# Date 2008-01-16 Time 06:06:42 PST -0800 (1200492402.43 s)
#phil __OFF__

Command line arguments: "../1012.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1110
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1012

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

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95125
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927905

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9513

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, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95125
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927905

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1767 [2205/2235]  1988   217   9.8%
  bin  2:  4.1767 -  3.3270 [2121/2140]  1906   215  10.1%
  bin  3:  3.3270 -  2.9099 [2096/2116]  1884   212  10.1%
  bin  4:  2.9099 -  2.6454 [2081/2106]  1880   201   9.7%
  bin  5:  2.6454 -  2.4566 [2056/2075]  1845   211  10.3%
  bin  6:  2.4566 -  2.3123 [2056/2103]  1855   201   9.8%
  bin  7:  2.3123 -  2.1969 [2046/2078]  1834   212  10.4%
  bin  8:  2.1969 -  2.1015 [2015/2052]  1819   196   9.7%
  bin  9:  2.1015 -  2.0208 [2039/2084]  1833   206  10.1%
  bin 10:  2.0208 -  1.9513 [ 874/2060]   786    88  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 24
        2.25 -     2.91: 1495
        2.91 -     3.58: 4521
        3.58 -     4.24: 9270
        4.24 -     4.90: 13267
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.589 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.688 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.757 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28572 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_1012/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/model_refine_001.geo

CPU time processing inputs: 8.97


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


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4144   r_free= 0.4183   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.214518                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.3333 0.3358      6.4711       6.484|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.3447 0.3187      6.6781       6.668|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.3825 0.3829      6.5614      6.6475|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.3900 0.4014      6.4227      6.4256|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.4308 0.4236      6.2897      6.2858|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.4574 0.4517      6.2156      6.1862|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.4426 0.4230      6.1784      6.1299|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.4567 0.4402      6.1076      6.1138|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.4548 0.4554      6.0766      6.0185|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.4693 0.5177      6.0397      6.1132|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.4629 0.5454      5.9971      6.0361|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.4676 0.5108      5.9155      5.9481|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.4880 0.4819      5.8536      5.8219|
| 14:  1.9999 -  1.9513 0.29    397   34 0.5279 0.4924      5.7997      5.7422|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.75  29.64   0.85     0.78      53465.41|
|  2:  4.6592 -  3.7165  1386   149  0.77  29.31   0.94     0.87      77173.03|
|  3:  3.7165 -  3.2521  1348   154  0.68  37.20   0.95     0.86      84591.02|
|  4:  3.2521 -  2.9572  1358   151  0.60  43.66   0.97     0.81      79318.61|
|  5:  2.9572 -  2.7466  1327   144  0.52  50.02   0.92     0.72      64916.73|
|  6:  2.7466 -  2.5855  1326   151  0.51  51.47   0.92     0.71      56693.49|
|  7:  2.5855 -  2.4566  1329   146  0.53  49.77   0.96     0.70      48782.59|
|  8:  2.4566 -  2.3501  1306   148  0.52  50.90   0.94     0.74      44867.87|
|  9:  2.3501 -  2.2600  1322   146  0.50  51.97   0.98     0.72      41620.62|
| 10:  2.2600 -  2.1822  1307   149  0.45  56.44   0.98     0.66      43503.13|
| 11:  2.1822 -  2.1142  1339   143  0.40  60.11   1.00     0.60      42939.51|
| 12:  2.1142 -  2.0539  1297   143  0.37  62.52   0.99     0.58      40154.75|
| 13:  2.0539 -  1.9999  1159   140  0.38  61.65   0.97     0.58      33698.07|
| 14:  1.9999 -  1.9513   397    34  0.37  62.46   0.93     0.56      28306.88|
|alpha:            min =        0.56 max =            0.87 mean =         0.72|
|beta:             min =    28306.88 max =        84591.02 mean =     54543.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.98 mean =        48.78|
|phase err.(test): min =        0.00 max =           89.98 mean =        49.03|
|-----------------------------------------------------------------------------|

