# Date 2008-01-16 Time 06:06:50 PST -0800 (1200492410.99 s)
#phil __OFF__

Command line arguments: "../1015.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1552
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1015

-------------------------------------------------------------------------------
  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: (71.3037, 46.6953, 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: 2.74, per 1000 atoms: 0.97


================================== 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: (71.3037, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98104
Completeness in resolution range: 0.958694
Completeness with d_max=infinity: 0.955794

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9810

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: (71.3037, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98104
Completeness in resolution range: 0.958694
Completeness with d_max=infinity: 0.955794

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2396 [2142/2168]  1931   211   9.9%
  bin  2:  4.2396 -  3.3774 [2064/2083]  1856   208  10.1%
  bin  3:  3.3774 -  2.9541 [2031/2050]  1826   205  10.1%
  bin  4:  2.9541 -  2.6857 [2015/2045]  1814   201  10.0%
  bin  5:  2.6857 -  2.4941 [2016/2035]  1819   197   9.8%
  bin  6:  2.4941 -  2.3476 [1983/2008]  1777   206  10.4%
  bin  7:  2.3476 -  2.2304 [1992/2020]  1793   199  10.0%
  bin  8:  2.2304 -  2.1336 [1970/2006]  1779   191   9.7%
  bin  9:  2.1336 -  2.0517 [1973/2015]  1772   201  10.2%
  bin 10:  2.0517 -  1.9810 [1403/2003]  1263   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/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: 0.12 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: 16
        2.42 -     3.04: 2194
        3.04 -     3.66: 4691
        3.66 -     4.28: 9066
        4.28 -     4.90: 12324
  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 107 " - " O   HOH Z 340 "  2.096 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.180 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.180 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.214 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28286 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_1015/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/model_refine_001.geo

CPU time processing inputs: 7.84


============================ 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 = 71.30375 46.69535 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 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3236   r_free= 0.3274   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.029612                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.2860 0.2766      6.3437      6.2955|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.2530 0.2526      6.4112      6.3955|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.2766 0.2567      6.3004      6.3768|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.2889 0.3273         6.2      6.2231|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.3264 0.3388      6.0883      6.1476|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.3431 0.3526      6.0277      6.0139|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.3478 0.3379      6.0151        6.01|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.3673 0.3390       5.958      5.9098|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.3510 0.3526      5.8975      5.8775|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.3588 0.4448      5.8881      6.0197|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.3842 0.3613      5.8702      5.8776|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.3834 0.3991      5.8105      5.8759|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.3810 0.3800      5.7146      5.6448|
| 14:  2.0305 -  1.9810 0.59    773   86 0.3842 0.4010       5.682      5.6485|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.80  25.23   0.86     0.82      40223.02|
|  2:  4.7289 -  3.7727  1342   146  0.85  21.73   0.98     0.92      44533.13|
|  3:  3.7727 -  3.3014  1314   147  0.80  26.16   1.00     0.95      45210.02|
|  4:  3.3014 -  3.0022  1315   153  0.77  29.35   1.00     0.93      41605.26|
|  5:  3.0022 -  2.7884  1297   139  0.70  35.14   0.98     0.89      36118.75|
|  6:  2.7884 -  2.6249  1286   143  0.70  35.61   1.00     0.89      31188.94|
|  7:  2.6249 -  2.4941  1300   139  0.72  34.09   1.00     0.91      27111.20|
|  8:  2.4941 -  2.3859  1261   151  0.71  35.07   0.99     0.93      24538.53|
|  9:  2.3859 -  2.2944  1281   145  0.70  35.61   1.04     0.92      23527.52|
| 10:  2.2944 -  2.2155  1279   138  0.67  38.04   1.04     0.91      24216.09|
| 11:  2.2155 -  2.1464  1286   138  0.65  40.29   1.06     0.89      23765.55|
| 12:  2.1464 -  2.0852  1241   139  0.66  39.67   1.03     0.91      21804.71|
| 13:  2.0852 -  2.0305  1263   140  0.64  40.81   1.03     0.90      18103.15|
| 14:  2.0305 -  1.9810   773    86  0.67  38.30   1.04     0.86      14055.97|
|alpha:            min =        0.82 max =            0.95 mean =         0.90|
|beta:             min =    14055.97 max =        45210.02 mean =     30373.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.94 mean =        33.67|
|phase err.(test): min =        0.00 max =           89.88 mean =        33.77|
|-----------------------------------------------------------------------------|

