# Date 2008-01-16 Time 05:07:39 PST -0800 (1200488859.12 s)
#phil __OFF__

Command line arguments: "../605.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27349
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 605

-------------------------------------------------------------------------------
  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, 45.7567, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95037
Completeness in resolution range: 0.962226
Completeness with d_max=infinity: 0.959305

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9504

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, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95037
Completeness in resolution range: 0.962226
Completeness with d_max=infinity: 0.959305

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1740 [2132/2157]  1922   210   9.8%
  bin  2:  4.1740 -  3.3251 [2062/2082]  1855   207  10.0%
  bin  3:  3.3251 -  2.9084 [2020/2039]  1815   205  10.1%
  bin  4:  2.9084 -  2.6441 [2005/2035]  1806   199   9.9%
  bin  5:  2.6441 -  2.4555 [2011/2030]  1815   196   9.7%
  bin  6:  2.4555 -  2.3113 [1987/2012]  1780   207  10.4%
  bin  7:  2.3113 -  2.1959 [1972/2000]  1772   200  10.1%
  bin  8:  2.1959 -  2.1006 [1970/2006]  1776   194   9.8%
  bin  9:  2.1006 -  2.0199 [1964/2006]  1771   193   9.8%
  bin 10:  2.0199 -  1.9504 [1466/1991]  1318   148  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/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:
        1.43 -     2.12: 31
        2.12 -     2.82: 930
        2.82 -     3.51: 4594
        3.51 -     4.21: 9535
        4.21 -     4.90: 13982
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.427 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.498 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.551 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.704 3.120 -x,y-1/2,-z+1/2
  ... (remaining 29067 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_605/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 45.75675 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4898   r_free= 0.4936   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.298953                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6558 0.99   1390  155 0.4081 0.4200      6.6165      6.6429|
|  2:  4.6558 -  3.7143 0.99   1335  146 0.4427 0.4442      6.8601       6.821|
|  3:  3.7143 -  3.2504 0.99   1316  144 0.4711 0.4706        6.73      6.8072|
|  4:  3.2504 -  2.9557 0.99   1296  153 0.4820 0.4636      6.5724      6.5165|
|  5:  2.9557 -  2.7453 0.99   1298  140 0.5174 0.4843      6.3898      6.3852|
|  6:  2.7453 -  2.5843 0.99   1287  140 0.5195 0.5824      6.2956      6.2805|
|  7:  2.5843 -  2.4555 0.99   1291  139 0.5091 0.4891      6.2587      6.2371|
|  8:  2.4555 -  2.3490 0.98   1256  149 0.5227 0.5075      6.1856      6.1735|
|  9:  2.3490 -  2.2589 0.98   1271  144 0.5355 0.5685      6.1348      6.2097|
| 10:  2.2589 -  2.1812 1.00   1280  139 0.5127 0.5131      6.1135      6.0935|
| 11:  2.1812 -  2.1132 0.98   1274  137 0.5224 0.5664      6.0485      6.0636|
| 12:  2.1132 -  2.0529 0.98   1251  140 0.5193 0.5260      5.9734      6.0276|
| 13:  2.0529 -  1.9990 0.99   1262  138 0.5140 0.5047      5.8839      5.8315|
| 14:  1.9990 -  1.9504 0.64    823   95 0.5534 0.4442      5.8917      5.7528|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6558  1390   155  0.64  39.51   0.81     0.71      91260.90|
|  2:  4.6558 -  3.7143  1335   146  0.64  40.38   0.88     0.77     135166.51|
|  3:  3.7143 -  3.2504  1316   144  0.53  49.10   0.91     0.74     139298.29|
|  4:  3.2504 -  2.9557  1296   153  0.43  57.34   0.92     0.62     123476.08|
|  5:  2.9557 -  2.7453  1298   140  0.33  65.05   0.87     0.48      94456.20|
|  6:  2.7453 -  2.5843  1287   140  0.26  70.27   0.88     0.39      86624.16|
|  7:  2.5843 -  2.4555  1291   139  0.25  71.48   0.92     0.34      74926.46|
|  8:  2.4555 -  2.3490  1256   149  0.25  71.69   0.91     0.37      68381.61|
|  9:  2.3490 -  2.2589  1271   144  0.27  69.88   0.90     0.39      58972.28|
| 10:  2.2589 -  2.1812  1280   139  0.28  69.19   0.95     0.42      55050.90|
| 11:  2.1812 -  2.1132  1274   137  0.23  72.79   0.98     0.36      52960.96|
| 12:  2.1132 -  2.0529  1251   140  0.26  70.89   0.98     0.42      47585.32|
| 13:  2.0529 -  1.9990  1262   138  0.33  65.40   0.96     0.53      36823.41|
| 14:  1.9990 -  1.9504   823    95  0.49  52.76   0.96     0.74      23915.83|
|alpha:            min =        0.34 max =            0.77 mean =         0.52|
|beta:             min =    23915.83 max =       139298.29 mean =     79746.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.81|
|phase err.(test): min =        0.00 max =           89.91 mean =        62.08|
|-----------------------------------------------------------------------------|

============================== 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 = 22.442159             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.416   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.887797              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.826   (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 |  1.427 -  1.774:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.774 -  2.121:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.121 -  2.469:       53 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.469 -  2.816:      877 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.816 -  3.163:     2117 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.163 -  3.511:     2477 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.511 -  3.858:     4710 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.858 -  4.205:     4825 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.205 -  4.553:     6324 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7658 |
|-----------------------------------------------------------------------------|
|-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 |        0.203 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.427 |       0.840 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4898   r_free= 0.4936   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.298953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4798   r_free= 0.4817   ksol= 0.35   Bsol= 20.54   scale= 0.906   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.58,1.31,1.26,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.296133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.706458             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.273   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.855264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.679   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4798      final r-factor (work) = 0.3954          |
| start r-factor (free) = 0.4817      final r-factor (free) = 0.4347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.9107 = 17.71 * 0.50 * 6.2923 + 1.00 * 0.2033                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.1231 = 17.71 * 0.50 * 6.2062 + 1.00 * 0.1786                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3954      final r-factor (work) = 0.3588          |
| start r-factor (free) = 0.4347      final r-factor (free) = 0.4442          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5202 = 1.86 * 1.00 * 6.2062 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3937 = 1.86 * 1.00 * 6.1284 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.17  18.98    None  None   None       |
|    all(noH): 2823   0      0.00    115.17  18.98    None  None   None       |
|    Sol.    : 438    0      0.00    115.17  33.44    None  None   None       |
|    Mac.    : 2385   0      0.00    91.63   16.32    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 -  11.517: 1049   |   5:    57.586 -  69.104:   46        |
|      1:    11.517 -  23.035:  886   |   6:    69.104 -  80.621:   14        |
|      2:    23.035 -  34.552:  498   |   7:    80.621 -  92.138:    3        |
|      3:    34.552 -  46.069:  224   |   8:    92.138 - 103.656:    1        |