============================== 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 = 6.550965              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.602024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.726   (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 |  1.589 -  1.920:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.920 -  2.251:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.251 -  2.582:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.582 -  2.914:     1462 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.914 -  3.245:     1922 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.245 -  3.576:     2599 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.576 -  3.907:     4739 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.907 -  4.238:     4531 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.238 -  4.569:     6054 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7213 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.589 |       0.406 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4144   r_free= 0.4183   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.214518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4030   r_free= 0.4074   ksol= 0.31   Bsol= 30.14   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-2.69,2.88,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.207504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.077603              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.295   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.735354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.565   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4030      final r-factor (work) = 0.2907          |
| start r-factor (free) = 0.4074      final r-factor (free) = 0.3226          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9232 = 5.08 * 0.50 * 6.2024 + 1.00 * 0.1766                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4413 = 5.08 * 0.50 * 6.0453 + 1.00 * 0.0934                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2907      final r-factor (work) = 0.2663          |
| start r-factor (free) = 0.3226      final r-factor (free) = 0.3291          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4518 = 0.74 * 1.00 * 6.0453 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3657 = 0.74 * 1.00 * 5.9002 + 1.00 * 0.0270                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 46     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.97   18.01    None  None   None       |
|    all(noH): 2823   0      0.00    85.97   18.01    None  None   None       |
|    Sol.    : 438    0      0.00    85.20   40.15    None  None   None       |
|    Mac.    : 2385   0      0.00    85.97   13.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.597:  764   |   5:    42.984 -  51.580:   96        |
|      1:     8.597 -  17.194: 1054   |   6:    51.580 -  60.177:   71        |
|      2:    17.194 -  25.790:  423   |   7:    60.177 -  68.774:   38        |
|      3:    25.790 -  34.387:  197   |   8:    68.774 -  77.371:   22        |
|      4:    34.387 -  42.984:  155   |   9:    77.371 -  85.967:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2663 r_free = 0.3291             target_work(ml) = 5.907         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2658 r_free = 0.3292             target_work(ml) = 5.905         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2658   r_free= 0.3292   ksol= 0.31   Bsol= 30.14   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-2.69,2.88,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.905306                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2652   r_free= 0.3278   ksol= 0.34   Bsol= 52.31   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-2.19,0.66,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.903183                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.644386              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.092   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2652      final r-factor (work) = 0.1944          |
| start r-factor (free) = 0.3278      final r-factor (free) = 0.2517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8449 = 3.64 * 0.50 * 5.9003 + 1.00 * 0.0934                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6189 = 3.64 * 0.50 * 5.7888 + 1.00 * 0.0705                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1944      final r-factor (work) = 0.1781          |
| start r-factor (free) = 0.2517      final r-factor (free) = 0.2371          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6959 = 0.64 * 1.00 * 5.7888 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5704 = 0.64 * 1.00 * 5.5980 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.83   18.00    None  None   None       |
|    all(noH): 2823   0      0.00    88.83   18.00    None  None   None       |
|    Sol.    : 438    0      4.18    88.83   42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    85.45   13.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.883:  799   |   5:    44.414 -  53.297:  117        |
|      1:     8.883 -  17.766: 1176   |   6:    53.297 -  62.180:   73        |
|      2:    17.766 -  26.648:  315   |   7:    62.180 -  71.062:   40        |
|      3:    26.648 -  35.531:  148   |   8:    71.062 -  79.945:   22        |
|      4:    35.531 -  44.414:  126   |   9:    79.945 -  88.828:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1781 r_free = 0.2371             target_work(ml) = 5.568         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1780 r_free = 0.2372             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1780   r_free= 0.2372   ksol= 0.34   Bsol= 52.31   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-2.19,0.66,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.567485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1774   r_free= 0.2356   ksol= 0.33   Bsol= 46.86   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-2.32,-0.83,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.562504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.790653              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.643   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.904  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1774      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2356      final r-factor (free) = 0.1868          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6814 = 3.79 * 0.50 * 5.5985 + 1.00 * 0.0705                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4272 = 3.79 * 0.50 * 5.4704 + 1.00 * 0.0590                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.1868      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7016 = 0.31 * 1.00 * 5.4704 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6492 = 0.31 * 1.00 * 5.3080 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    86.82   17.49    None  None   None       |
|    all(noH): 2823   0      1.33    86.82   17.49    None  None   None       |
|    Sol.    : 438    0      4.63    86.23   41.65    None  None   None       |
|    Mac.    : 2385   0      1.33    86.82   13.05    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:     1.331 -   9.880: 1004   |   5:    44.074 -  52.623:  107        |
|      1:     9.880 -  18.429: 1092   |   6:    52.623 -  61.172:   69        |
|      2:    18.429 -  26.977:  246   |   7:    61.172 -  69.720:   38        |
|      3:    26.977 -  35.526:  119   |   8:    69.720 -  78.269:   22        |
|      4:    35.526 -  44.074:  120   |   9:    78.269 -  86.818:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1305 r_free = 0.1757             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1304 r_free = 0.1754             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1754   ksol= 0.33   Bsol= 46.86   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-2.32,-0.83,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.269205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1306   r_free= 0.1753   ksol= 0.33   Bsol= 46.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.52,-1.65,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.269116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.233175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.400  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437592              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.598  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9890 = 2.23 * 0.50 * 5.3109 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8956 = 2.23 * 0.50 * 5.2285 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2968 = 0.44 * 1.00 * 5.2285 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2745 = 0.44 * 1.00 * 5.1774 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    93.53   17.29    None  None   None       |
|    all(noH): 2823   0      1.48    93.53   17.29    None  None   None       |
|    Sol.    : 438    0      5.43    83.67   41.05    None  None   None       |
|    Mac.    : 2385   0      1.48    93.53   12.93    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:     1.479 -  10.684: 1197   |   5:    47.507 -  56.712:  106        |
|      1:    10.684 -  19.890:  987   |   6:    56.712 -  65.918:   46        |
|      2:    19.890 -  29.096:  203   |   7:    65.918 -  75.124:   28        |
|      3:    29.096 -  38.301:  130   |   8:    75.124 -  84.329:    9        |
|      4:    38.301 -  47.507:  113   |   9:    84.329 -  93.535:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1603             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1601             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1601   ksol= 0.33   Bsol= 46.86   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.52,-1.65,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1600   ksol= 0.32   Bsol= 44.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.44,-1.83,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.934846              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0658 = 1.93 * 0.50 * 5.1769 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0435 = 1.93 * 0.50 * 5.1552 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0831 = 0.21 * 1.00 * 5.1552 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0805 = 0.21 * 1.00 * 5.1482 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.83    93.83   16.85    None  None   None       |
|    all(noH): 2823   0      1.83    93.83   16.85    None  None   None       |
|    Sol.    : 438    0      6.30    79.93   39.03    None  None   None       |
|    Mac.    : 2385   0      1.83    93.83   12.78    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:     1.832 -  11.032: 1275   |   5:    47.830 -  57.030:   89        |
|      1:    11.032 -  20.231:  932   |   6:    57.030 -  66.229:   37        |
|      2:    20.231 -  29.431:  200   |   7:    66.229 -  75.429:   20        |
|      3:    29.431 -  38.630:  145   |   8:    75.429 -  84.628:    4        |
|      4:    38.630 -  47.830:  117   |   9:    84.628 -  93.828:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1562             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1561             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1561   ksol= 0.32   Bsol= 44.91   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.44,-1.83,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145008                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.0985 0.1319      5.3838       5.575|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.0862 0.1066      5.4412      5.6246|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.1066 0.1606      5.4668      5.8486|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.1251 0.1564       5.462      5.5904|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.1304 0.1691      5.3038       5.492|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.1242 0.1751      5.1921      5.4086|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.1237 0.1723      5.1532      5.4002|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.1134 0.1636      5.0175      5.2294|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.1173 0.1822       4.998      5.2951|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.1140 0.1549      4.9427      5.1764|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.1136 0.1855      4.9406      5.2856|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.1142 0.1720      4.8801      5.0869|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.1150 0.1656      4.7712      5.0115|
| 14:  1.9999 -  1.9513 0.29    397   34 0.1001 0.1497      4.5796      4.8478|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.94   8.85   0.98     0.95       6963.32|
|  2:  4.6592 -  3.7165  1386   149  0.95   7.90   1.02     1.01       8951.62|
|  3:  3.7165 -  3.2521  1348   154  0.93  11.49   1.03     1.03      10283.26|
|  4:  3.2521 -  2.9572  1358   151  0.91  14.24   1.00     0.98      10313.71|
|  5:  2.9572 -  2.7466  1327   144  0.90  15.35   0.99     0.97       7816.46|
|  6:  2.7466 -  2.5855  1326   151  0.90  15.81   0.99     0.96       6689.65|
|  7:  2.5855 -  2.4566  1329   146  0.91  14.73   0.99     0.98       5926.48|
|  8:  2.4566 -  2.3501  1306   148  0.91  14.89   0.99     0.96       4774.85|
|  9:  2.3501 -  2.2600  1322   146  0.91  15.19   1.01     0.98       4589.95|
| 10:  2.2600 -  2.1822  1307   149  0.91  14.63   0.99     0.96       4086.07|
| 11:  2.1822 -  2.1142  1339   143  0.90  16.52   1.00     0.97       4474.96|
| 12:  2.1142 -  2.0539  1297   143  0.90  16.38   1.00     1.00       4091.28|
| 13:  2.0539 -  1.9999  1159   140  0.91  15.43   1.00     0.99       3145.68|
| 14:  1.9999 -  1.9513   397    34  0.91  14.75   0.99     0.96       2163.48|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2163.48 max =        10313.71 mean =      6284.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1561   ksol= 0.32   Bsol= 44.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.28,-1.76,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1561   ksol= 0.32   Bsol= 44.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.28,-1.76,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145035                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.0985 0.1320      5.3841      5.5754|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.0862 0.1066      5.4411      5.6245|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.1066 0.1606      5.4667      5.8485|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.1251 0.1564       5.462      5.5905|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.1303 0.1691      5.3039      5.4919|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.1242 0.1752      5.1922      5.4092|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.1237 0.1723      5.1534      5.4004|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.1133 0.1636      5.0177      5.2295|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.1173 0.1822      4.9981      5.2953|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.1140 0.1548      4.9428      5.1756|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.1136 0.1855      4.9404      5.2857|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.1142 0.1720      4.8798      5.0864|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.1150 0.1655      4.7712      5.0113|
| 14:  1.9999 -  1.9513 0.29    397   34 0.1002 0.1503        4.58      4.8506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.94   8.85   0.98     0.95       6967.28|
|  2:  4.6592 -  3.7165  1386   149  0.95   7.90   1.02     1.01       8952.24|
|  3:  3.7165 -  3.2521  1348   154  0.93  11.49   1.03     1.03      10279.76|
|  4:  3.2521 -  2.9572  1358   151  0.91  14.23   1.01     0.98      10312.25|
|  5:  2.9572 -  2.7466  1327   144  0.90  15.35   0.99     0.98       7819.22|
|  6:  2.7466 -  2.5855  1326   151  0.90  15.81   0.99     0.97       6692.79|
|  7:  2.5855 -  2.4566  1329   146  0.91  14.74   1.00     0.98       5930.13|
|  8:  2.4566 -  2.3501  1306   148  0.91  14.89   0.99     0.96       4778.26|
|  9:  2.3501 -  2.2600  1322   146  0.91  15.19   1.01     0.99       4590.12|
| 10:  2.2600 -  2.1822  1307   149  0.91  14.64   0.99     0.96       4087.16|
| 11:  2.1822 -  2.1142  1339   143  0.90  16.51   1.00     0.97       4471.98|
| 12:  2.1142 -  2.0539  1297   143  0.90  16.37   1.01     1.00       4088.71|
| 13:  2.0539 -  1.9999  1159   140  0.91  15.43   1.00     0.99       3146.48|
| 14:  1.9999 -  1.9513   397    34  0.91  14.75   0.99     0.96       2166.76|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2166.76 max =        10312.25 mean =      6285.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    93.76   16.78    None  None   None       |
|    all(noH): 2823   0      1.77    93.76   16.78    None  None   None       |
|    Sol.    : 438    0      6.23    79.86   38.96    None  None   None       |
|    Mac.    : 2385   0      1.77    93.76   12.71    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:     1.766 -  10.966: 1275   |   5:    47.764 -  56.964:   89        |
|      1:    10.966 -  20.165:  932   |   6:    56.964 -  66.163:   37        |
|      2:    20.165 -  29.365:  200   |   7:    66.163 -  75.363:   20        |
|      3:    29.365 -  38.565:  145   |   8:    75.363 -  84.563:    4        |
|      4:    38.565 -  47.764:  117   |   9:    84.563 -  93.762:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.661
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.723 - 5.661