============================== 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 = 4.537640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.893   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.696881              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.471   (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:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      203 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1991 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2839 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4670 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4396 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5618 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6706 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.163 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    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 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3236   r_free= 0.3274   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.029612                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3106   r_free= 0.3154   ksol= 0.32   Bsol= 45.42   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,-2.39,-0.53,-0.00,-0.00,-0.00); trace/3= -0.96                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.009704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.958157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.194   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.350965              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.189   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3106      final r-factor (work) = 0.1706          |
| start r-factor (free) = 0.3154      final r-factor (free) = 0.1926          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0703 = 3.96 * 0.50 * 6.0174 + 1.00 * 0.1615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3983 = 3.96 * 0.50 * 5.7293 + 1.00 * 0.0595                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1706      final r-factor (work) = 0.1593          |
| start r-factor (free) = 0.1926      final r-factor (free) = 0.1969          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0172 = 0.35 * 1.00 * 5.7293 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9431 = 0.35 * 1.00 * 5.4156 + 1.00 * 0.0424                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.02   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    69.02   16.53    None  None   None       |
|    Sol.    : 438    0      5.78    62.81   37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    69.02   12.68    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 -   6.902:  283   |   5:    34.511 -  41.413:  107        |
|      1:     6.902 -  13.804: 1348   |   6:    41.413 -  48.315:   83        |
|      2:    13.804 -  20.707:  604   |   7:    48.315 -  55.217:   69        |
|      3:    20.707 -  27.609:  159   |   8:    55.217 -  62.120:   36        |
|      4:    27.609 -  34.511:  132   |   9:    62.120 -  69.022:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1593 r_free = 0.1969             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1588 r_free = 0.1972             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1588   r_free= 0.1972   ksol= 0.32   Bsol= 45.42   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,-2.39,-0.53,-0.00,-0.00,-0.00); trace/3= -0.96                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.424222                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1578   r_free= 0.1955   ksol= 0.33   Bsol= 50.50   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-3.02,-1.76,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.423093                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.576631              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.111   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1578      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1955      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0637 = 2.58 * 0.50 * 5.4367 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9082 = 2.58 * 0.50 * 5.3179 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6906 = 0.31 * 1.00 * 5.3179 + 1.00 * 0.0520                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6063 = 0.31 * 1.00 * 5.1872 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    72.33   17.05    None  None   None       |
|    all(noH): 2823   0      1.48    72.33   17.05    None  None   None       |
|    Sol.    : 438    0      4.52    72.09   38.96    None  None   None       |
|    Mac.    : 2385   0      1.48    72.33   13.02    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:     1.478 -   8.563:  603   |   5:    36.904 -  43.989:   98        |
|      1:     8.563 -  15.649: 1295   |   6:    43.989 -  51.074:   89        |
|      2:    15.649 -  22.734:  379   |   7:    51.074 -  58.159:   70        |
|      3:    22.734 -  29.819:  139   |   8:    58.159 -  65.244:   36        |
|      4:    29.819 -  36.904:   99   |   9:    65.244 -  72.330:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1588             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1587             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1587   ksol= 0.33   Bsol= 50.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-3.02,-1.76,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168641                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1583   ksol= 0.33   Bsol= 50.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.80,-1.76,-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: 5.168603                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.400636              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.444  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340871              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.063  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2824 = 2.40 * 0.50 * 5.1865 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2340 = 2.40 * 0.50 * 5.1420 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7607 = 0.34 * 1.00 * 5.1420 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7555 = 0.34 * 1.00 * 5.1264 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    76.61   16.97    None  None   None       |
|    all(noH): 2823   0      1.31    76.61   16.97    None  None   None       |
|    Sol.    : 438    0      3.42    73.23   38.72    None  None   None       |
|    Mac.    : 2385   0      1.31    76.61   12.98    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:     1.310 -   8.840:  681   |   5:    38.959 -  46.489:  113        |
|      1:     8.840 -  16.370: 1281   |   6:    46.489 -  54.019:   84        |
|      2:    16.370 -  23.900:  347   |   7:    54.019 -  61.549:   56        |
|      3:    23.900 -  31.430:  129   |   8:    61.549 -  69.079:   18        |
|      4:    31.430 -  38.959:  103   |   9:    69.079 -  76.608:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1549             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1093 r_free = 0.1548             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1548   ksol= 0.33   Bsol= 50.50   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.80,-1.76,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1548   ksol= 0.33   Bsol= 50.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.62,-1.68,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125523                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.577058              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.442  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1043 = 1.58 * 0.50 * 5.1264 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0989 = 1.58 * 0.50 * 5.1324 + 1.00 * 0.0518                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8066 = 0.55 * 1.00 * 5.1324 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8086 = 0.55 * 1.00 * 5.1349 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    82.18   16.96    None  None   None       |
|    all(noH): 2823   0      0.76    82.18   16.96    None  None   None       |
|    Sol.    : 438    0      5.05    74.98   39.01    None  None   None       |
|    Mac.    : 2385   0      0.76    82.18   12.92    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:     0.760 -   8.903:  742   |   5:    41.472 -  49.615:  109        |
|      1:     8.903 -  17.045: 1280   |   6:    49.615 -  57.757:   80        |
|      2:    17.045 -  25.188:  311   |   7:    57.757 -  65.900:   39        |
|      3:    25.188 -  33.330:  133   |   8:    65.900 -  74.042:   13        |
|      4:    33.330 -  41.472:  108   |   9:    74.042 -  82.185:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1570             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1570             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1570   ksol= 0.33   Bsol= 50.50   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.62,-1.68,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1570   ksol= 0.33   Bsol= 50.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.44,-1.51,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.955650              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.798  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.499675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.757  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6411 = 2.96 * 0.50 * 5.1354 + 1.00 * 0.0518                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6372 = 2.96 * 0.50 * 5.1218 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5679 = 0.50 * 1.00 * 5.1218 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5656 = 0.50 * 1.00 * 5.1171 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    83.36   16.80    None  None   None       |
|    all(noH): 2823   0      0.78    83.36   16.80    None  None   None       |
|    Sol.    : 438    0      6.27    75.28   38.87    None  None   None       |
|    Mac.    : 2385   0      0.78    83.36   12.75    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:     0.779 -   9.037:  837   |   5:    42.067 -  50.325:  105        |
|      1:     9.037 -  17.294: 1217   |   6:    50.325 -  58.582:   76        |
|      2:    17.294 -  25.552:  286   |   7:    58.582 -  66.840:   33        |
|      3:    25.552 -  33.809:  135   |   8:    66.840 -  75.097:   14        |
|      4:    33.809 -  42.067:  114   |   9:    75.097 -  83.355:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1062 r_free = 0.1566             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1061 r_free = 0.1567             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1567   ksol= 0.33   Bsol= 50.50   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.44,-1.51,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116263                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.0968 0.1296      5.3693       5.527|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.0826 0.1109      5.4148      5.6153|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.1011 0.1524      5.4451      5.8572|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.1143 0.1526      5.4286      5.5701|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.1279 0.1817      5.3057      5.5545|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.1155 0.1724      5.1804      5.4289|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.1178 0.1583      5.1398      5.3307|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.1080 0.1757      5.0018       5.341|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.1092 0.1698      4.9922      5.2988|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.1027 0.1756      4.9109      5.2035|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.1086 0.1776      4.9283      5.2945|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.1050 0.1543      4.8651      5.0743|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.1106 0.1796      4.7666      5.0826|
| 14:  2.0305 -  1.9810 0.59    773   86 0.0966 0.1656      4.6071      4.8972|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.94   8.96   0.98     0.95       7014.54|
|  2:  4.7289 -  3.7727  1342   146  0.95   7.92   1.01     1.00       8904.91|
|  3:  3.7727 -  3.3014  1314   147  0.93  11.13   1.02     1.02      10085.61|
|  4:  3.3014 -  3.0022  1315   153  0.92  13.45   1.00     0.98      10164.46|
|  5:  3.0022 -  2.7884  1297   139  0.90  16.02   0.99     0.97       8231.24|
|  6:  2.7884 -  2.6249  1286   143  0.90  15.66   0.98     0.96       6910.26|
|  7:  2.6249 -  2.4941  1300   139  0.91  15.03   0.99     0.97       6078.96|
|  8:  2.4941 -  2.3859  1261   151  0.91  14.72   0.98     0.96       4784.18|
|  9:  2.3859 -  2.2944  1281   145  0.92  14.47   1.00     0.97       4654.11|
| 10:  2.2944 -  2.2155  1279   138  0.91  14.96   0.99     0.95       4095.96|
| 11:  2.2155 -  2.1464  1286   138  0.90  16.24   0.99     0.95       4375.68|
| 12:  2.1464 -  2.0852  1241   139  0.91  14.95   1.00     0.99       4005.87|
| 13:  2.0852 -  2.0305  1263   140  0.90  16.26   0.99     0.98       3288.16|
| 14:  2.0305 -  1.9810   773    86  0.92  13.69   0.97     0.94       2316.47|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2316.47 max =        10164.46 mean =      6215.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.76|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.31|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1567   ksol= 0.32   Bsol= 50.48   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.23,-1.31,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115922                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1567   ksol= 0.32   Bsol= 50.48   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.23,-1.31,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115922                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.0966 0.1294      5.3653      5.5251|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.0828 0.1110      5.4152      5.6156|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.1012 0.1525      5.4454      5.8571|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.1142 0.1526      5.4283      5.5699|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.1279 0.1817      5.3053      5.5539|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.1155 0.1723      5.1801      5.4285|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.1178 0.1582      5.1395      5.3304|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.1080 0.1756      5.0017      5.3407|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.1092 0.1698      4.9922      5.2988|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.1026 0.1756       4.911      5.2032|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.1086 0.1777      4.9283      5.2948|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.1050 0.1543      4.8651      5.0744|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.1106 0.1797      4.7666      5.0823|
| 14:  2.0305 -  1.9810 0.59    773   86 0.0966 0.1657      4.6073      4.8973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.94   8.89   0.98     0.95       6943.47|
|  2:  4.7289 -  3.7727  1342   146  0.95   7.90   1.01     1.00       8878.09|
|  3:  3.7727 -  3.3014  1314   147  0.93  11.14   1.03     1.02      10089.76|
|  4:  3.3014 -  3.0022  1315   153  0.92  13.44   1.01     0.99      10159.81|
|  5:  3.0022 -  2.7884  1297   139  0.90  16.01   1.00     0.97       8224.98|
|  6:  2.7884 -  2.6249  1286   143  0.90  15.65   0.99     0.96       6904.79|
|  7:  2.6249 -  2.4941  1300   139  0.91  15.02   1.00     0.97       6074.59|
|  8:  2.4941 -  2.3859  1261   151  0.91  14.72   0.99     0.97       4782.68|
|  9:  2.3859 -  2.2944  1281   145  0.92  14.47   1.00     0.97       4653.02|
| 10:  2.2944 -  2.2155  1279   138  0.91  14.97   1.00     0.96       4096.17|
| 11:  2.2155 -  2.1464  1286   138  0.90  16.24   1.00     0.96       4374.99|
| 12:  2.1464 -  2.0852  1241   139  0.91  14.95   1.01     1.00       4005.94|
| 13:  2.0852 -  2.0305  1263   140  0.90  16.27   1.00     0.99       3288.04|
| 14:  2.0305 -  1.9810   773    86  0.92  13.70   0.98     0.95       2317.32|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2317.32 max =        10159.81 mean =      6206.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.76|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.29|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    83.33   16.78    None  None   None       |
|    all(noH): 2823   0      0.75    83.33   16.78    None  None   None       |
|    Sol.    : 438    0      6.24    75.25   38.85    None  None   None       |
|    Mac.    : 2385   0      0.75    83.33   12.72    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:     0.753 -   9.010:  837   |   5:    42.041 -  50.298:  105        |
|      1:     9.010 -  17.268: 1217   |   6:    50.298 -  58.556:   76        |
|      2:    17.268 -  25.526:  286   |   7:    58.556 -  66.814:   33        |
|      3:    25.526 -  33.783:  135   |   8:    66.814 -  75.071:   14        |
|      4:    33.783 -  42.041:  114   |   9:    75.071 -  83.329:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 4.605
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 285
   mapped sites are within: 0.722 - 4.605