|      4:    46.069 -  57.586:  101   |   9:   103.656 - 115.173:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3588 r_free = 0.4442             target_work(ml) = 6.138         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3582 r_free = 0.4440             target_work(ml) = 6.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3582   r_free= 0.4440   ksol= 0.35   Bsol= 20.54   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.58,1.31,1.26,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.137384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3570   r_free= 0.4431   ksol= 0.36   Bsol= 53.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.63,0.76,0.00,0.00,0.00); trace/3= 0.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.138633                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.449812             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.901  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.761273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.213  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3570      final r-factor (work) = 0.3105          |
| start r-factor (free) = 0.4431      final r-factor (free) = 0.3891          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.4118 = 13.45 * 0.50 * 6.1316 + 1.00 * 0.1774                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.0631 = 13.45 * 0.50 * 6.0918 + 1.00 * 0.0962                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3105      final r-factor (work) = 0.2974          |
| start r-factor (free) = 0.3891      final r-factor (free) = 0.3784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6613 = 0.76 * 1.00 * 6.0918 + 1.00 * 0.0238                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5960 = 0.76 * 1.00 * 6.0138 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.82  17.69    None  None   None       |
|    all(noH): 2823   0      0.00    117.82  17.69    None  None   None       |
|    Sol.    : 438    0      0.00    117.82  33.00    None  None   None       |
|    Mac.    : 2385   0      0.00    97.11   14.88    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 -  11.782: 1171   |   5:    58.909 -  70.691:   21        |
|      1:    11.782 -  23.564:  942   |   6:    70.691 -  82.473:    3        |
|      2:    23.564 -  35.346:  420   |   7:    82.473 -  94.255:    5        |
|      3:    35.346 -  47.127:  166   |   8:    94.255 - 106.037:    1        |
|      4:    47.127 -  58.909:   93   |   9:   106.037 - 117.818:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2974 r_free = 0.3784             target_work(ml) = 6.002         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2971 r_free = 0.3788             target_work(ml) = 6.002         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2971   r_free= 0.3788   ksol= 0.36   Bsol= 53.93   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.63,0.76,0.00,0.00,0.00); trace/3= 0.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.001688                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2973   r_free= 0.3789   ksol= 0.36   Bsol= 55.41   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,0.13,0.60,0.00,0.00,0.00); trace/3= 0.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.001008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.269844              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.649  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.614  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2973      final r-factor (work) = 0.2521          |
| start r-factor (free) = 0.3789      final r-factor (free) = 0.3312          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9423 = 5.27 * 0.50 * 6.0139 + 1.00 * 0.0962                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7286 = 5.27 * 0.50 * 5.9429 + 1.00 * 0.0695                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2521      final r-factor (work) = 0.2380          |
| start r-factor (free) = 0.3312      final r-factor (free) = 0.3173          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0410 = 0.51 * 1.00 * 5.9429 + 1.00 * 0.0285                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9711 = 0.51 * 1.00 * 5.8384 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.92  17.27    None  None   None       |
|    all(noH): 2823   0      0.00    112.92  17.27    None  None   None       |
|    Sol.    : 438    0      1.36    112.92  37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    97.06   13.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.292: 1258   |   5:    56.458 -  67.750:   54        |
|      1:    11.292 -  22.583:  874   |   6:    67.750 -  79.042:    7        |
|      2:    22.583 -  33.875:  313   |   7:    79.042 -  90.333:    3        |
|      3:    33.875 -  45.167:  198   |   8:    90.333 - 101.625:    2        |
|      4:    45.167 -  56.458:  113   |   9:   101.625 - 112.917:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2380 r_free = 0.3173             target_work(ml) = 5.820         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2379 r_free = 0.3171             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2379   r_free= 0.3171   ksol= 0.36   Bsol= 55.41   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,0.13,0.60,0.00,0.00,0.00); trace/3= 0.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.819416                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2382   r_free= 0.3158   ksol= 0.33   Bsol= 43.58   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,-0.58,-0.02,-0.00,-0.00,-0.00); trace/3= -0.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.817865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.213071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.986858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.387  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2382      final r-factor (work) = 0.1837          |
| start r-factor (free) = 0.3158      final r-factor (free) = 0.2446          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2065 = 6.21 * 0.50 * 5.8383 + 1.00 * 0.0695                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8381 = 6.21 * 0.50 * 5.7180 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1837      final r-factor (work) = 0.1632          |
| start r-factor (free) = 0.2446      final r-factor (free) = 0.2242          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6543 = 0.99 * 1.00 * 5.7180 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4627 = 0.99 * 1.00 * 5.5226 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.07  17.50    None  None   None       |
|    all(noH): 2823   0      0.00    110.07  17.50    None  None   None       |
|    Sol.    : 438    0      3.66    110.07  44.32    None  None   None       |
|    Mac.    : 2385   0      0.00    100.93  12.58    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 -  11.007: 1403   |   5:    55.034 -  66.041:   97        |
|      1:    11.007 -  22.014:  802   |   6:    66.041 -  77.047:   50        |
|      2:    22.014 -  33.020:  187   |   7:    77.047 -  88.054:    8        |
|      3:    33.020 -  44.027:  147   |   8:    88.054 -  99.061:    2        |
|      4:    44.027 -  55.034:  125   |   9:    99.061 - 110.068:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1632 r_free = 0.2242             target_work(ml) = 5.482         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1630 r_free = 0.2235             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2235   ksol= 0.33   Bsol= 43.58   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,-0.58,-0.02,-0.00,-0.00,-0.00); trace/3= -0.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.480091                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2223   ksol= 0.32   Bsol= 40.69   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.36,-0.47,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.476982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.738773              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.782  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.043  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2223      final r-factor (free) = 0.1942          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4020 = 3.74 * 0.50 * 5.5242 + 1.00 * 0.0750                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1873 = 3.74 * 0.50 * 5.4157 + 1.00 * 0.0633                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1389      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1942      final r-factor (free) = 0.1835          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3309 = 0.43 * 1.00 * 5.4157 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2864 = 0.43 * 1.00 * 5.3168 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.42  16.84    None  None   None       |
|    all(noH): 2823   0      0.00    104.42  16.84    None  None   None       |
|    Sol.    : 438    0      4.92    104.42  43.41    None  None   None       |