peak=    5.852 closest distance to " NH2 ARG A  56 " =    2.167
peak=    5.457 closest distance to " CG  PRO A  54 " =    1.230
peak=    5.387 closest distance to " CB  GLN A 223 " =    1.473
peak=    5.225 closest distance to " CB  SER A  63 " =    1.290
peak=    5.149 closest distance to " NE2 GLN A  11 " =    1.154
peak=    4.977 closest distance to " O   HOH Z 126 " =    1.919
peak=    4.939 closest distance to " CB  ARG A 275 " =    0.926
peak=    4.801 closest distance to " CG  PRO A 198 " =    1.342
peak=    4.771 closest distance to " CG  PRO A  90 " =    1.091
peak=    4.768 closest distance to " O   HOH Z 193 " =    1.928
peak=    4.765 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.729 closest distance to " O   HOH Z 144 " =    1.649
peak=    4.700 closest distance to " O   HOH Z 232 " =    2.223
peak=    4.696 closest distance to " O   HOH Z 278 " =    1.065
peak=    4.660 closest distance to " CB  PRO A  54 " =    0.907
peak=    4.637 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.607 closest distance to " O   HOH Z 108 " =    1.743
peak=    4.601 closest distance to " OD1 ASN A  69 " =    2.547
peak=    4.580 closest distance to " O   HOH Z 260 " =    1.243
peak=    4.515 closest distance to " OD2 ASP A 286 " =    2.821
peak=    4.485 closest distance to " CB  GLU A 128 " =    1.080
peak=    4.479 closest distance to " O   HOH Z  15 " =    2.151
peak=    4.464 closest distance to " C   PRO A 198 " =    1.545
peak=    4.460 closest distance to " CB  GLU A 152 " =    1.200
peak=    4.422 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.416 closest distance to " O   HOH Z 368 " =    1.931
peak=    4.400 closest distance to " O   HOH Z 236 " =    1.951
peak=    4.400 closest distance to " CA  ALA A  21 " =    1.115
peak=    4.364 closest distance to " CB  SER A   3 " =    1.425
peak=    4.357 closest distance to " CA  TYR A  30 " =    1.033
peak=    4.320 closest distance to " O   HOH Z 369 " =    1.979
peak=    4.278 closest distance to " O   HOH Z  78 " =    1.922
peak=    4.260 closest distance to " O   HOH Z 234 " =    3.749
peak=    4.193 closest distance to " CB  LEU A 228 " =    1.089
peak=    4.192 closest distance to " ND2 ASN A 187 " =    1.615
peak=    4.180 closest distance to " O   HOH Z 134 " =    1.503
peak=    4.163 closest distance to " O   HOH Z 427 " =    2.840
peak=    4.120 closest distance to " O   HOH Z  48 " =    1.538
peak=    4.097 closest distance to " CA  THR A 264 " =    0.849
peak=    4.097 closest distance to " O   HOH Z 295 " =    1.581
peak=    4.092 closest distance to " O   HOH Z 282 " =    1.653
peak=    4.090 closest distance to " CB  TRP A 266 " =    0.985
peak=    4.078 closest distance to " O   HOH Z 298 " =    1.828
peak=    4.057 closest distance to " O   HOH Z 207 " =    1.765
peak=    4.030 closest distance to " CB  TRP A 179 " =    1.379
peak=    4.019 closest distance to " O   HOH Z 316 " =    3.067
peak=    4.007 closest distance to " O   HOH Z  21 " =    1.650
peak=    3.959 closest distance to " O   HOH Z 135 " =    1.754
peak=    3.953 closest distance to " NH2BARG A 102 " =    1.021
peak=    3.938 closest distance to " O   HOH Z  10 " =    1.889
peak=    3.933 closest distance to " CD BLYS A 290 " =    1.145
peak=    3.932 closest distance to " CA  THR A 221 " =    0.947
peak=    3.931 closest distance to " O   HOH Z 126 " =    1.543
peak=    3.930 closest distance to " O   HOH Z 425 " =    1.421
peak=    3.922 closest distance to " O   HOH Z  61 " =    1.613
peak=    3.919 closest distance to " O   HOH Z 344 " =    3.050
peak=    3.919 closest distance to " O   HOH Z 214 " =    1.112
peak=    3.909 closest distance to " O   SER A  87 " =    2.226
peak=    3.909 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.900 closest distance to " O   HOH Z 389 " =    1.926
peak=    3.899 closest distance to " CA  GLY A 241 " =    3.734
peak=    3.897 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.891 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.891 closest distance to " CG  PRO A 243 " =    1.102
peak=    3.873 closest distance to " O   HOH Z 193 " =    2.067
peak=    3.873 closest distance to " O   HOH Z  59 " =    1.991
peak=    3.852 closest distance to " O   HOH Z 128 " =    2.106
peak=    3.849 closest distance to " O   HOH Z 132 " =    1.068
peak=    3.849 closest distance to " CB  ARG A 139 " =    0.944
peak=    3.842 closest distance to " NH2 ARG A 156 " =    1.249
peak=    3.839 closest distance to " O   HOH Z 371 " =    3.212
peak=    3.829 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.828 closest distance to " CA  ASN A 215 " =    1.290
peak=    3.826 closest distance to " O   HOH Z 227 " =    1.682
peak=    3.793 closest distance to " CD1 LEU A 300 " =    1.265
peak=    3.790 closest distance to " O   HOH Z 133 " =    1.664
peak=    3.781 closest distance to " O   HOH Z 281 " =    4.301
peak=    3.780 closest distance to " O   HOH Z  68 " =    1.584
peak=    3.779 closest distance to " O   HOH Z 203 " =    1.937
peak=    3.773 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.770 closest distance to " CB  VAL A 202 " =    1.639
peak=    3.767 closest distance to " ND1 HIS A  86 " =    1.677
peak=    3.766 closest distance to " O   HOH Z 132 " =    2.254
peak=    3.766 closest distance to " CD  LYS A 166 " =    1.308
peak=    3.763 closest distance to " O   HOH Z 247 " =    1.304
peak=    3.761 closest distance to " O   HOH Z  88 " =    3.545
peak=    3.752 closest distance to " CB  SER A 216 " =    0.761
peak=    3.751 closest distance to " O   MET A 105 " =    1.669
peak=    3.750 closest distance to " O   HOH Z  20 " =    1.763
peak=    3.740 closest distance to " O   HOH Z 180 " =    2.146
peak=    3.729 closest distance to " O   HOH Z 189 " =    2.116
peak=    3.726 closest distance to " CB  ASN A 187 " =    1.209
peak=    3.726 closest distance to " O   HOH Z   6 " =    2.105
peak=    3.714 closest distance to " CB  GLU A 152 " =    1.478
peak=    3.685 closest distance to " CD  ARG A 159 " =    0.832
peak=    3.679 closest distance to " O   HOH Z 303 " =    2.106
peak=    3.666 closest distance to " NH1AARG A 145 " =    1.043
peak=    3.664 closest distance to " O   HOH Z 263 " =    2.230
peak=    3.644 closest distance to " NE AARG A 275 " =    1.496
peak=    3.640 closest distance to " O   HOH Z 273 " =    2.892
peak=    3.631 closest distance to " O   HOH Z 346 " =    1.674