peak=    5.496 closest distance to " CG  PRO A  54 " =    1.199
peak=    5.420 closest distance to " NH2 ARG A  56 " =    2.207
peak=    5.419 closest distance to " O   HOH Z 126 " =    1.941
peak=    5.353 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.209 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.137 closest distance to " CB  SER A  63 " =    1.218
peak=    5.117 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.815 closest distance to " C   PRO A 198 " =    1.515
peak=    4.768 closest distance to " O   HOH Z 142 " =    1.754
peak=    4.732 closest distance to " CB  GLN A 183 " =    1.212
peak=    4.707 closest distance to " O   HOH Z  78 " =    1.705
peak=    4.650 closest distance to " CG  PRO A 213 " =    1.185
peak=    4.647 closest distance to " O   HOH Z  15 " =    2.242
peak=    4.644 closest distance to " O   HOH Z 298 " =    1.947
peak=    4.592 closest distance to " CB  LEU A 228 " =    1.089
peak=    4.587 closest distance to " CB  PRO A  54 " =    0.896
peak=    4.573 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.554 closest distance to " CB  GLU A 152 " =    1.238
peak=    4.508 closest distance to " O   HOH Z 369 " =    2.099
peak=    4.426 closest distance to " O   HOH Z 236 " =    2.006
peak=    4.415 closest distance to " O   HOH Z 193 " =    1.835
peak=    4.375 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.331 closest distance to " OD1 ASN A  69 " =    2.599
peak=    4.331 closest distance to " CB  ASN A 187 " =    1.073
peak=    4.327 closest distance to " CB  ARG A  79 " =    1.411
peak=    4.282 closest distance to " CB  ASN A 148 " =    1.361
peak=    4.273 closest distance to " ND2 ASN A 187 " =    1.488
peak=    4.261 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.253 closest distance to " O   HOH Z 427 " =    2.943
peak=    4.124 closest distance to " O   HOH Z 303 " =    2.130
peak=    4.092 closest distance to " CB  TYR A 169 " =    0.758
peak=    4.084 closest distance to " O   HOH Z 261 " =    2.275
peak=    4.080 closest distance to " O   HOH Z 234 " =    3.737
peak=    4.063 closest distance to " O   HOH Z 132 " =    2.459
peak=    4.061 closest distance to " O   HOH Z 272 " =    1.850
peak=    4.058 closest distance to " O   HOH Z 193 " =    1.764
peak=    4.026 closest distance to " OD2 ASP A 286 " =    2.857
peak=    4.005 closest distance to " O   HOH Z 316 " =    3.093
peak=    4.004 closest distance to " O   HOH Z 214 " =    2.000
peak=    4.001 closest distance to " O   HOH Z 158 " =    2.969
peak=    3.986 closest distance to " NH1AARG A 145 " =    1.132
peak=    3.984 closest distance to " CB  SER A 212 " =    1.119
peak=    3.981 closest distance to " CB  SER A   3 " =    1.404
peak=    3.979 closest distance to " O   HOH Z 368 " =    2.021
peak=    3.977 closest distance to " CB  TRP A 266 " =    0.949
peak=    3.961 closest distance to " O   HOH Z 250 " =    1.486
peak=    3.945 closest distance to " O   HOH Z 346 " =    1.647
peak=    3.944 closest distance to " NZ  LYS A 117 " =    3.209
peak=    3.943 closest distance to " CB  VAL A 265 " =    1.281
peak=    3.924 closest distance to " ND1 HIS A  86 " =    1.721
peak=    3.917 closest distance to " CG1 ILE A  33 " =    1.229
peak=    3.902 closest distance to " CB  ARG A 190 " =    1.613
peak=    3.899 closest distance to " CG  PRO A  90 " =    1.035
peak=    3.896 closest distance to " O   HOH Z 180 " =    2.124
peak=    3.893 closest distance to " O   HOH Z 133 " =    1.666
peak=    3.891 closest distance to " O   HOH Z 344 " =    3.153
peak=    3.889 closest distance to " CA  ALA A  21 " =    1.196
peak=    3.883 closest distance to " CD  ARG A  66 " =    2.276
peak=    3.864 closest distance to " CA  ASN A 215 " =    1.194
peak=    3.855 closest distance to " O   HOH Z   1 " =    1.877
peak=    3.854 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.841 closest distance to " O   HOH Z 197 " =    3.123
peak=    3.824 closest distance to " CG2 VAL A 257 " =    0.942
peak=    3.821 closest distance to " CB  GLU A 277 " =    3.605
peak=    3.820 closest distance to " O   HOH Z 203 " =    1.846
peak=    3.814 closest distance to " CD2 LEU A 255 " =    1.521
peak=    3.802 closest distance to " CA  MET A  40 " =    1.126
peak=    3.795 closest distance to " CG  PRO A 198 " =    1.174
peak=    3.792 closest distance to " CA  THR A 264 " =    0.849
peak=    3.792 closest distance to " O   HOH Z  10 " =    1.860
peak=    3.780 closest distance to " O   HOH Z 403 " =    1.700
peak=    3.768 closest distance to " CB  TRP A 179 " =    1.401
peak=    3.760 closest distance to " O   HOH Z 213 " =    1.859
peak=    3.759 closest distance to " O   HOH Z 219 " =    2.079
peak=    3.759 closest distance to " CD  ARG A 159 " =    0.764
peak=    3.756 closest distance to " O   MET A 105 " =    1.804
peak=    3.736 closest distance to " CE  LYS A  76 " =    0.861
peak=    3.734 closest distance to " NH2 ARG A 156 " =    1.203
peak=    3.731 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.724 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.719 closest distance to " CG  PRO A 243 " =    1.115
peak=    3.712 closest distance to " CB  SER A 216 " =    0.827
peak=    3.701 closest distance to " O   HOH Z 389 " =    1.945
peak=    3.690 closest distance to " O   HOH Z 108 " =    2.318
peak=    3.687 closest distance to " CD BLYS A 290 " =    1.145
peak=    3.684 closest distance to " CZ  PHE A 218 " =    1.059
peak=    3.681 closest distance to " O   HOH Z  64 " =    2.178
peak=    3.679 closest distance to " CD1 LEU A 300 " =    1.236
peak=    3.678 closest distance to " O   HOH Z  66 " =    2.136
peak=    3.673 closest distance to " ND2 ASN A 110 " =    1.824
peak=    3.662 closest distance to " O   HOH Z 425 " =    2.090
peak=    3.654 closest distance to " O   HOH Z 189 " =    2.392
peak=    3.653 closest distance to " O   HOH Z 135 " =    1.701
peak=    3.635 closest distance to " O   HOH Z 371 " =    3.062
peak=    3.631 closest distance to " CB  ASP A 140 " =    0.929
peak=    3.627 closest distance to " O   HOH Z 411 " =    3.842
peak=    3.623 closest distance to " CA  THR A 221 " =    0.979
peak=    3.621 closest distance to " O   HOH Z 280 " =    3.040
peak=    3.615 closest distance to " O   HOH Z 426 " =    1.556
peak=    3.610 closest distance to " O   HOH Z  21 " =    1.704
peak=    3.609 closest distance to " O   HOH Z 368 " =    3.609
peak=    3.607 closest distance to " O   HOH Z 305 " =    3.627
peak=    3.599 closest distance to " O   HOH Z 425 " =    1.227
peak=    3.594 closest distance to " CA  PRO A  54 " =    1.324
peak=    3.586 closest distance to " CG  LEU A 167 " =    1.236
peak=    3.585 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.566 closest distance to " CD  ARG A 219 " =    1.077
peak=    3.566 closest distance to " O   HOH Z 133 " =    2.460
peak=    3.563 closest distance to " CB  ARG A 139 " =    0.998
peak=    3.555 closest distance to " CB  ASN A 142 " =    0.951
peak=    3.545 closest distance to " CB  ALA A  34 " =    1.096
peak=    3.537 closest distance to " O   HOH Z  40 " =    1.867
peak=    3.529 closest distance to " CB  TYR A 169 " =    0.785
peak=    3.525 closest distance to " N   ARG A 156 " =    1.312
peak=    3.520 closest distance to " CD2 TRP A 179 " =    1.345
peak=    3.516 closest distance to " NH2BARG A 145 " =    2.043
peak=    3.511 closest distance to " O   HOH Z 172 " =    3.327
peak=    3.509 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.503 closest distance to " O   HOH Z 407 " =    2.377
peak=    3.502 closest distance to " O   HOH Z  40 " =    1.826
peak=    3.501 closest distance to " CD  ARG A 269 " =    0.898
peak=    3.500 closest distance to " CA  ALA A 291 " =    0.913
peak=    3.499 closest distance to " O   SER A  87 " =    2.272
peak=    3.497 closest distance to " OG  SER A  22 " =    2.763
peak=    3.491 closest distance to " O   HOH Z 193 " =    2.069
peak=    3.489 closest distance to " O   HOH Z  88 " =    3.544
peak=    3.488 closest distance to " O   HOH Z  59 " =    1.928
peak=    3.484 closest distance to " OD1 ASN A 217 " =    1.641
peak=    3.474 closest distance to " O   HOH Z 245 " =    1.295
peak=    3.467 closest distance to " O   HOH Z   1 " =    1.709
peak=    3.455 closest distance to " CD  LYS A 166 " =    1.241
peak=    3.437 closest distance to " CB  LEU A 143 " =    1.103
peak=    3.435 closest distance to " ND1 HIS A  81 " =    1.585
peak=    3.434 closest distance to " O   HOH Z 437 " =    1.474
peak=    3.425 closest distance to " N   ASN A 127 " =    1.246
peak=    3.422 closest distance to " CB  ALA A   1 " =    4.605
peak=    3.422 closest distance to " O   HOH Z 327 " =    1.814
peak=    3.420 closest distance to " OD1BASN A 224 " =    2.379
peak=    3.416 closest distance to " CB  MET A  47 " =    1.051
peak=    3.409 closest distance to " CB  GLN A  88 " =    1.270
peak=    3.408 closest distance to " O   HOH Z 209 " =    2.385