|    Mac.    : 2385   0      0.00    102.09  11.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.442: 1389   |   5:    52.208 -  62.650:   94        |
|      1:    10.442 -  20.883:  842   |   6:    62.650 -  73.091:   55        |
|      2:    20.883 -  31.325:  191   |   7:    73.091 -  83.533:   23        |
|      3:    31.325 -  41.766:  116   |   8:    83.533 -  93.974:    5        |
|      4:    41.766 -  52.208:  105   |   9:    93.974 - 104.416:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1835             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1317 r_free = 0.1830             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1830   ksol= 0.32   Bsol= 40.69   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.36,-0.47,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.284274                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6558 0.99   1390  155 0.1075 0.1371      5.4547      5.6208|
|  2:  4.6558 -  3.7143 0.99   1335  146 0.0952 0.1301      5.5537      5.7906|
|  3:  3.7143 -  3.2504 0.99   1316  144 0.1231 0.1652      5.6184      5.9617|
|  4:  3.2504 -  2.9557 0.99   1296  153 0.1451 0.2000      5.6366      5.8179|
|  5:  2.9557 -  2.7453 0.99   1298  140 0.1541 0.2107      5.4521      5.7007|
|  6:  2.7453 -  2.5843 0.99   1287  140 0.1422 0.1807      5.3396      5.4861|
|  7:  2.5843 -  2.4555 0.99   1291  139 0.1467 0.1937      5.2919      5.5368|
|  8:  2.4555 -  2.3490 0.98   1256  149 0.1488 0.2209      5.2484      5.5324|
|  9:  2.3490 -  2.2589 0.98   1271  144 0.1472 0.1992      5.2086      5.4123|
| 10:  2.2589 -  2.1812 1.00   1280  139 0.1367 0.2184      5.1312      5.4025|
| 11:  2.1812 -  2.1132 0.98   1274  137 0.1334 0.2119      5.0816      5.3919|
| 12:  2.1132 -  2.0529 0.98   1251  140 0.1273 0.1782      4.9853      5.2097|
| 13:  2.0529 -  1.9990 0.99   1262  138 0.1337 0.2238      4.9128      5.2634|
| 14:  1.9990 -  1.9504 0.64    823   95 0.1401 0.1730      4.8548      5.0095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6558  1390   155  0.93  10.69   0.98     0.96       8840.46|
|  2:  4.6558 -  3.7143  1335   146  0.94   9.86   1.04     1.02      11706.27|
|  3:  3.7143 -  3.2504  1316   144  0.91  13.91   1.06     1.04      14175.69|
|  4:  3.2504 -  2.9557  1296   153  0.89  17.14   1.04     1.01      15201.83|
|  5:  2.9557 -  2.7453  1298   140  0.88  18.54   1.01     0.98      10547.74|
|  6:  2.7453 -  2.5843  1287   140  0.88  18.22   1.01     0.97       9114.87|
|  7:  2.5843 -  2.4555  1291   139  0.88  18.82   1.01     0.98       8170.91|
|  8:  2.4555 -  2.3490  1256   149  0.87  19.65   1.00     0.97       7727.69|
|  9:  2.3490 -  2.2589  1271   144  0.88  19.06   1.01     0.97       7263.49|
| 10:  2.2589 -  2.1812  1280   139  0.87  19.58   1.02     0.97       6410.67|
| 11:  2.1812 -  2.1132  1274   137  0.88  18.95   1.02     0.98       5808.73|
| 12:  2.1132 -  2.0529  1251   140  0.89  17.90   1.02     1.00       5013.80|
| 13:  2.0529 -  1.9990  1262   138  0.88  18.91   1.02     1.01       4245.71|
| 14:  1.9990 -  1.9504   823    95  0.89  17.45   1.01     0.98       3448.73|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     3448.73 max =        15201.83 mean =      8579.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.96|
|phase err.(test): min =        0.00 max =           89.98 mean =        16.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1836   ksol= 0.31   Bsol= 40.10   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-1.36,-0.47,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285684                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1836   ksol= 0.31   Bsol= 40.10   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-1.36,-0.47,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285684                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6558 0.99   1390  155 0.1086 0.1413      5.4638      5.6273|
|  2:  4.6558 -  3.7143 0.99   1335  146 0.0963 0.1323      5.5645      5.8012|
|  3:  3.7143 -  3.2504 0.99   1316  144 0.1236 0.1650      5.6215      5.9588|
|  4:  3.2504 -  2.9557 0.99   1296  153 0.1458 0.1992      5.6371      5.8167|
|  5:  2.9557 -  2.7453 0.99   1298  140 0.1539 0.2109      5.4507      5.7004|
|  6:  2.7453 -  2.5843 0.99   1287  140 0.1421 0.1801      5.3393      5.4842|
|  7:  2.5843 -  2.4555 0.99   1291  139 0.1468 0.1939      5.2917      5.5383|
|  8:  2.4555 -  2.3490 0.98   1256  149 0.1483 0.2211      5.2482      5.5317|
|  9:  2.3490 -  2.2589 0.98   1271  144 0.1471 0.1994      5.2084      5.4129|
| 10:  2.2589 -  2.1812 1.00   1280  139 0.1364 0.2188      5.1306       5.403|
| 11:  2.1812 -  2.1132 0.98   1274  137 0.1332 0.2120      5.0803      5.3914|
| 12:  2.1132 -  2.0529 0.98   1251  140 0.1271 0.1773      4.9847      5.2069|
| 13:  2.0529 -  1.9990 0.99   1262  138 0.1338 0.2237      4.9121      5.2629|
| 14:  1.9990 -  1.9504 0.64    823   95 0.1401 0.1729      4.8546      5.0101|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6558  1390   155  0.93  10.92   0.98     0.96       9107.77|
|  2:  4.6558 -  3.7143  1335   146  0.94   9.95   1.04     1.02      11908.77|
|  3:  3.7143 -  3.2504  1316   144  0.91  13.96   1.06     1.05      14239.13|
|  4:  3.2504 -  2.9557  1296   153  0.89  17.15   1.04     1.01      15195.36|
|  5:  2.9557 -  2.7453  1298   140  0.88  18.53   1.01     0.98      10537.53|
|  6:  2.7453 -  2.5843  1287   140  0.88  18.20   1.01     0.97       9101.54|
|  7:  2.5843 -  2.4555  1291   139  0.88  18.80   1.01     0.98       8168.02|
|  8:  2.4555 -  2.3490  1256   149  0.87  19.67   1.00     0.97       7751.26|
|  9:  2.3490 -  2.2589  1271   144  0.88  19.07   1.01     0.97       7267.49|
| 10:  2.2589 -  2.1812  1280   139  0.87  19.61   1.02     0.97       6420.99|
| 11:  2.1812 -  2.1132  1274   137  0.88  18.92   1.02     0.98       5795.29|
| 12:  2.1132 -  2.0529  1251   140  0.89  17.88   1.02     1.00       5006.72|
| 13:  2.0529 -  1.9990  1262   138  0.88  18.91   1.02     1.01       4237.91|
| 14:  1.9990 -  1.9504   823    95  0.89  17.45   1.01     0.98       3446.37|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     3446.37 max =        15195.36 mean =      8618.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.88 mean =        16.99|
|phase err.(test): min =        0.00 max =           89.86 mean =        16.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.297)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.42  16.85    None  None   None       |
|    all(noH): 2823   0      0.00    104.42  16.85    None  None   None       |
|    Sol.    : 438    0      4.92    104.42  43.41    None  None   None       |
|    Mac.    : 2385   0      0.00    102.09  11.97    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 -  10.445: 1389   |   5:    52.211 -  62.653:   94        |
|      1:    10.445 -  20.886:  842   |   6:    62.653 -  73.094:   55        |
|      2:    20.886 -  31.328:  191   |   7:    73.094 -  83.536:   23        |
|      3:    31.328 -  41.769:  116   |   8:    83.536 -  93.977:    5        |
|      4:    41.769 -  52.211:  105   |   9:    93.977 - 104.419:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.570 - 5.511
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 316
   mapped sites are within: 0.726 - 5.511

peak=    7.847 closest distance to " O   HOH Z 390 " =    1.299
peak=    7.277 closest distance to " O   HOH Z 101 " =    1.003
peak=    7.108 closest distance to " O   HOH Z  61 " =    1.596
peak=    7.081 closest distance to " OD1 ASP A 298 " =    2.225
peak=    6.813 closest distance to " O   HOH Z 138 " =    1.098
peak=    6.721 closest distance to " O   HOH Z 385 " =    1.924
peak=    6.576 closest distance to " O   HOH Z 205 " =    1.449
peak=    6.449 closest distance to " O   HOH Z 289 " =    1.659
peak=    6.402 closest distance to " O   HOH Z 130 " =    1.283
peak=    6.193 closest distance to " O   HOH Z 222 " =    1.806
peak=    5.926 closest distance to " NE2 GLN A  11 " =    1.505
peak=    5.911 closest distance to " O   HOH Z  65 " =    2.011
peak=    5.899 closest distance to " O   HOH Z 278 " =    1.723
peak=    5.603 closest distance to " O   HOH Z  97 " =    1.652
peak=    5.594 closest distance to " O   HOH Z   7 " =    1.976
peak=    5.523 closest distance to " O   HOH Z 214 " =    1.688
peak=    5.457 closest distance to " O   HOH Z  29 " =    1.418
peak=    5.294 closest distance to " O   HOH Z 403 " =    1.754
peak=    5.282 closest distance to " O   HOH Z 144 " =    1.952
peak=    5.255 closest distance to " O   HOH Z 126 " =    1.916