peak=    3.630 closest distance to " CG2 THR A 221 " =    1.064
peak=    3.629 closest distance to " CB  LEU A 143 " =    1.093
peak=    3.621 closest distance to " O   HOH Z 163 " =    1.966
peak=    3.619 closest distance to " NH2AARG A 190 " =    1.400
peak=    3.618 closest distance to " O   HOH Z 284 " =    2.969
peak=    3.614 closest distance to " N   ARG A 156 " =    1.354
peak=    3.607 closest distance to " O   HOH Z   3 " =    1.754
peak=    3.606 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.599 closest distance to " O   HOH Z 214 " =    2.353
peak=    3.598 closest distance to " CB  MET A  47 " =    1.038
peak=    3.596 closest distance to " OG BSER A 164 " =    2.404
peak=    3.595 closest distance to " CG  PRO A 280 " =    0.725
peak=    3.593 closest distance to " CA  MET A  40 " =    1.086
peak=    3.591 closest distance to " N   ASN A  39 " =    1.319
peak=    3.585 closest distance to " O   HOH Z  93 " =    2.461
peak=    3.573 closest distance to " CD2 LEU A 255 " =    1.433
peak=    3.573 closest distance to " O   HOH Z 374 " =    2.634
peak=    3.572 closest distance to " NH1BARG A 145 " =    0.920
peak=    3.559 closest distance to " O   ALA A 165 " =    1.358
peak=    3.550 closest distance to " O   HOH Z  40 " =    1.976
peak=    3.549 closest distance to " N   ASN A 127 " =    1.235
peak=    3.549 closest distance to " O   HOH Z  49 " =    2.096
peak=    3.548 closest distance to " O   HOH Z  66 " =    2.048
peak=    3.546 closest distance to " O   HOH Z  54 " =    1.600
peak=    3.542 closest distance to " OD1BASN A 224 " =    2.278
peak=    3.540 closest distance to " O   HOH Z 183 " =    1.525
peak=    3.536 closest distance to " O   HOH Z 426 " =    1.488
peak=    3.529 closest distance to " O   HOH Z 334 " =    1.432
peak=    3.529 closest distance to " O   HOH Z 133 " =    2.287
peak=    3.528 closest distance to " OG  SER A  22 " =    2.807
peak=    3.528 closest distance to " O   HOH Z 272 " =    1.914
peak=    3.525 closest distance to " CA  LEU A 282 " =    1.135
peak=    3.522 closest distance to " O   HOH Z 175 " =    3.581
peak=    3.521 closest distance to " OD1 ASN A 217 " =    1.654
peak=    3.520 closest distance to " O   GLY A  57 " =    2.523
peak=    3.518 closest distance to " O   ALA A   1 " =    1.558
peak=    3.516 closest distance to " O   HOH Z 313 " =    1.711
peak=    3.516 closest distance to " O   HOH Z  73 " =    1.535
peak=    3.508 closest distance to " O   HOH Z 437 " =    1.735
peak=    3.505 closest distance to " O   HOH Z 280 " =    1.753
peak=    3.498 closest distance to " CB  ARG A  79 " =    1.446
peak=    3.491 closest distance to " CG  MET A 113 " =    1.270
peak=    3.488 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.483 closest distance to " O   HOH Z 410 " =    1.743
peak=    3.481 closest distance to " CD  LYS A 119 " =    1.181
peak=    3.477 closest distance to " O   HOH Z 124 " =    1.366
peak=    3.475 closest distance to " O   HOH Z 261 " =    2.299
peak=    3.473 closest distance to " O   HOH Z 106 " =    2.256
peak=    3.469 closest distance to " CA  ALA A  51 " =    1.052
peak=    3.469 closest distance to " CB  ILE A 234 " =    0.958
peak=    3.468 closest distance to " NZ  LYS A 117 " =    3.362
peak=    3.467 closest distance to " CA  ASP A 191 " =    0.761
peak=    3.466 closest distance to " CA  TYR A 186 " =    1.450
peak=    3.464 closest distance to " CA  SER A  87 " =    0.926
peak=    3.463 closest distance to " O   HOH Z 188 " =    2.033
peak=    3.456 closest distance to " CB  PRO A 198 " =    0.917
peak=    3.453 closest distance to " CB  ALA A 248 " =    0.942
peak=    3.453 closest distance to " O   HOH Z  97 " =    1.938
peak=    3.443 closest distance to " CB  MET A  40 " =    0.828
peak=    3.427 closest distance to " O   HOH Z 409 " =    2.657
peak=    3.426 closest distance to " SD AMET A  47 " =    1.193
peak=    3.423 closest distance to " CG1BVAL A  72 " =    1.568
peak=    3.414 closest distance to " N   PHE A 130 " =    1.303
peak=    3.414 closest distance to " O   HOH Z 359 " =    3.866
peak=    3.412 closest distance to " O   HOH Z  66 " =    2.062
peak=    3.411 closest distance to " O   HOH Z 108 " =    2.012
peak=    3.408 closest distance to " O   THR A 220 " =    1.450
peak=    3.408 closest distance to " O   HOH Z 345 " =    1.731
peak=    3.402 closest distance to " O   HOH Z 271 " =    2.256
peak=    3.397 closest distance to " O   HOH Z 353 " =    2.575
peak=    3.394 closest distance to " CG2 VAL A 257 " =    0.960
peak=    3.383 closest distance to " O   HOH Z 276 " =    1.233
peak=    3.382 closest distance to " C   TYR A 214 " =    1.570
peak=    3.382 closest distance to " O   HOH Z 172 " =    3.582
peak=    3.382 closest distance to " O   HOH Z 250 " =    1.418
peak=    3.369 closest distance to " CB  ALA A 291 " =    1.446
peak=    3.368 closest distance to " O   HOH Z 291 " =    1.818
peak=    3.366 closest distance to " CB  THR A 157 " =    1.091
peak=    3.365 closest distance to " CG  GLN A  88 " =    0.996
peak=    3.362 closest distance to " CG  GLN A  55 " =    1.973
peak=    3.362 closest distance to " O   HOH Z 211 " =    2.127
peak=    3.358 closest distance to " O   HOH Z 407 " =    2.253
peak=    3.358 closest distance to " O   HOH Z 227 " =    2.140
peak=    3.356 closest distance to " OD1 ASP A 231 " =    1.834
peak=    3.349 closest distance to " O   HOH Z  44 " =    1.748
peak=    3.345 closest distance to " O   HOH Z  43 " =    1.907
peak=    3.335 closest distance to " O   HOH Z   1 " =    1.798
peak=    3.335 closest distance to " ND1 HIS A  81 " =    1.512
peak=    3.331 closest distance to " O   HOH Z 214 " =    1.805
peak=    3.326 closest distance to " O   HOH Z  40 " =    1.661
peak=    3.324 closest distance to " O   HOH Z 163 " =    1.848
peak=    3.320 closest distance to " CA  VAL A  41 " =    0.956
peak=    3.317 closest distance to " O   HOH Z 329 " =    3.466
peak=    3.317 closest distance to " O   HOH Z 337 " =    3.734
peak=    3.316 closest distance to " CB  ARG A 102 " =    0.723
peak=    3.314 closest distance to " O   HOH Z  58 " =    1.679
peak=    3.306 closest distance to " O   HOH Z 139 " =    3.090
peak=    3.306 closest distance to " CA  LYS A 290 " =    1.369
peak=    3.303 closest distance to " CG1 ILE A 151 " =    0.868
peak=    3.302 closest distance to " O   HOH Z  44 " =    3.341
peak=    3.299 closest distance to " O   HOH Z  64 " =    2.141