peak=    3.406 closest distance to " O   HOH Z  93 " =    2.651
peak=    3.404 closest distance to " O   HOH Z 329 " =    3.724
peak=    3.399 closest distance to " CB  ASN A  39 " =    0.928
peak=    3.399 closest distance to " O   HOH Z 128 " =    2.226
peak=    3.398 closest distance to " O   HOH Z 295 " =    1.513
peak=    3.392 closest distance to " CA  ALA A  51 " =    0.929
peak=    3.388 closest distance to " CB  MET A  40 " =    0.786
peak=    3.383 closest distance to " NH2AARG A 275 " =    3.669
peak=    3.381 closest distance to " CG  LYS A  76 " =    0.972
peak=    3.378 closest distance to " O   HOH Z 227 " =    1.661
peak=    3.376 closest distance to " CB  ASN A 224 " =    1.053
peak=    3.372 closest distance to " N   SER A 134 " =    1.353
peak=    3.369 closest distance to " O   HOH Z  97 " =    1.927
peak=    3.367 closest distance to " O   HOH Z 163 " =    1.793
peak=    3.364 closest distance to " OG BSER A 164 " =    2.338
peak=    3.364 closest distance to " N   VAL A 126 " =    1.283
peak=    3.358 closest distance to " O  BHOH Z 338 " =    2.349
peak=    3.353 closest distance to " CB  THR A 157 " =    1.106
peak=    3.349 closest distance to " O   HOH Z 273 " =    2.727
peak=    3.347 closest distance to " O   HOH Z 391 " =    2.934
peak=    3.347 closest distance to " CA  ALA A 158 " =    1.178
peak=    3.346 closest distance to " O   HOH Z 419 " =    1.942
peak=    3.345 closest distance to " O   HOH Z 291 " =    1.665
peak=    3.343 closest distance to " O   GLY A  57 " =    2.632
peak=    3.341 closest distance to " CG1BVAL A  72 " =    1.595
peak=    3.338 closest distance to " O   HOH Z  54 " =    2.433
peak=    3.334 closest distance to " CD2 LEU A 297 " =    0.862
peak=    3.333 closest distance to " CA  ALA A 233 " =    1.169
peak=    3.332 closest distance to " CA  ALA A  84 " =    1.482
peak=    3.317 closest distance to " O   HOH Z  44 " =    3.148
peak=    3.317 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.314 closest distance to " O   HOH Z 211 " =    2.776
peak=    3.311 closest distance to " CB  ALA A 233 " =    1.369
peak=    3.311 closest distance to " CB  ALA A 248 " =    0.898
peak=    3.309 closest distance to " O   HOH Z 345 " =    3.530
peak=    3.309 closest distance to " CD1 ILE A 106 " =    0.821
peak=    3.306 closest distance to " O   HOH Z 134 " =    1.334
peak=    3.303 closest distance to " O   HOH Z 409 " =    2.777
peak=    3.300 closest distance to " O   HOH Z 261 " =    2.195
peak=    3.299 closest distance to " O   HOH Z  53 " =    2.564
peak=    3.292 closest distance to " O   HOH Z 281 " =    4.066
peak=    3.286 closest distance to " CA  ALA A 154 " =    0.958
peak=    3.286 closest distance to " CA  ARG A 195 " =    1.213
peak=    3.285 closest distance to " O   HOH Z 128 " =    2.157
peak=    3.283 closest distance to " O   HOH Z 271 " =    2.428
peak=    3.282 closest distance to " CB  GLU A 236 " =    1.112
peak=    3.278 closest distance to " CB  ILE A 120 " =    1.241
peak=    3.277 closest distance to " CB  ALA A   9 " =    1.564
peak=    3.276 closest distance to " CB  LEU A 255 " =    0.756
peak=    3.275 closest distance to " OE1 GLN A  11 " =    2.188
peak=    3.274 closest distance to " O   THR A 220 " =    1.450
peak=    3.270 closest distance to " CB  TYR A 116 " =    0.827
peak=    3.270 closest distance to " CG  MET A 113 " =    1.446
peak=    3.269 closest distance to " O   HOH Z 345 " =    1.682
peak=    3.268 closest distance to " CE BLYS A 290 " =    1.132
peak=    3.268 closest distance to " CD  PRO A 243 " =    1.623
peak=    3.266 closest distance to " CG BARG A 275 " =    1.492
peak=    3.265 closest distance to " CB  HIS A 108 " =    0.802
peak=    3.264 closest distance to " CB  GLU A  46 " =    1.010
peak=    3.260 closest distance to " O   HOH Z 166 " =    3.716
peak=    3.259 closest distance to " CB  ARG A 138 " =    0.998
peak=    3.254 closest distance to " O   HOH Z 423 " =    2.816
peak=    3.248 closest distance to " O   HOH Z  20 " =    1.575
peak=    3.247 closest distance to " CD  LYS A 119 " =    1.228
peak=    3.245 closest distance to " CG  GLN A  11 " =    1.822
peak=    3.245 closest distance to " O   HOH Z 148 " =    3.281
peak=    3.245 closest distance to " O   HOH Z  44 " =    1.651
peak=    3.243 closest distance to " CG1 ILE A 151 " =    0.936
peak=    3.239 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.238 closest distance to " O   HOH Z 406 " =    1.614
peak=    3.237 closest distance to " O   HOH Z 188 " =    2.084
peak=    3.233 closest distance to " CB  ASN A 110 " =    1.171
peak=    3.232 closest distance to " O   ALA A 158 " =    1.303
peak=    3.231 closest distance to " O   HOH Z 411 " =    1.814
peak=    3.231 closest distance to " N   PHE A 130 " =    1.271
peak=    3.224 closest distance to " O   HOH Z 353 " =    2.778
peak=    3.223 closest distance to " O   HOH Z 359 " =    3.906
peak=    3.219 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.217 closest distance to " O   HOH Z 334 " =    1.444
peak=    3.216 closest distance to " O   HOH Z 248 " =    1.729
peak=    3.216 closest distance to " CA  ASP A 140 " =    1.173
peak=    3.214 closest distance to " O   HOH Z  54 " =    1.607
peak=    3.213 closest distance to " O   ALA A 165 " =    1.412
peak=    3.211 closest distance to " CB  GLN A  89 " =    1.290
peak=    3.209 closest distance to " O   HOH Z 371 " =    1.752
peak=    3.203 closest distance to " O   HOH Z 213 " =    2.281
peak=    3.202 closest distance to " CG  GLN A  77 " =    2.169
peak=    3.201 closest distance to " O   HOH Z 234 " =    1.721
peak=    3.200 closest distance to " CA  ARG A  36 " =    1.100
peak=    3.194 closest distance to " O   HOH Z 263 " =    1.735
peak=    3.185 closest distance to " O   HOH Z 144 " =    1.791
peak=    3.185 closest distance to " CB  ALA A 291 " =    1.461
peak=    3.178 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.177 closest distance to " NH2 ARG A 219 " =    1.818
peak=    3.177 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.176 closest distance to " CG2 ILE A 120 " =    1.209
peak=    3.173 closest distance to " CA  SER A  87 " =    1.055
peak=    3.166 closest distance to " CA  MET A 105 " =    0.999
peak=    3.164 closest distance to " O   THR A 251 " =    1.205
peak=    3.163 closest distance to " CB  VAL A 265 " =    1.946
peak=    3.161 closest distance to " CG  ARG A 159 " =    0.862
peak=    3.160 closest distance to " CD2 HIS A  81 " =    1.193
peak=    3.156 closest distance to " CG  MET A 185 " =    1.051
peak=    3.152 closest distance to " CB  SER A  62 " =    1.212
peak=    3.151 closest distance to " CA  ALA A 248 " =    1.270
peak=    3.149 closest distance to " CB  PHE A  16 " =    1.013
peak=    3.146 closest distance to " CA  TYR A 116 " =    1.355
peak=    3.144 closest distance to " O   TYR A 116 " =    1.296
peak=    3.139 closest distance to " CA  GLY A 267 " =    1.182
peak=    3.130 closest distance to " O   HOH Z  49 " =    2.788
peak=    3.126 closest distance to " OG  SER A 206 " =    1.312
peak=    3.125 closest distance to " O   HOH Z 371 " =    3.347
peak=    3.123 closest distance to " NZ  LYS A 166 " =    3.019
peak=    3.123 closest distance to " CB  ASN A 285 " =    0.874
peak=    3.120 closest distance to " O   TRP A 274 " =    1.808
peak=    3.119 closest distance to " O   HOH Z  43 " =    1.913
peak=    3.113 closest distance to " CZ3 TRP A 123 " =    1.214
peak=    3.106 closest distance to " CA  ASP A 191 " =    0.773
peak=    3.106 closest distance to " O   HOH Z  88 " =    2.935
peak=    3.105 closest distance to " CB  TYR A  30 " =    1.444
peak=    3.102 closest distance to " N   SER A 135 " =    1.300
peak=    3.097 closest distance to " O   HOH Z 298 " =    2.640
peak=    3.095 closest distance to " CZ2 TRP A 179 " =    1.665
peak=    3.091 closest distance to " CG BARG A 102 " =    1.829
peak=    3.088 closest distance to " CB  TRP A 150 " =    1.343
peak=    3.088 closest distance to " OG BSER A  99 " =    2.159
peak=    3.087 closest distance to " CA  GLU A  46 " =    0.722
peak=    3.082 closest distance to " N   ASN A 252 " =    1.405
peak=    3.079 closest distance to " N   GLN A 278 " =    1.065
peak=    3.076 closest distance to " O   HOH Z 419 " =    2.953
peak=    3.062 closest distance to " O   HOH Z 287 " =    2.088
peak=    3.058 closest distance to " CB  ASP A 171 " =    0.814
peak=    3.053 closest distance to " O   ALA A   1 " =    1.557
peak=    3.044 closest distance to " O   HOH Z 386 " =    2.613
peak=    3.042 closest distance to " OD1 ASN A 187 " =    1.759
peak=    3.041 closest distance to " O   HOH Z 302 " =    1.857
peak=    3.036 closest distance to " O   HOH Z 218 " =    2.423
peak=    3.031 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.030 closest distance to " CA  LYS A 290 " =    1.394
peak=    3.030 closest distance to " O   HOH Z 365 " =    2.921
peak=    2.996 closest distance to " O   HOH Z 180 " =    1.968