peak=    5.216 closest distance to " O   HOH Z 427 " =    2.016
peak=    5.171 closest distance to " O   HOH Z 124 " =    1.704
peak=    5.129 closest distance to " O   HOH Z  28 " =    1.827
peak=    5.106 closest distance to " O   HOH Z 245 " =    1.325
peak=    4.985 closest distance to " NH2 ARG A  56 " =    2.008
peak=    4.953 closest distance to " O   SER A  62 " =    0.877
peak=    4.927 closest distance to " O   HOH Z 211 " =    1.606
peak=    4.911 closest distance to " O   HOH Z  78 " =    1.773
peak=    4.903 closest distance to " O   PRO A 198 " =    1.274
peak=    4.899 closest distance to " OD1 ASP A  50 " =    1.125
peak=    4.898 closest distance to " O   HOH Z 358 " =    1.369
peak=    4.870 closest distance to " O   HOH Z 424 " =    1.278
peak=    4.853 closest distance to " O   HOH Z 316 " =    2.894
peak=    4.839 closest distance to " O   HOH Z 112 " =    1.622
peak=    4.787 closest distance to " O   HOH Z 287 " =    1.758
peak=    4.767 closest distance to " O   HOH Z 427 " =    1.335
peak=    4.746 closest distance to " O   HOH Z 276 " =    1.619
peak=    4.705 closest distance to " O   HOH Z 381 " =    1.157
peak=    4.656 closest distance to " O   HOH Z 363 " =    1.202
peak=    4.641 closest distance to " O   HOH Z 417 " =    2.005
peak=    4.626 closest distance to " O   HOH Z 375 " =    1.098
peak=    4.603 closest distance to " O   HOH Z 135 " =    1.684
peak=    4.586 closest distance to " O   HOH Z  54 " =    1.258
peak=    4.586 closest distance to " O   HOH Z 402 " =    1.554
peak=    4.561 closest distance to " O   HOH Z 215 " =    2.016
peak=    4.561 closest distance to " O   HOH Z 139 " =    1.754
peak=    4.547 closest distance to " O   HOH Z 282 " =    1.814
peak=    4.521 closest distance to " O   HOH Z 117 " =    1.374
peak=    4.514 closest distance to " O   HOH Z 133 " =    1.441
peak=    4.480 closest distance to " O   HOH Z 415 " =    1.048
peak=    4.464 closest distance to " O   HOH Z 414 " =    1.477
peak=    4.461 closest distance to " CG  PRO A  90 " =    1.117
peak=    4.437 closest distance to " O   HOH Z  63 " =    1.874
peak=    4.431 closest distance to " O   HOH Z 416 " =    1.366
peak=    4.421 closest distance to " O   HOH Z  59 " =    1.571
peak=    4.403 closest distance to " CG  PRO A  54 " =    1.274
peak=    4.398 closest distance to " O   HOH Z  92 " =    1.394
peak=    4.344 closest distance to " NZ  LYS A 117 " =    1.228
peak=    4.326 closest distance to " O   HOH Z 302 " =    1.526
peak=    4.324 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.300 closest distance to " O   HOH Z 116 " =    1.258
peak=    4.285 closest distance to " O   HOH Z 250 " =    2.159
peak=    4.263 closest distance to " O   HOH Z 193 " =    1.793
peak=    4.261 closest distance to " CB  PRO A  54 " =    1.139
peak=    4.213 closest distance to " O   HOH Z 234 " =    3.729
peak=    4.211 closest distance to " O   HOH Z 158 " =    1.521
peak=    4.210 closest distance to " CB  GLN A 183 " =    1.074
peak=    4.207 closest distance to " CB  ALA A   1 " =    1.218
peak=    4.173 closest distance to " O   HOH Z 217 " =    2.887
peak=    4.144 closest distance to " O   HOH Z 261 " =    2.194
peak=    4.126 closest distance to " CB  ASN A 148 " =    1.434
peak=    4.112 closest distance to " O   HOH Z 109 " =    1.751
peak=    4.107 closest distance to " O   HOH Z 400 " =    0.827
peak=    4.101 closest distance to " N   GLU A   2 " =    1.289
peak=    4.100 closest distance to " CB  SER A   3 " =    1.234
peak=    4.088 closest distance to " OG BSER A 258 " =    1.057
peak=    4.088 closest distance to " NH2 ARG A 219 " =    1.751
peak=    4.083 closest distance to " O   HOH Z 352 " =    1.619
peak=    4.082 closest distance to " O   HOH Z 371 " =    1.850
peak=    4.075 closest distance to " O   SER A  87 " =    2.242
peak=    4.059 closest distance to " O   HOH Z 134 " =    1.512
peak=    4.055 closest distance to " O   HOH Z   9 " =    1.023
peak=    4.025 closest distance to " O   ALA A 165 " =    1.244
peak=    4.013 closest distance to " O   HOH Z 423 " =    2.006
peak=    4.008 closest distance to " O   HOH Z 393 " =    1.504
peak=    4.005 closest distance to " O   HOH Z 258 " =    1.357
peak=    3.995 closest distance to " O   HOH Z 350 " =    1.239
peak=    3.972 closest distance to " O   HOH Z 371 " =    2.997
peak=    3.969 closest distance to " O   HOH Z  88 " =    2.775
peak=    3.964 closest distance to " O   HOH Z 394 " =    1.771
peak=    3.957 closest distance to " O   HOH Z   5 " =    1.422
peak=    3.952 closest distance to " CA  TYR A  30 " =    1.017
peak=    3.950 closest distance to " O   HOH Z 166 " =    1.765
peak=    3.948 closest distance to " CE  MET A  93 " =    1.425
peak=    3.940 closest distance to " N   GLN A 278 " =    1.167
peak=    3.934 closest distance to " O   HOH Z 405 " =    1.511
peak=    3.931 closest distance to " CB  SER A 216 " =    1.013
peak=    3.921 closest distance to " O   HOH Z 347 " =    1.119
peak=    3.919 closest distance to " O   HOH Z 344 " =    1.226
peak=    3.916 closest distance to " O   HOH Z 132 " =    1.085
peak=    3.915 closest distance to " CG  PRO A 243 " =    1.107
peak=    3.913 closest distance to " CB  GLU A 128 " =    0.979
peak=    3.909 closest distance to " CB  TRP A 179 " =    1.388
peak=    3.888 closest distance to " O   HOH Z 209 " =    2.357
peak=    3.880 closest distance to " O   HOH Z 392 " =    1.270
peak=    3.879 closest distance to " NE AARG A 275 " =    1.454
peak=    3.877 closest distance to " O   HOH Z 389 " =    1.587
peak=    3.861 closest distance to " OD2 ASP A 286 " =    2.444
peak=    3.860 closest distance to " CB  TYR A 169 " =    0.726
peak=    3.857 closest distance to " O   HOH Z   6 " =    1.904
peak=    3.832 closest distance to " O   HOH Z 369 " =    2.214
peak=    3.816 closest distance to " O   HOH Z 311 " =    1.460
peak=    3.807 closest distance to " O   HOH Z 250 " =    1.313
peak=    3.805 closest distance to " O   HOH Z 104 " =    1.833
peak=    3.800 closest distance to " CB  ARG A 102 " =    0.907
peak=    3.791 closest distance to " O   HOH Z 105 " =    1.286
peak=    3.790 closest distance to " O   HOH Z 269 " =    3.164
peak=    3.783 closest distance to " O   HOH Z 110 " =    1.533
peak=    3.771 closest distance to " O   HOH Z 171 " =    2.391
peak=    3.770 closest distance to " CB  ARG A 275 " =    1.074
peak=    3.767 closest distance to " O   HOH Z 186 " =    1.273
peak=    3.765 closest distance to " O   HOH Z 145 " =    1.838
peak=    3.761 closest distance to " O   HOH Z 236 " =    1.541
peak=    3.755 closest distance to " CG  PRO A 198 " =    1.340
peak=    3.754 closest distance to " O   HOH Z 202 " =    1.723
peak=    3.753 closest distance to " O   HOH Z 298 " =    1.979
peak=    3.753 closest distance to " O   HOH Z 409 " =    1.845
peak=    3.747 closest distance to " O   HOH Z 128 " =    2.096
peak=    3.733 closest distance to " O   HOH Z  53 " =    2.293
peak=    3.732 closest distance to " CA  LEU A 282 " =    1.127
peak=    3.723 closest distance to " CD  LYS A 166 " =    1.566
peak=    3.717 closest distance to " NZ BLYS A 290 " =    1.089
peak=    3.715 closest distance to " NE1 TRP A 274 " =    1.099
peak=    3.713 closest distance to " O   HOH Z 272 " =    1.799
peak=    3.712 closest distance to " CE AMET A  47 " =    1.168
peak=    3.701 closest distance to " OG  SER A  62 " =    3.361
peak=    3.700 closest distance to " O   HOH Z 269 " =    1.294
peak=    3.699 closest distance to " N   SER A  63 " =    0.825
peak=    3.692 closest distance to " CB  GLU A 152 " =    1.192
peak=    3.692 closest distance to " CD  ARG A 138 " =    0.906
peak=    3.691 closest distance to " O   HOH Z 120 " =    0.907
peak=    3.690 closest distance to " CB  GLU A 277 " =    1.100
peak=    3.678 closest distance to " N   ALA A   1 " =    1.406
peak=    3.664 closest distance to " CB  VAL A 265 " =    1.327
peak=    3.664 closest distance to " CD2 TRP A 179 " =    1.553
peak=    3.664 closest distance to " O   HOH Z 384 " =    1.479
peak=    3.664 closest distance to " O   HOH Z  68 " =    1.731
peak=    3.663 closest distance to " CD2 TRP A 179 " =    2.119
peak=    3.653 closest distance to " CG  ASN A  60 " =    1.394
peak=    3.651 closest distance to " O   ASP A 286 " =    2.452
peak=    3.643 closest distance to " O   HOH Z   2 " =    1.794
peak=    3.641 closest distance to " O   HOH Z 412 " =    1.820
peak=    3.636 closest distance to " OE1 GLN A  77 " =    1.210
peak=    3.633 closest distance to " O   HOH Z 227 " =    1.725
peak=    3.632 closest distance to " CG1BVAL A 121 " =    1.799
