# Date 2008-01-16 Time 05:47:52 PST -0800 (1200491272.26 s)
#phil __OFF__

Command line arguments: "../883.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14204
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 883

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 85.5261, 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: 3.24, 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: (70.9525, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98037
Completeness in resolution range: 0.967358
Completeness with d_max=infinity: 0.964405

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98037
Completeness in resolution range: 0.967358
Completeness with d_max=infinity: 0.964405

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0612 -  4.2379 [2122/2147]  1912   210   9.9%
  bin  2:  4.2379 -  3.3762 [2045/2065]  1840   205  10.0%
  bin  3:  3.3762 -  2.9531 [2018/2037]  1813   205  10.2%
  bin  4:  2.9531 -  2.6847 [1997/2027]  1801   196   9.8%
  bin  5:  2.6847 -  2.4932 [1986/2005]  1792   194   9.8%
  bin  6:  2.4932 -  2.3468 [1992/2017]  1788   204  10.2%
  bin  7:  2.3468 -  2.2297 [1937/1965]  1741   196  10.1%
  bin  8:  2.2297 -  2.1329 [1976/2012]  1777   199  10.1%
  bin  9:  2.1329 -  2.0510 [1953/1995]  1758   195  10.0%
  bin 10:  2.0510 -  1.9804 [1563/1980]  1408   155   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2205
        3.04 -     3.66: 4729
        3.66 -     4.28: 9092
        4.28 -     4.90: 12351
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.107 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.255 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.264 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28393 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_883/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 85.5261 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: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.3421   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.076461                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7269 0.99   1385  155 0.2934 0.2913      6.3662      6.3235|
|  2:  4.7269 -  3.7712 0.99   1330  146 0.2712 0.2604      6.4763      6.4334|
|  3:  3.7712 -  3.3003 0.99   1301  142 0.2919 0.2662      6.3549      6.4527|
|  4:  3.3003 -  3.0011 0.99   1294  153 0.3114 0.3557      6.2645      6.2842|
|  5:  3.0011 -  2.7875 0.99   1289  138 0.3531 0.3461      6.1471      6.1355|
|  6:  2.7875 -  2.6240 0.99   1281  141 0.3551 0.3798      6.0675      6.0668|
|  7:  2.6240 -  2.4932 0.99   1278  135 0.3682 0.3359      6.0514      6.0164|
|  8:  2.4932 -  2.3851 0.98   1267  151 0.3852 0.3785      6.0112      6.0017|
|  9:  2.3851 -  2.2936 0.98   1245  138 0.3703 0.3607       5.945      5.8963|
| 10:  2.2936 -  2.2148 1.00   1290  140 0.3858 0.3970      5.9342      5.9583|
| 11:  2.2148 -  2.1457 0.97   1258  139 0.4080 0.3959      5.9155      5.9343|
| 12:  2.1457 -  2.0845 0.98   1247  141 0.4041 0.4304      5.8617      5.9202|
| 13:  2.0845 -  2.0298 1.00   1264  136 0.4017 0.3985      5.7632      5.7012|
| 14:  2.0298 -  1.9804 0.71    901  104 0.4251 0.4102      5.7547      5.6707|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7269  1385   155  0.79  25.97   0.86     0.81      42480.43|
|  2:  4.7269 -  3.7712  1330   146  0.84  22.81   0.97     0.92      49511.06|
|  3:  3.7712 -  3.3003  1301   142  0.78  27.72   1.00     0.95      51227.28|
|  4:  3.3003 -  3.0011  1294   153  0.75  31.44   0.99     0.92      47110.51|
|  5:  3.0011 -  2.7875  1289   138  0.69  35.94   0.97     0.89      39420.46|
|  6:  2.7875 -  2.6240  1281   141  0.69  36.49   1.00     0.89      33829.23|
|  7:  2.6240 -  2.4932  1278   135  0.70  35.98   0.99     0.90      29756.36|
|  8:  2.4932 -  2.3851  1267   151  0.68  37.48   0.99     0.91      27486.51|
|  9:  2.3851 -  2.2936  1245   138  0.69  36.82   1.02     0.90      25578.61|
| 10:  2.2936 -  2.2148  1290   140  0.66  39.28   1.04     0.90      25465.54|
| 11:  2.2148 -  2.1457  1258   139  0.63  41.60   1.04     0.89      25334.82|
| 12:  2.1457 -  2.0845  1247   141  0.63  42.00   1.04     0.88      23841.46|
| 13:  2.0845 -  2.0298  1264   136  0.60  44.11   1.03     0.86      20610.94|
| 14:  2.0298 -  1.9804   901   104  0.63  41.74   1.01     0.84      16325.88|
|alpha:            min =        0.81 max =            0.95 mean =         0.89|
|beta:             min =    16325.88 max =        51227.28 mean =     33258.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.98 mean =        35.40|
|phase err.(test): min =        0.00 max =           89.93 mean =        35.44|
|-----------------------------------------------------------------------------|

============================== 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 = 4.377337              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.337   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.823087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.422   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      205 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2000 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2856 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4666 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4426 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5622 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6729 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.177 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    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: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.3421   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.076461                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3306   r_free= 0.3313   ksol= 0.34   Bsol= 47.20   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.16,-0.45,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.060763                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.804525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.535   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397966              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.239   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3306      final r-factor (work) = 0.1860          |
| start r-factor (free) = 0.3313      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6981 = 3.80 * 0.50 * 6.0645 + 1.00 * 0.1619                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0497 = 3.80 * 0.50 * 5.7751 + 1.00 * 0.0639                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1860      final r-factor (work) = 0.1703          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.2147          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3045 = 0.40 * 1.00 * 5.7751 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1891 = 0.40 * 1.00 * 5.4777 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.54   17.16    None  None   None       |
|    all(noH): 2823   0      0.00    72.54   17.16    None  None   None       |
|    Sol.    : 438    0      6.60    72.54   39.42    None  None   None       |
|    Mac.    : 2385   0      0.00    66.87   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.254:  386   |   5:    36.271 -  43.525:  113        |
|      1:     7.254 -  14.508: 1337   |   6:    43.525 -  50.779:   99        |
|      2:    14.508 -  21.763:  500   |   7:    50.779 -  58.033:   64        |
|      3:    21.763 -  29.017:  162   |   8:    58.033 -  65.288:   38        |