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.694 - 5.587
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.782 - 5.587

peak=   -4.604 closest distance to " O   HOH Z 266 " =    4.781
peak=   -4.593 closest distance to " CB  PRO A 243 " =    2.604
peak=   -4.430 closest distance to " CD  ARG A 156 " =    1.997
peak=   -4.376 closest distance to " O   HOH Z 377 " =    2.063
peak=   -4.365 closest distance to " CG  GLN A 223 " =    1.949
peak=   -4.272 closest distance to " O   VAL A  67 " =    2.734
peak=   -4.165 closest distance to " SG  CYS A 254 " =    3.345
peak=   -4.153 closest distance to " O   HOH Z 389 " =    1.894
peak=   -4.110 closest distance to " O   HOH Z 290 " =    1.185
peak=   -4.098 closest distance to " O   HOH Z 372 " =    2.464
peak=   -4.087 closest distance to " N   ALA A  43 " =    2.606
peak=   -4.076 closest distance to " O   HOH Z 198 " =    2.072
peak=   -4.070 closest distance to " CE2 TYR A  30 " =    2.829
peak=   -4.061 closest distance to " O   HOH Z 126 " =    1.873
peak=   -4.030 closest distance to " CG1 VAL A 112 " =    2.821
peak=   -4.003 closest distance to " O   ILE A 109 " =    2.595
peak=   -3.991 closest distance to " O   HOH Z 231 " =    2.138
peak=   -3.959 closest distance to " O   HOH Z 353 " =    2.144
peak=   -3.943 closest distance to " O   HOH Z 435 " =    2.756
peak=   -3.941 closest distance to " OG BSER A 134 " =    1.224
peak=   -3.925 closest distance to " CZ3 TRP A 179 " =    1.120
peak=   -3.893 closest distance to " O   HOH Z  43 " =    1.578
peak=   -3.893 closest distance to " C   HIS A 108 " =    1.112
peak=   -3.886 closest distance to " CD1 PHE A  59 " =    1.834
peak=   -3.886 closest distance to " ND2 ASN A  45 " =    1.607
peak=   -3.854 closest distance to " CZ  PHE A  59 " =    1.604
peak=   -3.833 closest distance to " O   HOH Z 118 " =    3.130
peak=   -3.799 closest distance to " O   HOH Z  10 " =    1.493
peak=   -3.798 closest distance to " N   ASP A 286 " =    2.482
peak=   -3.792 closest distance to " CG  PHE A 283 " =    2.839
peak=   -3.788 closest distance to " O   HOH Z 313 " =    1.981
peak=   -3.764 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.750 closest distance to " CE2 PHE A 218 " =    2.477
peak=   -3.748 closest distance to " CB  ALA A 291 " =    2.361
peak=   -3.742 closest distance to " O   HOH Z  52 " =    1.331
peak=   -3.729 closest distance to " CD2 LEU A 143 " =    2.633
peak=   -3.709 closest distance to " NH2AARG A 275 " =    5.479
peak=   -3.706 closest distance to " SG ACYS A 201 " =    1.875
peak=   -3.690 closest distance to " CE  MET A 105 " =    2.271
peak=   -3.679 closest distance to " CB  ALA A  43 " =    2.478
peak=   -3.679 closest distance to " O   PRO A 163 " =    2.042
peak=   -3.678 closest distance to " O   HOH Z 211 " =    1.627
peak=   -3.675 closest distance to " CG  ARG A 269 " =    2.646
peak=   -3.670 closest distance to " CD1 LEU A 228 " =    2.314
peak=   -3.665 closest distance to " O   HOH Z  38 " =    1.483
peak=   -3.655 closest distance to " NH2BARG A 275 " =    1.831
peak=   -3.653 closest distance to " O   HOH Z 185 " =    2.195
peak=   -3.640 closest distance to " CA  GLY A 203 " =    2.275
peak=   -3.639 closest distance to " O   VAL A 189 " =    2.544
peak=   -3.630 closest distance to " CD2 PHE A 192 " =    2.069
peak=   -3.618 closest distance to " CD  ARG A 139 " =    1.578
peak=   -3.613 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.613 closest distance to " O   GLY A 211 " =    1.527
peak=   -3.602 closest distance to " ND2 ASN A 249 " =    2.360
peak=   -3.596 closest distance to " O   HOH Z 351 " =    1.495
peak=   -3.593 closest distance to " O   HOH Z 407 " =    3.212
peak=   -3.588 closest distance to " O   HOH Z 198 " =    1.400
peak=   -3.584 closest distance to " CB  ASN A  39 " =    2.268
peak=   -3.582 closest distance to " CG2 ILE A 263 " =    2.291
peak=   -3.577 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -3.573 closest distance to " O   VAL A  67 " =    2.679
peak=   -3.572 closest distance to " CD  ARG A 195 " =    5.241
peak=   -3.566 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.563 closest distance to " OD1 ASN A 187 " =    1.618
peak=   -3.558 closest distance to " NH1 ARG A 195 " =    2.578
peak=   -3.558 closest distance to " CB  PRO A 163 " =    2.519
peak=   -3.557 closest distance to " CD  GLN A  58 " =    1.085
peak=   -3.549 closest distance to " CZ  TYR A 169 " =    1.694
peak=   -3.548 closest distance to " CG  MET A 105 " =    1.006
peak=   -3.541 closest distance to " O   HOH Z  93 " =    2.244
peak=   -3.537 closest distance to " OD1 ASP A 171 " =    1.607
peak=   -3.531 closest distance to " C   ALA A 158 " =    1.327
peak=   -3.528 closest distance to " N   SER A 212 " =    2.007
peak=   -3.518 closest distance to " NE2 GLN A  88 " =    1.918
peak=   -3.515 closest distance to " CB  TYR A  15 " =    2.146
peak=   -3.509 closest distance to " OD1 ASN A 148 " =    1.657
peak=   -3.508 closest distance to " OG  SER A  97 " =    2.146
peak=   -3.508 closest distance to " C   LEU A 143 " =    1.290
peak=   -3.501 closest distance to " CG1 VAL A 250 " =    2.620
peak=   -3.501 closest distance to " OD1 ASP A 191 " =    1.757
peak=   -3.497 closest distance to " OXT GLY A 302 " =    2.871
peak=   -3.485 closest distance to " OG BSER A 134 " =    1.684
peak=   -3.482 closest distance to " N   GLN A  58 " =    1.727
peak=   -3.467 closest distance to " OG  SER A  62 " =    1.589
peak=   -3.464 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.460 closest distance to " O   ARG A 145 " =    1.548
peak=   -3.448 closest distance to " O   HOH Z  13 " =    1.589
peak=   -3.443 closest distance to " O   HOH Z 311 " =    3.687
peak=   -3.436 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.423 closest distance to " CG1 VAL A 197 " =    2.239
peak=   -3.420 closest distance to " CA  GLY A  98 " =    1.941
peak=   -3.416 closest distance to " CB  CYS A 201 " =    2.572
peak=   -3.411 closest distance to " CB  CYS A 254 " =    2.193
peak=   -3.407 closest distance to " O   SER A 135 " =    1.475
peak=   -3.399 closest distance to " CA  GLY A 241 " =    2.260
peak=   -3.394 closest distance to " CD2 LEU A 237 " =    2.723
peak=   -3.386 closest distance to " CB  TRP A  85 " =    2.468
peak=   -3.382 closest distance to " OG  SER A  87 " =    1.428
peak=   -3.379 closest distance to " O   HOH Z 350 " =    1.689
peak=   -3.377 closest distance to " O   HOH Z  73 " =    2.170
peak=   -3.377 closest distance to " O   HOH Z 281 " =    2.694
peak=   -3.373 closest distance to " NE  ARG A  36 " =    1.935
peak=   -3.371 closest distance to " O   HOH Z  11 " =    1.806
