# Date 2008-01-16 Time 06:21:30 PST -0800 (1200493290.21 s)
#phil __OFF__

Command line arguments: "../1110.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4895
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1110

-------------------------------------------------------------------------------
  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: (71.655, 45.9914, 88.5498, 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: 3.23, per 1000 atoms: 1.14


================================== 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: (71.655, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.96439
Completeness in resolution range: 0.912602
Completeness with d_max=infinity: 0.910058

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   1.9644

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: (71.655, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.96439
Completeness in resolution range: 0.912602
Completeness with d_max=infinity: 0.910058

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.2057 [2251/2278]  2027   224  10.0%
  bin  2:  4.2057 -  3.3497 [2173/2193]  1960   213   9.8%
  bin  3:  3.3497 -  2.9296 [2132/2151]  1912   220  10.3%
  bin  4:  2.9296 -  2.6633 [2110/2140]  1894   216  10.2%
  bin  5:  2.6633 -  2.4732 [2121/2140]  1909   212  10.0%
  bin  6:  2.4732 -  2.3280 [2089/2114]  1880   209  10.0%
  bin  7:  2.3280 -  2.2117 [2098/2126]  1893   205   9.8%
  bin  8:  2.2117 -  2.1157 [2062/2098]  1850   212  10.3%
  bin  9:  2.1157 -  2.0344 [2000/2113]  1812   188   9.4%
  bin 10:  2.0344 -  1.9644 [ 553/2112]   493    60  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 35
        2.42 -     3.04: 2203
        3.04 -     3.66: 4650
        3.66 -     4.28: 8945
        4.28 -     4.90: 12194
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.972 3.040 -x,y-1/2,-z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28022 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_1110/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/model_refine_001.geo

CPU time processing inputs: 8.62


============================ 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 = 71.655 45.9914 88.54975 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: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4968   r_free= 0.4997   ksol= 0.00   Bsol= 0.00   scale= 0.859    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.304897                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6919 0.99   1462  164 0.4047 0.3792      6.6343      6.5843|
|  2:  4.6919 -  3.7420 0.99   1411  156 0.4423 0.4469        6.87      6.8714|
|  3:  3.7420 -  3.2743 0.99   1366  153 0.4635 0.4376      6.6817      6.6593|
|  4:  3.2743 -  2.9773 0.99   1400  150 0.5041 0.5352      6.5456      6.5418|
|  5:  2.9773 -  2.7652 0.99   1347  154 0.5268 0.5515      6.3737      6.4106|
|  6:  2.7652 -  2.6030 0.99   1372  152 0.5282 0.5247      6.2941      6.2191|
|  7:  2.6030 -  2.4732 0.99   1344  156 0.5373 0.5260      6.2397      6.1906|
|  8:  2.4732 -  2.3660 0.98   1345  145 0.5484 0.5768      6.1779      6.1652|
|  9:  2.3660 -  2.2752 0.98   1338  150 0.5449 0.5670      6.1318      6.2131|
| 10:  2.2752 -  2.1969 1.00   1353  151 0.5460 0.5522      6.0679      6.0609|
| 11:  2.1969 -  2.1284 0.98   1327  147 0.5258 0.5066      6.0198      6.0301|
| 12:  2.1284 -  2.0677 0.98   1350  145 0.5375 0.5606       5.934      5.9418|
| 13:  2.0677 -  2.0134 0.74    993  113 0.5372 0.5012      5.8873      5.7818|
| 14:  2.0134 -  1.9644 0.16    222   23 0.5275 0.4722      5.8367      5.9633|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6919  1462   164  0.71  33.61   0.80     0.75      71682.17|
|  2:  4.6919 -  3.7420  1411   156  0.67  37.97   0.87     0.77     124963.13|
|  3:  3.7420 -  3.2743  1366   153  0.49  52.77   0.88     0.67     142647.04|
|  4:  3.2743 -  2.9773  1400   150  0.33  65.01   0.85     0.49     138612.26|
|  5:  2.9773 -  2.7652  1347   154  0.25  71.19   0.84     0.38     105883.66|
|  6:  2.7652 -  2.6030  1372   152  0.21  74.47   0.87     0.31      90716.36|
|  7:  2.6030 -  2.4732  1344   156  0.21  74.38   0.87     0.30      77235.54|
|  8:  2.4732 -  2.3660  1345   145  0.17  76.95   0.86     0.26      70453.02|
|  9:  2.3660 -  2.2752  1338   150  0.21  74.60   0.89     0.31      63399.03|
| 10:  2.2752 -  2.1969  1353   151  0.22  73.65   0.88     0.34      56053.07|
| 11:  2.1969 -  2.1284  1327   147  0.24  72.17   0.92     0.38      52706.78|
| 12:  2.1284 -  2.0677  1350   145  0.23  72.74   0.88     0.38      46929.10|
| 13:  2.0677 -  2.0134   993   113  0.23  72.69   0.91     0.39      41010.31|
| 14:  2.0134 -  1.9644   222    23  0.29  68.85   0.95     0.41      32500.23|
|alpha:            min =        0.26 max =            0.77 mean =         0.45|
|beta:             min =    32500.23 max =       142647.04 mean =     83811.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.99 mean =        65.13|
|phase err.(test): min =        0.00 max =           90.00 mean =        65.39|
|-----------------------------------------------------------------------------|

============================== 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 = 23.246335             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.057   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.325051              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.678   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2007 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1849 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2801 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4604 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4341 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5556 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6638 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.298 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    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: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4968   r_free= 0.4997   ksol= 0.00   Bsol= 0.00   scale= 0.859    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.304897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4900   r_free= 0.4975   ksol= 0.32   Bsol= 64.46   scale= 0.901   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.10,2.95,-0.00,0.00,0.00); trace/3= 0.72                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.302927                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.562736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.887   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.835247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.100   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4900      final r-factor (work) = 0.3980          |