|      4:    29.017 -  36.271:  110   |   9:    65.288 -  72.542:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1703 r_free = 0.2147             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1699 r_free = 0.2148             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1699   r_free= 0.2148   ksol= 0.34   Bsol= 47.20   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.16,-0.45,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.490504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1688   r_free= 0.2130   ksol= 0.33   Bsol= 52.43   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.32,-1.69,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.488399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.167128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.204  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1688      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.2130      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5251 = 4.17 * 0.50 * 5.5007 + 1.00 * 0.0639                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2330 = 4.17 * 0.50 * 5.3612 + 1.00 * 0.0627                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0874 = 0.20 * 1.00 * 5.3612 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0527 = 0.20 * 1.00 * 5.1979 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    70.58   16.96    None  None   None       |
|    all(noH): 2823   0      1.86    70.58   16.96    None  None   None       |
|    Sol.    : 438    0      5.95    70.46   38.55    None  None   None       |
|    Mac.    : 2385   0      1.86    70.58   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.860 -   8.732:  618   |   5:    36.221 -  43.093:  114        |
|      1:     8.732 -  15.604: 1286   |   6:    43.093 -  49.965:   85        |
|      2:    15.604 -  22.477:  377   |   7:    49.965 -  56.837:   69        |
|      3:    22.477 -  29.349:  123   |   8:    56.837 -  63.710:   34        |
|      4:    29.349 -  36.221:  100   |   9:    63.710 -  70.582:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1585             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1585             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1585   ksol= 0.33   Bsol= 52.43   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.32,-1.69,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.163803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1584   ksol= 0.32   Bsol= 47.58   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.62,-1.71,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.163696                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.273621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.805  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.717786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.193  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5692 = 3.27 * 0.50 * 5.1970 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4693 = 3.27 * 0.50 * 5.1316 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6907 = 0.72 * 1.00 * 5.1316 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6718 = 0.72 * 1.00 * 5.1035 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    81.85   17.13    None  None   None       |
|    all(noH): 2823   0      1.06    81.85   17.13    None  None   None       |
|    Sol.    : 438    0      4.99    75.99   39.59    None  None   None       |
|    Mac.    : 2385   0      1.06    81.85   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.063 -   9.141:  789   |   5:    41.455 -  49.534:  113        |
|      1:     9.141 -  17.220: 1236   |   6:    49.534 -  57.612:   75        |
|      2:    17.220 -  25.298:  306   |   7:    57.612 -  65.690:   45        |
|      3:    25.298 -  33.377:  132   |   8:    65.690 -  73.769:   19        |
|      4:    33.377 -  41.455:  102   |   9:    73.769 -  81.847:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1535             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1535             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1535   ksol= 0.32   Bsol= 47.58   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.62,-1.71,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1535   ksol= 0.32   Bsol= 47.58   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.58,-1.63,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104269                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.626825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.684  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.017  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7729 = 2.63 * 0.50 * 5.1035 + 1.00 * 0.0698                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7667 = 2.63 * 0.50 * 5.1037 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8611 = 0.56 * 1.00 * 5.1037 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8611 = 0.56 * 1.00 * 5.1034 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    83.78   17.00    None  None   None       |
|    all(noH): 2823   0      0.81    83.78   17.00    None  None   None       |
|    Sol.    : 438    0      5.77    77.10   39.42    None  None   None       |
|    Mac.    : 2385   0      0.81    83.78   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.806 -   9.103:  808   |   5:    42.293 -  50.590:  107        |
|      1:     9.103 -  17.400: 1241   |   6:    50.590 -  58.887:   76        |
|      2:    17.400 -  25.698:  290   |   7:    58.887 -  67.185:   39        |
|      3:    25.698 -  33.995:  135   |   8:    67.185 -  75.482:   15        |
|      4:    33.995 -  42.293:  107   |   9:    75.482 -  83.780:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1061 r_free = 0.1544             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1544             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1544   ksol= 0.32   Bsol= 47.58   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.58,-1.63,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105083                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1544   ksol= 0.32   Bsol= 47.58   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.43,-1.44,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.083176              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 168.935  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.155490              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.836  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1060      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3798 = 2.08 * 0.50 * 5.1041 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3786 = 2.08 * 0.50 * 5.1084 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1067      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8031 = 0.16 * 1.00 * 5.1084 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8028 = 0.16 * 1.00 * 5.1178 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    80.95   16.37    None  None   None       |
|    all(noH): 2823   0      1.63    80.95   16.37    None  None   None       |
|    Sol.    : 438    0      6.43    77.76   36.79    None  None   None       |
|    Mac.    : 2385   0      1.63    80.95   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.627 -   9.559:  942   |   5:    41.288 -  49.220:   98        |
|      1:     9.559 -  17.491: 1138   |   6:    49.220 -  57.152:   66        |
|      2:    17.491 -  25.423:  269   |   7:    57.152 -  65.084:   18        |
|      3:    25.423 -  33.355:  139   |   8:    65.084 -  73.016:   10        |
|      4:    33.355 -  41.288:  138   |   9:    73.016 -  80.948:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1544             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1545             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1545   ksol= 0.32   Bsol= 47.58   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.43,-1.44,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114678                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7269 0.99   1385  155 0.0987 0.1273      5.3751       5.525|