peak=   -3.369 closest distance to " CD2 TYR A 247 " =    2.565
peak=   -3.365 closest distance to " CB  ALA A 131 " =    2.001
peak=   -3.361 closest distance to " CB  ASP A 286 " =    2.219
peak=   -3.352 closest distance to " N   THR A 235 " =    1.315
peak=   -3.352 closest distance to " OD2 ASP A 171 " =    1.800
peak=   -3.351 closest distance to " O   HOH Z 111 " =    2.144
peak=   -3.351 closest distance to " O   HOH Z 196 " =    2.166
peak=   -3.337 closest distance to " O   GLY A 196 " =    1.119
peak=   -3.337 closest distance to " O   HOH Z 426 " =    1.668
peak=   -3.337 closest distance to " OD1 ASP A 191 " =    1.543
peak=   -3.330 closest distance to " CD  GLN A  88 " =    0.914
peak=   -3.326 closest distance to " CG  TRP A 266 " =    1.769
peak=   -3.318 closest distance to " O   HOH Z  98 " =    2.228
peak=   -3.307 closest distance to " CD2 LEU A 300 " =    2.868
peak=   -3.303 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.301 closest distance to " O   HOH Z 168 " =    1.813
peak=   -3.299 closest distance to " CD1 LEU A 297 " =    2.444
peak=   -3.297 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.292 closest distance to " O   HOH Z 253 " =    3.913
peak=   -3.290 closest distance to " O   TRP A  70 " =    1.528
peak=   -3.289 closest distance to " ND2 ASN A  60 " =    1.417
peak=   -3.289 closest distance to " OH  TYR A 214 " =    1.243
peak=   -3.279 closest distance to " CG  PRO A 163 " =    2.485
peak=   -3.269 closest distance to " O   HOH Z  51 " =    1.713
peak=   -3.267 closest distance to " O   HOH Z 417 " =    2.496
peak=   -3.266 closest distance to " CA  GLY A 241 " =    3.061
peak=   -3.262 closest distance to " O   HOH Z 298 " =    1.273
peak=   -3.261 closest distance to " O   HOH Z 394 " =    1.419
peak=   -3.259 closest distance to " OG  SER A  26 " =    1.248
peak=   -3.257 closest distance to " O   HOH Z 388 " =    1.996
peak=   -3.247 closest distance to " CB  ALA A 248 " =    2.005
peak=   -3.246 closest distance to " O   PHE A 218 " =    1.611
peak=   -3.240 closest distance to " O   HOH Z  88 " =    2.202
peak=   -3.236 closest distance to " O   HOH Z 298 " =    2.563
peak=   -3.230 closest distance to " N   ALA A 248 " =    1.558
peak=   -3.230 closest distance to " N   THR A 157 " =    1.505
peak=   -3.224 closest distance to " CA  ASP A  27 " =    2.495
peak=   -3.222 closest distance to " CG  ASN A 301 " =    1.928
peak=   -3.222 closest distance to " O   HOH Z 359 " =    3.150
peak=   -3.220 closest distance to " O   ALA A 161 " =    1.649
peak=   -3.220 closest distance to " CE  LYS A  76 " =    2.773
peak=   -3.217 closest distance to " CD1 ILE A 239 " =    2.135
peak=   -3.216 closest distance to " N   ALA A 226 " =    2.150
peak=   -3.213 closest distance to " OE1 GLN A  88 " =    1.234
peak=   -3.207 closest distance to " CD2 TYR A 293 " =    2.037
peak=   -3.203 closest distance to " CD2 PHE A  61 " =    2.556
peak=   -3.199 closest distance to " O   HOH Z 191 " =    5.587
peak=   -3.199 closest distance to " CE BMET A  47 " =    1.940
peak=   -3.196 closest distance to " O   HOH Z 137 " =    1.518
peak=   -3.188 closest distance to " O   GLY A 267 " =    2.474
peak=   -3.187 closest distance to " CB  ALA A 248 " =    2.441
peak=   -3.186 closest distance to " CE  MET A  93 " =    1.274
peak=   -3.185 closest distance to " CG1BVAL A  41 " =    2.797
peak=   -3.179 closest distance to " CB  ASP A 132 " =    2.280
peak=   -3.177 closest distance to " CG  ARG A  66 " =    2.294
peak=   -3.177 closest distance to " O   VAL A 174 " =    2.080
peak=   -3.176 closest distance to " N   PHE A  59 " =    2.109
peak=   -3.169 closest distance to " O   HOH Z 317 " =    2.365
peak=   -3.167 closest distance to " CG  GLU A   2 " =    1.953
peak=   -3.167 closest distance to " O   HOH Z 174 " =    2.903
peak=   -3.166 closest distance to " O   HOH Z 222 " =    1.211
peak=   -3.164 closest distance to " O   HOH Z  51 " =    1.290
peak=   -3.162 closest distance to " O   HOH Z 111 " =    1.268
peak=   -3.161 closest distance to " CE3 TRP A 123 " =    1.254
peak=   -3.160 closest distance to " CG1 VAL A 112 " =    2.600
peak=   -3.159 closest distance to " NZ  LYS A 119 " =    3.414
peak=   -3.158 closest distance to " NH2 ARG A  79 " =    1.587
peak=   -3.157 closest distance to " CE3 TRP A 274 " =    2.442
peak=   -3.156 closest distance to " CE3 TRP A 150 " =    2.024
peak=   -3.155 closest distance to " CG2 VAL A 189 " =    1.999
peak=   -3.146 closest distance to " CB  ALA A   7 " =    2.126
peak=   -3.144 closest distance to " OG1 THR A 178 " =    1.312
peak=   -3.143 closest distance to " O   HOH Z 166 " =    1.454
peak=   -3.140 closest distance to " O   HOH Z 241 " =    1.370
peak=   -3.139 closest distance to " O   GLN A 240 " =    2.422
peak=   -3.137 closest distance to " O   HOH Z 414 " =    1.841
peak=   -3.136 closest distance to " O   HOH Z 295 " =    1.487
peak=   -3.132 closest distance to " O   HOH Z 357 " =    2.158
peak=   -3.132 closest distance to " O   ALA A 180 " =    1.377
peak=   -3.126 closest distance to " O   HOH Z 393 " =    1.402
peak=   -3.118 closest distance to " O   HOH Z 148 " =    1.835
peak=   -3.116 closest distance to " CG  GLU A 152 " =    1.200
peak=   -3.116 closest distance to " O   SER A  22 " =    2.400
peak=   -3.114 closest distance to " O   HOH Z 361 " =    3.390
peak=   -3.112 closest distance to " CZ2 TRP A 179 " =    2.315
peak=   -3.112 closest distance to " O   ASN A 301 " =    1.508
peak=   -3.108 closest distance to " O   HOH Z 166 " =    1.955
peak=   -3.107 closest distance to " CA  SER A 135 " =    1.375
peak=   -3.105 closest distance to " CD  GLU A 236 " =    1.067
peak=   -3.105 closest distance to " O   HOH Z 207 " =    2.166
peak=   -3.104 closest distance to " C   MET A 188 " =    1.462
peak=   -3.101 closest distance to " CD1 ILE A 199 " =    2.595
peak=   -3.101 closest distance to " CG2 THR A 221 " =    2.242
peak=   -3.096 closest distance to " O   HOH Z  63 " =    1.447
peak=   -3.077 closest distance to " OXT GLY A 302 " =    3.383
peak=   -3.073 closest distance to " CD2 PHE A  61 " =    2.016
peak=   -3.070 closest distance to " O   HOH Z 324 " =    2.258
peak=   -3.067 closest distance to " CG  ARG A 269 " =    2.049
peak=   -3.064 closest distance to " O   HOH Z 323 " =    1.339
peak=   -3.064 closest distance to " O   GLY A  80 " =    2.440
peak=   -3.061 closest distance to " CB  PHE A 208 " =    2.257
peak=   -3.056 closest distance to " O   HOH Z 139 " =    2.934
peak=   -3.031 closest distance to " O   VAL A 125 " =    2.346
peak=   -3.006 closest distance to " N   ALA A 248 " =    1.870