peak=    3.631 closest distance to " O   HOH Z 411 " =    3.288
peak=    3.629 closest distance to " O   HOH Z 158 " =    2.373
peak=    3.623 closest distance to " CB  GLN A 223 " =    1.436
peak=    3.618 closest distance to " O   HOH Z  57 " =    1.176
peak=    3.597 closest distance to " O   HOH Z 244 " =    1.519
peak=    3.595 closest distance to " N   TYR A  15 " =    1.169
peak=    3.589 closest distance to " O   HOH Z 353 " =    2.051
peak=    3.585 closest distance to " O   HOH Z  97 " =    2.251
peak=    3.581 closest distance to " O   HOH Z  15 " =    1.526
peak=    3.578 closest distance to " CD  GLN A  58 " =    5.511
peak=    3.567 closest distance to " CA  ASN A  74 " =    1.283
peak=    3.563 closest distance to " O   HOH Z 291 " =    1.558
peak=    3.555 closest distance to " O   HOH Z 426 " =    1.179
peak=    3.548 closest distance to " O   HOH Z 112 " =    2.112
peak=    3.548 closest distance to " O   HOH Z 126 " =    1.473
peak=    3.541 closest distance to " O   HOH Z 239 " =    1.553
peak=    3.540 closest distance to " O   HOH Z 227 " =    2.052
peak=    3.539 closest distance to " O   HOH Z 155 " =    2.199
peak=    3.538 closest distance to " O   HOH Z 361 " =    2.519
peak=    3.536 closest distance to " O   HOH Z  40 " =    2.617
peak=    3.533 closest distance to " CG  LYS A 166 " =    1.352
peak=    3.526 closest distance to " C   ALA A 299 " =    0.978
peak=    3.525 closest distance to " CG  LEU A 167 " =    1.251
peak=    3.518 closest distance to " CG  GLN A  77 " =    2.249
peak=    3.507 closest distance to " O   HOH Z 213 " =    2.240
peak=    3.506 closest distance to " O   HOH Z 422 " =    2.722
peak=    3.504 closest distance to " O   HOH Z 247 " =    1.124
peak=    3.499 closest distance to " OE2 GLU A  53 " =    2.001
peak=    3.491 closest distance to " CG1 VAL A 202 " =    2.084
peak=    3.477 closest distance to " O   HOH Z 223 " =    1.022
peak=    3.471 closest distance to " O   HOH Z 286 " =    2.530
peak=    3.471 closest distance to " CA  ALA A  51 " =    1.153
peak=    3.470 closest distance to " CB  ALA A 104 " =    1.204
peak=    3.468 closest distance to " O   HOH Z 366 " =    2.495
peak=    3.467 closest distance to " O   HOH Z 259 " =    2.037
peak=    3.466 closest distance to " CB  ASP A 200 " =    0.948
peak=    3.463 closest distance to " CB  PHE A  16 " =    1.022
peak=    3.463 closest distance to " O   HOH Z 433 " =    1.324
peak=    3.461 closest distance to " CA  GLU A 152 " =    1.149
peak=    3.458 closest distance to " CA  ALA A  21 " =    1.160
peak=    3.437 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.428 closest distance to " O   HOH Z 151 " =    1.955
peak=    3.421 closest distance to " O   ASN A 217 " =    0.990
peak=    3.421 closest distance to " O   HOH Z 380 " =    2.069
peak=    3.418 closest distance to " NH2BARG A 145 " =    1.926
peak=    3.418 closest distance to " NH2AARG A 190 " =    1.487
peak=    3.417 closest distance to " O   HOH Z 425 " =    2.073
peak=    3.416 closest distance to " O   HOH Z  32 " =    2.274
peak=    3.412 closest distance to " O   HOH Z 119 " =    4.104
peak=    3.411 closest distance to " O   HOH Z  44 " =    1.516
peak=    3.407 closest distance to " CB  LYS A 290 " =    1.527
peak=    3.405 closest distance to " O   HOH Z  47 " =    1.786
peak=    3.399 closest distance to " N   SER A 210 " =    1.160
peak=    3.381 closest distance to " O   HOH Z  22 " =    1.920
peak=    3.379 closest distance to " O   HOH Z 158 " =    3.033
peak=    3.378 closest distance to " O   HOH Z 313 " =    1.889
peak=    3.376 closest distance to " O   HOH Z 410 " =    1.754
peak=    3.375 closest distance to " CG  GLN A 240 " =    3.305
peak=    3.371 closest distance to " O   HOH Z 365 " =    5.319
peak=    3.369 closest distance to " O   HOH Z  11 " =    1.302
peak=    3.369 closest distance to " O   HOH Z  89 " =    1.351
peak=    3.364 closest distance to " O   HOH Z 357 " =    1.576
peak=    3.363 closest distance to " CB  SER A  63 " =    1.432
peak=    3.362 closest distance to " O   HOH Z 291 " =    1.881
peak=    3.349 closest distance to " OG BSER A  12 " =    1.117
peak=    3.346 closest distance to " O   HOH Z  46 " =    1.095
peak=    3.339 closest distance to " CB  LEU A 228 " =    1.152
peak=    3.331 closest distance to " O   HOH Z 128 " =    1.902
peak=    3.329 closest distance to " CB  ASP A 124 " =    1.033
peak=    3.325 closest distance to " CB  LEU A 300 " =    1.049
peak=    3.321 closest distance to " CG  GLN A  88 " =    1.023
peak=    3.315 closest distance to " O   HOH Z 364 " =    1.573
peak=    3.315 closest distance to " O   HOH Z 368 " =    1.795
peak=    3.315 closest distance to " CB  MET A 105 " =    0.935
peak=    3.311 closest distance to " N   GLN A  73 " =    1.407
peak=    3.309 closest distance to " NE2 GLN A  58 " =    3.298
peak=    3.309 closest distance to " CG AARG A 275 " =    1.053
peak=    3.309 closest distance to " O   HOH Z 108 " =    2.077
peak=    3.306 closest distance to " O   HOH Z 378 " =    1.203
peak=    3.306 closest distance to " OD1 ASP A 238 " =    0.905
peak=    3.303 closest distance to " CG2 THR A 251 " =    1.694
peak=    3.302 closest distance to " O   HOH Z 388 " =    2.161
peak=    3.300 closest distance to " OG ASER A  99 " =    1.168
peak=    3.300 closest distance to " CZ3 TRP A 274 " =    2.059
peak=    3.291 closest distance to " O   HOH Z 368 " =    3.617
peak=    3.289 closest distance to " O   HOH Z 145 " =    2.508
peak=    3.287 closest distance to " CG  ARG A  66 " =    2.435
peak=    3.286 closest distance to " O   HOH Z 286 " =    2.341
peak=    3.283 closest distance to " CG2 THR A 221 " =    1.346
peak=    3.274 closest distance to " O   HOH Z 207 " =    2.050
peak=    3.274 closest distance to " O   HOH Z 180 " =    2.068
peak=    3.270 closest distance to " CB  GLN A  11 " =    1.374
peak=    3.268 closest distance to " O   SER A 271 " =    1.315
peak=    3.261 closest distance to " O   HOH Z 100 " =    1.194
peak=    3.261 closest distance to " CA  PRO A 280 " =    1.534
peak=    3.261 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.260 closest distance to " O   HOH Z 116 " =    2.166
peak=    3.255 closest distance to " O   HOH Z 290 " =    1.047
peak=    3.255 closest distance to " O   HOH Z 152 " =    2.151
peak=    3.253 closest distance to " O   HOH Z 106 " =    2.343
peak=    3.252 closest distance to " O   HOH Z 133 " =    2.506
peak=    3.247 closest distance to " O   HOH Z 166 " =    1.643
peak=    3.245 closest distance to " CB  SER A 276 " =    1.142
peak=    3.226 closest distance to " O   HOH Z 288 " =    1.725
peak=    3.226 closest distance to " CG2 THR A 220 " =    0.951
peak=    3.222 closest distance to " O   HOH Z 334 " =    1.596
peak=    3.218 closest distance to " OD1 ASP A 286 " =    1.063
peak=    3.212 closest distance to " CA  ASN A 215 " =    1.140
peak=    3.212 closest distance to " O   HOH Z 147 " =    1.341
peak=    3.210 closest distance to " C   ASN A 285 " =    0.890
peak=    3.210 closest distance to " O   HOH Z 189 " =    1.691
peak=    3.209 closest distance to " CG1 VAL A 232 " =    1.527
peak=    3.209 closest distance to " N   TRP A 150 " =    1.524
peak=    3.209 closest distance to " CG BARG A 102 " =    1.885
peak=    3.208 closest distance to " CB  GLU A 277 " =    3.443
peak=    3.205 closest distance to " CG  GLN A  11 " =    1.983
peak=    3.200 closest distance to " SD BMET A  47 " =    1.460
peak=    3.194 closest distance to " N   ARG A 156 " =    1.193
peak=    3.192 closest distance to " N   PHE A 130 " =    1.124
peak=    3.192 closest distance to " O   HOH Z  55 " =    1.817
peak=    3.190 closest distance to " CD1 LEU A 228 " =    1.747
peak=    3.190 closest distance to " O   HOH Z  32 " =    1.589
peak=    3.185 closest distance to " O   HOH Z 334 " =    2.747
peak=    3.182 closest distance to " O   HOH Z 276 " =    2.063
peak=    3.181 closest distance to " CA  ARG A  36 " =    1.320
peak=    3.173 closest distance to " NH1AARG A 145 " =    0.926
peak=    3.171 closest distance to " O   HOH Z 413 " =    1.605
peak=    3.170 closest distance to " CB  VAL A 121 " =    0.977
peak=    3.169 closest distance to " OD1 ASN A  45 " =    1.126
peak=    3.169 closest distance to " OG BSER A 212 " =    2.889
peak=    3.165 closest distance to " O   HOH Z 102 " =    1.860
peak=    3.164 closest distance to " O   HOH Z 193 " =    1.995
peak=    3.163 closest distance to " CB  ALA A 131 " =    1.538
peak=    3.163 closest distance to " CB  ASP A 140 " =    0.746
peak=    3.161 closest distance to " O   HOH Z 371 " =    1.647
peak=    3.159 closest distance to " O   HOH Z 344 " =    2.918