|  2:  4.7269 -  3.7712 0.99   1330  146 0.0860 0.1125      5.4422      5.6325|
|  3:  3.7712 -  3.3003 0.99   1301  142 0.1038 0.1530      5.4636      5.8749|
|  4:  3.3003 -  3.0011 0.99   1294  153 0.1181 0.1499      5.4438      5.5561|
|  5:  3.0011 -  2.7875 0.99   1289  138 0.1284 0.1815      5.3096      5.5779|
|  6:  2.7875 -  2.6240 0.99   1281  141 0.1158 0.1679       5.186      5.3884|
|  7:  2.6240 -  2.4932 0.99   1278  135 0.1226 0.1579      5.1435      5.3558|
|  8:  2.4932 -  2.3851 0.98   1267  151 0.1093 0.1671      5.0001      5.3144|
|  9:  2.3851 -  2.2936 0.98   1245  138 0.1091 0.1714      4.9859      5.2441|
| 10:  2.2936 -  2.2148 1.00   1290  140 0.1059 0.1759      4.9068      5.2606|
| 11:  2.2148 -  2.1457 0.97   1258  139 0.1094 0.1689       4.921      5.2426|
| 12:  2.1457 -  2.0845 0.98   1247  141 0.1053 0.1579      4.8464      5.1003|
| 13:  2.0845 -  2.0298 1.00   1264  136 0.1083 0.1745      4.7545       5.089|
| 14:  2.0298 -  1.9804 0.71    901  104 0.1006 0.1585      4.6172      4.8375|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7269  1385   155  0.94   8.81   0.98     0.95       6854.13|
|  2:  4.7269 -  3.7712  1330   146  0.95   7.87   1.02     1.01       9036.81|
|  3:  3.7712 -  3.3003  1301   142  0.94  11.07   1.02     1.02      10199.96|
|  4:  3.3003 -  3.0011  1294   153  0.92  13.51   1.01     0.98      10189.44|
|  5:  3.0011 -  2.7875  1289   138  0.90  15.60   0.99     0.96       8059.51|
|  6:  2.7875 -  2.6240  1281   141  0.91  15.34   0.98     0.96       6806.62|
|  7:  2.6240 -  2.4932  1278   135  0.91  15.16   0.99     0.97       5928.59|
|  8:  2.4932 -  2.3851  1267   151  0.92  13.97   0.99     0.96       4570.63|
|  9:  2.3851 -  2.2936  1245   138  0.92  14.08   1.00     0.98       4503.69|
| 10:  2.2936 -  2.2148  1290   140  0.91  14.24   1.00     0.97       3874.11|
| 11:  2.2148 -  2.1457  1258   139  0.90  15.80   0.99     0.95       4149.40|
| 12:  2.1457 -  2.0845  1247   141  0.92  14.18   1.01     1.00       3756.00|
| 13:  2.0845 -  2.0298  1264   136  0.91  15.55   1.00     0.99       3127.25|
| 14:  2.0298 -  1.9804   901   104  0.92  13.39   0.98     0.96       2277.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2277.66 max =        10199.96 mean =      6066.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.85 mean =        12.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1545   ksol= 0.32   Bsol= 47.52   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.32,-1.30,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1545   ksol= 0.32   Bsol= 47.52   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.32,-1.30,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114709                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7269 0.99   1385  155 0.0987 0.1273      5.3754      5.5253|
|  2:  4.7269 -  3.7712 0.99   1330  146 0.0860 0.1124      5.4423      5.6323|
|  3:  3.7712 -  3.3003 0.99   1301  142 0.1038 0.1530      5.4635      5.8748|
|  4:  3.3003 -  3.0011 0.99   1294  153 0.1181 0.1500      5.4437      5.5561|
|  5:  3.0011 -  2.7875 0.99   1289  138 0.1284 0.1815      5.3096      5.5779|
|  6:  2.7875 -  2.6240 0.99   1281  141 0.1158 0.1678      5.1859      5.3882|
|  7:  2.6240 -  2.4932 0.99   1278  135 0.1226 0.1579      5.1434      5.3557|
|  8:  2.4932 -  2.3851 0.98   1267  151 0.1093 0.1671      5.0001      5.3144|
|  9:  2.3851 -  2.2936 0.98   1245  138 0.1091 0.1714       4.986       5.244|
| 10:  2.2936 -  2.2148 1.00   1290  140 0.1059 0.1759      4.9069      5.2608|
| 11:  2.2148 -  2.1457 0.97   1258  139 0.1094 0.1690      4.9212      5.2429|
| 12:  2.1457 -  2.0845 0.98   1247  141 0.1053 0.1580      4.8464      5.1005|
| 13:  2.0845 -  2.0298 1.00   1264  136 0.1083 0.1746      4.7545      5.0892|
| 14:  2.0298 -  1.9804 0.71    901  104 0.1006 0.1584       4.617      4.8369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7269  1385   155  0.94   8.81   0.98     0.95       6858.63|
|  2:  4.7269 -  3.7712  1330   146  0.95   7.87   1.02     1.01       9039.13|
|  3:  3.7712 -  3.3003  1301   142  0.94  11.07   1.02     1.02      10198.25|
|  4:  3.3003 -  3.0011  1294   153  0.92  13.51   1.01     0.98      10189.63|
|  5:  3.0011 -  2.7875  1289   138  0.90  15.60   0.99     0.96       8057.92|
|  6:  2.7875 -  2.6240  1281   141  0.91  15.34   0.99     0.96       6805.75|
|  7:  2.6240 -  2.4932  1278   135  0.91  15.16   1.00     0.97       5927.15|
|  8:  2.4932 -  2.3851  1267   151  0.92  13.97   0.99     0.97       4570.19|
|  9:  2.3851 -  2.2936  1245   138  0.92  14.08   1.01     0.98       4503.56|
| 10:  2.2936 -  2.2148  1290   140  0.91  14.24   1.00     0.97       3874.73|
| 11:  2.2148 -  2.1457  1258   139  0.90  15.81   1.00     0.96       4150.95|
| 12:  2.1457 -  2.0845  1247   141  0.92  14.18   1.01     1.01       3757.45|
| 13:  2.0845 -  2.0298  1264   136  0.91  15.55   1.01     1.00       3127.00|
| 14:  2.0298 -  1.9804   901   104  0.92  13.39   0.99     0.96       2276.14|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2276.14 max =        10198.25 mean =      6066.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.85 mean =        12.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    80.89   16.31    None  None   None       |
|    all(noH): 2823   0      1.57    80.89   16.31    None  None   None       |
|    Sol.    : 438    0      6.37    77.70   36.73    None  None   None       |
|    Mac.    : 2385   0      1.57    80.89   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.569 -   9.501:  942   |   5:    41.229 -  49.162:   98        |
|      1:     9.501 -  17.433: 1138   |   6:    49.162 -  57.094:   66        |
|      2:    17.433 -  25.365:  269   |   7:    57.094 -  65.026:   18        |
|      3:    25.365 -  33.297:  139   |   8:    65.026 -  72.958:   10        |
|      4:    33.297 -  41.229:  138   |   9:    72.958 -  80.890:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 284         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 4.586
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 284
   mapped sites are within: 0.704 - 4.586

peak=    5.668 closest distance to " O   HOH Z 126 " =    1.975
peak=    5.610 closest distance to " CG  PRO A  54 " =    1.310
peak=    5.512 closest distance to " NE2 GLN A  11 " =    1.214
peak=    5.360 closest distance to " NH2 ARG A  56 " =    2.152
peak=    5.254 closest distance to " CB  GLN A 223 " =    1.432
peak=    5.234 closest distance to " CB  SER A  63 " =    1.219
peak=    5.201 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.935 closest distance to " O   HOH Z 144 " =    1.740
peak=    4.890 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.843 closest distance to " CB  GLN A 183 " =    1.185
peak=    4.817 closest distance to " O   HOH Z 236 " =    1.977
peak=    4.791 closest distance to " CB  PRO A  54 " =    0.952
peak=    4.781 closest distance to " O   HOH Z 232 " =    2.348
peak=    4.742 closest distance to " C   PRO A 198 " =    1.497
peak=    4.676 closest distance to " CB  ASN A 187 " =    1.360
peak=    4.577 closest distance to " CB  GLU A 152 " =    1.245
peak=    4.532 closest distance to " ND2 ASN A 187 " =    1.519
peak=    4.514 closest distance to " O   HOH Z  78 " =    1.757
peak=    4.474 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.461 closest distance to " CG  PRO A  90 " =    1.097
peak=    4.444 closest distance to " O   HOH Z 298 " =    1.933
peak=    4.426 closest distance to " O   HOH Z 369 " =    2.084
peak=    4.425 closest distance to " CB  ARG A  79 " =    1.372
peak=    4.409 closest distance to " O   HOH Z  15 " =    2.303
peak=    4.389 closest distance to " O   HOH Z 193 " =    1.871
peak=    4.361 closest distance to " O   HOH Z 303 " =    2.146
peak=    4.342 closest distance to " CG  PRO A 243 " =    1.087