| start r-factor (free) = 0.4975      final r-factor (free) = 0.4378          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.6187 = 18.56 * 0.50 * 6.2972 + 1.00 * 0.1720                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.8987 = 18.56 * 0.50 * 6.2214 + 1.00 * 0.1560                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3980      final r-factor (work) = 0.3604          |
| start r-factor (free) = 0.4378      final r-factor (free) = 0.4504          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4239 = 1.84 * 1.00 * 6.2214 + 1.00 * 0.0062                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2759 = 1.84 * 1.00 * 6.1309 + 1.00 * 0.0242                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.11   20.62    None  None   None       |
|    all(noH): 2823   0      0.00    86.11   20.62    None  None   None       |
|    Sol.    : 438    0      0.00    86.11   39.23    None  None   None       |
|    Mac.    : 2385   0      0.00    81.12   17.20    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 -   8.612:  694   |   5:    43.057 -  51.669:  132        |
|      1:     8.612 -  17.223:  742   |   6:    51.669 -  60.280:   72        |
|      2:    17.223 -  25.834:  561   |   7:    60.280 -  68.891:   53        |
|      3:    25.834 -  34.446:  331   |   8:    68.891 -  77.503:   21        |
|      4:    34.446 -  43.057:  204   |   9:    77.503 -  86.114:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3604 r_free = 0.4504             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3598 r_free = 0.4516             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3598   r_free= 0.4516   ksol= 0.32   Bsol= 64.46   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.10,2.95,-0.00,0.00,0.00); trace/3= 0.72                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.135865                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3602   r_free= 0.4501   ksol= 0.37   Bsol= 96.56   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.69,2.08,-0.00,0.00,0.00); trace/3= 0.36                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.137467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.327822             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.030   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.786512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.704  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3602      final r-factor (work) = 0.2986          |
| start r-factor (free) = 0.4501      final r-factor (free) = 0.3721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8883 = 11.33 * 0.50 * 6.1322 + 1.00 * 0.1558                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5467 = 11.33 * 0.50 * 6.0815 + 1.00 * 0.1013                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2986      final r-factor (work) = 0.2794          |
| start r-factor (free) = 0.3721      final r-factor (free) = 0.3609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8072 = 0.79 * 1.00 * 6.0815 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7181 = 0.79 * 1.00 * 5.9614 + 1.00 * 0.0293                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.47   20.47    None  None   None       |
|    all(noH): 2823   0      0.00    85.47   20.47    None  None   None       |
|    Sol.    : 438    0      0.00    85.47   40.42    None  None   None       |
|    Mac.    : 2385   0      0.00    78.84   16.81    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 -   8.547:  622   |   5:    42.735 -  51.282:  125        |
|      1:     8.547 -  17.094:  847   |   6:    51.282 -  59.829:   67        |
|      2:    17.094 -  25.641:  562   |   7:    59.829 -  68.376:   48        |
|      3:    25.641 -  34.188:  331   |   8:    68.376 -  76.922:   27        |
|      4:    34.188 -  42.735:  185   |   9:    76.922 -  85.469:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2794 r_free = 0.3609             target_work(ml) = 5.948         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2794 r_free = 0.3611             target_work(ml) = 5.948         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2794   r_free= 0.3611   ksol= 0.37   Bsol= 96.56   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.69,2.08,-0.00,0.00,0.00); trace/3= 0.36                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.947933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2795   r_free= 0.3609   ksol= 0.35   Bsol= 85.99   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-1.35,0.80,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.947959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.304701              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.260623              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.630   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2795      final r-factor (work) = 0.2355          |
| start r-factor (free) = 0.3609      final r-factor (free) = 0.3107          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9126 = 5.30 * 0.50 * 5.9612 + 1.00 * 0.1013                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6791 = 5.30 * 0.50 * 5.8867 + 1.00 * 0.0655                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2355      final r-factor (work) = 0.2140          |
| start r-factor (free) = 0.3107      final r-factor (free) = 0.2955          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4384 = 1.26 * 1.00 * 5.8867 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2922 = 1.26 * 1.00 * 5.7705 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.65  20.65    None  None   None       |
|    all(noH): 2823   0      0.00    101.65  20.65    None  None   None       |
|    Sol.    : 438    0      1.90    101.65  48.30    None  None   None       |