peak=    3.154 closest distance to " NH2BARG A 190 " =    1.507
peak=    3.154 closest distance to " O   HOH Z  24 " =    1.651
peak=    3.153 closest distance to " CA  SER A  62 " =    1.072
peak=    3.152 closest distance to " O   HOH Z 271 " =    1.837
peak=    3.144 closest distance to " O   HOH Z 135 " =    1.730
peak=    3.143 closest distance to " O   HOH Z  88 " =    3.906
peak=    3.139 closest distance to " O   HOH Z 326 " =    1.371
peak=    3.137 closest distance to " O   HOH Z 406 " =    1.357
peak=    3.136 closest distance to " CD2 LEU A  25 " =    1.133
peak=    3.133 closest distance to " CB  ALA A   7 " =    1.279
peak=    3.131 closest distance to " OE1 GLN A 240 " =    1.697
peak=    3.128 closest distance to " N   TRP A 177 " =    1.745
peak=    3.111 closest distance to " O   HOH Z 332 " =    1.354
peak=    3.106 closest distance to " O   HOH Z   7 " =    2.915
peak=    3.103 closest distance to " CG2 THR A 279 " =    1.261
peak=    3.100 closest distance to " O   HOH Z 277 " =    2.352
peak=    3.099 closest distance to " O   HOH Z 197 " =    1.373
peak=    3.097 closest distance to " O   HOH Z 375 " =    2.170
peak=    3.082 closest distance to " NE BARG A 275 " =    1.066
peak=    3.077 closest distance to " NE  ARG A  14 " =    1.293
peak=    3.072 closest distance to " O   ALA A 242 " =    0.968
peak=    3.066 closest distance to " O   ASN A 301 " =    2.119
peak=    3.040 closest distance to " CB  TYR A 116 " =    1.232
peak=    3.024 closest distance to " OG BSER A  99 " =    2.547

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.572 - 5.392
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 218
   mapped sites are within: 0.717 - 5.392

peak=   -4.824 closest distance to " O   SER A  62 " =    1.013
peak=   -4.822 closest distance to " O   HOH Z  60 " =    1.898
peak=   -4.627 closest distance to " O   PRO A 198 " =    1.247
peak=   -4.359 closest distance to " O   HOH Z 409 " =    3.133
peak=   -4.279 closest distance to " O   HOH Z 381 " =    0.820
peak=   -4.257 closest distance to " CD  ARG A  14 " =    3.017
peak=   -4.233 closest distance to " O   TRP A  70 " =    1.323
peak=   -4.219 closest distance to " ND2 ASN A 209 " =    1.731
peak=   -4.165 closest distance to " O   HOH Z  24 " =    1.051
peak=   -4.148 closest distance to " O   HOH Z  65 " =    0.727
peak=   -4.141 closest distance to " CG  GLN A  88 " =    0.858
peak=   -4.088 closest distance to " CG  ASP A  50 " =    0.943
peak=   -4.045 closest distance to " O   HOH Z 163 " =    1.618
peak=   -4.030 closest distance to " O   HOH Z 377 " =    1.921
peak=   -4.028 closest distance to " CA  GLY A 133 " =    1.896
peak=   -4.021 closest distance to " O   HOH Z 347 " =    0.794
peak=   -4.001 closest distance to " CG  MET A 105 " =    0.945
peak=   -3.992 closest distance to " O   HOH Z 388 " =    1.940
peak=   -3.962 closest distance to " CZ  PHE A  59 " =    1.411
peak=   -3.956 closest distance to " CB  ALA A 248 " =    1.919
peak=   -3.854 closest distance to " O   HOH Z  98 " =    1.658
peak=   -3.842 closest distance to " NH2 ARG A  79 " =    1.853
peak=   -3.835 closest distance to " O   ILE A  49 " =    1.500
peak=   -3.822 closest distance to " O   HOH Z 415 " =    1.144
peak=   -3.802 closest distance to " CD1 TRP A 179 " =    1.162
peak=   -3.792 closest distance to " O   HOH Z  88 " =    2.072
peak=   -3.785 closest distance to " O   HOH Z 132 " =    0.730
peak=   -3.781 closest distance to " OG  SER A  97 " =    2.228
peak=   -3.780 closest distance to " O   HOH Z  54 " =    0.717
peak=   -3.766 closest distance to " O   HOH Z  39 " =    1.418
peak=   -3.762 closest distance to " CG  GLU A 152 " =    2.670
peak=   -3.744 closest distance to " O   HOH Z 290 " =    1.130
peak=   -3.743 closest distance to " O   GLY A  98 " =    2.179
peak=   -3.734 closest distance to " O   HOH Z 397 " =    1.278
peak=   -3.730 closest distance to " O   HOH Z 139 " =    2.299
peak=   -3.719 closest distance to " C   ALA A 114 " =    1.962
peak=   -3.692 closest distance to " O   PRO A 198 " =    1.180
peak=   -3.690 closest distance to " O   HOH Z 410 " =    2.254
peak=   -3.686 closest distance to " O   SER A 146 " =    1.382
peak=   -3.679 closest distance to " O   SER A  22 " =    2.589
peak=   -3.678 closest distance to " O   HOH Z 198 " =    2.181
peak=   -3.675 closest distance to " O   HOH Z  13 " =    1.343
peak=   -3.670 closest distance to " N   GLN A  58 " =    1.232
peak=   -3.664 closest distance to " O   SER A 135 " =    1.561
peak=   -3.661 closest distance to " O   HOH Z 138 " =    0.923
peak=   -3.661 closest distance to " N   GLN A  58 " =    1.830
peak=   -3.659 closest distance to " CD2 LEU A 237 " =    2.338
peak=   -3.636 closest distance to " CB  ALA A 227 " =    2.208
peak=   -3.595 closest distance to " O   VAL A 197 " =    1.408
peak=   -3.591 closest distance to " C   GLN A 205 " =    2.013
peak=   -3.581 closest distance to " CB  ASN A 285 " =    2.059
peak=   -3.558 closest distance to " CB  ASP A  27 " =    2.437
peak=   -3.556 closest distance to " O   THR A 235 " =    1.287
peak=   -3.548 closest distance to " CG  ARG A 219 " =    2.265
peak=   -3.547 closest distance to " O   HOH Z 316 " =    1.787
peak=   -3.542 closest distance to " OD1 ASN A 301 " =    2.061
peak=   -3.535 closest distance to " CG  ARG A 139 " =    1.179
peak=   -3.532 closest distance to " OH  TYR A 214 " =    1.231
peak=   -3.529 closest distance to " O   PRO A  54 " =    1.418
peak=   -3.521 closest distance to " OD1 ASN A  39 " =    2.047
peak=   -3.521 closest distance to " CZ3 TRP A 123 " =    1.699
peak=   -3.519 closest distance to " O   HOH Z 197 " =    3.485
peak=   -3.512 closest distance to " O   PRO A 243 " =    2.389
peak=   -3.502 closest distance to " O   HOH Z 150 " =    2.823
peak=   -3.501 closest distance to " O   HOH Z 372 " =    2.457
peak=   -3.495 closest distance to " O   ALA A  51 " =    1.240
peak=   -3.494 closest distance to " O   ASN A 301 " =    1.384
peak=   -3.492 closest distance to " O   HOH Z  77 " =    1.702
peak=   -3.486 closest distance to " C   SER A  63 " =    1.251
peak=   -3.476 closest distance to " O   GLN A 194 " =    1.288
peak=   -3.473 closest distance to " O   HOH Z 126 " =    1.834
peak=   -3.464 closest distance to " O   HOH Z 185 " =    1.915
peak=   -3.461 closest distance to " NH2AARG A 275 " =    5.392
peak=   -3.456 closest distance to " O   HOH Z 250 " =    1.247
peak=   -3.455 closest distance to " O   HOH Z 208 " =    0.986
peak=   -3.452 closest distance to " O   HOH Z 101 " =    1.073
peak=   -3.451 closest distance to " O   HOH Z  73 " =    1.466
peak=   -3.449 closest distance to " O   HOH Z 425 " =    0.951
peak=   -3.448 closest distance to " O   HOH Z  93 " =    1.357
peak=   -3.435 closest distance to " CD2 TYR A 293 " =    1.977
peak=   -3.434 closest distance to " O   HOH Z 234 " =    4.663
peak=   -3.433 closest distance to " CB  CYS A 201 " =    2.158
peak=   -3.432 closest distance to " C   HIS A 108 " =    1.178
peak=   -3.428 closest distance to " OD2 ASP A 140 " =    1.506
peak=   -3.424 closest distance to " OG ASER A 134 " =    1.212
peak=   -3.422 closest distance to " CB  VAL A  72 " =    0.912
peak=   -3.421 closest distance to " CZ2 TRP A  92 " =    2.395
peak=   -3.418 closest distance to " OG1 THR A 246 " =    1.758
peak=   -3.412 closest distance to " OE1 GLN A  58 " =    2.511
peak=   -3.411 closest distance to " O   HOH Z 385 " =    0.950
peak=   -3.411 closest distance to " O   HOH Z 404 " =    1.525
peak=   -3.407 closest distance to " N   THR A 157 " =    1.595
peak=   -3.404 closest distance to " O   HOH Z 413 " =    4.366
peak=   -3.397 closest distance to " O   ASN A 215 " =    1.693
peak=   -3.395 closest distance to " OG1 THR A 178 " =    1.025
peak=   -3.394 closest distance to " OG BSER A 134 " =    1.538
peak=   -3.393 closest distance to " O   ARG A  56 " =    1.422
peak=   -3.388 closest distance to " O   HOH Z  22 " =    2.090
peak=   -3.386 closest distance to " O   HOH Z 274 " =    3.008
peak=   -3.385 closest distance to " CG  ARG A  66 " =    2.271
peak=   -3.384 closest distance to " CB  ALA A   7 " =    1.949
peak=   -3.383 closest distance to " NH1 ARG A  56 " =    2.416
peak=   -3.381 closest distance to " O   HOH Z  14 " =    1.263
peak=   -3.375 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.372 closest distance to " OD1 ASP A 171 " =    1.497
peak=   -3.365 closest distance to " OG  SER A   3 " =    1.050
peak=   -3.364 closest distance to " OG1 THR A 279 " =    1.205
peak=   -3.363 closest distance to " N   LYS A 166 " =    1.843