peak=    3.297 closest distance to " O   HOH Z 147 " =    1.650
peak=    3.296 closest distance to " O   HOH Z 158 " =    2.856
peak=    3.294 closest distance to " O   HOH Z 287 " =    1.824
peak=    3.294 closest distance to " O   HOH Z 258 " =    1.826
peak=    3.290 closest distance to " CZ  PHE A 192 " =    0.886
peak=    3.288 closest distance to " O   HOH Z   1 " =    1.815
peak=    3.288 closest distance to " NH2 ARG A 219 " =    1.791
peak=    3.285 closest distance to " CZ  PHE A 208 " =    1.178
peak=    3.283 closest distance to " O   HOH Z 106 " =    2.296
peak=    3.282 closest distance to " CB  ARG A 190 " =    1.720
peak=    3.281 closest distance to " O   HOH Z  61 " =    1.637
peak=    3.279 closest distance to " O   HOH Z 234 " =    1.775
peak=    3.275 closest distance to " CB  TYR A  30 " =    1.433
peak=    3.274 closest distance to " O   HOH Z 286 " =    2.205
peak=    3.273 closest distance to " O   HOH Z 173 " =    1.844
peak=    3.267 closest distance to " CG2 THR A 220 " =    1.147
peak=    3.266 closest distance to " CG  GLN A  58 " =    2.550
peak=    3.265 closest distance to " CB  TRP A 179 " =    1.710
peak=    3.262 closest distance to " O   HOH Z 236 " =    1.553
peak=    3.261 closest distance to " CA  ALA A 158 " =    1.140
peak=    3.256 closest distance to " O   HOH Z 388 " =    1.984
peak=    3.255 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.253 closest distance to " O   HOH Z 287 " =    2.144
peak=    3.252 closest distance to " CB  PHE A 283 " =    0.781
peak=    3.252 closest distance to " CE1 TYR A 186 " =    1.241
peak=    3.243 closest distance to " CG BARG A 102 " =    1.930
peak=    3.242 closest distance to " CG  MET A 185 " =    1.111
peak=    3.241 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.241 closest distance to " O   HOH Z 411 " =    1.794
peak=    3.238 closest distance to " CG1 VAL A 202 " =    1.931
peak=    3.236 closest distance to " NZ  LYS A  76 " =    1.244
peak=    3.234 closest distance to " CA  VAL A 126 " =    0.964
peak=    3.232 closest distance to " CG  ARG A 159 " =    0.916
peak=    3.232 closest distance to " CD  ARG A  66 " =    2.383
peak=    3.231 closest distance to " CD2 HIS A  81 " =    1.232
peak=    3.227 closest distance to " OE1 GLN A  11 " =    2.050
peak=    3.227 closest distance to " CA  ALA A 154 " =    1.028
peak=    3.226 closest distance to " CA  ASP A 140 " =    1.140
peak=    3.225 closest distance to " O   HOH Z 151 " =    2.175
peak=    3.224 closest distance to " O   HOH Z 365 " =    2.854
peak=    3.223 closest distance to " CB  SER A  62 " =    1.336
peak=    3.222 closest distance to " CB  GLU A  46 " =    1.032
peak=    3.220 closest distance to " O   HOH Z 332 " =    1.584
peak=    3.217 closest distance to " O   HOH Z 357 " =    1.803
peak=    3.214 closest distance to " NZ ALYS A 290 " =    1.067
peak=    3.212 closest distance to " CA  LYS A 117 " =    1.214
peak=    3.209 closest distance to " O   GLY A 229 " =    1.704
peak=    3.191 closest distance to " CZ  PHE A 218 " =    0.991
peak=    3.190 closest distance to " CA  ILE A 234 " =    0.936
peak=    3.187 closest distance to " O   HOH Z  63 " =    2.308
peak=    3.187 closest distance to " O   HOH Z 128 " =    1.597
peak=    3.187 closest distance to " O   HOH Z 248 " =    1.857
peak=    3.182 closest distance to " CB  PHE A  16 " =    1.034
peak=    3.179 closest distance to " O   HOH Z 329 " =    2.675
peak=    3.179 closest distance to " CA  ARG A  56 " =    2.176
peak=    3.174 closest distance to " O   HOH Z 263 " =    1.632
peak=    3.166 closest distance to " N   GLN A 278 " =    0.906
peak=    3.164 closest distance to " NH1 ARG A 138 " =    1.134
peak=    3.163 closest distance to " O   HOH Z  43 " =    2.731
peak=    3.160 closest distance to " O   HOH Z 116 " =    1.732
peak=    3.160 closest distance to " OG1 THR A 294 " =    1.603
peak=    3.160 closest distance to " O   HOH Z 422 " =    2.739
peak=    3.157 closest distance to " O   HOH Z 334 " =    1.825
peak=    3.155 closest distance to " O   HOH Z   4 " =    1.969
peak=    3.153 closest distance to " O   HOH Z 387 " =    3.120
peak=    3.153 closest distance to " N   SER A  12 " =    1.640
peak=    3.152 closest distance to " CD BARG A 102 " =    1.262
peak=    3.152 closest distance to " CD  PRO A 243 " =    1.602
peak=    3.151 closest distance to " OE1 GLU A 277 " =    1.831
peak=    3.151 closest distance to " O   HOH Z 166 " =    3.635
peak=    3.150 closest distance to " O   HOH Z 194 " =    2.076
peak=    3.149 closest distance to " N   ASN A 252 " =    1.370
peak=    3.146 closest distance to " CD1 ILE A  33 " =    1.531
peak=    3.146 closest distance to " CB  ASP A 132 " =    4.010
peak=    3.144 closest distance to " CG2 ILE A 120 " =    1.295
peak=    3.143 closest distance to " NH2BARG A 145 " =    2.006
peak=    3.143 closest distance to " CD1 LEU A 228 " =    1.986
peak=    3.139 closest distance to " CG2 VAL A 174 " =    1.339
peak=    3.131 closest distance to " O   HOH Z 215 " =    1.586
peak=    3.129 closest distance to " NE2 GLN A  58 " =    5.661
peak=    3.128 closest distance to " O   HOH Z 112 " =    1.477
peak=    3.128 closest distance to " O   TRP A 274 " =    1.691
peak=    3.119 closest distance to " O   HOH Z  80 " =    1.585
peak=    3.116 closest distance to " CA  ALA A  43 " =    1.197
peak=    3.108 closest distance to " CB  TYR A 116 " =    0.920
peak=    3.107 closest distance to " OE1 GLU A 236 " =    1.504
peak=    3.107 closest distance to " OD1 ASP A 238 " =    1.028
peak=    3.106 closest distance to " CG  PRO A 213 " =    1.003
peak=    3.101 closest distance to " CB  ARG A 138 " =    0.992
peak=    3.095 closest distance to " CB  SER A 276 " =    1.109
peak=    3.093 closest distance to " C   ALA A 299 " =    0.984
peak=    3.086 closest distance to " N   SER A 135 " =    1.341
peak=    3.084 closest distance to " CG BARG A 275 " =    1.461
peak=    3.081 closest distance to " O   HOH Z 345 " =    3.392
peak=    3.075 closest distance to " CG  GLU A   2 " =    1.210
peak=    3.066 closest distance to " O   HOH Z 213 " =    1.551
peak=    3.064 closest distance to " NH1 ARG A  56 " =    0.989
peak=    3.049 closest distance to " O   HOH Z 115 " =    1.953
peak=    3.023 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.016 closest distance to " O   ALA A 158 " =    1.271
peak=    3.003 closest distance to " CB  HIS A 108 " =    1.056