|    Mac.    : 2385   0      0.00    91.77   15.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.165:  890   |   5:    50.827 -  60.992:  114        |
|      1:    10.165 -  20.331: 1008   |   6:    60.992 -  71.157:   81        |
|      2:    20.331 -  30.496:  366   |   7:    71.157 -  81.323:   40        |
|      3:    30.496 -  40.661:  173   |   8:    81.323 -  91.488:   21        |
|      4:    40.661 -  50.827:  123   |   9:    91.488 - 101.653:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2140 r_free = 0.2955             target_work(ml) = 5.745         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2140 r_free = 0.2951             target_work(ml) = 5.744         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2951   ksol= 0.35   Bsol= 85.99   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-1.35,0.80,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.744163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2951   ksol= 0.35   Bsol= 97.87   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.33,-0.04,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.743827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.785412              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.107  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.178  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1786          |
| start r-factor (free) = 0.2951      final r-factor (free) = 0.2490          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9919 = 3.79 * 0.50 * 5.7729 + 1.00 * 0.0655                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8002 = 3.79 * 0.50 * 5.6752 + 1.00 * 0.0587                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1786      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.2490      final r-factor (free) = 0.2312          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5312 = 0.62 * 1.00 * 5.6752 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4536 = 0.62 * 1.00 * 5.5558 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.02  19.78    None  None   None       |
|    all(noH): 2823   0      0.00    107.02  19.78    None  None   None       |
|    Sol.    : 438    0      4.97    107.02  49.11    None  None   None       |
|    Mac.    : 2385   0      0.00    95.70   14.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.702: 1043   |   5:    53.508 -  64.210:  107        |
|      1:    10.702 -  21.403: 1051   |   6:    64.210 -  74.912:   72        |
|      2:    21.403 -  32.105:  267   |   7:    74.912 -  85.613:   39        |
|      3:    32.105 -  42.807:  115   |   8:    85.613 -  96.315:   18        |
|      4:    42.807 -  53.508:  110   |   9:    96.315 - 107.017:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1682 r_free = 0.2312             target_work(ml) = 5.519         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1682 r_free = 0.2311             target_work(ml) = 5.518         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1682   r_free= 0.2311   ksol= 0.35   Bsol= 97.87   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.33,-0.04,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.518020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1685   r_free= 0.2308   ksol= 0.34   Bsol= 87.47   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.73,-0.47,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.517300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.023882              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.411  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580437              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1685      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2308      final r-factor (free) = 0.1999          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4597 = 3.02 * 0.50 * 5.5564 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3206 = 3.02 * 0.50 * 5.4618 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1460      final r-factor (work) = 0.1396          |
| start r-factor (free) = 0.1999      final r-factor (free) = 0.1932          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1841 = 0.58 * 1.00 * 5.4618 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1248 = 0.58 * 1.00 * 5.3616 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    105.10  19.36    None  None   None       |
|    all(noH): 2823   0      0.43    105.10  19.36    None  None   None       |
|    Sol.    : 438    0      6.97    105.10  49.12    None  None   None       |
|    Mac.    : 2385   0      0.43    93.86   13.90    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:     0.434 -  10.901: 1118   |   5:    52.769 -  63.236:   84        |
|      1:    10.901 -  21.368: 1034   |   6:    63.236 -  73.703:   88        |
|      2:    21.368 -  31.835:  226   |   7:    73.703 -  84.170:   36        |
|      3:    31.835 -  42.302:  107   |   8:    84.170 -  94.637:   22        |
|      4:    42.302 -  52.769:  103   |   9:    94.637 - 105.104:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1396 r_free = 0.1932             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1395 r_free = 0.1931             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1395   r_free= 0.1931   ksol= 0.34   Bsol= 87.47   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.73,-0.47,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338938                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6919 0.99   1462  164 0.0970 0.1446      5.3929      5.6561|
|  2:  4.6919 -  3.7420 0.99   1411  156 0.0918 0.1372      5.5293      5.8116|
|  3:  3.7420 -  3.2743 0.99   1366  153 0.1321 0.1860      5.6461      5.9741|
|  4:  3.2743 -  2.9773 0.99   1400  150 0.1657 0.2110       5.676      5.8383|
|  5:  2.9773 -  2.7652 0.99   1347  154 0.1684 0.2185      5.5357      5.7556|
|  6:  2.7652 -  2.6030 0.99   1372  152 0.1641 0.2374      5.4215      5.6285|
|  7:  2.6030 -  2.4732 0.99   1344  156 0.1595 0.2070      5.3492      5.5203|
|  8:  2.4732 -  2.3660 0.98   1345  145 0.1588 0.2087      5.3008      5.5174|
|  9:  2.3660 -  2.2752 0.98   1338  150 0.1607 0.2252      5.2657      5.5003|
| 10:  2.2752 -  2.1969 1.00   1353  151 0.1457 0.2029      5.1491      5.3272|
| 11:  2.1969 -  2.1284 0.98   1327  147 0.1450 0.2134      5.1102      5.4466|