peak=   -3.361 closest distance to " O   HOH Z 137 " =    1.446
peak=   -3.357 closest distance to " CA  ASN A 127 " =    1.350
peak=   -3.357 closest distance to " O   HOH Z  95 " =    1.375
peak=   -3.356 closest distance to " O   HOH Z   1 " =    3.520
peak=   -3.350 closest distance to " O   HOH Z 231 " =    1.711
peak=   -3.346 closest distance to " O   HOH Z 266 " =    4.246
peak=   -3.341 closest distance to " O   HOH Z  76 " =    1.085
peak=   -3.339 closest distance to " O   HOH Z 418 " =    1.087
peak=   -3.324 closest distance to " O   HOH Z 264 " =    0.958
peak=   -3.324 closest distance to " N   VAL A  72 " =    1.692
peak=   -3.316 closest distance to " N   ALA A   1 " =    1.338
peak=   -3.314 closest distance to " OD2 ASP A 298 " =    0.973
peak=   -3.313 closest distance to " CD  LYS A 289 " =    2.475
peak=   -3.311 closest distance to " OG  SER A  87 " =    1.024
peak=   -3.307 closest distance to " O   HOH Z  40 " =    3.956
peak=   -3.307 closest distance to " O   ARG A  14 " =    2.295
peak=   -3.307 closest distance to " CA  LYS A 290 " =    1.431
peak=   -3.305 closest distance to " CG2AVAL A  41 " =    2.838
peak=   -3.304 closest distance to " O   HOH Z 102 " =    2.135
peak=   -3.300 closest distance to " ND2 ASN A  45 " =    1.168
peak=   -3.300 closest distance to " O   HOH Z 385 " =    2.630
peak=   -3.299 closest distance to " O   HOH Z  51 " =    0.836
peak=   -3.296 closest distance to " CE3 TRP A  70 " =    2.098
peak=   -3.295 closest distance to " N   GLN A 122 " =    1.443
peak=   -3.294 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.293 closest distance to " O   HOH Z  97 " =    1.171
peak=   -3.285 closest distance to " CD2 LEU A 297 " =    1.219
peak=   -3.281 closest distance to " O   HOH Z 247 " =    0.974
peak=   -3.278 closest distance to " O   VAL A 174 " =    2.508
peak=   -3.278 closest distance to " O   HOH Z 426 " =    1.476
peak=   -3.277 closest distance to " CD  PRO A 198 " =    1.250
peak=   -3.275 closest distance to " O   HOH Z 393 " =    3.243
peak=   -3.274 closest distance to " CE3 TRP A 274 " =    2.568
peak=   -3.271 closest distance to " CG  PRO A 163 " =    2.479
peak=   -3.264 closest distance to " O   ILE A 239 " =    1.247
peak=   -3.261 closest distance to " O   ALA A   1 " =    1.103
peak=   -3.261 closest distance to " CB  ALA A 291 " =    2.116
peak=   -3.260 closest distance to " CB  TRP A  85 " =    2.335
peak=   -3.258 closest distance to " N   ALA A 114 " =    2.276
peak=   -3.258 closest distance to " N   GLY A  35 " =    1.742
peak=   -3.251 closest distance to " CG  ARG A 259 " =    2.820
peak=   -3.244 closest distance to " O   HOH Z 412 " =    5.075
peak=   -3.244 closest distance to " O   HOH Z 221 " =    1.119
peak=   -3.240 closest distance to " O   HOH Z 388 " =    2.163
peak=   -3.238 closest distance to " O   LEU A 297 " =    0.742
peak=   -3.237 closest distance to " O   HOH Z 210 " =    2.011
peak=   -3.235 closest distance to " CG BLYS A 290 " =    1.026
peak=   -3.229 closest distance to " CD  ARG A 156 " =    1.925
peak=   -3.224 closest distance to " CA  GLY A 211 " =    1.366
peak=   -3.221 closest distance to " NZ  LYS A 289 " =    1.468
peak=   -3.219 closest distance to " CD1 LEU A  96 " =    2.091
peak=   -3.219 closest distance to " N   GLN A  88 " =    1.819
peak=   -3.216 closest distance to " O   HOH Z 114 " =    4.532
peak=   -3.213 closest distance to " O   ASP A  65 " =    1.004
peak=   -3.211 closest distance to " O   HOH Z 140 " =    4.484
peak=   -3.207 closest distance to " ND2 ASN A 173 " =    1.802
peak=   -3.201 closest distance to " O   HOH Z 117 " =    0.771
peak=   -3.200 closest distance to " CD BARG A 145 " =    2.474
peak=   -3.199 closest distance to " O   SER A 216 " =    1.862
peak=   -3.199 closest distance to " NH2 ARG A 159 " =    2.527
peak=   -3.198 closest distance to " O   HOH Z 427 " =    0.990
peak=   -3.196 closest distance to " O   THR A  29 " =    1.781
peak=   -3.196 closest distance to " O   HOH Z 100 " =    1.293
peak=   -3.193 closest distance to " CB  PRO A 213 " =    1.570
peak=   -3.191 closest distance to " OG  SER A 245 " =    1.157
peak=   -3.186 closest distance to " O   HOH Z 246 " =    1.953
peak=   -3.186 closest distance to " OE2 GLU A 152 " =    2.150
peak=   -3.185 closest distance to " O   VAL A 232 " =    1.836
peak=   -3.182 closest distance to " O   HOH Z 292 " =    3.436
peak=   -3.176 closest distance to " CG  PRO A 243 " =    1.145
peak=   -3.175 closest distance to " OXT GLY A 302 " =    3.078
peak=   -3.170 closest distance to " O   HOH Z  64 " =    1.037
peak=   -3.168 closest distance to " CG1 ILE A 234 " =    1.855
peak=   -3.167 closest distance to " O   HOH Z 298 " =    1.080
peak=   -3.166 closest distance to " CD1 TYR A 214 " =    1.370
peak=   -3.166 closest distance to " C   VAL A 265 " =    0.915
peak=   -3.164 closest distance to " O   HOH Z  43 " =    1.718
peak=   -3.164 closest distance to " CB  ASP A 132 " =    2.265
peak=   -3.162 closest distance to " OD1 ASP A  27 " =    1.969
peak=   -3.151 closest distance to " O   HOH Z 412 " =    4.885
peak=   -3.149 closest distance to " O   SER A  97 " =    1.228
peak=   -3.148 closest distance to " ND2 ASN A 285 " =    1.539
peak=   -3.148 closest distance to " O   PHE A 218 " =    1.413
peak=   -3.147 closest distance to " O   HOH Z 143 " =    1.446
peak=   -3.146 closest distance to " O   HOH Z 253 " =    1.576
peak=   -3.139 closest distance to " CG  GLU A 277 " =    1.267
peak=   -3.136 closest distance to " O   HOH Z 389 " =    4.626
peak=   -3.128 closest distance to " CB  SER A 245 " =    2.498
peak=   -3.126 closest distance to " O   HOH Z 377 " =    1.158
peak=   -3.125 closest distance to " SD  MET A 188 " =    1.189
peak=   -3.118 closest distance to " NE2 GLN A  55 " =    0.783
peak=   -3.104 closest distance to " C   VAL A  72 " =    1.077
peak=   -3.101 closest distance to " O   HOH Z 128 " =    2.346
peak=   -3.100 closest distance to " O   VAL A 197 " =    1.068
peak=   -3.097 closest distance to " N   ASN A 127 " =    1.611
peak=   -3.093 closest distance to " CG  ASN A  60 " =    1.066
peak=   -3.085 closest distance to " OE1 GLN A  77 " =    1.687
peak=   -3.085 closest distance to " O   HOH Z 147 " =    1.424
peak=   -3.072 closest distance to " O   HOH Z 258 " =    4.846
peak=   -3.069 closest distance to " O   HOH Z  46 " =    0.826
peak=   -3.063 closest distance to " N   GLY A 302 " =    1.563
peak=   -3.049 closest distance to " O   GLY A  80 " =    2.384
peak=   -3.036 closest distance to " CG  PHE A  61 " =    1.883
peak=   -3.029 closest distance to " O   HOH Z 383 " =    1.259
peak=   -3.023 closest distance to " O   ALA A 161 " =    1.898
peak=   -3.017 closest distance to " O   HOH Z 111 " =    2.300

================= 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    :  0.4898 0.4936   6.298953e+00   6.293932e+00
   1_bss:  0.4798 0.4817   6.296133e+00   6.282119e+00
   1_xyz:  0.3954 0.4347   6.172156e+00   6.230576e+00
   1_adp:  0.3588 0.4442   6.137614e+00   6.238532e+00
   1_occ:  0.3582 0.4440   6.137384e+00   6.238140e+00
   2_bss:  0.3570 0.4431   6.138633e+00   6.238253e+00
   2_xyz:  0.3105 0.3891   6.026206e+00   6.167915e+00
   2_adp:  0.2974 0.3784   6.001775e+00   6.151240e+00
   2_occ:  0.2971 0.3788   6.001688e+00   6.151311e+00
   3_bss:  0.2973 0.3789   6.001008e+00   6.150812e+00
   3_xyz:  0.2521 0.3312   5.860929e+00   6.035753e+00
   3_adp:  0.2380 0.3173   5.819697e+00   6.004928e+00
   3_occ:  0.2379 0.3171   5.819416e+00   6.004942e+00
   4_bss:  0.2382 0.3158   5.817865e+00   6.002793e+00
   4_xyz:  0.1837 0.2446   5.575290e+00   5.787038e+00
   4_adp:  0.1632 0.2242   5.481689e+00   5.715542e+00
   4_occ:  0.1630 0.2235   5.480091e+00   5.713689e+00
   5_bss:  0.1632 0.2223   5.476982e+00   5.709181e+00
   5_xyz:  0.1389 0.1942   5.334712e+00   5.581999e+00
   5_adp:  0.1320 0.1835   5.285563e+00   5.527440e+00
   5_occ:  0.1317 0.1830   5.284274e+00   5.526286e+00
   5_bss:  0.1321 0.1836   5.285684e+00   5.527026e+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:  0.352  20.540  -3.583   1.311   1.264   0.000   0.000   0.000
   1_xyz:  0.352  20.540  -3.583   1.311   1.264   0.000   0.000   0.000
   1_adp:  0.352  20.540  -3.583   1.311   1.264   0.000   0.000   0.000
   1_occ:  0.352  20.540  -3.583   1.311   1.264   0.000   0.000   0.000
   2_bss:  0.362  53.930  -0.861   0.628   0.765   0.000   0.000   0.000
   2_xyz:  0.362  53.930  -0.861   0.628   0.765   0.000   0.000   0.000
   2_adp:  0.362  53.930  -0.861   0.628   0.765   0.000   0.000   0.000
   2_occ:  0.362  53.930  -0.861   0.628   0.765   0.000   0.000   0.000