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.488
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 202
   mapped sites are within: 0.790 - 5.488

peak=   -4.846 closest distance to " O   HOH Z 290 " =    0.977
peak=   -4.517 closest distance to " O   HOH Z 377 " =    1.648
peak=   -4.443 closest distance to " CB  PRO A 243 " =    2.593
peak=   -4.373 closest distance to " O   HOH Z 198 " =    2.291
peak=   -4.355 closest distance to " CG  LYS A 193 " =    2.439
peak=   -4.156 closest distance to " O   HOH Z 266 " =    4.271
peak=   -4.090 closest distance to " N   GLN A  58 " =    1.745
peak=   -4.084 closest distance to " CG  GLN A 223 " =    1.893
peak=   -4.069 closest distance to " SG  CYS A 254 " =    3.326
peak=   -4.023 closest distance to " O   PRO A 198 " =    1.250
peak=   -4.012 closest distance to " O   HOH Z 231 " =    1.727
peak=   -4.005 closest distance to " C   ASN A 285 " =    2.555
peak=   -3.989 closest distance to " O   HOH Z  98 " =    1.796
peak=   -3.971 closest distance to " O   ILE A 109 " =    2.626
peak=   -3.958 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.947 closest distance to " O   VAL A 153 " =    2.394
peak=   -3.922 closest distance to " CD  ARG A 156 " =    1.944
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    0.937
peak=   -3.889 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.885 closest distance to " O   HOH Z 388 " =    1.911
peak=   -3.885 closest distance to " CD1 LEU A 228 " =    2.346
peak=   -3.825 closest distance to " CB  CYS A 201 " =    2.527
peak=   -3.824 closest distance to " CB  TYR A  15 " =    2.194
peak=   -3.792 closest distance to " N   ALA A  43 " =    2.350
peak=   -3.791 closest distance to " N   MET A 188 " =    1.798
peak=   -3.788 closest distance to " CB  ASP A  27 " =    2.379
peak=   -3.779 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.765 closest distance to " O   HOH Z  92 " =    1.734
peak=   -3.763 closest distance to " C   ALA A 158 " =    1.341
peak=   -3.750 closest distance to " O   HOH Z  13 " =    1.256
peak=   -3.750 closest distance to " O   GLY A 211 " =    1.389
peak=   -3.730 closest distance to " CE  MET A 105 " =    2.162
peak=   -3.729 closest distance to " CB  CYS A 254 " =    2.320
peak=   -3.724 closest distance to " O   HOH Z 185 " =    2.065
peak=   -3.719 closest distance to " OXT GLY A 302 " =    2.854
peak=   -3.716 closest distance to " O   HOH Z  43 " =    1.517
peak=   -3.707 closest distance to " O   HOH Z  52 " =    1.156
peak=   -3.700 closest distance to " CD2 LEU A 300 " =    2.910
peak=   -3.697 closest distance to " O   HOH Z 353 " =    2.181
peak=   -3.693 closest distance to " CZ  PHE A  59 " =    1.626
peak=   -3.691 closest distance to " CB  PHE A 283 " =    2.964
peak=   -3.686 closest distance to " CE2 TYR A  30 " =    2.841
peak=   -3.685 closest distance to " O   HOH Z 395 " =    5.139
peak=   -3.673 closest distance to " CA  SER A 146 " =    2.342
peak=   -3.659 closest distance to " O   HOH Z 407 " =    3.219
peak=   -3.659 closest distance to " OD1 ASP A 191 " =    1.728
peak=   -3.648 closest distance to " ND2 ASN A  45 " =    1.184
peak=   -3.640 closest distance to " CZ3 TRP A 179 " =    1.252
peak=   -3.627 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.623 closest distance to " CD  GLN A  88 " =    0.795
peak=   -3.623 closest distance to " CB  ALA A 291 " =    2.234
peak=   -3.622 closest distance to " O   HOH Z  24 " =    1.456
peak=   -3.610 closest distance to " O   HOH Z  93 " =    2.102
peak=   -3.605 closest distance to " O   PRO A 163 " =    1.940
peak=   -3.604 closest distance to " O   GLY A 196 " =    1.077
peak=   -3.603 closest distance to " SD BMET A  47 " =    0.863
peak=   -3.582 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.581 closest distance to " CB  ASN A  39 " =    2.092
peak=   -3.564 closest distance to " C   LEU A 143 " =    1.448
peak=   -3.561 closest distance to " OG  SER A  97 " =    2.135
peak=   -3.558 closest distance to " CB  ALA A 291 " =    2.418
peak=   -3.552 closest distance to " O   HOH Z  38 " =    1.664
peak=   -3.550 closest distance to " O   HOH Z  71 " =    1.083
peak=   -3.528 closest distance to " CE  MET A  93 " =    1.194
peak=   -3.525 closest distance to " CE  LYS A  76 " =    2.738
peak=   -3.517 closest distance to " N   THR A 157 " =    1.592
peak=   -3.498 closest distance to " O   HOH Z 436 " =    1.262
peak=   -3.494 closest distance to " O   HOH Z  15 " =    1.801
peak=   -3.494 closest distance to " OG BSER A 134 " =    1.193
peak=   -3.493 closest distance to " NH1 ARG A 195 " =    2.569
peak=   -3.489 closest distance to " O   HOH Z  97 " =    1.926
peak=   -3.488 closest distance to " CG1 VAL A 250 " =    2.666
peak=   -3.481 closest distance to " OG ASER A 134 " =    1.238
peak=   -3.478 closest distance to " CD1 LEU A 101 " =    2.522
peak=   -3.462 closest distance to " SG ACYS A 201 " =    2.120
peak=   -3.459 closest distance to " NH2BARG A 275 " =    2.028
peak=   -3.458 closest distance to " CZ  TYR A 169 " =    1.705
peak=   -3.454 closest distance to " O   HOH Z  88 " =    2.301
peak=   -3.452 closest distance to " N   SER A 212 " =    2.002
peak=   -3.446 closest distance to " O   MET A  40 " =    2.784
peak=   -3.435 closest distance to " O   HOH Z 111 " =    2.405
peak=   -3.435 closest distance to " O   HOH Z 435 " =    2.699
peak=   -3.431 closest distance to " O   ALA A 161 " =    1.540
peak=   -3.430 closest distance to " C   HIS A 108 " =    1.159
peak=   -3.429 closest distance to " N   GLN A 122 " =    1.532
peak=   -3.428 closest distance to " O   SER A  62 " =    2.152
peak=   -3.425 closest distance to " O   VAL A  67 " =    2.627
peak=   -3.423 closest distance to " OG ASER A 216 " =    1.021
peak=   -3.421 closest distance to " CD2 LEU A 237 " =    2.662
peak=   -3.420 closest distance to " O   HOH Z 389 " =    1.843
peak=   -3.418 closest distance to " O   HOH Z 313 " =    2.041
peak=   -3.414 closest distance to " CB  TRP A  85 " =    2.580
peak=   -3.414 closest distance to " CG  GLU A 152 " =    2.317
peak=   -3.412 closest distance to " N   GLN A  58 " =    1.479
peak=   -3.410 closest distance to " O   HOH Z 283 " =    1.801
peak=   -3.409 closest distance to " O   HOH Z 351 " =    1.523
peak=   -3.405 closest distance to " O   HOH Z 166 " =    1.294
peak=   -3.404 closest distance to " O   HOH Z  11 " =    1.917
