.128 closest distance to " O   ARG A  79 " =    1.196
peak=   -3.128 closest distance to " CG2 ILE A 263 " =    2.227
peak=   -3.123 closest distance to " OH  TYR A 172 " =    1.897
peak=   -3.122 closest distance to " CA  ASN A 127 " =    1.105
peak=   -3.119 closest distance to " CG  GLN A 103 " =    2.369
peak=   -3.116 closest distance to " CE1 HIS A  81 " =    1.475
peak=   -3.107 closest distance to " O   HOH Z 378 " =    1.386
peak=   -3.106 closest distance to " NH2 ARG A 159 " =    2.413
peak=   -3.102 closest distance to " CZ  TYR A  68 " =    1.078
peak=   -3.093 closest distance to " CB  HIS A  86 " =    1.206
peak=   -3.086 closest distance to " O   HOH Z 120 " =    4.530
peak=   -3.080 closest distance to " O   HOH Z 265 " =    1.914
peak=   -3.053 closest distance to " O   HOH Z  91 " =    2.335
peak=   -3.050 closest distance to " O   HOH Z 150 " =    1.814

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4692 0.4592   6.283559e+00   6.261078e+00
   1_bss:  0.4587 0.4477   6.276653e+00   6.250386e+00
   1_xyz:  0.3664 0.3975   6.127655e+00   6.172173e+00
   1_adp:  0.3368 0.4081   6.082760e+00   6.184474e+00
   1_occ:  0.3365 0.4071   6.082043e+00   6.184103e+00
   2_bss:  0.3351 0.4048   6.083980e+00   6.186307e+00
   2_xyz:  0.2892 0.3560   5.970131e+00   6.105829e+00
   2_adp:  0.2824 0.3496   5.959032e+00   6.095377e+00
   2_occ:  0.2823 0.3497   5.958893e+00   6.095687e+00
   3_bss:  0.2825 0.3495   5.959786e+00   6.095371e+00
   3_xyz:  0.2239 0.2795   5.743743e+00   5.917336e+00
   3_adp:  0.2041 0.2646   5.676007e+00   5.868243e+00
   3_occ:  0.2039 0.2646   5.675584e+00   5.868340e+00
   4_bss:  0.2039 0.2640   5.675338e+00   5.867557e+00
   4_xyz:  0.1719 0.2201   5.513046e+00   5.716280e+00
   4_adp:  0.1634 0.2075   5.465834e+00   5.661433e+00
   4_occ:  0.1633 0.2074   5.465024e+00   5.660915e+00
   5_bss:  0.1637 0.2072   5.466862e+00   5.660829e+00
   5_xyz:  0.1393 0.1851   5.330401e+00   5.543531e+00
   5_adp:  0.1343 0.1829   5.302281e+00   5.521558e+00
   5_occ:  0.1341 0.1829   5.301836e+00   5.521232e+00
   5_bss:  0.1346 0.1827   5.302905e+00   5.520335e+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:  0.284  39.964  -3.980   4.221   2.517   0.000   0.000   0.000
   1_xyz:  0.284  39.964  -3.980   4.221   2.517   0.000   0.000   0.000
   1_adp:  0.284  39.964  -3.980   4.221   2.517   0.000   0.000   0.000
   1_occ:  0.284  39.964  -3.980   4.221   2.517   0.000   0.000   0.000
   2_bss:  0.298  52.609  -1.452   2.493   1.511   0.000   0.000   0.000
   2_xyz:  0.298  52.609  -1.452   2.493   1.511   0.000   0.000   0.000
   2_adp:  0.298  52.609  -1.452   2.493   1.511   0.000   0.000   0.000
   2_occ:  0.298  52.609  -1.452   2.493   1.511   0.000   0.000   0.000
   3_bss:  0.315  64.787  -1.304   2.022   1.035   0.000   0.000   0.000
   3_xyz:  0.315  64.787  -1.304   2.022   1.035   0.000   0.000   0.000
   3_adp:  0.315  64.787  -1.304   2.022   1.035   0.000   0.000   0.000
   3_occ:  0.315  64.787  -1.304   2.022   1.035   0.000   0.000   0.000
   4_bss:  0.332  82.979  -1.280   0.921   0.655   0.000   0.000   0.000
   4_xyz:  0.332  82.979  -1.280   0.921   0.655   0.000   0.000   0.000
   4_adp:  0.332  82.979  -1.280   0.921   0.655   0.000   0.000   0.000
   4_occ:  0.332  82.979  -1.280   0.921   0.655   0.000   0.000   0.000
   5_bss:  0.336  83.997  -1.492   0.206   0.499   0.000   0.000   0.000
   5_xyz:  0.336  83.997  -1.492   0.206   0.499   0.000   0.000   0.000
   5_adp:  0.336  83.997  -1.492   0.206   0.499   0.000   0.000   0.000
   5_occ:  0.336  83.997  -1.492   0.206   0.499   0.000   0.000   0.000
   5_bss:  0.333  79.105  -1.347  -0.059   0.649  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.161 0.4562  0.5942    65946.574
   1_bss:  53.745 0.4731  0.6378    62728.508