| 12:  2.1284 -  2.0677 0.98   1350  145 0.1473 0.2176      5.0416      5.2583|
| 13:  2.0677 -  2.0134 0.74    993  113 0.1329 0.1950      4.9323       5.104|
| 14:  2.0134 -  1.9644 0.16    222   23 0.1229 0.1741      4.8155      5.1312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6919  1462   164  0.94   9.64   0.96     0.94       7960.72|
|  2:  4.6919 -  3.7420  1411   156  0.94   9.69   1.02     1.01      11442.28|
|  3:  3.7420 -  3.2743  1366   153  0.91  14.80   1.04     1.04      14891.79|
|  4:  3.2743 -  2.9773  1400   150  0.87  19.70   1.03     1.00      16776.55|
|  5:  2.9773 -  2.7652  1347   154  0.87  19.95   1.01     0.99      12858.41|
|  6:  2.7652 -  2.6030  1372   152  0.85  21.06   1.00     0.95      10497.27|
|  7:  2.6030 -  2.4732  1344   156  0.87  19.87   1.02     0.98       9149.17|
|  8:  2.4732 -  2.3660  1345   145  0.86  20.53   1.01     0.97       8449.82|
|  9:  2.3660 -  2.2752  1338   150  0.85  21.45   1.01     0.96       8035.06|
| 10:  2.2752 -  2.1969  1353   151  0.86  20.38   1.02     0.98       6658.91|
| 11:  2.1969 -  2.1284  1327   147  0.87  20.19   1.01     0.95       6219.28|
| 12:  2.1284 -  2.0677  1350   145  0.87  20.21   1.01     1.00       5538.05|
| 13:  2.0677 -  2.0134   993   113  0.87  20.18   1.01     0.98       4669.12|
| 14:  2.0134 -  1.9644   222    23  0.91  16.01   0.98     0.97       3474.41|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     3474.41 max =        16776.55 mean =      9523.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.13|
|phase err.(test): min =        0.00 max =           89.97 mean =        17.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1932   ksol= 0.33   Bsol= 77.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-3.11,-0.86,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1932   ksol= 0.33   Bsol= 77.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-3.11,-0.86,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6919 0.99   1462  164 0.0976 0.1424      5.3842      5.6361|
|  2:  4.6919 -  3.7420 0.99   1411  156 0.0919 0.1375      5.5258       5.813|
|  3:  3.7420 -  3.2743 0.99   1366  153 0.1324 0.1855      5.6468      5.9716|
|  4:  3.2743 -  2.9773 0.99   1400  150 0.1660 0.2114      5.6769      5.8386|
|  5:  2.9773 -  2.7652 0.99   1347  154 0.1686 0.2188       5.537      5.7577|
|  6:  2.7652 -  2.6030 0.99   1372  152 0.1643 0.2376      5.4223      5.6292|
|  7:  2.6030 -  2.4732 0.99   1344  156 0.1597 0.2070      5.3501      5.5209|
|  8:  2.4732 -  2.3660 0.98   1345  145 0.1587 0.2089       5.301      5.5185|
|  9:  2.3660 -  2.2752 0.98   1338  150 0.1608 0.2251      5.2658      5.5001|
| 10:  2.2752 -  2.1969 1.00   1353  151 0.1457 0.2028      5.1492      5.3277|
| 11:  2.1969 -  2.1284 0.98   1327  147 0.1450 0.2134      5.1098      5.4457|
| 12:  2.1284 -  2.0677 0.98   1350  145 0.1473 0.2178      5.0422      5.2593|
| 13:  2.0677 -  2.0134 0.74    993  113 0.1330 0.1950      4.9324      5.1042|
| 14:  2.0134 -  1.9644 0.16    222   23 0.1229 0.1739      4.8154      5.1299|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6919  1462   164  0.94   9.38   0.96     0.94       7669.53|
|  2:  4.6919 -  3.7420  1411   156  0.94   9.58   1.02     1.00      11252.21|
|  3:  3.7420 -  3.2743  1366   153  0.91  14.79   1.03     1.03      14876.17|
|  4:  3.2743 -  2.9773  1400   150  0.87  19.68   1.02     0.99      16767.10|
|  5:  2.9773 -  2.7652  1347   154  0.87  19.97   1.00     0.98      12890.93|
|  6:  2.7652 -  2.6030  1372   152  0.85  21.07   0.98     0.94      10523.81|
|  7:  2.6030 -  2.4732  1344   156  0.87  19.88   1.00     0.97       9167.03|
|  8:  2.4732 -  2.3660  1345   145  0.86  20.54   0.99     0.95       8462.24|
|  9:  2.3660 -  2.2752  1338   150  0.85  21.46   0.99     0.94       8047.44|
| 10:  2.2752 -  2.1969  1353   151  0.86  20.37   1.00     0.96       6662.79|
| 11:  2.1969 -  2.1284  1327   147  0.87  20.17   0.98     0.93       6218.27|
| 12:  2.1284 -  2.0677  1350   145  0.87  20.20   0.99     0.98       5538.68|
| 13:  2.0677 -  2.0134   993   113  0.87  20.17   0.98     0.96       4670.25|
| 14:  2.0134 -  1.9644   222    23  0.91  15.99   0.96     0.95       3471.06|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3471.06 max =        16767.10 mean =      9490.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.10|
|phase err.(test): min =        0.00 max =           89.77 mean =        17.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.085)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.42    105.09  19.35    None  None   None       |
|    all(noH): 2823   0      0.42    105.09  19.35    None  None   None       |
|    Sol.    : 438    0      6.96    105.09  49.10    None  None   None       |
|    Mac.    : 2385   0      0.42    93.84   13.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.421 -  10.888: 1118   |   5:    52.756 -  63.223:   84        |
|      1:    10.888 -  21.355: 1034   |   6:    63.223 -  73.690:   88        |
|      2:    21.355 -  31.822:  226   |   7:    73.690 -  84.157:   36        |
|      3:    31.822 -  42.289:  107   |   8:    84.157 -  94.624:   22        |
|      4:    42.289 -  52.756:  103   |   9:    94.624 - 105.090:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.612 - 5.346
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 347
   mapped sites are within: 0.736 - 5.346

peak=    8.342 closest distance to " O   HOH Z 103 " =    1.273
peak=    5.791 closest distance to " O   HOH Z 222 " =    1.761
peak=    5.605 closest distance to " O   HOH Z 182 " =    1.471
peak=    5.461 closest distance to " O   HOH Z 295 " =    1.498
peak=    5.236 closest distance to " O   HOH Z  11 " =    1.304
peak=    5.232 closest distance to " O   HOH Z 245 " =    1.125
peak=    5.219 closest distance to " O   HOH Z  63 " =    1.728
peak=    5.190 closest distance to " O   HOH Z  70 " =    1.314
peak=    5.177 closest distance to " O   HOH Z 131 " =    1.526
peak=    5.100 closest distance to " OE1 GLN A  73 " =    2.062
peak=    5.077 closest distance to " O   HOH Z  65 " =    1.491
peak=    5.050 closest distance to " CG  PRO A  90 " =    1.404
peak=    4.943 closest distance to " O   HOH Z 417 " =    2.537
peak=    4.913 closest distance to " CG  PRO A  54 " =    1.525
peak=    4.843 closest distance to " O   HOH Z 207 " =    1.395