================= 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    :  0.3236 0.3274   6.029612e+00   6.037877e+00
   1_bss:  0.3106 0.3154   6.009704e+00   6.011454e+00
   1_xyz:  0.1706 0.1926   5.469473e+00   5.582544e+00
   1_adp:  0.1593 0.1969   5.426489e+00   5.608638e+00
   1_occ:  0.1588 0.1972   5.424222e+00   5.607293e+00
   2_bss:  0.1578 0.1955   5.423093e+00   5.604425e+00
   2_xyz:  0.1247 0.1640   5.216250e+00   5.430110e+00
   2_adp:  0.1175 0.1588   5.168998e+00   5.397575e+00
   2_occ:  0.1174 0.1587   5.168641e+00   5.397694e+00
   3_bss:  0.1175 0.1583   5.168603e+00   5.397219e+00
   3_xyz:  0.1105 0.1553   5.130809e+00   5.376013e+00
   3_adp:  0.1094 0.1549   5.125536e+00   5.373476e+00
   3_occ:  0.1093 0.1548   5.125499e+00   5.373740e+00
   4_bss:  0.1093 0.1548   5.125523e+00   5.373684e+00
   4_xyz:  0.1109 0.1562   5.137780e+00   5.383327e+00
   4_adp:  0.1104 0.1570   5.138378e+00   5.387565e+00
   4_occ:  0.1104 0.1570   5.138419e+00   5.387828e+00
   5_bss:  0.1103 0.1570   5.138527e+00   5.387863e+00
   5_xyz:  0.1063 0.1570   5.118259e+00   5.382850e+00
   5_adp:  0.1062 0.1566   5.116156e+00   5.380334e+00
   5_occ:  0.1061 0.1567   5.116263e+00   5.380664e+00
   5_bss:  0.1061 0.1567   5.115922e+00   5.380404e+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:  0.323  45.422   0.046  -2.388  -0.531  -0.000  -0.000  -0.000
   1_xyz:  0.323  45.422   0.046  -2.388  -0.531  -0.000  -0.000  -0.000
   1_adp:  0.323  45.422   0.046  -2.388  -0.531  -0.000  -0.000  -0.000
   1_occ:  0.323  45.422   0.046  -2.388  -0.531  -0.000  -0.000  -0.000
   2_bss:  0.330  50.503  -1.943  -3.017  -1.763  -0.000  -0.000  -0.000
   2_xyz:  0.330  50.503  -1.943  -3.017  -1.763  -0.000  -0.000  -0.000
   2_adp:  0.330  50.503  -1.943  -3.017  -1.763  -0.000  -0.000  -0.000
   2_occ:  0.330  50.503  -1.943  -3.017  -1.763  -0.000  -0.000  -0.000
   3_bss:  0.330  50.503  -2.242  -2.796  -1.760  -0.000  -0.000  -0.000
   3_xyz:  0.330  50.503  -2.242  -2.796  -1.760  -0.000  -0.000  -0.000
   3_adp:  0.330  50.503  -2.242  -2.796  -1.760  -0.000  -0.000  -0.000
   3_occ:  0.330  50.503  -2.242  -2.796  -1.760  -0.000  -0.000  -0.000
   4_bss:  0.330  50.503  -2.233  -2.620  -1.679  -0.000  -0.000  -0.000
   4_xyz:  0.330  50.503  -2.233  -2.620  -1.679  -0.000  -0.000  -0.000
   4_adp:  0.330  50.503  -2.233  -2.620  -1.679  -0.000  -0.000  -0.000
   4_occ:  0.330  50.503  -2.233  -2.620  -1.679  -0.000  -0.000  -0.000
   5_bss:  0.330  50.503  -2.107  -2.436  -1.511  -0.000  -0.000  -0.000
   5_xyz:  0.330  50.503  -2.107  -2.436  -1.511  -0.000  -0.000  -0.000
   5_adp:  0.330  50.503  -2.107  -2.436  -1.511  -0.000  -0.000  -0.000
   5_occ:  0.330  50.503  -2.107  -2.436  -1.511  -0.000  -0.000  -0.000
   5_bss:  0.322  50.476  -1.916  -2.226  -1.307  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.682 0.7197  0.9027    30373.450
   1_bss:  32.476 0.7314  0.8910    27411.260
   1_xyz:  17.892 0.8831  1.0078     9641.395
   1_adp:  18.601 0.8762  1.0047    10160.463
   1_occ:  18.578 0.8763  1.0047    10110.014
   2_bss:  18.496 0.8770  0.9599    10030.598
   2_xyz:  14.777 0.9086  0.9776     6923.182
   2_adp:  14.077 0.9144  0.9795     6453.414
   2_occ:  14.075 0.9144  0.9794     6449.455
   3_bss:  14.069 0.9145  0.9778     6441.572
   3_xyz:  13.643 0.9180  0.9780     6162.909
   3_adp:  13.579 0.9186  0.9737     6133.826
   3_occ:  13.585 0.9185  0.9736     6133.045
   4_bss:  13.586 0.9185  0.9767     6131.838
   4_xyz:  13.745 0.9174  0.9757     6245.085
   4_adp:  13.828 0.9167  0.9706     6292.530
   4_occ:  13.833 0.9167  0.9705     6294.374
   5_bss:  13.836 0.9167  0.9760     6295.155
   5_xyz:  13.762 0.9171  0.9763     6249.731
   5_adp:  13.712 0.9175  0.9708     6213.750
   5_occ:  13.718 0.9175  0.9707     6215.689
   5_bss:  13.711 0.9175  0.9768     6206.633
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6146e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6146e-01
   1_xyz:   0.986  0.007  0.068 14.800  0.005  4.112   5.9522e-02
   1_adp:   0.986  0.007  0.068 14.800  0.005  4.112   5.9522e-02
   1_occ:   0.986  0.007  0.068 14.800  0.005  4.112   5.9522e-02
   2_bss:   0.986  0.007  0.068 14.800  0.005  4.112   5.9522e-02
   2_xyz:   0.982  0.007  0.074 14.508  0.004  4.119   5.7035e-02
   2_adp:   0.982  0.007  0.074 14.508  0.004  4.119   5.7035e-02
   2_occ:   0.982  0.007  0.074 14.508  0.004  4.119   5.7035e-02
   3_bss:   0.982  0.007  0.074 14.508  0.004  4.119   5.7035e-02
   3_xyz:   1.013  0.008  0.077 14.736  0.004  4.122   6.1960e-02
   3_adp:   1.013  0.008  0.077 14.736  0.004  4.122   6.1960e-02
   3_occ:   1.013  0.008  0.077 14.736  0.004  4.122   6.1960e-02
   4_bss:   1.013  0.008  0.077 14.736  0.004  4.122   6.1960e-02
   4_xyz:   0.918  0.006  0.070 14.410  0.004  4.122   5.1805e-02
   4_adp:   0.918  0.006  0.070 14.410  0.004  4.122   5.1805e-02
   4_occ:   0.918  0.006  0.070 14.410  0.004  4.122   5.1805e-02
   5_bss:   0.918  0.006  0.070 14.410  0.004  4.122   5.1805e-02
   5_xyz:   1.063  0.009  0.080 14.796  0.004  4.124   6.8056e-02
   5_adp:   1.063  0.009  0.080 14.796  0.004  4.124   6.8056e-02
   5_occ:   1.063  0.009  0.080 14.796  0.004  4.124   6.8056e-02