   1_xyz:  45.972 0.5693  0.7501    46689.397
   1_adp:  46.586 0.5617  0.7403    48305.297
   1_occ:  46.575 0.5618  0.7396    48227.714
   2_bss:  46.257 0.5660  0.7477    48113.138
   2_xyz:  39.301 0.6506  0.8461    36523.777
   2_adp:  38.312 0.6626  0.8438    35294.664
   2_occ:  38.307 0.6627  0.8436    35315.463
   3_bss:  38.261 0.6634  0.8371    35315.910
   3_xyz:  29.260 0.7654  0.9397    21078.348
   3_adp:  27.026 0.7900  0.9373    18537.389
   3_occ:  27.019 0.7901  0.9373    18524.038
   4_bss:  26.913 0.7913  0.9240    18428.621
   4_xyz:  21.932 0.8423  0.9578    12583.909
   4_adp:  20.196 0.8601  0.9567    11237.628
   4_occ:  20.176 0.8603  0.9571    11226.968
   5_bss:  20.171 0.8604  0.9455    11228.346
   5_xyz:  17.442 0.8856  0.9615     8768.485
   5_adp:  16.911 0.8906  0.9550     8470.164
   5_occ:  16.903 0.8907  0.9549     8468.739
   5_bss:  16.889 0.8908  0.9553     8446.307
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6786e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6786e-01
   1_xyz:   1.644  0.013  0.101 16.155  0.006  4.112   1.4107e-01
   1_adp:   1.644  0.013  0.101 16.155  0.006  4.112   1.4107e-01
   1_occ:   1.644  0.013  0.101 16.155  0.006  4.112   1.4107e-01
   2_bss:   1.644  0.013  0.101 16.155  0.006  4.112   1.4107e-01
   2_xyz:   1.155  0.008  0.077 14.842  0.004  4.111   7.3723e-02
   2_adp:   1.155  0.008  0.077 14.842  0.004  4.111   7.3723e-02
   2_occ:   1.155  0.008  0.077 14.842  0.004  4.111   7.3723e-02
   3_bss:   1.155  0.008  0.077 14.842  0.004  4.111   7.3723e-02
   3_xyz:   1.165  0.009  0.078 14.885  0.005  4.125   7.8354e-02
   3_adp:   1.165  0.009  0.078 14.885  0.005  4.125   7.8354e-02
   3_occ:   1.165  0.009  0.078 14.885  0.005  4.125   7.8354e-02
   4_bss:   1.165  0.009  0.078 14.885  0.005  4.125   7.8354e-02
   4_xyz:   0.980  0.007  0.073 14.328  0.003  4.114   5.8244e-02
   4_adp:   0.980  0.007  0.073 14.328  0.003  4.114   5.8244e-02
   4_occ:   0.980  0.007  0.073 14.328  0.003  4.114   5.8244e-02
   5_bss:   0.980  0.007  0.073 14.328  0.003  4.114   5.8244e-02
   5_xyz:   1.097  0.009  0.079 14.385  0.003  4.127   6.9447e-02
   5_adp:   1.097  0.009  0.079 14.385  0.003  4.127   6.9447e-02
   5_occ:   1.097  0.009  0.079 14.385  0.003  4.127   6.9447e-02
   5_bss:   1.097  0.009  0.079 14.385  0.003  4.127   6.9447e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.658   2.4493e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.658   2.4493e-01
   1_xyz:   9.150  0.083  0.354 83.279  0.037  1.976   1.1630e-01
   1_adp:   9.150  0.083  0.354 83.279  0.037  1.976   1.1630e-01
   1_occ:   9.150  0.083  0.354 83.279  0.037  1.976   1.1630e-01
   2_bss:   9.150  0.083  0.354 83.279  0.037  1.976   1.1630e-01
   2_xyz:   7.628  0.043  0.244 86.253  0.017  2.250   9.3104e-02
   2_adp:   7.628  0.043  0.244 86.253  0.017  2.250   9.3104e-02
   2_occ:   7.628  0.043  0.244 86.253  0.017  2.250   9.3104e-02
   3_bss:   7.628  0.043  0.244 86.253  0.017  2.250   9.3104e-02
   3_xyz:   7.279  0.042  0.242 88.667  0.040  2.222   7.5714e-02
   3_adp:   7.279  0.042  0.242 88.667  0.040  2.222   7.5714e-02
   3_occ:   7.279  0.042  0.242 88.667  0.040  2.222   7.5714e-02
   4_bss:   7.279  0.042  0.242 88.667  0.040  2.222   7.5714e-02
   4_xyz:   7.015  0.045  0.239 85.692  0.023  2.217   3.9243e-02
   4_adp:   7.015  0.045  0.239 85.692  0.023  2.217   3.9243e-02
   4_occ:   7.015  0.045  0.239 85.692  0.023  2.217   3.9243e-02
   5_bss:   7.015  0.045  0.239 85.692  0.023  2.217   3.9243e-02
   5_xyz:   8.062  0.049  0.254 83.460  0.027  2.291   5.0936e-02
   5_adp:   8.062  0.049  0.254 83.460  0.027  2.291   5.0936e-02
   5_occ:   8.062  0.049  0.254 83.460  0.027  2.291   5.0936e-02