peak=    4.793 closest distance to " CB  SER A  63 " =    1.442
peak=    4.754 closest distance to " NE2 GLN A  11 " =    1.224
peak=    4.719 closest distance to " O   HOH Z  67 " =    1.642
peak=    4.710 closest distance to " O   HOH Z   7 " =    1.924
peak=    4.701 closest distance to " NH1AARG A 145 " =    1.228
peak=    4.698 closest distance to " CB  PRO A  90 " =    1.184
peak=    4.665 closest distance to " O   HOH Z 287 " =    2.005
peak=    4.602 closest distance to " CB  PRO A  54 " =    1.244
peak=    4.582 closest distance to " CB  SER A 216 " =    1.153
peak=    4.542 closest distance to " O   HOH Z 105 " =    1.222
peak=    4.470 closest distance to " O   HOH Z 403 " =    1.392
peak=    4.462 closest distance to " O   HOH Z 117 " =    1.067
peak=    4.459 closest distance to " O   HOH Z 296 " =    1.235
peak=    4.452 closest distance to " O   HOH Z 147 " =    1.237
peak=    4.430 closest distance to " O   HOH Z 374 " =    1.178
peak=    4.430 closest distance to " O   HOH Z 427 " =    2.382
peak=    4.430 closest distance to " O   HOH Z  66 " =    1.032
peak=    4.421 closest distance to " CB  GLN A 223 " =    1.521
peak=    4.407 closest distance to " OE1 GLN A 240 " =    1.654
peak=    4.363 closest distance to " O   HOH Z 130 " =    1.108
peak=    4.347 closest distance to " O   PRO A 198 " =    1.360
peak=    4.333 closest distance to " O   HOH Z 390 " =    1.342
peak=    4.324 closest distance to " CB  ASN A 148 " =    1.487
peak=    4.276 closest distance to " O   HOH Z 126 " =    1.660
peak=    4.253 closest distance to " O   HOH Z 126 " =    1.985
peak=    4.212 closest distance to " O   GLN A  55 " =    1.439
peak=    4.193 closest distance to " O   HOH Z 132 " =    1.408
peak=    4.182 closest distance to " O   HOH Z  46 " =    1.186
peak=    4.170 closest distance to " O   HOH Z 419 " =    1.919
peak=    4.137 closest distance to " O   HOH Z 414 " =    2.218
peak=    4.125 closest distance to " O   HOH Z 148 " =    1.570
peak=    4.119 closest distance to " O   HOH Z 431 " =    1.239
peak=    4.108 closest distance to " CG2 THR A 221 " =    1.241
peak=    4.107 closest distance to " CE3 TRP A 274 " =    1.500
peak=    4.086 closest distance to " O   HOH Z 425 " =    1.698
peak=    4.074 closest distance to " NH2 ARG A  56 " =    1.076
peak=    4.072 closest distance to " O   HOH Z 380 " =    2.019
peak=    4.072 closest distance to " O   HOH Z 232 " =    2.154
peak=    4.069 closest distance to " O   HOH Z 410 " =    1.499
peak=    4.066 closest distance to " O   HOH Z 273 " =    1.521
peak=    4.066 closest distance to " O   HOH Z 427 " =    1.328
peak=    4.035 closest distance to " O   HOH Z  69 " =    1.627
peak=    4.033 closest distance to " O   HOH Z  28 " =    1.251
peak=    4.033 closest distance to " O   HOH Z  61 " =    1.895
peak=    4.028 closest distance to " O   HOH Z  39 " =    1.201
peak=    4.026 closest distance to " CB  ALA A 114 " =    0.925
peak=    4.018 closest distance to " CE  MET A  93 " =    1.422
peak=    4.008 closest distance to " CB  PHE A  61 " =    1.191
peak=    4.002 closest distance to " NE2 HIS A 207 " =    1.019
peak=    4.001 closest distance to " CB  LYS A 290 " =    0.932
peak=    3.980 closest distance to " O   HOH Z 158 " =    1.231
peak=    3.979 closest distance to " O   HOH Z  77 " =    1.333
peak=    3.965 closest distance to " ND2BASN A 224 " =    0.906
peak=    3.961 closest distance to " CZ3 TRP A 266 " =    1.199
peak=    3.957 closest distance to " O   HOH Z 145 " =    2.247
peak=    3.952 closest distance to " C   PRO A  54 " =    0.920
peak=    3.932 closest distance to " OE1 GLN A  77 " =    1.368
peak=    3.932 closest distance to " O   HOH Z 411 " =    3.157
peak=    3.928 closest distance to " O   HOH Z  88 " =    3.737
peak=    3.928 closest distance to " O   HOH Z  91 " =    2.435
peak=    3.925 closest distance to " O   HOH Z 255 " =    1.176
peak=    3.925 closest distance to " CG  GLN A  55 " =    0.829
peak=    3.913 closest distance to " O   HOH Z 217 " =    2.879
peak=    3.913 closest distance to " O   HOH Z 303 " =    1.315
peak=    3.909 closest distance to " C   ASN A 209 " =    1.508
peak=    3.898 closest distance to " CB  MET A  40 " =    0.917
peak=    3.883 closest distance to " O   HOH Z 183 " =    1.643
peak=    3.851 closest distance to " CA  VAL A 125 " =    1.145
peak=    3.845 closest distance to " O   HOH Z 193 " =    1.631
peak=    3.843 closest distance to " O   HOH Z 112 " =    0.924
peak=    3.841 closest distance to " CD  GLN A  55 " =    1.311
peak=    3.837 closest distance to " CB  TRP A 266 " =    1.022
peak=    3.836 closest distance to " O   HOH Z 414 " =    1.408
peak=    3.832 closest distance to " CG  LEU A 167 " =    1.313
peak=    3.830 closest distance to " O   HOH Z 369 " =    2.012
peak=    3.819 closest distance to " CB  PHE A 225 " =    1.568
peak=    3.810 closest distance to " CA  GLU A 152 " =    1.126
peak=    3.804 closest distance to " O   HOH Z 298 " =    2.398
peak=    3.801 closest distance to " O   HOH Z 102 " =    1.064
peak=    3.788 closest distance to " O   HOH Z 180 " =    2.147
peak=    3.781 closest distance to " CB  ARG A 275 " =    1.042
peak=    3.779 closest distance to " O   HOH Z  58 " =    1.971
peak=    3.775 closest distance to " CB  ASN A  60 " =    0.935
peak=    3.772 closest distance to " CA  ALA A  51 " =    1.043
peak=    3.765 closest distance to " ND2 ASN A  60 " =    2.834
peak=    3.764 closest distance to " N   VAL A 296 " =    1.836
peak=    3.759 closest distance to " CA  ASN A 127 " =    1.203
peak=    3.756 closest distance to " CB  MET A  47 " =    1.088
peak=    3.753 closest distance to " O   HOH Z 218 " =    1.670
peak=    3.748 closest distance to " O   HOH Z  53 " =    2.348
peak=    3.746 closest distance to " O   HOH Z 362 " =    2.013
peak=    3.739 closest distance to " O   HOH Z 112 " =    1.108
peak=    3.739 closest distance to " CD  ARG A 159 " =    0.806
peak=    3.738 closest distance to " O   TYR A 116 " =    1.313
peak=    3.736 closest distance to " CB  ALA A  43 " =    0.932
peak=    3.731 closest distance to " O   HOH Z 278 " =    1.213
peak=    3.731 closest distance to " CD  ARG A 195 " =    3.464
peak=    3.728 closest distance to " O   HOH Z 316 " =    3.041
peak=    3.713 closest distance to " O   HOH Z  97 " =    1.492
peak=    3.710 closest distance to " CA  ARG A 195 " =    1.518