peak=    4.326 closest distance to " CB  LEU A 228 " =    1.067
peak=    4.256 closest distance to " O   HOH Z 427 " =    2.871
peak=    4.206 closest distance to " O   HOH Z 132 " =    2.352
peak=    4.159 closest distance to " O   HOH Z 234 " =    3.727
peak=    4.145 closest distance to " O   HOH Z 144 " =    2.270
peak=    4.141 closest distance to " CG2 VAL A 257 " =    0.996
peak=    4.136 closest distance to " OD1 ASN A  69 " =    2.622
peak=    4.124 closest distance to " CB  GLU A 128 " =    0.996
peak=    4.108 closest distance to " CA  ASN A 215 " =    1.182
peak=    4.090 closest distance to " CB  VAL A 265 " =    1.312
peak=    4.089 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.073 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.043 closest distance to " CB  SER A 216 " =    0.789
peak=    4.040 closest distance to " CB  SER A   3 " =    1.377
peak=    4.027 closest distance to " O   HOH Z   1 " =    1.965
peak=    4.025 closest distance to " O   HOH Z  40 " =    1.927
peak=    3.971 closest distance to " O   HOH Z 209 " =    2.294
peak=    3.970 closest distance to " OD2 ASP A 286 " =    2.850
peak=    3.969 closest distance to " O   HOH Z 272 " =    1.819
peak=    3.968 closest distance to " O   HOH Z 250 " =    1.488
peak=    3.955 closest distance to " CA  THR A 264 " =    0.859
peak=    3.949 closest distance to " O   HOH Z 368 " =    1.929
peak=    3.940 closest distance to " O   HOH Z 346 " =    1.649
peak=    3.938 closest distance to " O   HOH Z  21 " =    1.746
peak=    3.937 closest distance to " O   HOH Z 217 " =    3.193
peak=    3.930 closest distance to " CG1 ILE A  33 " =    1.263
peak=    3.929 closest distance to " O   HOH Z 389 " =    1.929
peak=    3.917 closest distance to " O   HOH Z 158 " =    3.006
peak=    3.914 closest distance to " O   HOH Z 193 " =    1.730
peak=    3.909 closest distance to " O   HOH Z 219 " =    2.228
peak=    3.899 closest distance to " O   HOH Z   9 " =    2.030
peak=    3.885 closest distance to " O   HOH Z  68 " =    2.190
peak=    3.867 closest distance to " CA  ALA A  21 " =    1.187
peak=    3.867 closest distance to " O   HOH Z 344 " =    3.137
peak=    3.863 closest distance to " O   HOH Z 316 " =    3.086
peak=    3.852 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.845 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.835 closest distance to " O   HOH Z 214 " =    2.019
peak=    3.834 closest distance to " CE  LYS A  76 " =    0.918
peak=    3.824 closest distance to " CD  ARG A  66 " =    2.247
peak=    3.821 closest distance to " O   HOH Z 403 " =    1.683
peak=    3.818 closest distance to " O   HOH Z 368 " =    3.577
peak=    3.815 closest distance to " ND1 HIS A  86 " =    1.665
peak=    3.815 closest distance to " CB  TRP A 266 " =    0.934
peak=    3.814 closest distance to " O   HOH Z 133 " =    1.634
peak=    3.807 closest distance to " CB  ARG A 190 " =    1.551
peak=    3.781 closest distance to " CB  SER A 212 " =    1.146
peak=    3.776 closest distance to " OD1BASN A 224 " =    2.253
peak=    3.771 closest distance to " O   HOH Z 419 " =    2.038
peak=    3.771 closest distance to " O   HOH Z 189 " =    2.208
peak=    3.757 closest distance to " CB  ALA A  34 " =    1.042
peak=    3.756 closest distance to " O   HOH Z 425 " =    2.099
peak=    3.756 closest distance to " O   HOH Z 197 " =    3.216
peak=    3.755 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.749 closest distance to " NH1AARG A 145 " =    1.168
peak=    3.719 closest distance to " CD  ARG A 159 " =    0.752
peak=    3.718 closest distance to " O   HOH Z  10 " =    1.864
peak=    3.714 closest distance to " O   HOH Z 327 " =    1.682
peak=    3.713 closest distance to " O   HOH Z 305 " =    3.561
peak=    3.706 closest distance to " CZ  PHE A 218 " =    1.020
peak=    3.696 closest distance to " N   PHE A 130 " =    1.263
peak=    3.693 closest distance to " O   HOH Z  64 " =    2.258
peak=    3.686 closest distance to " O   HOH Z 128 " =    2.156
peak=    3.683 closest distance to " CB  ARG A 139 " =    0.984
peak=    3.675 closest distance to " CD2 LEU A 255 " =    1.554
peak=    3.666 closest distance to " O   SER A  87 " =    2.190
peak=    3.664 closest distance to " CB  TRP A 179 " =    1.385
peak=    3.659 closest distance to " O   HOH Z 207 " =    1.762
peak=    3.640 closest distance to " CA  SER A  87 " =    0.993
peak=    3.634 closest distance to " O   HOH Z 180 " =    2.095
peak=    3.631 closest distance to " O   HOH Z 203 " =    1.849
peak=    3.629 closest distance to " CA  ALA A 233 " =    1.155
peak=    3.627 closest distance to " CB  MET A  40 " =    0.809
peak=    3.626 closest distance to " CD BLYS A 290 " =    1.211
peak=    3.620 closest distance to " O   HOH Z 371 " =    1.717
peak=    3.617 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.596 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.587 closest distance to " O   HOH Z 245 " =    1.316
peak=    3.586 closest distance to " CB  ASN A 142 " =    0.926
peak=    3.560 closest distance to " O   HOH Z 273 " =    2.665
peak=    3.557 closest distance to " CA  MET A  40 " =    1.114
peak=    3.535 closest distance to " CB  ASP A 140 " =    0.843
peak=    3.530 closest distance to " N   ARG A 156 " =    1.321
peak=    3.526 closest distance to " O   HOH Z 213 " =    1.735
peak=    3.523 closest distance to " NH2BARG A 145 " =    2.044
peak=    3.513 closest distance to " O   HOH Z   3 " =    1.885
peak=    3.509 closest distance to " CB  LEU A 143 " =    1.108
peak=    3.508 closest distance to " O   HOH Z 371 " =    2.889
peak=    3.507 closest distance to " CD2 TRP A 179 " =    1.326
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.498 closest distance to " CB  GLU A 277 " =    3.540
peak=    3.494 closest distance to " CD1 ILE A 106 " =    0.863
peak=    3.489 closest distance to " CA  THR A 221 " =    0.995
peak=    3.489 closest distance to " CB  VAL A 202 " =    1.623
peak=    3.488 closest distance to " CG  LEU A 167 " =    1.202
peak=    3.485 closest distance to " O   HOH Z 135 " =    1.708
peak=    3.479 closest distance to " CD  ARG A 219 " =    1.092
peak=    3.478 closest distance to " CD  LYS A 166 " =    1.241
peak=    3.476 closest distance to " O   HOH Z 407 " =    2.300
peak=    3.474 closest distance to " O   HOH Z 193 " =    1.978
peak=    3.467 closest distance to " CG1BVAL A  72 " =    1.552
peak=    3.462 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.461 closest distance to " O   HOH Z 248 " =    1.672
peak=    3.461 closest distance to " O   HOH Z 411 " =    3.814
peak=    3.459 closest distance to " O   HOH Z  44 " =    1.691
peak=    3.459 closest distance to " O   HOH Z   1 " =    1.750
peak=    3.457 closest distance to " CB  ASN A 224 " =    1.062
peak=    3.448 closest distance to " O   HOH Z 234 " =    1.696
peak=    3.445 closest distance to " O   HOH Z 353 " =    2.710
peak=    3.436 closest distance to " O   HOH Z  54 " =    1.654
peak=    3.435 closest distance to " O   HOH Z  55 " =    2.394
peak=    3.427 closest distance to " O   HOH Z 133 " =    2.387
peak=    3.425 closest distance to " CB  ALA A   1 " =    4.586
peak=    3.424 closest distance to " O   HOH Z 406 " =    1.664
peak=    3.423 closest distance to " O   HOH Z 280 " =    3.006
peak=    3.421 closest distance to " CB  SER A  62 " =    1.207
peak=    3.414 closest distance to " CD  PRO A 243 " =    1.627
peak=    3.413 closest distance to " O   HOH Z 261 " =    2.189
peak=    3.411 closest distance to " O   HOH Z 227 " =    2.148
peak=    3.410 closest distance to " OG  SER A  22 " =    2.740
peak=    3.404 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.402 closest distance to " O   HOH Z  59 " =    1.819
peak=    3.402 closest distance to " O   HOH Z  93 " =    2.506
peak=    3.400 closest distance to " O   HOH Z 402 " =    1.451