peak=   -3.402 closest distance to " O   HOH Z 275 " =    1.564
peak=   -3.398 closest distance to " O   HOH Z 222 " =    1.203
peak=   -3.392 closest distance to " O   HOH Z  47 " =    1.418
peak=   -3.380 closest distance to " OE1 GLN A  88 " =    1.066
peak=   -3.377 closest distance to " O   HOH Z 128 " =    2.505
peak=   -3.372 closest distance to " NH2AARG A 275 " =    5.488
peak=   -3.370 closest distance to " O   HOH Z 298 " =    1.177
peak=   -3.366 closest distance to " OG  SER A 245 " =    0.926
peak=   -3.365 closest distance to " O   HOH Z 213 " =    1.064
peak=   -3.363 closest distance to " O   HOH Z 281 " =    2.910
peak=   -3.361 closest distance to " CE3 TRP A 274 " =    2.496
peak=   -3.360 closest distance to " CA  TRP A 274 " =    1.665
peak=   -3.358 closest distance to " CB  PRO A 163 " =    2.589
peak=   -3.356 closest distance to " CD  GLN A  88 " =    2.151
peak=   -3.355 closest distance to " C   GLN A 240 " =    2.293
peak=   -3.352 closest distance to " CA  GLY A 241 " =    2.260
peak=   -3.345 closest distance to " CG  LEU A  83 " =    1.907
peak=   -3.340 closest distance to " OD1 ASN A 148 " =    1.729
peak=   -3.334 closest distance to " O   HOH Z  11 " =    1.956
peak=   -3.333 closest distance to " O   HOH Z   3 " =    1.798
peak=   -3.332 closest distance to " CA  GLY A 203 " =    2.149
peak=   -3.332 closest distance to " CB  ALA A  43 " =    2.394
peak=   -3.332 closest distance to " CB  SER A 245 " =    2.496
peak=   -3.331 closest distance to " O   HOH Z 266 " =    4.524
peak=   -3.325 closest distance to " O   HOH Z 278 " =    2.520
peak=   -3.320 closest distance to " O   HOH Z 292 " =    4.463
peak=   -3.319 closest distance to " N   SER A 276 " =    1.223
peak=   -3.318 closest distance to " O   HOH Z  97 " =    1.508
peak=   -3.317 closest distance to " ND2 ASN A 249 " =    1.926
peak=   -3.314 closest distance to " O   HOH Z 166 " =    1.840
peak=   -3.311 closest distance to " O   HOH Z 385 " =    2.061
peak=   -3.304 closest distance to " OD1 ASN A 176 " =    1.102
peak=   -3.302 closest distance to " O   VAL A 174 " =    2.035
peak=   -3.299 closest distance to " CE3 TRP A 150 " =    1.846
peak=   -3.298 closest distance to " O   SER A 135 " =    1.527
peak=   -3.298 closest distance to " CD  LYS A 289 " =    2.598
peak=   -3.297 closest distance to " O   TRP A  70 " =    1.512
peak=   -3.292 closest distance to " CB  ASP A 132 " =    2.253
peak=   -3.290 closest distance to " CE2 PHE A 218 " =    2.487
peak=   -3.286 closest distance to " OD2 ASP A 171 " =    2.083
peak=   -3.281 closest distance to " OG  SER A   3 " =    1.757
peak=   -3.280 closest distance to " CD1 PHE A  59 " =    1.774
peak=   -3.280 closest distance to " NH2 ARG A  79 " =    1.749
peak=   -3.273 closest distance to " N   HIS A 115 " =    1.891
peak=   -3.260 closest distance to " O   PRO A 198 " =    1.323
peak=   -3.260 closest distance to " CD1 ILE A 239 " =    1.966
peak=   -3.256 closest distance to " CG1 VAL A 197 " =    2.280
peak=   -3.256 closest distance to " O   HOH Z 426 " =    1.726
peak=   -3.250 closest distance to " O   HOH Z 310 " =    3.460
peak=   -3.250 closest distance to " O   HOH Z  90 " =    3.051
peak=   -3.248 closest distance to " OG BSER A 134 " =    1.675
peak=   -3.246 closest distance to " N   ALA A 226 " =    2.134
peak=   -3.246 closest distance to " O   HOH Z 350 " =    2.491
peak=   -3.240 closest distance to " CG  PRO A 163 " =    2.439
peak=   -3.240 closest distance to " CZ  ARG A 259 " =    0.922
peak=   -3.222 closest distance to " CD2 LEU A 143 " =    2.558
peak=   -3.221 closest distance to " O   HOH Z 198 " =    1.428
peak=   -3.221 closest distance to " O   GLY A 267 " =    2.424
peak=   -3.219 closest distance to " O   HOH Z 323 " =    1.366
peak=   -3.217 closest distance to " CA  GLY A 133 " =    1.942
peak=   -3.211 closest distance to " O   GLY A 118 " =    2.229
peak=   -3.209 closest distance to " O   HOH Z 396 " =    1.614
peak=   -3.206 closest distance to " O   HOH Z 148 " =    1.851
peak=   -3.204 closest distance to " CG  TRP A 266 " =    1.538
peak=   -3.191 closest distance to " OD1 ASP A 200 " =    1.303
peak=   -3.188 closest distance to " CG1 VAL A 112 " =    2.804
peak=   -3.188 closest distance to " O   HOH Z 256 " =    1.566
peak=   -3.187 closest distance to " CB  ALA A 131 " =    2.006
peak=   -3.185 closest distance to " O   HOH Z 184 " =    1.862
peak=   -3.182 closest distance to " OXT GLY A 302 " =    3.304
peak=   -3.182 closest distance to " OG  SER A  87 " =    1.289
peak=   -3.177 closest distance to " CE3 TRP A 123 " =    1.208
peak=   -3.164 closest distance to " O   HOH Z 118 " =    2.660
peak=   -3.163 closest distance to " O   HOH Z 176 " =    0.790
peak=   -3.157 closest distance to " O   SER A 146 " =    0.917
peak=   -3.154 closest distance to " O   HOH Z 417 " =    2.440
peak=   -3.153 closest distance to " NE2 GLN A  88 " =    0.925
peak=   -3.149 closest distance to " O   HOH Z 100 " =    1.037
peak=   -3.149 closest distance to " OE1 GLN A  77 " =    1.928
peak=   -3.146 closest distance to " O   GLY A 203 " =    2.553
peak=   -3.145 closest distance to " O   HOH Z 317 " =    2.693
peak=   -3.145 closest distance to " O   HOH Z 371 " =    1.731
peak=   -3.144 closest distance to " O   HOH Z 423 " =    1.086
peak=   -3.144 closest distance to " O   SER A  22 " =    2.366
peak=   -3.133 closest distance to " O   VAL A 197 " =    1.233
peak=   -3.126 closest distance to " CB  LEU A 167 " =    2.050
peak=   -3.121 closest distance to " SG BCYS A 201 " =    2.259
peak=   -3.120 closest distance to " CD1 TRP A 179 " =    0.981
peak=   -3.120 closest distance to " O   HOH Z 234 " =    4.150
peak=   -3.119 closest distance to " O   HOH Z  63 " =    1.263
peak=   -3.112 closest distance to " OD1 ASP A 191 " =    1.311
peak=   -3.111 closest distance to " CD2 TYR A 293 " =    2.040
peak=   -3.091 closest distance to " O   HOH Z 119 " =    4.166
peak=   -3.088 closest distance to " CG  GLN A 278 " =    2.278
peak=   -3.082 closest distance to " O   HOH Z 438 " =    1.353
peak=   -3.063 closest distance to " CD1 ILE A 199 " =    2.544
peak=   -3.059 closest distance to " N   ALA A 248 " =    1.648
peak=   -3.035 closest distance to " NH2 ARG A 156 " =    1.154
peak=   -3.029 closest distance to " CD1 TYR A 247 " =    2.823
peak=   -3.026 closest distance to " O   HOH Z 378 " =    1.908