peak=    3.692 closest distance to " OH  TYR A 116 " =    1.949
peak=    3.683 closest distance to " O   HOH Z 393 " =    1.584
peak=    3.683 closest distance to " CB  SER A  62 " =    1.025
peak=    3.682 closest distance to " NZ  LYS A 166 " =    0.961
peak=    3.682 closest distance to " CB  SER A   3 " =    1.665
peak=    3.681 closest distance to " O   HOH Z  26 " =    1.510
peak=    3.678 closest distance to " CD  LYS A  76 " =    1.673
peak=    3.674 closest distance to " CB  ARG A 102 " =    0.951
peak=    3.670 closest distance to " O   HOH Z 361 " =    1.498
peak=    3.670 closest distance to " CA  TYR A  30 " =    1.224
peak=    3.659 closest distance to " CB  GLU A 152 " =    1.090
peak=    3.646 closest distance to " O   HOH Z  52 " =    1.213
peak=    3.644 closest distance to " CG  PRO A 198 " =    1.261
peak=    3.640 closest distance to " N   GLN A 278 " =    1.149
peak=    3.638 closest distance to " O   HOH Z 139 " =    1.065
peak=    3.631 closest distance to " CZ  PHE A 218 " =    1.207
peak=    3.629 closest distance to " N   TYR A  15 " =    1.135
peak=    3.623 closest distance to " O   HOH Z 375 " =    1.109
peak=    3.622 closest distance to " CD  ARG A  56 " =    0.974
peak=    3.617 closest distance to " O   HOH Z 135 " =    1.411
peak=    3.616 closest distance to " CB  VAL A 265 " =    1.412
peak=    3.614 closest distance to " O   HOH Z 201 " =    1.803
peak=    3.604 closest distance to " O   HOH Z 248 " =    1.288
peak=    3.601 closest distance to " CG  GLN A  89 " =    1.515
peak=    3.599 closest distance to " O   HOH Z  92 " =    1.257
peak=    3.596 closest distance to " CG  PRO A 213 " =    1.384
peak=    3.579 closest distance to " N   PHE A 130 " =    1.257
peak=    3.573 closest distance to " O   HOH Z 216 " =    3.910
peak=    3.567 closest distance to " O   HOH Z 220 " =    1.511
peak=    3.567 closest distance to " O   HOH Z 437 " =    1.759
peak=    3.565 closest distance to " CB  SER A  99 " =    0.887
peak=    3.563 closest distance to " CB  TYR A  30 " =    1.283
peak=    3.562 closest distance to " CG2 ILE A  20 " =    1.516
peak=    3.556 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.553 closest distance to " CB  HIS A  86 " =    1.002
peak=    3.546 closest distance to " CB  SER A 141 " =    1.055
peak=    3.546 closest distance to " CB  ALA A 160 " =    1.474
peak=    3.538 closest distance to " O   ALA A 291 " =    1.470
peak=    3.531 closest distance to " O   HOH Z   9 " =    1.917
peak=    3.529 closest distance to " O   HOH Z 171 " =    2.277
peak=    3.528 closest distance to " O   HOH Z 147 " =    1.656
peak=    3.528 closest distance to " CB  TRP A 150 " =    1.150
peak=    3.527 closest distance to " O   HOH Z 327 " =    1.644
peak=    3.526 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.525 closest distance to " O   HOH Z 154 " =    2.368
peak=    3.519 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.517 closest distance to " NZ  LYS A 119 " =    2.461
peak=    3.517 closest distance to " O   HOH Z 313 " =    1.875
peak=    3.517 closest distance to " CA  TRP A  92 " =    1.234
peak=    3.515 closest distance to " O   HOH Z 293 " =    1.440
peak=    3.514 closest distance to " O   HOH Z 352 " =    1.787
peak=    3.514 closest distance to " CZ  PHE A  38 " =    1.334
peak=    3.513 closest distance to " O   HOH Z 189 " =    3.920
peak=    3.510 closest distance to " CB  ALA A 233 " =    1.094
peak=    3.508 closest distance to " O   HOH Z 171 " =    1.873
peak=    3.501 closest distance to " O   HOH Z 359 " =    1.471
peak=    3.500 closest distance to " CD2 TRP A 179 " =    2.088
peak=    3.498 closest distance to " CB  GLU A 175 " =    1.129
peak=    3.498 closest distance to " O   HOH Z 181 " =    2.337
peak=    3.492 closest distance to " CG1 VAL A 296 " =    1.214
peak=    3.492 closest distance to " CB  ASN A  39 " =    0.922
peak=    3.490 closest distance to " CB  GLU A 128 " =    1.003
peak=    3.487 closest distance to " O   HOH Z 124 " =    1.960
peak=    3.483 closest distance to " CE3 TRP A 150 " =    1.151
peak=    3.475 closest distance to " O   HOH Z 257 " =    1.213
peak=    3.466 closest distance to " O   HOH Z 380 " =    1.414
peak=    3.464 closest distance to " O   HOH Z  27 " =    1.018
peak=    3.456 closest distance to " O   HOH Z 207 " =    2.748
peak=    3.454 closest distance to " NH1BARG A 102 " =    1.041
peak=    3.450 closest distance to " O   THR A 251 " =    1.217
peak=    3.447 closest distance to " O   HOH Z 155 " =    1.933
peak=    3.445 closest distance to " C   GLN A  73 " =    1.181
peak=    3.438 closest distance to " N   ARG A 156 " =    1.287
peak=    3.434 closest distance to " OG ASER A 212 " =    1.437
peak=    3.431 closest distance to " NE2 GLN A 103 " =    1.039
peak=    3.428 closest distance to " O   HOH Z 240 " =    2.028
peak=    3.420 closest distance to " O   HOH Z 185 " =    2.282
peak=    3.418 closest distance to " CB  GLU A 277 " =    3.553
peak=    3.418 closest distance to " CD1 ILE A  33 " =    1.904
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.502
peak=    3.413 closest distance to " O   HOH Z 211 " =    1.683
peak=    3.408 closest distance to " CG  GLU A 277 " =    1.983
peak=    3.405 closest distance to " OG  SER A  26 " =    1.606
peak=    3.396 closest distance to " CD1 LEU A 300 " =    1.061
peak=    3.391 closest distance to " O   MET A 105 " =    1.708
peak=    3.389 closest distance to " CB  LEU A 300 " =    1.066
peak=    3.389 closest distance to " O   HOH Z 394 " =    1.676
peak=    3.387 closest distance to " CB  SER A 210 " =    0.996
peak=    3.386 closest distance to " O   HOH Z 251 " =    1.733
peak=    3.379 closest distance to " CG2 VAL A 257 " =    0.910
peak=    3.378 closest distance to " N   GLU A 152 " =    1.425
peak=    3.378 closest distance to " CB  ALA A  10 " =    1.032
peak=    3.373 closest distance to " O   HOH Z 434 " =    1.867
peak=    3.368 closest distance to " O   HOH Z 170 " =    1.200
peak=    3.362 closest distance to " CE  LYS A  76 " =    0.906
peak=    3.350 closest distance to " O   HOH Z 172 " =    5.214
peak=    3.348 closest distance to " O   HOH Z 205 " =    1.142
peak=    3.347 closest distance to " CG1 ILE A  20 " =    1.320
peak=    3.346 closest distance to " CA  ARG A 156 " =    1.077
peak=    3.345 closest distance to " O   HOH Z 119 " =    1.676