peak=    3.398 closest distance to " CB  ILE A 120 " =    1.177
peak=    3.390 closest distance to " O   HOH Z 188 " =    2.093
peak=    3.389 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.385 closest distance to " O   HOH Z 426 " =    1.583
peak=    3.384 closest distance to " O   HOH Z 108 " =    2.140
peak=    3.381 closest distance to " NH2 ARG A 156 " =    1.205
peak=    3.378 closest distance to " O   HOH Z 295 " =    1.535
peak=    3.377 closest distance to " O   HOH Z 286 " =    2.323
peak=    3.371 closest distance to " OG BSER A 164 " =    2.325
peak=    3.368 closest distance to " CG1 VAL A 153 " =    0.892
peak=    3.368 closest distance to " CA  ALA A  84 " =    1.447
peak=    3.368 closest distance to " CA  PHE A 283 " =    1.209
peak=    3.368 closest distance to " O   HOH Z 329 " =    3.665
peak=    3.360 closest distance to " CG  ARG A 159 " =    0.813
peak=    3.359 closest distance to " CB  GLN A 278 " =    0.845
peak=    3.357 closest distance to " CB  THR A 157 " =    1.087
peak=    3.356 closest distance to " OG  SER A 206 " =    1.289
peak=    3.351 closest distance to " CG2 ILE A 120 " =    1.193
peak=    3.346 closest distance to " O   HOH Z 128 " =    2.169
peak=    3.334 closest distance to " O   HOH Z 271 " =    2.374
peak=    3.334 closest distance to " CA  ALA A 291 " =    0.965
peak=    3.332 closest distance to " O   HOH Z  88 " =    3.238
peak=    3.331 closest distance to " CG1 ILE A 151 " =    1.026
peak=    3.330 closest distance to " CB  TYR A 116 " =    0.842
peak=    3.328 closest distance to " CB  LYS A 117 " =    1.205
peak=    3.327 closest distance to " O   HOH Z 172 " =    3.158
peak=    3.326 closest distance to " CB  GLU A  46 " =    0.965
peak=    3.322 closest distance to " O   ASN A 209 " =    1.294
peak=    3.320 closest distance to " CA  ALA A 158 " =    1.124
peak=    3.319 closest distance to " O   HOH Z 211 " =    2.733
peak=    3.318 closest distance to " O   HOH Z 153 " =    1.652
peak=    3.317 closest distance to " O   MET A 105 " =    1.739
peak=    3.316 closest distance to " CD2 LEU A 297 " =    0.873
peak=    3.314 closest distance to " O   HOH Z 425 " =    1.265
peak=    3.314 closest distance to " CZ  PHE A 208 " =    1.133
peak=    3.311 closest distance to " O   HOH Z 263 " =    1.699
peak=    3.311 closest distance to " O   HOH Z 423 " =    1.579
peak=    3.307 closest distance to " CE BLYS A 290 " =    1.192
peak=    3.298 closest distance to " CA  ALA A  51 " =    0.897
peak=    3.298 closest distance to " CA  ALA A 154 " =    0.936
peak=    3.295 closest distance to " ND1 HIS A  81 " =    1.656
peak=    3.291 closest distance to " O   HOH Z 437 " =    1.596
peak=    3.288 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.287 closest distance to " CB  ALA A 248 " =    0.952
peak=    3.278 closest distance to " NH2AARG A 275 " =    3.693
peak=    3.278 closest distance to " CG AARG A 275 " =    1.196
peak=    3.275 closest distance to " CG  MET A 113 " =    1.214
peak=    3.271 closest distance to " OG  SER A  97 " =    3.512
peak=    3.267 closest distance to " CD1 ILE A 263 " =    1.342
peak=    3.262 closest distance to " N   ASN A 127 " =    1.278
peak=    3.262 closest distance to " O   HOH Z 423 " =    2.667
peak=    3.258 closest distance to " NH1BARG A 145 " =    1.196
peak=    3.258 closest distance to " O   HOH Z 345 " =    1.774
peak=    3.257 closest distance to " CA  LYS A 290 " =    1.293
peak=    3.257 closest distance to " O   HOH Z 345 " =    3.470
peak=    3.256 closest distance to " CD  GLN A 240 " =    1.603
peak=    3.250 closest distance to " NE2 HIS A 207 " =    1.420
peak=    3.249 closest distance to " O   HOH Z  85 " =    2.160
peak=    3.242 closest distance to " CD2 HIS A  81 " =    1.187
peak=    3.241 closest distance to " O   HOH Z 148 " =    3.285
peak=    3.239 closest distance to " O   HOH Z 163 " =    1.832
peak=    3.239 closest distance to " NH1 ARG A 138 " =    1.120
peak=    3.238 closest distance to " CG  LYS A  76 " =    0.930
peak=    3.235 closest distance to " CB  ALA A 291 " =    1.341
peak=    3.235 closest distance to " O   HOH Z 166 " =    3.729
peak=    3.234 closest distance to " O   HOH Z  97 " =    1.933
peak=    3.227 closest distance to " CB  ARG A 138 " =    1.020
peak=    3.225 closest distance to " CA  ARG A 195 " =    1.196
peak=    3.222 closest distance to " O   HOH Z  63 " =    1.413
peak=    3.221 closest distance to " CG  GLU A 277 " =    2.161
peak=    3.219 closest distance to " O   HOH Z 213 " =    2.165
peak=    3.214 closest distance to " CB  GLU A 236 " =    1.119
peak=    3.212 closest distance to " OD1 ASN A 217 " =    1.682
peak=    3.210 closest distance to " O  BHOH Z 338 " =    2.439
peak=    3.209 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.208 closest distance to " O   GLY A  57 " =    2.596
peak=    3.207 closest distance to " CB  ASN A 110 " =    1.102
peak=    3.204 closest distance to " CA  VAL A 126 " =    0.982
peak=    3.203 closest distance to " N   ASN A  39 " =    1.293
peak=    3.201 closest distance to " CB  LEU A 255 " =    0.734
peak=    3.184 closest distance to " CB  TRP A 150 " =    1.435
peak=    3.184 closest distance to " O   HOH Z 199 " =    1.633
peak=    3.183 closest distance to " O   HOH Z  44 " =    3.117
peak=    3.179 closest distance to " O   HOH Z 336 " =    2.024
peak=    3.176 closest distance to " O   HOH Z  49 " =    2.098
peak=    3.172 closest distance to " CB  ALA A   9 " =    1.571
peak=    3.167 closest distance to " O   HOH Z  88 " =    2.625
peak=    3.162 closest distance to " CB  ILE A 234 " =    0.984
peak=    3.162 closest distance to " O   HOH Z  66 " =    2.126
peak=    3.161 closest distance to " CA  ILE A 234 " =    0.949
peak=    3.157 closest distance to " OG  SER A  62 " =    2.986
peak=    3.155 closest distance to " O   HOH Z 411 " =    1.784
peak=    3.149 closest distance to " N   SER A 135 " =    1.264
peak=    3.145 closest distance to " O   HOH Z 175 " =    2.146
peak=    3.143 closest distance to " CG  GLN A  89 " =    1.496
peak=    3.142 closest distance to " O   HOH Z 433 " =    1.784
peak=    3.137 closest distance to " O   HOH Z 217 " =    1.486
peak=    3.136 closest distance to " O   HOH Z 409 " =    2.664
peak=    3.125 closest distance to " O   HOH Z 417 " =    1.997
peak=    3.122 closest distance to " CB  SER A 210 " =    0.704
peak=    3.120 closest distance to " O   HOH Z 391 " =    2.941
peak=    3.118 closest distance to " N   SER A 134 " =    1.376
peak=    3.116 closest distance to " CA  ASP A 140 " =    1.187
peak=    3.116 closest distance to " O   HOH Z 144 " =    1.801
peak=    3.116 closest distance to " CB  LYS A 193 " =    0.997
peak=    3.116 closest distance to " O   HOH Z 302 " =    1.891
peak=    3.111 closest distance to " O   HOH Z 292 " =    1.782
peak=    3.108 closest distance to " O   HOH Z 359 " =    4.019
peak=    3.106 closest distance to " CG  GLN A 278 " =    1.333
peak=    3.106 closest distance to " N   SER A 146 " =    1.689
peak=    3.104 closest distance to " CA  TYR A 186 " =    1.571
peak=    3.103 closest distance to " CG  GLN A 240 " =    3.533
peak=    3.100 closest distance to " O   HOH Z 435 " =    1.883
peak=    3.096 closest distance to " N   SER A  12 " =    1.582
peak=    3.095 closest distance to " O   HOH Z  71 " =    2.271
peak=    3.092 closest distance to " N   ASN A 252 " =    1.449
peak=    3.091 closest distance to " OD1 ASN A 187 " =    1.754
peak=    3.091 closest distance to " CB  ALA A 114 " =    1.192
peak=    3.087 closest distance to " O   ALA A   1 " =    1.535
peak=    3.085 closest distance to " CG BARG A 102 " =    1.838
peak=    3.081 closest distance to " O   HOH Z 291 " =    1.795
peak=    3.074 closest distance to " O   HOH Z 298 " =    2.549
peak=    3.064 closest distance to " CG1 VAL A 189 " =    1.860