   5_bss:   8.062  0.049  0.254 83.460  0.027  2.291   5.0936e-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: 105.82   0.00  18.83  84.78   0.00  15.39 105.82   0.00  37.55
   1_occ: 105.82   0.00  18.83  84.78   0.00  15.39 105.82   0.00  37.55
   2_bss: 105.82   0.00  18.83  84.78   0.00  15.39 105.82   0.00  37.55
   2_xyz: 105.82   0.00  18.83  84.78   0.00  15.39 105.82   0.00  37.55
   2_adp: 107.05   0.00  17.98  83.46   0.00  14.57 107.05   0.00  36.54
   2_occ: 107.05   0.00  17.98  83.46   0.00  14.57 107.05   0.00  36.54
   3_bss: 107.05   0.00  17.98  83.46   0.00  14.57 107.05   0.00  36.54
   3_xyz: 107.05   0.00  17.98  83.46   0.00  14.57 107.05   0.00  36.54
   3_adp: 111.43   0.00  18.55 102.00   0.00  13.73 111.43   2.00  44.84
   3_occ: 111.43   0.00  18.55 102.00   0.00  13.73 111.43   2.00  44.84
   4_bss: 111.43   0.00  18.55 102.00   0.00  13.73 111.43   2.00  44.84
   4_xyz: 111.43   0.00  18.55 102.00   0.00  13.73 111.43   2.00  44.84
   4_adp: 107.35   0.00  17.44  98.92   0.00  12.56 107.35   3.84  44.01
   4_occ: 107.35   0.00  17.44  98.92   0.00  12.56 107.35   3.84  44.01
   5_bss: 107.35   0.00  17.44  98.92   0.00  12.56 107.35   3.84  44.01
   5_xyz: 107.35   0.00  17.44  98.92   0.00  12.56 107.35   3.84  44.01
   5_adp: 107.53   0.00  16.98  97.68   0.00  12.04 107.53   0.00  43.87
   5_occ: 107.53   0.00  16.98  97.68   0.00  12.04 107.53   0.00  43.87
   5_bss: 107.53   0.00  16.98  97.69   0.00  12.04 107.53   0.00  43.88
------------------------------------------------------------------------
 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:    1.567    0.021    0.382
   1_adp:    1.567    0.021    0.382
   1_occ:    1.567    0.021    0.382
   2_bss:    1.567    0.021    0.382
   2_xyz:    1.340    0.038    0.482
   2_adp:    1.340    0.038    0.482
   2_occ:    1.340    0.038    0.482
   3_bss:    1.340    0.038    0.482
   3_xyz:    1.503    0.042    0.678
   3_adp:    1.503    0.042    0.678
   3_occ:    1.503    0.042    0.678
   4_bss:    1.503    0.042    0.678
   4_xyz:    1.559    0.104    0.770
   4_adp:    1.559    0.104    0.770
   4_occ:    1.559    0.104    0.770
   5_bss:    1.559    0.104    0.770
   5_xyz:    1.677    0.091    0.835
   5_adp:    1.677    0.091    0.835
   5_occ:    1.677    0.091    0.835
   5_bss:    1.677    0.091    0.835
------------------------------------------------------------------------

CPU time actual refinement: 346.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/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_724/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_724/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.55 
  Macro-tasks:
    bulk solvent and scale       = 50.03  
    individual site refinement   = 136.23 
    weights calculation          = 29.50  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 222.39 
  Micro-tasks:
    mask                            = 2.79   
    f_calc                          = 110.20 
    alpha_beta                      = 8.38   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 112.67 
    fmodel                         = 8.29   
    r_factors                      = 0.27   
    phase_errors                   = 11.22  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 255.33 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.955 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    631 calls, 109.87 s
gradients_fft:          576 calls, 101.92 s

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

# Date 2008-01-16 Time 05:30:50 PST -0800 (1200490250.05 s)
Start R-work = 0.4692, R-free = 0.4592 (no bulk solvent and anisotropic scale)
Final R-work = 0.1506, R-free = 0.1974 (no bulk solvent and anisotropic scale)

Start R-work = 0.4587, R-free = 0.4477
Final R-work = 0.1346, R-free = 0.1827