peak=    3.344 closest distance to " O   HOH Z 167 " =    1.777
peak=    3.340 closest distance to " O   HOH Z 153 " =    3.809
peak=    3.337 closest distance to " CB  ILE A 120 " =    1.280
peak=    3.334 closest distance to " CG2BVAL A  41 " =    1.106
peak=    3.333 closest distance to " O   HOH Z  32 " =    1.926
peak=    3.329 closest distance to " O   HOH Z  30 " =    1.760
peak=    3.329 closest distance to " O   HOH Z 184 " =    1.646
peak=    3.328 closest distance to " CG1 VAL A 202 " =    1.800
peak=    3.326 closest distance to " CB  TYR A 169 " =    0.828
peak=    3.325 closest distance to " O   HOH Z 288 " =    1.816
peak=    3.323 closest distance to " O   ALA A 158 " =    1.350
peak=    3.322 closest distance to " CB  GLN A 183 " =    1.190
peak=    3.322 closest distance to " O   HOH Z  88 " =    3.018
peak=    3.322 closest distance to " CB  GLU A 236 " =    1.514
peak=    3.320 closest distance to " CB  ASP A 200 " =    0.954
peak=    3.316 closest distance to " CA  ARG A  36 " =    1.250
peak=    3.315 closest distance to " CG1 ILE A 151 " =    1.112
peak=    3.315 closest distance to " CB  ALA A 137 " =    1.031
peak=    3.315 closest distance to " NH2BARG A 190 " =    1.290
peak=    3.314 closest distance to " O   THR A 220 " =    1.546
peak=    3.310 closest distance to " CA  ALA A   7 " =    0.977
peak=    3.309 closest distance to " O   HOH Z 152 " =    1.745
peak=    3.307 closest distance to " CB  ASP A 124 " =    0.899
peak=    3.305 closest distance to " CG2 ILE A 239 " =    0.991
peak=    3.303 closest distance to " OE2 GLU A  53 " =    1.073
peak=    3.302 closest distance to " ND2 ASN A 187 " =    1.757
peak=    3.297 closest distance to " O   HOH Z 280 " =    1.376
peak=    3.296 closest distance to " CB  ARG A  79 " =    1.084
peak=    3.293 closest distance to " O   HOH Z 371 " =    2.888
peak=    3.291 closest distance to " O   HOH Z 217 " =    1.419
peak=    3.285 closest distance to " O   HOH Z 373 " =    1.970
peak=    3.283 closest distance to " O   HOH Z 214 " =    2.519
peak=    3.281 closest distance to " CB  PHE A 130 " =    1.081
peak=    3.281 closest distance to " O   HOH Z  51 " =    1.924
peak=    3.280 closest distance to " O   HOH Z 332 " =    1.593
peak=    3.278 closest distance to " O   HOH Z 213 " =    2.190
peak=    3.275 closest distance to " O   HOH Z 422 " =    1.089
peak=    3.273 closest distance to " O   HOH Z 272 " =    1.894
peak=    3.271 closest distance to " O   HOH Z 199 " =    1.596
peak=    3.270 closest distance to " CA  ASN A 284 " =    1.045
peak=    3.270 closest distance to " CA  ALA A 160 " =    1.047
peak=    3.268 closest distance to " CD  LYS A 119 " =    1.722
peak=    3.267 closest distance to " O   HOH Z 298 " =    4.045
peak=    3.266 closest distance to " CB  SER A 276 " =    1.152
peak=    3.264 closest distance to " CE  LYS A 119 " =    1.189
peak=    3.263 closest distance to " CD2 TYR A  15 " =    1.356
peak=    3.256 closest distance to " CB  LEU A  83 " =    0.794
peak=    3.251 closest distance to " O   HOH Z 329 " =    4.200
peak=    3.248 closest distance to " O   HOH Z  47 " =    1.508
peak=    3.243 closest distance to " O   HOH Z 393 " =    3.225
peak=    3.240 closest distance to " O   HOH Z 328 " =    1.580
peak=    3.237 closest distance to " NZ ALYS A 290 " =    0.982
peak=    3.232 closest distance to " O   HOH Z 120 " =    1.082
peak=    3.231 closest distance to " O   HOH Z 116 " =    3.261
peak=    3.230 closest distance to " CD2 LEU A   5 " =    1.334
peak=    3.226 closest distance to " CA  VAL A 230 " =    1.160
peak=    3.221 closest distance to " O   HOH Z 171 " =    2.833
peak=    3.220 closest distance to " O   HOH Z 153 " =    4.206
peak=    3.218 closest distance to " O   HOH Z 215 " =    1.765
peak=    3.217 closest distance to " O   HOH Z 186 " =    3.025
peak=    3.213 closest distance to " CB  ASP A 191 " =    1.440
peak=    3.212 closest distance to " O   HOH Z 325 " =    2.191
peak=    3.211 closest distance to " CA  ILE A 234 " =    1.100
peak=    3.210 closest distance to " CB  ASP A  50 " =    1.121
peak=    3.209 closest distance to " O   HOH Z 258 " =    2.012
peak=    3.207 closest distance to " N   ALA A 165 " =    1.278
peak=    3.207 closest distance to " CD1 LEU A 228 " =    1.765
peak=    3.206 closest distance to " OE1 GLN A 278 " =    1.096
peak=    3.205 closest distance to " O   HOH Z   1 " =    1.618
peak=    3.205 closest distance to " CB  ARG A 156 " =    1.204
peak=    3.204 closest distance to " CA  SER A  95 " =    0.968
peak=    3.203 closest distance to " O   HOH Z 158 " =    2.891
peak=    3.201 closest distance to " CB  ALA A 161 " =    0.961
peak=    3.200 closest distance to " NE2 GLN A  73 " =    1.808
peak=    3.200 closest distance to " CB  ASN A 142 " =    0.942
peak=    3.199 closest distance to " O   HOH Z 412 " =    5.346
peak=    3.195 closest distance to " CD2 PHE A  59 " =    2.025
peak=    3.195 closest distance to " CD  LYS A 166 " =    1.591
peak=    3.194 closest distance to " O   HOH Z 106 " =    1.532
peak=    3.194 closest distance to " O   HOH Z   7 " =    3.127
peak=    3.193 closest distance to " CB  ALA A 299 " =    1.209
peak=    3.192 closest distance to " O   HOH Z 368 " =    2.005
peak=    3.190 closest distance to " N   CYS A 260 " =    0.923
peak=    3.181 closest distance to " O   HOH Z 284 " =    1.464
peak=    3.179 closest distance to " O   HOH Z 385 " =    0.973
peak=    3.179 closest distance to " O   HOH Z  40 " =    1.998
peak=    3.179 closest distance to " O   HOH Z 357 " =    1.973
peak=    3.179 closest distance to " CB  ALA A 184 " =    1.106
peak=    3.176 closest distance to " O   HOH Z 140 " =    1.816
peak=    3.176 closest distance to " CA  ALA A 291 " =    1.053
peak=    3.175 closest distance to " CD  GLN A  55 " =    0.894
peak=    3.169 closest distance to " O   PHE A  59 " =    0.867
peak=    3.167 closest distance to " OD2 ASP A  65 " =    3.183
peak=    3.164 closest distance to " O   HOH Z 368 " =    3.765
peak=    3.160 closest distance to " CE AMET A  47 " =    1.717
peak=    3.158 closest distance to " OE2 GLU A  53 " =    2.082
peak=    3.153 closest distance to " O   HOH Z  84 " =    1.429
peak=    3.152 closest distance to " N   PHE A  59 " =    0.736
peak=    3.151 closest distance to " N   SER A  97 " =    0.819
peak=    3.149 closest distance to " O   HOH Z 115 " =    1.653