peak=    3.063 closest distance to " CA  MET A 105 " =    0.912
peak=    3.063 closest distance to " O   HOH Z  49 " =    2.488
peak=    3.036 closest distance to " O   HOH Z 365 " =    2.982
peak=    3.028 closest distance to " O   HOH Z 386 " =    2.750
peak=    3.025 closest distance to " O   HOH Z 258 " =    1.885
peak=    3.019 closest distance to " O   HOH Z 163 " =    1.580

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.484 - 5.593
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 202
   mapped sites are within: 0.751 - 5.593

peak=   -4.813 closest distance to " CB  PRO A 243 " =    2.612
peak=   -4.770 closest distance to " O   HOH Z 290 " =    1.060
peak=   -4.636 closest distance to " O   HOH Z 266 " =    4.714
peak=   -4.344 closest distance to " CD  ARG A 156 " =    1.995
peak=   -4.315 closest distance to " O   HOH Z 389 " =    1.884
peak=   -4.260 closest distance to " O   HOH Z 377 " =    2.046
peak=   -4.258 closest distance to " O   HOH Z 435 " =    2.776
peak=   -4.213 closest distance to " CG  GLN A 223 " =    1.758
peak=   -4.197 closest distance to " O   VAL A  67 " =    2.618
peak=   -4.134 closest distance to " CG1 VAL A 112 " =    2.864
peak=   -4.038 closest distance to " C   HIS A 108 " =    1.135
peak=   -4.017 closest distance to " SG  CYS A 254 " =    3.368
peak=   -3.955 closest distance to " CZ3 TRP A 179 " =    1.142
peak=   -3.942 closest distance to " O   HOH Z 372 " =    2.465
peak=   -3.926 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.918 closest distance to " OG BSER A 134 " =    1.222
peak=   -3.904 closest distance to " CZ  TYR A 169 " =    1.591
peak=   -3.872 closest distance to " ND2 ASN A  45 " =    1.595
peak=   -3.872 closest distance to " CG  PHE A 283 " =    2.777
peak=   -3.870 closest distance to " O   HOH Z 185 " =    2.201
peak=   -3.863 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -3.843 closest distance to " N   ALA A  43 " =    2.554
peak=   -3.831 closest distance to " CG  ASP A 231 " =    0.753
peak=   -3.809 closest distance to " O   HOH Z 351 " =    1.448
peak=   -3.807 closest distance to " N   GLN A  58 " =    1.879
peak=   -3.800 closest distance to " O   HOH Z 313 " =    1.963
peak=   -3.787 closest distance to " CZ  PHE A  59 " =    1.495
peak=   -3.761 closest distance to " C   ALA A 158 " =    1.385
peak=   -3.752 closest distance to " O   HOH Z 114 " =    3.127
peak=   -3.749 closest distance to " O   VAL A  67 " =    2.691
peak=   -3.748 closest distance to " O   HOH Z  43 " =    1.676
peak=   -3.733 closest distance to " O   HOH Z 407 " =    3.164
peak=   -3.729 closest distance to " O   HOH Z 231 " =    2.170
peak=   -3.729 closest distance to " O   HOH Z  60 " =    2.465
peak=   -3.724 closest distance to " O   HOH Z 198 " =    1.955
peak=   -3.724 closest distance to " CB  ALA A 161 " =    2.619
peak=   -3.706 closest distance to " N   ASP A 286 " =    2.415
peak=   -3.704 closest distance to " CB  ASN A  39 " =    2.187
peak=   -3.673 closest distance to " O   ARG A 145 " =    1.529
peak=   -3.666 closest distance to " CG  GLU A 152 " =    0.793
peak=   -3.661 closest distance to " OD1 ASP A 171 " =    1.595
peak=   -3.660 closest distance to " CD  GLN A  58 " =    1.034
peak=   -3.651 closest distance to " CD  ARG A 139 " =    1.593
peak=   -3.647 closest distance to " CE  MET A 105 " =    2.273
peak=   -3.647 closest distance to " CE2 PHE A 218 " =    2.452
peak=   -3.640 closest distance to " CB  CYS A 201 " =    2.612
peak=   -3.631 closest distance to " CB  ALA A 291 " =    2.306
peak=   -3.628 closest distance to " CD1 PHE A  59 " =    1.816
peak=   -3.627 closest distance to " CB  PHE A 192 " =    1.953
peak=   -3.627 closest distance to " O   HOH Z 353 " =    2.163
peak=   -3.625 closest distance to " O   HOH Z 282 " =    1.032
peak=   -3.624 closest distance to " O   HOH Z 211 " =    1.559
peak=   -3.619 closest distance to " ND2 ASN A  45 " =    1.088
peak=   -3.618 closest distance to " O   HOH Z 198 " =    1.354
peak=   -3.618 closest distance to " CB  PRO A 163 " =    2.564
peak=   -3.617 closest distance to " O   HOH Z  52 " =    1.193
peak=   -3.605 closest distance to " O   HOH Z 377 " =    0.751
peak=   -3.601 closest distance to " CA  GLY A  98 " =    1.893
peak=   -3.593 closest distance to " CD1 LEU A 228 " =    2.292
peak=   -3.591 closest distance to " OG BSER A 134 " =    1.649
peak=   -3.587 closest distance to " O   HOH Z 126 " =    1.872
peak=   -3.579 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.578 closest distance to " OXT GLY A 302 " =    2.832
peak=   -3.576 closest distance to " CZ BARG A 275 " =    1.787
peak=   -3.571 closest distance to " O   HOH Z  10 " =    1.455
peak=   -3.570 closest distance to " OD1 ASN A 148 " =    1.617
peak=   -3.565 closest distance to " NH2AARG A 275 " =    5.370
peak=   -3.565 closest distance to " CA  GLY A 203 " =    2.168
peak=   -3.548 closest distance to " CB  ALA A  43 " =    2.454
peak=   -3.545 closest distance to " CD  GLN A  88 " =    0.833
peak=   -3.536 closest distance to " O   VAL A 189 " =    2.560
peak=   -3.534 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.534 closest distance to " O   GLY A 211 " =    1.369
peak=   -3.526 closest distance to " O   PRO A 198 " =    1.220
peak=   -3.509 closest distance to " O   SER A 135 " =    1.451
peak=   -3.505 closest distance to " CA  GLY A 241 " =    2.271
peak=   -3.503 closest distance to " OD1 ASP A 191 " =    1.738
peak=   -3.503 closest distance to " C   LEU A 143 " =    1.251
peak=   -3.488 closest distance to " CB  CYS A 254 " =    2.267
peak=   -3.483 closest distance to " CG  ARG A 269 " =    2.313
peak=   -3.477 closest distance to " CG  MET A 105 " =    0.991
peak=   -3.475 closest distance to " N   SER A 212 " =    1.823
peak=   -3.466 closest distance to " O   PRO A 163 " =    1.968
peak=   -3.462 closest distance to " O   HOH Z 395 " =    5.185
peak=   -3.454 closest distance to " O   HOH Z 298 " =    1.204
peak=   -3.444 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.441 closest distance to " C   LEU A 222 " =    0.777
peak=   -3.437 closest distance to " O   HOH Z  98 " =    2.233
peak=   -3.433 closest distance to " O   PRO A 243 " =    2.561
peak=   -3.426 closest distance to " NH1 ARG A 195 " =    2.551
peak=   -3.420 closest distance to " CD1 LEU A 101 " =    2.361
peak=   -3.416 closest distance to " OD1 ASN A 187 " =    1.663
peak=   -3.413 closest distance to " CD2 LEU A 300 " =    2.880
peak=   -3.408 closest distance to " NH2 ARG A  79 " =    1.908
peak=   -3.399 closest distance to " O   HOH Z 322 " =    1.499
peak=   -3.390 closest distance to " O   GLN A 240 " =    2.141
peak=   -3.388 closest distance to " O   SER A  95 " =    1.484
peak=   -3.387 closest distance to " O   HOH Z  51 " =    1.133
peak=   -3.378 closest distance to " CG2 ILE A 263 " =    2.284
peak=   -3.373 closest distance to " C   ILE A 234 " =    1.273
peak=   -3.371 closest distance to " OG  SER A  97 " =    2.170
peak=   -3.367 closest distance to " NE  ARG A  36 " =    1.960
peak=   -3.363 closest distance to " CD2 LEU A 237 " =    2.748
peak=   -3.357 closest distance to " O   TRP A  70 " =    1.505
peak=   -3.356 closest distance to " CE3 TRP A 274 " =    1.063
peak=   -3.350 closest distance to " OD2 ASP A 171 " =    2.195
peak=   -3.346 closest distance to " O   HOH Z 359 " =    3.274
peak=   -3.343 closest distance to " O   HOH Z 385 " =    2.026
peak=   -3.343 closest distance to " O   HOH Z 394 " =    1.396
peak=   -3.341 closest distance to " CB  ALA A 248 " =    2.440
peak=   -3.340 closest distance to " N   PHE A  59 " =    2.123
peak=   -3.340 closest distance to " OD1 ASP A 191 " =    1.570
peak=   -3.333 closest distance to " CB  ASP A 286 " =    2.101
peak=   -3.330 closest distance to " CB  ASP A 132 " =    2.358
peak=   -3.327 closest distance to " O   HOH Z  11 " =    1.831