   3_bss:  0.355  55.413  -0.185   0.127   0.598   0.000   0.000   0.000
   3_xyz:  0.355  55.413  -0.185   0.127   0.598   0.000   0.000   0.000
   3_adp:  0.355  55.413  -0.185   0.127   0.598   0.000   0.000   0.000
   3_occ:  0.355  55.413  -0.185   0.127   0.598   0.000   0.000   0.000
   4_bss:  0.334  43.575  -0.605  -0.578  -0.019  -0.000  -0.000  -0.000
   4_xyz:  0.334  43.575  -0.605  -0.578  -0.019  -0.000  -0.000  -0.000
   4_adp:  0.334  43.575  -0.605  -0.578  -0.019  -0.000  -0.000  -0.000
   4_occ:  0.334  43.575  -0.605  -0.578  -0.019  -0.000  -0.000  -0.000
   5_bss:  0.317  40.688  -0.982  -1.361  -0.466  -0.000  -0.000  -0.000
   5_xyz:  0.317  40.688  -0.982  -1.361  -0.466  -0.000  -0.000  -0.000
   5_adp:  0.317  40.688  -0.982  -1.361  -0.466  -0.000  -0.000  -0.000
   5_occ:  0.317  40.688  -0.982  -1.361  -0.466  -0.000  -0.000  -0.000
   5_bss:  0.314  40.095  -0.985  -1.364  -0.469  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.837 0.3702  0.5162    79744.924
   1_bss:  59.866 0.3946  0.5476    75003.442
   1_xyz:  50.570 0.5128  0.6971    57277.782
   1_adp:  52.352 0.4895  0.6609    59384.340
   1_occ:  52.388 0.4890  0.6600    59443.416
   2_bss:  52.266 0.4906  0.6779    59464.919
   2_xyz:  43.966 0.5940  0.8185    44948.967
   2_adp:  41.825 0.6206  0.8354    42424.113
   2_occ:  41.886 0.6198  0.8338    42426.048
   3_bss:  41.846 0.6201  0.8340    42265.416
   3_xyz:  34.306 0.7091  0.9304    29629.303
   3_adp:  32.220 0.7335  0.9393    27151.348
   3_occ:  32.221 0.7335  0.9384    27159.470
   4_bss:  32.119 0.7345  0.9190    26902.464
   4_xyz:  24.105 0.8207  0.9900    15562.476
   4_adp:  21.846 0.8440  0.9918    13172.798
   4_occ:  21.790 0.8446  0.9918    13089.012
   5_bss:  21.677 0.8454  0.9729    12880.948
   5_xyz:  18.361 0.8768  0.9899     9548.067
   5_adp:  16.936 0.8902  0.9903     8622.977
   5_occ:  16.901 0.8905  0.9903     8580.869
   5_bss:  16.933 0.8903  0.9903     8620.168
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0331e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0331e-01
   1_xyz:   1.830  0.015  0.121 16.839  0.007  4.106   1.7857e-01
   1_adp:   1.830  0.015  0.121 16.839  0.007  4.106   1.7857e-01
   1_occ:   1.830  0.015  0.121 16.839  0.007  4.106   1.7857e-01
   2_bss:   1.830  0.015  0.121 16.839  0.007  4.106   1.7857e-01
   2_xyz:   1.318  0.009  0.089 15.645  0.005  4.102   9.6174e-02
   2_adp:   1.318  0.009  0.089 15.645  0.005  4.102   9.6174e-02
   2_occ:   1.318  0.009  0.089 15.645  0.005  4.102   9.6174e-02
   3_bss:   1.318  0.009  0.089 15.645  0.005  4.102   9.6174e-02
   3_xyz:   1.037  0.008  0.066 14.611  0.004  4.108   6.9528e-02
   3_adp:   1.037  0.008  0.066 14.611  0.004  4.108   6.9528e-02
   3_occ:   1.037  0.008  0.066 14.611  0.004  4.108   6.9528e-02
   4_bss:   1.037  0.008  0.066 14.611  0.004  4.108   6.9528e-02
   4_xyz:   1.144  0.008  0.074 14.773  0.004  4.109   7.5019e-02
   4_adp:   1.144  0.008  0.074 14.773  0.004  4.109   7.5019e-02
   4_occ:   1.144  0.008  0.074 14.773  0.004  4.109   7.5019e-02
   5_bss:   1.144  0.008  0.074 14.773  0.004  4.109   7.5019e-02
   5_xyz:   1.041  0.007  0.070 14.630  0.004  4.107   6.3296e-02
   5_adp:   1.041  0.007  0.070 14.630  0.004  4.107   6.3296e-02
   5_occ:   1.041  0.007  0.070 14.630  0.004  4.107   6.3296e-02
   5_bss:   1.041  0.007  0.070 14.630  0.004  4.107   6.3296e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.427   2.3773e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.427   2.3773e-01
   1_xyz:  10.676  0.110  0.448 86.186  0.053  1.866   1.2884e-01
   1_adp:  10.676  0.110  0.448 86.186  0.053  1.866   1.2884e-01
   1_occ:  10.676  0.110  0.448 86.186  0.053  1.866   1.2884e-01
   2_bss:  10.676  0.110  0.448 86.186  0.053  1.866   1.2884e-01
   2_xyz:   8.559  0.070  0.295 81.229  0.052  2.144   7.3172e-02
   2_adp:   8.559  0.070  0.295 81.229  0.052  2.144   7.3172e-02
   2_occ:   8.559  0.070  0.295 81.229  0.052  2.144   7.3172e-02
   3_bss:   8.559  0.070  0.295 81.229  0.052  2.144   7.3172e-02
   3_xyz:   7.198  0.056  0.264 80.961  0.028  2.223   1.3670e-01
   3_adp:   7.198  0.056  0.264 80.961  0.028  2.223   1.3670e-01
   3_occ:   7.198  0.056  0.264 80.961  0.028  2.223   1.3670e-01
   4_bss:   7.198  0.056  0.264 80.961  0.028  2.223   1.3670e-01
   4_xyz:   7.542  0.048  0.225 79.418  0.035  2.215   6.6216e-02
   4_adp:   7.542  0.048  0.225 79.418  0.035  2.215   6.6216e-02
   4_occ:   7.542  0.048  0.225 79.418  0.035  2.215   6.6216e-02
   5_bss:   7.542  0.048  0.225 79.418  0.035  2.215   6.6216e-02
   5_xyz:   7.227  0.045  0.215 79.984  0.038  2.308   7.9240e-02
   5_adp:   7.227  0.045  0.215 79.984  0.038  2.308   7.9240e-02
   5_occ:   7.227  0.045  0.215 79.984  0.038  2.308   7.9240e-02
   5_bss:   7.227  0.045  0.215 79.984  0.038  2.308   7.9240e-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: 115.17   0.00  18.98  91.63   0.00  16.32 115.17   0.00  33.44
   1_occ: 115.17   0.00  18.98  91.63   0.00  16.32 115.17   0.00  33.44
   2_bss: 115.17   0.00  18.98  91.63   0.00  16.32 115.17   0.00  33.44
   2_xyz: 115.17   0.00  18.98  91.63   0.00  16.32 115.17   0.00  33.44
   2_adp: 117.82   0.00  17.69  97.11   0.00  14.88 117.82   0.00  33.00
   2_occ: 117.82   0.00  17.69  97.11   0.00  14.88 117.82   0.00  33.00
   3_bss: 117.82   0.00  17.69  97.11   0.00  14.88 117.82   0.00  33.00
   3_xyz: 117.82   0.00  17.69  97.11   0.00  14.88 117.82   0.00  33.00
   3_adp: 112.92   0.00  17.27  97.06   0.00  13.55 112.92   1.36  37.50
   3_occ: 112.92   0.00  17.27  97.06   0.00  13.55 112.92   1.36  37.50
   4_bss: 112.92   0.00  17.27  97.06   0.00  13.55 112.92   1.36  37.50
   4_xyz: 112.92   0.00  17.27  97.06   0.00  13.55 112.92   1.36  37.50
   4_adp: 110.07   0.00  17.50 100.93   0.00  12.58 110.07   3.66  44.32
   4_occ: 110.07   0.00  17.50 100.93   0.00  12.58 110.07   3.66  44.32
   5_bss: 110.07   0.00  17.50 100.93   0.00  12.58 110.07   3.66  44.32
   5_xyz: 110.07   0.00  17.50 100.93   0.00  12.58 110.07   3.66  44.32
   5_adp: 104.42   0.00  16.84 102.09   0.00  11.96 104.42   4.92  43.41
   5_occ: 104.42   0.00  16.84 102.09   0.00  11.96 104.42   4.92  43.41
   5_bss: 104.42   0.00  16.85 102.09   0.00  11.97 104.42   4.92  43.41
------------------------------------------------------------------------
 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:    1.902    0.016    0.417
   1_adp:    1.902    0.016    0.417
   1_occ:    1.902    0.016    0.417
   2_bss:    1.902    0.016    0.417
   2_xyz:    1.671    0.069    0.577
   2_adp:    1.671    0.069    0.577
   2_occ:    1.671    0.069    0.577
   3_bss:    1.671    0.069    0.577
   3_xyz:    1.696    0.078    0.699
   3_adp:    1.696    0.078    0.699
   3_occ:    1.696    0.078    0.699
   4_bss:    1.696    0.078    0.699
   4_xyz:    1.776    0.040    0.855
   4_adp:    1.776    0.040    0.855
   4_occ:    1.776    0.040    0.855
   5_bss:    1.776    0.040    0.855
   5_xyz:    1.770    0.097    0.901
   5_adp:    1.770    0.097    0.901
   5_occ:    1.770    0.097    0.901
   5_bss:    1.770    0.097    0.901
------------------------------------------------------------------------

CPU time actual refinement: 367.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/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_605/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_605/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.40 
  Macro-tasks:
    bulk solvent and scale       = 44.05  
    individual site refinement   = 153.81 
    weights calculation          = 30.60  
    collect and process          = 6.38   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 234.96 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 121.23 
    alpha_beta                      = 8.44   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 129.29 
    fmodel                         = 7.23   
    r_factors                      = 0.25   
    phase_errors                   = 10.09  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 281.02 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.184 micro seconds
Total CPU time: 6.35 minutes
from_scatterers_fft:    656 calls, 120.83 s
gradients_fft:          601 calls, 116.05 s

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

# Date 2008-01-16 Time 05:14:00 PST -0800 (1200489240.65 s)
Start R-work = 0.4898, R-free = 0.4936 (no bulk solvent and anisotropic scale)
Final R-work = 0.1490, R-free = 0.1988 (no bulk solvent and anisotropic scale)

Start R-work = 0.4798, R-free = 0.4817
Final R-work = 0.1321, R-free = 0.1836