================= 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    :  0.4144 0.4183   6.214518e+00   6.219562e+00
   1_bss:  0.4030 0.4074   6.207504e+00   6.202781e+00
   1_xyz:  0.2907 0.3226   5.956876e+00   6.043818e+00
   1_adp:  0.2663 0.3291   5.906546e+00   6.058165e+00
   1_occ:  0.2658 0.3292   5.905306e+00   6.057199e+00
   2_bss:  0.2652 0.3278   5.903183e+00   6.052813e+00
   2_xyz:  0.1944 0.2517   5.636670e+00   5.825644e+00
   2_adp:  0.1781 0.2371   5.567834e+00   5.772669e+00
   2_occ:  0.1780 0.2372   5.567485e+00   5.772480e+00
   3_bss:  0.1774 0.2356   5.562504e+00   5.767734e+00
   3_xyz:  0.1403 0.1868   5.336903e+00   5.563405e+00
   3_adp:  0.1305 0.1757   5.270281e+00   5.494316e+00
   3_occ:  0.1304 0.1754   5.269205e+00   5.493295e+00
   4_bss:  0.1306 0.1753   5.269116e+00   5.492565e+00
   4_xyz:  0.1187 0.1630   5.187798e+00   5.420509e+00
   4_adp:  0.1157 0.1603   5.167916e+00   5.402864e+00
   4_occ:  0.1156 0.1601   5.167177e+00   5.402329e+00
   5_bss:  0.1156 0.1600   5.166930e+00   5.402219e+00
   5_xyz:  0.1121 0.1574   5.147264e+00   5.387305e+00
   5_adp:  0.1121 0.1562   5.145564e+00   5.382888e+00
   5_occ:  0.1119 0.1561   5.145008e+00   5.382586e+00
   5_bss:  0.1119 0.1561   5.145035e+00   5.382609e+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:  0.314  30.143  -0.550  -2.685   2.878  -0.000   0.000   0.000
   1_xyz:  0.314  30.143  -0.550  -2.685   2.878  -0.000   0.000   0.000
   1_adp:  0.314  30.143  -0.550  -2.685   2.878  -0.000   0.000   0.000
   1_occ:  0.314  30.143  -0.550  -2.685   2.878  -0.000   0.000   0.000
   2_bss:  0.336  52.313  -1.235  -2.189   0.664  -0.000   0.000   0.000
   2_xyz:  0.336  52.313  -1.235  -2.189   0.664  -0.000   0.000   0.000
   2_adp:  0.336  52.313  -1.235  -2.189   0.664  -0.000   0.000   0.000
   2_occ:  0.336  52.313  -1.235  -2.189   0.664  -0.000   0.000   0.000
   3_bss:  0.325  46.856  -1.648  -2.323  -0.827  -0.000  -0.000  -0.000
   3_xyz:  0.325  46.856  -1.648  -2.323  -0.827  -0.000  -0.000  -0.000
   3_adp:  0.325  46.856  -1.648  -2.323  -0.827  -0.000  -0.000  -0.000
   3_occ:  0.325  46.856  -1.648  -2.323  -0.827  -0.000  -0.000  -0.000
   4_bss:  0.325  46.856  -2.073  -2.524  -1.651  -0.000  -0.000  -0.000
   4_xyz:  0.325  46.856  -2.073  -2.524  -1.651  -0.000  -0.000  -0.000
   4_adp:  0.325  46.856  -2.073  -2.524  -1.651  -0.000  -0.000  -0.000
   4_occ:  0.325  46.856  -2.073  -2.524  -1.651  -0.000  -0.000  -0.000
   5_bss:  0.319  44.907  -2.064  -2.436  -1.833  -0.000  -0.000  -0.000
   5_xyz:  0.319  44.907  -2.064  -2.436  -1.833  -0.000  -0.000  -0.000
   5_adp:  0.319  44.907  -2.064  -2.436  -1.833  -0.000  -0.000  -0.000
   5_occ:  0.319  44.907  -2.064  -2.436  -1.833  -0.000  -0.000  -0.000
   5_bss:  0.319  44.842  -1.950  -2.281  -1.757  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.802 0.5359  0.7168    54546.530
   1_bss:  47.414 0.5511  0.7363    50685.822
   1_xyz:  34.760 0.7041  0.9053    29818.074
   1_adp:  35.789 0.6912  0.8932    30988.041
   1_occ:  35.765 0.6913  0.8930    30891.729
   2_bss:  35.423 0.6953  0.8746    30546.481
   2_xyz:  25.702 0.8036  0.9758    16994.796
   2_adp:  23.744 0.8246  0.9847    14960.330
   2_occ:  23.741 0.8246  0.9842    14954.736
   3_bss:  23.538 0.8265  0.9614    14719.140
   3_xyz:  18.045 0.8793  0.9928     9104.521
   3_adp:  16.338 0.8951  0.9965     7992.728
   3_occ:  16.302 0.8955  0.9964     7963.154
   4_bss:  16.275 0.8956  0.9792     7950.160
   4_xyz:  14.740 0.9087  0.9839     6778.351
   4_adp:  14.333 0.9123  0.9811     6574.588
   4_occ:  14.307 0.9125  0.9810     6556.877
   5_bss:  14.304 0.9125  0.9798     6553.923
   5_xyz:  14.002 0.9150  0.9810     6330.863
   5_adp:  13.866 0.9163  0.9795     6289.381
   5_occ:  13.853 0.9165  0.9795     6284.827
   5_bss:  13.854 0.9165  0.9811     6285.593
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7664e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7664e-01
   1_xyz:   1.262  0.010  0.081 15.660  0.005  4.109   9.3401e-02
   1_adp:   1.262  0.010  0.081 15.660  0.005  4.109   9.3401e-02
   1_occ:   1.262  0.010  0.081 15.660  0.005  4.109   9.3401e-02
   2_bss:   1.262  0.010  0.081 15.660  0.005  4.109   9.3401e-02
   2_xyz:   1.127  0.008  0.074 14.299  0.004  4.123   7.0480e-02
   2_adp:   1.127  0.008  0.074 14.299  0.004  4.123   7.0480e-02
   2_occ:   1.127  0.008  0.074 14.299  0.004  4.123   7.0480e-02
   3_bss:   1.127  0.008  0.074 14.299  0.004  4.123   7.0480e-02
   3_xyz:   1.015  0.006  0.072 14.573  0.004  4.115   5.8974e-02
   3_adp:   1.015  0.006  0.072 14.573  0.004  4.115   5.8974e-02
   3_occ:   1.015  0.006  0.072 14.573  0.004  4.115   5.8974e-02
   4_bss:   1.015  0.006  0.072 14.573  0.004  4.115   5.8974e-02
   4_xyz:   0.993  0.006  0.071 14.634  0.004  4.118   5.7508e-02
   4_adp:   0.993  0.006  0.071 14.634  0.004  4.118   5.7508e-02
   4_occ:   0.993  0.006  0.071 14.634  0.004  4.118   5.7508e-02
   5_bss:   0.993  0.006  0.071 14.634  0.004  4.118   5.7508e-02
   5_xyz:   0.977  0.006  0.071 14.625  0.004  4.119   5.6279e-02
   5_adp:   0.977  0.006  0.071 14.625  0.004  4.119   5.6279e-02
   5_occ:   0.977  0.006  0.071 14.625  0.004  4.119   5.6279e-02
   5_bss:   0.977  0.006  0.071 14.625  0.004  4.119   5.6279e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.589   2.3979e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.589   2.3979e-01
   1_xyz:   8.618  0.055  0.322 88.690  0.032  2.189   8.7743e-02
   1_adp:   8.618  0.055  0.322 88.690  0.032  2.189   8.7743e-02
   1_occ:   8.618  0.055  0.322 88.690  0.032  2.189   8.7743e-02
   2_bss:   8.618  0.055  0.322 88.690  0.032  2.189   8.7743e-02
   2_xyz:   6.782  0.044  0.225 86.186  0.017  2.368   1.2451e-01
   2_adp:   6.782  0.044  0.225 86.186  0.017  2.368   1.2451e-01
   2_occ:   6.782  0.044  0.225 86.186  0.017  2.368   1.2451e-01
   3_bss:   6.782  0.044  0.225 86.186  0.017  2.368   1.2451e-01
   3_xyz:   7.833  0.032  0.339 82.699  0.030  2.327   5.4756e-02
   3_adp:   7.833  0.032  0.339 82.699  0.030  2.327   5.4756e-02
   3_occ:   7.833  0.032  0.339 82.699  0.030  2.327   5.4756e-02
   4_bss:   7.833  0.032  0.339 82.699  0.030  2.327   5.4756e-02
   4_xyz:   6.904  0.044  0.214 84.905  0.034  2.354   4.3905e-02
   4_adp:   6.904  0.044  0.214 84.905  0.034  2.354   4.3905e-02
   4_occ:   6.904  0.044  0.214 84.905  0.034  2.354   4.3905e-02
   5_bss:   6.904  0.044  0.214 84.905  0.034  2.354   4.3905e-02
   5_xyz:   7.517  0.043  0.222 83.526  0.033  2.324   4.3871e-02
   5_adp:   7.517  0.043  0.222 83.526  0.033  2.324   4.3871e-02
   5_occ:   7.517  0.043  0.222 83.526  0.033  2.324   4.3871e-02
   5_bss:   7.517  0.043  0.222 83.526  0.033  2.324   4.3871e-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:  85.97   0.00  18.01  85.97   0.00  13.94  85.20   0.00  40.15
   1_occ:  85.97   0.00  18.01  85.97   0.00  13.94  85.20   0.00  40.15
   2_bss:  85.97   0.00  18.01  85.97   0.00  13.94  85.20   0.00  40.15
   2_xyz:  85.97   0.00  18.01  85.97   0.00  13.94  85.20   0.00  40.15
   2_adp:  88.83   0.00  18.00  85.45   0.00  13.50  88.83   4.18  42.56
   2_occ:  88.83   0.00  18.00  85.45   0.00  13.50  88.83   4.18  42.56
   3_bss:  88.83   0.00  18.00  85.45   0.00  13.50  88.83   4.18  42.56
   3_xyz:  88.83   0.00  18.00  85.45   0.00  13.50  88.83   4.18  42.56
   3_adp:  86.82   1.33  17.49  86.82   1.33  13.05  86.23   4.63  41.65
   3_occ:  86.82   1.33  17.49  86.82   1.33  13.05  86.23   4.63  41.65
   4_bss:  86.82   1.33  17.49  86.82   1.33  13.05  86.23   4.63  41.65
   4_xyz:  86.82   1.33  17.49  86.82   1.33  13.05  86.23   4.63  41.65
   4_adp:  93.53   1.48  17.29  93.53   1.48  12.93  83.67   5.43  41.05
   4_occ:  93.53   1.48  17.29  93.53   1.48  12.93  83.67   5.43  41.05
   5_bss:  93.53   1.48  17.29  93.53   1.48  12.93  83.67   5.43  41.05
   5_xyz:  93.53   1.48  17.29  93.53   1.48  12.93  83.67   5.43  41.05
   5_adp:  93.83   1.83  16.85  93.83   1.83  12.78  79.93   6.30  39.03
   5_occ:  93.83   1.83  16.85  93.83   1.83  12.78  79.93   6.30  39.03
   5_bss:  93.76   1.77  16.78  93.76   1.77  12.71  79.86   6.23  38.96
------------------------------------------------------------------------
 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:    1.841    0.011    0.303
   1_adp:    1.841    0.011    0.303
   1_occ:    1.841    0.011    0.303
   2_bss:    1.841    0.011    0.303
   2_xyz:    1.179    0.021    0.462
   2_adp:    1.179    0.021    0.462
   2_occ:    1.179    0.021    0.462
   3_bss:    1.179    0.021    0.462
   3_xyz:    1.189    0.048    0.551
   3_adp:    1.189    0.048    0.551
   3_occ:    1.189    0.048    0.551
   4_bss:    1.189    0.048    0.551
   4_xyz:    1.234    0.023    0.578
   4_adp:    1.234    0.023    0.578
   4_occ:    1.234    0.023    0.578
   5_bss:    1.234    0.023    0.578
   5_xyz:    1.300    0.070    0.593
   5_adp:    1.300    0.070    0.593
   5_occ:    1.300    0.070    0.593
   5_bss:    1.300    0.070    0.593
------------------------------------------------------------------------

CPU time actual refinement: 370.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/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_1012/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1012/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 370.59 
  Macro-tasks:
    bulk solvent and scale       = 39.23  
    individual site refinement   = 168.67 
    weights calculation          = 30.77  
    collect and process          = 6.69   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 245.46 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 124.41 
    alpha_beta                      = 8.58   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 131.38 
    fmodel                         = 6.90   
    r_factors                      = 0.21   
    phase_errors                   = 11.67  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 286.40 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.030 micro seconds
Total CPU time: 6.40 minutes
from_scatterers_fft:    684 calls, 123.99 s
gradients_fft:          629 calls, 118.12 s

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

# Date 2008-01-16 Time 06:13:06 PST -0800 (1200492787.00 s)
Start R-work = 0.4144, R-free = 0.4183 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.4030, R-free = 0.4074
Final R-work = 0.1119, R-free = 0.1561