peak=   -3.324 closest distance to " CG1 VAL A 197 " =    2.185
peak=   -3.323 closest distance to " CB  ALA A 248 " =    1.971
peak=   -3.322 closest distance to " O   HOH Z 111 " =    2.108
peak=   -3.318 closest distance to " OG  SER A  62 " =    1.510
peak=   -3.316 closest distance to " N   THR A 157 " =    1.517
peak=   -3.316 closest distance to " CD1 LEU A 297 " =    2.442
peak=   -3.312 closest distance to " O   HOH Z 266 " =    4.567
peak=   -3.308 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.301 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.301 closest distance to " O   HOH Z 417 " =    2.454
peak=   -3.301 closest distance to " O   HOH Z 281 " =    2.708
peak=   -3.301 closest distance to " O   HOH Z 176 " =    0.773
peak=   -3.296 closest distance to " ND2 ASN A 249 " =    2.307
peak=   -3.288 closest distance to " O   HOH Z 222 " =    1.168
peak=   -3.285 closest distance to " ND2 ASN A 187 " =    1.498
peak=   -3.285 closest distance to " O   ALA A 161 " =    1.544
peak=   -3.285 closest distance to " NH1AARG A 275 " =    1.819
peak=   -3.273 closest distance to " CD  GLU A 277 " =    1.165
peak=   -3.271 closest distance to " OE1 GLN A  88 " =    1.189
peak=   -3.270 closest distance to " OE1 GLN A 223 " =    1.928
peak=   -3.267 closest distance to " C   MET A 188 " =    1.480
peak=   -3.267 closest distance to " O   HOH Z 311 " =    3.609
peak=   -3.262 closest distance to " O   LEU A 101 " =    2.603
peak=   -3.259 closest distance to " N   ALA A 248 " =    1.573
peak=   -3.253 closest distance to " CE3 TRP A 123 " =    1.242
peak=   -3.252 closest distance to " CG1 VAL A 250 " =    2.679
peak=   -3.248 closest distance to " O   HOH Z  76 " =    1.849
peak=   -3.247 closest distance to " CG  TRP A 266 " =    1.830
peak=   -3.247 closest distance to " O   HOH Z  93 " =    2.271
peak=   -3.242 closest distance to " O   HOH Z  13 " =    1.382
peak=   -3.238 closest distance to " CE  LYS A  76 " =    2.864
peak=   -3.237 closest distance to " CB  ALA A 131 " =    2.023
peak=   -3.236 closest distance to " CE3 TRP A 274 " =    2.422
peak=   -3.233 closest distance to " O   HOH Z 377 " =    1.039
peak=   -3.222 closest distance to " CE1 TYR A 169 " =    2.511
peak=   -3.221 closest distance to " SG ACYS A 201 " =    1.959
peak=   -3.221 closest distance to " O   HOH Z 148 " =    1.799
peak=   -3.214 closest distance to " O   HOH Z  63 " =    1.659
peak=   -3.213 closest distance to " ND2 ASN A  60 " =    1.394
peak=   -3.213 closest distance to " O   HOH Z 137 " =    1.541
peak=   -3.210 closest distance to " CD1 ILE A 239 " =    2.113
peak=   -3.210 closest distance to " OG  SER A  87 " =    1.368
peak=   -3.202 closest distance to " CD2 PHE A  61 " =    1.988
peak=   -3.198 closest distance to " O   HOH Z  24 " =    1.467
peak=   -3.196 closest distance to " NZ  LYS A 119 " =    3.309
peak=   -3.195 closest distance to " CA  GLY A 241 " =    3.348
peak=   -3.186 closest distance to " O   HOH Z 196 " =    2.197
peak=   -3.184 closest distance to " NE2 GLN A 278 " =    1.694
peak=   -3.184 closest distance to " ND2 ASN A 252 " =    1.605
peak=   -3.183 closest distance to " O   HOH Z 174 " =    2.509
peak=   -3.183 closest distance to " O   HOH Z 253 " =    3.883
peak=   -3.183 closest distance to " CG1 VAL A 230 " =    2.028
peak=   -3.183 closest distance to " O   SER A  22 " =    2.410
peak=   -3.174 closest distance to " O   HOH Z 241 " =    1.316
peak=   -3.173 closest distance to " O   HOH Z 323 " =    1.199
peak=   -3.172 closest distance to " O   GLY A  17 " =    1.260
peak=   -3.171 closest distance to " O   HOH Z  73 " =    2.241
peak=   -3.169 closest distance to " O   HOH Z 114 " =    0.812
peak=   -3.149 closest distance to " O   VAL A 174 " =    2.083
peak=   -3.149 closest distance to " O   PHE A 218 " =    1.586
peak=   -3.141 closest distance to " CG2 THR A 178 " =    2.263
peak=   -3.140 closest distance to " O   HOH Z 210 " =    1.030
peak=   -3.139 closest distance to " CD  GLU A 236 " =    1.019
peak=   -3.137 closest distance to " O   HOH Z 298 " =    2.517
peak=   -3.131 closest distance to " N   GLN A 122 " =    1.479
peak=   -3.129 closest distance to " CB  ALA A   7 " =    2.089
peak=   -3.115 closest distance to " O   HOH Z 111 " =    1.192
peak=   -3.115 closest distance to " CB  PHE A 208 " =    2.219
peak=   -3.113 closest distance to " O   HOH Z 317 " =    2.383
peak=   -3.108 closest distance to " O   HOH Z 250 " =    1.505
peak=   -3.106 closest distance to " O   HOH Z 168 " =    1.831
peak=   -3.104 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.103 closest distance to " O   HOH Z 423 " =    1.069
peak=   -3.088 closest distance to " O   ALA A  34 " =    2.845
peak=   -3.083 closest distance to " CG1 VAL A 125 " =    1.922
peak=   -3.080 closest distance to " O   HOH Z 244 " =    1.933
peak=   -3.079 closest distance to " NH2 ARG A  79 " =    1.627
peak=   -3.067 closest distance to " OD1AASN A 224 " =    1.764
peak=   -3.060 closest distance to " OXT GLY A 302 " =    3.494
peak=   -3.057 closest distance to " CZ2 TRP A 150 " =    2.159
peak=   -3.046 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -3.044 closest distance to " CB  LEU A  83 " =    2.378
peak=   -3.041 closest distance to " O   HOH Z 324 " =    2.207
peak=   -3.018 closest distance to " O   HOH Z 283 " =    5.593

================= 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    :  0.3426 0.3421   6.076461e+00   6.069608e+00
   1_bss:  0.3306 0.3313   6.060763e+00   6.044813e+00
   1_xyz:  0.1860 0.2085   5.543603e+00   5.645500e+00
   1_adp:  0.1703 0.2147   5.491756e+00   5.679921e+00
   1_occ:  0.1699 0.2148   5.490504e+00   5.679161e+00
   2_bss:  0.1688 0.2130   5.488399e+00   5.674743e+00
   2_xyz:  0.1238 0.1678   5.220415e+00   5.457560e+00
   2_adp:  0.1172 0.1585   5.164200e+00   5.397691e+00
   2_occ:  0.1171 0.1585   5.163803e+00   5.397613e+00
   3_bss:  0.1172 0.1584   5.163696e+00   5.397737e+00
   3_xyz:  0.1087 0.1531   5.113031e+00   5.364244e+00
   3_adp:  0.1065 0.1535   5.104153e+00   5.362573e+00
   3_occ:  0.1065 0.1535   5.104272e+00   5.362929e+00
   4_bss:  0.1065 0.1535   5.104269e+00   5.362935e+00
   4_xyz:  0.1064 0.1541   5.105249e+00   5.366154e+00
   4_adp:  0.1061 0.1544   5.104975e+00   5.367827e+00
   4_occ:  0.1060 0.1544   5.105083e+00   5.368139e+00
   5_bss:  0.1060 0.1544   5.105163e+00   5.368182e+00
   5_xyz:  0.1067 0.1554   5.111999e+00   5.374452e+00
   5_adp:  0.1081 0.1544   5.114580e+00   5.370415e+00
   5_occ:  0.1081 0.1545   5.114678e+00   5.370744e+00
   5_bss:  0.1081 0.1545   5.114709e+00   5.370754e+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:  0.337  47.203  -1.398  -0.156  -0.449  -0.000  -0.000  -0.000
   1_xyz:  0.337  47.203  -1.398  -0.156  -0.449  -0.000  -0.000  -0.000
   1_adp:  0.337  47.203  -1.398  -0.156  -0.449  -0.000  -0.000  -0.000
   1_occ:  0.337  47.203  -1.398  -0.156  -0.449  -0.000  -0.000  -0.000
   2_bss:  0.333  52.432  -2.377  -2.324  -1.690  -0.000  -0.000  -0.000
   2_xyz:  0.333  52.432  -2.377  -2.324  -1.690  -0.000  -0.000  -0.000
   2_adp:  0.333  52.432  -2.377  -2.324  -1.690  -0.000  -0.000  -0.000
   2_occ:  0.333  52.432  -2.377  -2.324  -1.690  -0.000  -0.000  -0.000
   3_bss:  0.324  47.575  -2.476  -2.621  -1.712  -0.000  -0.000  -0.000
   3_xyz:  0.324  47.575  -2.476  -2.621  -1.712  -0.000  -0.000  -0.000
   3_adp:  0.324  47.575  -2.476  -2.621  -1.712  -0.000  -0.000  -0.000
   3_occ:  0.324  47.575  -2.476  -2.621  -1.712  -0.000  -0.000  -0.000
   4_bss:  0.324  47.575  -2.357  -2.581  -1.627  -0.000  -0.000  -0.000
   4_xyz:  0.324  47.575  -2.357  -2.581  -1.627  -0.000  -0.000  -0.000
   4_adp:  0.324  47.575  -2.357  -2.581  -1.627  -0.000  -0.000  -0.000
   4_occ:  0.324  47.575  -2.357  -2.581  -1.627  -0.000  -0.000  -0.000