   5_bss:   1.063  0.009  0.080 14.796  0.004  4.124   6.8056e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4094e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4094e-01
   1_xyz:   8.777  0.071  0.270 83.848  0.035  2.349   6.1280e-02
   1_adp:   8.777  0.071  0.270 83.848  0.035  2.349   6.1280e-02
   1_occ:   8.777  0.071  0.270 83.848  0.035  2.349   6.1280e-02
   2_bss:   8.777  0.071  0.270 83.848  0.035  2.349   6.1280e-02
   2_xyz:   7.706  0.038  0.225 82.664  0.038  2.336   4.6911e-02
   2_adp:   7.706  0.038  0.225 82.664  0.038  2.336   4.6911e-02
   2_occ:   7.706  0.038  0.225 82.664  0.038  2.336   4.6911e-02
   3_bss:   7.706  0.038  0.225 82.664  0.038  2.336   4.6911e-02
   3_xyz:   7.785  0.038  0.235 83.597  0.037  2.293   4.5791e-02
   3_adp:   7.785  0.038  0.235 83.597  0.037  2.293   4.5791e-02
   3_occ:   7.785  0.038  0.235 83.597  0.037  2.293   4.5791e-02
   4_bss:   7.785  0.038  0.235 83.597  0.037  2.293   4.5791e-02
   4_xyz:   7.460  0.036  0.215 83.665  0.035  2.377   3.2444e-02
   4_adp:   7.460  0.036  0.215 83.665  0.035  2.377   3.2444e-02
   4_occ:   7.460  0.036  0.215 83.665  0.035  2.377   3.2444e-02
   5_bss:   7.460  0.036  0.215 83.665  0.035  2.377   3.2444e-02
   5_xyz:   7.228  0.045  0.247 83.661  0.038  2.276   5.3654e-02
   5_adp:   7.228  0.045  0.247 83.661  0.038  2.276   5.3654e-02
   5_occ:   7.228  0.045  0.247 83.661  0.038  2.276   5.3654e-02
   5_bss:   7.228  0.045  0.247 83.661  0.038  2.276   5.3654e-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:  69.02   0.00  16.53  69.02   0.00  12.68  62.81   5.78  37.50
   1_occ:  69.02   0.00  16.53  69.02   0.00  12.68  62.81   5.78  37.50
   2_bss:  69.02   0.00  16.53  69.02   0.00  12.68  62.81   5.78  37.50
   2_xyz:  69.02   0.00  16.53  69.02   0.00  12.68  62.81   5.78  37.50
   2_adp:  72.33   1.48  17.05  72.33   1.48  13.02  72.09   4.52  38.96
   2_occ:  72.33   1.48  17.05  72.33   1.48  13.02  72.09   4.52  38.96
   3_bss:  72.33   1.48  17.05  72.33   1.48  13.02  72.09   4.52  38.96
   3_xyz:  72.33   1.48  17.05  72.33   1.48  13.02  72.09   4.52  38.96
   3_adp:  76.61   1.31  16.97  76.61   1.31  12.98  73.23   3.42  38.72
   3_occ:  76.61   1.31  16.97  76.61   1.31  12.98  73.23   3.42  38.72
   4_bss:  76.61   1.31  16.97  76.61   1.31  12.98  73.23   3.42  38.72
   4_xyz:  76.61   1.31  16.97  76.61   1.31  12.98  73.23   3.42  38.72
   4_adp:  82.18   0.76  16.96  82.18   0.76  12.92  74.98   5.05  39.01
   4_occ:  82.18   0.76  16.96  82.18   0.76  12.92  74.98   5.05  39.01
   5_bss:  82.18   0.76  16.96  82.18   0.76  12.92  74.98   5.05  39.01
   5_xyz:  82.18   0.76  16.96  82.18   0.76  12.92  74.98   5.05  39.01
   5_adp:  83.36   0.78  16.80  83.36   0.78  12.75  75.28   6.27  38.87
   5_occ:  83.36   0.78  16.80  83.36   0.78  12.75  75.28   6.27  38.87
   5_bss:  83.33   0.75  16.78  83.33   0.75  12.72  75.25   6.24  38.85
------------------------------------------------------------------------
 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:    1.151    0.019    0.292
   1_adp:    1.151    0.019    0.292
   1_occ:    1.151    0.019    0.292
   2_bss:    1.151    0.019    0.292
   2_xyz:    0.795    0.025    0.353
   2_adp:    0.795    0.025    0.353
   2_occ:    0.795    0.025    0.353
   3_bss:    0.795    0.025    0.353
   3_xyz:    0.775    0.028    0.378
   3_adp:    0.775    0.028    0.378
   3_occ:    0.775    0.028    0.378
   4_bss:    0.775    0.028    0.378
   4_xyz:    0.856    0.043    0.385
   4_adp:    0.856    0.043    0.385
   4_occ:    0.856    0.043    0.385
   5_bss:    0.856    0.043    0.385
   5_xyz:    0.930    0.028    0.391
   5_adp:    0.930    0.028    0.391
   5_occ:    0.930    0.028    0.391
   5_bss:    0.930    0.028    0.391
------------------------------------------------------------------------

CPU time actual refinement: 277.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/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_1015/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1015/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 277.52 
  Macro-tasks:
    bulk solvent and scale       = 31.30  
    individual site refinement   = 114.13 
    weights calculation          = 24.52  
    collect and process          = 5.52   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 175.55 
  Micro-tasks:
    mask                            = 1.02   
    f_calc                          = 88.64  
    alpha_beta                      = 6.69   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 97.29  
    fmodel                         = 5.51   
    r_factors                      = 0.18   
    phase_errors                   = 9.41   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 209.96 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.903 micro seconds
Total CPU time: 4.82 minutes
from_scatterers_fft:    669 calls, 88.35 s
gradients_fft:          614 calls, 85.30 s

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

# Date 2008-01-16 Time 06:11:39 PST -0800 (1200492699.64 s)
Start R-work = 0.3236, R-free = 0.3274 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.3106, R-free = 0.3154
Final R-work = 0.1061, R-free = 0.1567