   5_bss:  0.324  47.575  -2.179  -2.433  -1.440  -0.000  -0.000  -0.000
   5_xyz:  0.324  47.575  -2.179  -2.433  -1.440  -0.000  -0.000  -0.000
   5_adp:  0.324  47.575  -2.179  -2.433  -1.440  -0.000  -0.000  -0.000
   5_occ:  0.324  47.575  -2.179  -2.433  -1.440  -0.000  -0.000  -0.000
   5_bss:  0.324  47.517  -2.072  -2.323  -1.300  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.407 0.6999  0.8910    33258.782
   1_bss:  34.222 0.7114  0.8865    30080.432
   1_xyz:  19.437 0.8691  1.0121    11130.233
   1_adp:  20.378 0.8595  1.0070    11897.514
   1_occ:  20.367 0.8596  1.0066    11862.172
   2_bss:  20.227 0.8607  0.9563    11688.121
   2_xyz:  15.398 0.9028  0.9840     7181.419
   2_adp:  14.080 0.9140  0.9884     6446.179
   2_occ:  14.077 0.9140  0.9883     6439.834
   3_bss:  14.077 0.9140  0.9829     6435.508
   3_xyz:  13.348 0.9200  0.9835     5969.872
   3_adp:  13.312 0.9205  0.9783     5940.572
   3_occ:  13.319 0.9204  0.9782     5943.852
   4_bss:  13.319 0.9204  0.9812     5944.923
   4_xyz:  13.364 0.9201  0.9805     5996.654
   4_adp:  13.375 0.9201  0.9752     6014.607
   4_occ:  13.382 0.9201  0.9751     6016.226
   5_bss:  13.384 0.9201  0.9812     6017.716
   5_xyz:  13.474 0.9195  0.9805     6092.800
   5_adp:  13.365 0.9203  0.9765     6065.155
   5_occ:  13.373 0.9202  0.9764     6066.689
   5_bss:  13.374 0.9202  0.9786     6066.943
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6192e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6192e-01
   1_xyz:   1.048  0.007  0.071 14.933  0.005  4.109   6.3945e-02
   1_adp:   1.048  0.007  0.071 14.933  0.005  4.109   6.3945e-02
   1_occ:   1.048  0.007  0.071 14.933  0.005  4.109   6.3945e-02
   2_bss:   1.048  0.007  0.071 14.933  0.005  4.109   6.3945e-02
   2_xyz:   1.036  0.007  0.075 14.730  0.004  4.116   6.2679e-02
   2_adp:   1.036  0.007  0.075 14.730  0.004  4.116   6.2679e-02
   2_occ:   1.036  0.007  0.075 14.730  0.004  4.116   6.2679e-02
   3_bss:   1.036  0.007  0.075 14.730  0.004  4.116   6.2679e-02
   3_xyz:   1.076  0.009  0.081 15.043  0.004  4.118   6.9831e-02
   3_adp:   1.076  0.009  0.081 15.043  0.004  4.118   6.9831e-02
   3_occ:   1.076  0.009  0.081 15.043  0.004  4.118   6.9831e-02
   4_bss:   1.076  0.009  0.081 15.043  0.004  4.118   6.9831e-02
   4_xyz:   1.025  0.008  0.077 14.802  0.004  4.118   6.3438e-02
   4_adp:   1.025  0.008  0.077 14.802  0.004  4.118   6.3438e-02
   4_occ:   1.025  0.008  0.077 14.802  0.004  4.118   6.3438e-02
   5_bss:   1.025  0.008  0.077 14.802  0.004  4.118   6.3438e-02
   5_xyz:   0.974  0.007  0.074 14.609  0.004  4.118   5.7752e-02
   5_adp:   0.974  0.007  0.074 14.609  0.004  4.118   5.7752e-02
   5_occ:   0.974  0.007  0.074 14.609  0.004  4.118   5.7752e-02
   5_bss:   0.974  0.007  0.074 14.609  0.004  4.118   5.7752e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4021e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4021e-01
   1_xyz:   7.712  0.049  0.347 85.654  0.048  2.303   6.6353e-02
   1_adp:   7.712  0.049  0.347 85.654  0.048  2.303   6.6353e-02
   1_occ:   7.712  0.049  0.347 85.654  0.048  2.303   6.6353e-02
   2_bss:   7.712  0.049  0.347 85.654  0.048  2.303   6.6353e-02
   2_xyz:   7.375  0.038  0.240 83.883  0.045  2.314   5.9227e-02
   2_adp:   7.375  0.038  0.240 83.883  0.045  2.314   5.9227e-02
   2_occ:   7.375  0.038  0.240 83.883  0.045  2.314   5.9227e-02
   3_bss:   7.375  0.038  0.240 83.883  0.045  2.314   5.9227e-02
   3_xyz:   7.415  0.042  0.265 84.682  0.037  2.240   5.7904e-02
   3_adp:   7.415  0.042  0.265 84.682  0.037  2.240   5.7904e-02
   3_occ:   7.415  0.042  0.265 84.682  0.037  2.240   5.7904e-02
   4_bss:   7.415  0.042  0.265 84.682  0.037  2.240   5.7904e-02
   4_xyz:   7.008  0.043  0.243 84.062  0.041  2.313   4.9488e-02
   4_adp:   7.008  0.043  0.243 84.062  0.041  2.313   4.9488e-02
   4_occ:   7.008  0.043  0.243 84.062  0.041  2.313   4.9488e-02
   5_bss:   7.008  0.043  0.243 84.062  0.041  2.313   4.9488e-02
   5_xyz:   7.257  0.041  0.232 84.216  0.037  2.308   4.2256e-02
   5_adp:   7.257  0.041  0.232 84.216  0.037  2.308   4.2256e-02
   5_occ:   7.257  0.041  0.232 84.216  0.037  2.308   4.2256e-02
   5_bss:   7.257  0.041  0.232 84.216  0.037  2.308   4.2256e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  72.54   0.00  17.16  66.87   0.00  13.08  72.54   6.60  39.42
   1_occ:  72.54   0.00  17.16  66.87   0.00  13.08  72.54   6.60  39.42
   2_bss:  72.54   0.00  17.16  66.87   0.00  13.08  72.54   6.60  39.42
   2_xyz:  72.54   0.00  17.16  66.87   0.00  13.08  72.54   6.60  39.42
   2_adp:  70.58   1.86  16.96  70.58   1.86  12.99  70.46   5.95  38.55
   2_occ:  70.58   1.86  16.96  70.58   1.86  12.99  70.46   5.95  38.55
   3_bss:  70.58   1.86  16.96  70.58   1.86  12.99  70.46   5.95  38.55
   3_xyz:  70.58   1.86  16.96  70.58   1.86  12.99  70.46   5.95  38.55
   3_adp:  81.85   1.06  17.13  81.85   1.06  13.01  75.99   4.99  39.59
   3_occ:  81.85   1.06  17.13  81.85   1.06  13.01  75.99   4.99  39.59
   4_bss:  81.85   1.06  17.13  81.85   1.06  13.01  75.99   4.99  39.59
   4_xyz:  81.85   1.06  17.13  81.85   1.06  13.01  75.99   4.99  39.59
   4_adp:  83.78   0.81  17.00  83.78   0.81  12.89  77.10   5.77  39.42
   4_occ:  83.78   0.81  17.00  83.78   0.81  12.89  77.10   5.77  39.42
   5_bss:  83.78   0.81  17.00  83.78   0.81  12.89  77.10   5.77  39.42
   5_xyz:  83.78   0.81  17.00  83.78   0.81  12.89  77.10   5.77  39.42
   5_adp:  80.95   1.63  16.37  80.95   1.63  12.62  77.76   6.43  36.79
   5_occ:  80.95   1.63  16.37  80.95   1.63  12.62  77.76   6.43  36.79
   5_bss:  80.89   1.57  16.31  80.89   1.57  12.56  77.70   6.37  36.73
------------------------------------------------------------------------
 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:    1.350    0.014    0.329
   1_adp:    1.350    0.014    0.329
   1_occ:    1.350    0.014    0.329
   2_bss:    1.350    0.014    0.329
   2_xyz:    0.798    0.021    0.396
   2_adp:    0.798    0.021    0.396
   2_occ:    0.798    0.021    0.396
   3_bss:    0.798    0.021    0.396
   3_xyz:    0.864    0.030    0.422
   3_adp:    0.864    0.030    0.422
   3_occ:    0.864    0.030    0.422
   4_bss:    0.864    0.030    0.422
   4_xyz:    1.037    0.039    0.430
   4_adp:    1.037    0.039    0.430
   4_occ:    1.037    0.039    0.430
   5_bss:    1.037    0.039    0.430
   5_xyz:    1.139    0.056    0.435
   5_adp:    1.139    0.056    0.435
   5_occ:    1.139    0.056    0.435
   5_bss:    1.139    0.056    0.435
------------------------------------------------------------------------

CPU time actual refinement: 322.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/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_883/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_883/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.03 
  Macro-tasks:
    bulk solvent and scale       = 37.67  
    individual site refinement   = 131.83 
    weights calculation          = 28.98  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.24 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 102.46 
    alpha_beta                      = 8.28   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.30 
    fmodel                         = 6.63   
    r_factors                      = 0.21   
    phase_errors                   = 11.21  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 242.73 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.574 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    644 calls, 102.21 s
gradients_fft:          589 calls,  97.91 s

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

# Date 2008-01-16 Time 05:53:28 PST -0800 (1200491608.70 s)
Start R-work = 0.3426, R-free = 0.3421 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.3306, R-free = 0.3313
Final R-work = 0.1081, R-free = 0.1545