peak=    3.147 closest distance to " O   GLY A 302 " =    1.791
peak=    3.145 closest distance to " O   HOH Z 279 " =    4.242
peak=    3.143 closest distance to " O   HOH Z  44 " =    2.852
peak=    3.143 closest distance to " O   HOH Z 353 " =    1.659
peak=    3.143 closest distance to " CA  PHE A 283 " =    1.211
peak=    3.142 closest distance to " CB  ARG A 190 " =    1.531
peak=    3.141 closest distance to " O   ASN A  69 " =    1.754
peak=    3.138 closest distance to " CA  PRO A  54 " =    1.108
peak=    3.137 closest distance to " CA  SER A  87 " =    0.987
peak=    3.133 closest distance to " O   HOH Z 128 " =    1.774
peak=    3.128 closest distance to " O   HOH Z 313 " =    1.533
peak=    3.123 closest distance to " CA  ASP A 162 " =    0.904
peak=    3.121 closest distance to " O   HOH Z 421 " =    2.955
peak=    3.120 closest distance to " CA  VAL A 121 " =    0.981
peak=    3.118 closest distance to " O   HOH Z 438 " =    2.486
peak=    3.117 closest distance to " CG AARG A 275 " =    1.291
peak=    3.114 closest distance to " O   HOH Z  43 " =    1.110
peak=    3.112 closest distance to " O   HOH Z 409 " =    4.796
peak=    3.110 closest distance to " O   HOH Z 357 " =    1.969
peak=    3.101 closest distance to " O   HOH Z 287 " =    1.870
peak=    3.096 closest distance to " NH2AARG A 145 " =    1.184
peak=    3.082 closest distance to " CB  ARG A 259 " =    1.484
peak=    3.080 closest distance to " CE1 PHE A 218 " =    1.120
peak=    3.075 closest distance to " CA  GLU A  46 " =    0.779
peak=    3.070 closest distance to " CB  SER A 212 " =    1.129
peak=    3.068 closest distance to " O   HOH Z  22 " =    2.659
peak=    3.057 closest distance to " CA  ALA A 129 " =    1.249
peak=    3.055 closest distance to " O   HOH Z 130 " =    3.162
peak=    3.033 closest distance to " NH2AARG A 190 " =    1.961

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.550 - 5.685
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 203
   mapped sites are within: 0.723 - 5.685

peak=   -4.804 closest distance to " OE1 GLN A  88 " =    0.936
peak=   -4.664 closest distance to " O   PRO A 198 " =    1.264
peak=   -4.479 closest distance to " CG  GLN A  88 " =    0.884
peak=   -4.389 closest distance to " O   HOH Z  32 " =    1.533
peak=   -4.356 closest distance to " CD  ARG A  14 " =    3.224
peak=   -4.176 closest distance to " CG  MET A 105 " =    1.012
peak=   -4.117 closest distance to " OG  SER A  97 " =    2.054
peak=   -4.106 closest distance to " CB  ASP A  27 " =    2.542
peak=   -4.046 closest distance to " O   HOH Z 389 " =    2.490
peak=   -4.033 closest distance to " O   HOH Z  60 " =    1.245
peak=   -4.019 closest distance to " O   HOH Z 216 " =    1.322
peak=   -4.016 closest distance to " O   ALA A  10 " =    1.659
peak=   -4.007 closest distance to " CB  GLN A  55 " =    1.200
peak=   -3.996 closest distance to " CD1 TYR A 247 " =    2.696
peak=   -3.990 closest distance to " CB  PRO A 243 " =    2.537
peak=   -3.986 closest distance to " CB  ALA A 291 " =    2.183
peak=   -3.980 closest distance to " O   HOH Z 111 " =    1.585
peak=   -3.980 closest distance to " C   PHE A  59 " =    1.082
peak=   -3.980 closest distance to " CG  ARG A 219 " =    2.387
peak=   -3.979 closest distance to " CD2 TYR A 293 " =    1.982
peak=   -3.947 closest distance to " O   HOH Z 257 " =    1.054
peak=   -3.941 closest distance to " O   HOH Z 100 " =    0.988
peak=   -3.928 closest distance to " CD2 LEU A 167 " =    1.836
peak=   -3.895 closest distance to " CD  ARG A 156 " =    1.943
peak=   -3.873 closest distance to " CD2 TYR A 116 " =    2.115
peak=   -3.870 closest distance to " NE1 TRP A 179 " =    1.221
peak=   -3.866 closest distance to " C   ILE A 239 " =    1.958
peak=   -3.852 closest distance to " CB  ALA A  43 " =    2.646
peak=   -3.828 closest distance to " CG2 ILE A  49 " =    2.873
peak=   -3.828 closest distance to " O   HOH Z 143 " =    1.245
peak=   -3.826 closest distance to " O   VAL A 125 " =    2.412
peak=   -3.808 closest distance to " O   PRO A 163 " =    1.904
peak=   -3.797 closest distance to " N   ALA A  43 " =    2.589
peak=   -3.796 closest distance to " O   HOH Z  39 " =    0.953
peak=   -3.795 closest distance to " O   GLY A  80 " =    2.583
peak=   -3.762 closest distance to " NE2 GLN A  55 " =    0.723
peak=   -3.752 closest distance to " CD  GLN A  55 " =    0.940
peak=   -3.751 closest distance to " O   HOH Z 313 " =    1.497
peak=   -3.744 closest distance to " O   GLN A 240 " =    3.091
peak=   -3.739 closest distance to " NZ  LYS A 166 " =    1.371
peak=   -3.724 closest distance to " CB  ALA A   9 " =    2.531
peak=   -3.699 closest distance to " CA  GLY A  98 " =    1.944
peak=   -3.694 closest distance to " O   HOH Z 103 " =    1.269
peak=   -3.690 closest distance to " NE2 GLN A 194 " =    2.030
peak=   -3.682 closest distance to " O   HOH Z  28 " =    1.116
peak=   -3.672 closest distance to " NE2 GLN A 223 " =    1.477
peak=   -3.668 closest distance to " O   HOH Z 193 " =    1.441
peak=   -3.635 closest distance to " O   SER A  22 " =    2.921
peak=   -3.625 closest distance to " O   SER A 135 " =    1.381
peak=   -3.599 closest distance to " O   HOH Z 298 " =    2.215
peak=   -3.588 closest distance to " CD  GLN A  55 " =    1.157
peak=   -3.581 closest distance to " O   GLY A 203 " =    2.572
peak=   -3.580 closest distance to " CB  ALA A 131 " =    1.898
peak=   -3.573 closest distance to " N   PRO A  54 " =    0.976
peak=   -3.571 closest distance to " N   LEU A 282 " =    2.159
peak=   -3.570 closest distance to " O   HOH Z 163 " =    1.709
peak=   -3.565 closest distance to " O   ASP A 253 " =    1.850
peak=   -3.565 closest distance to " CB  ALA A 227 " =    2.332
peak=   -3.561 closest distance to " CA  ASN A 110 " =    0.935
peak=   -3.561 closest distance to " OG  SER A  63 " =    1.172
peak=   -3.559 closest distance to " CZ3 TRP A 179 " =    1.264
peak=   -3.550 closest distance to " CA  HIS A 207 " =    1.116
peak=   -3.536 closest distance to " CG  ARG A 259 " =    2.538
peak=   -3.531 closest distance to " O   HOH Z  69 " =    1.408
peak=   -3.516 closest distance to " O   HOH Z 316 " =    1.717
peak=   -3.510 closest distance to " CA  GLY A 133 " =    2.011
peak=   -3.508 closest distance to " O   HOH Z  68 " =    1.388
peak=   -3.507 closest distance to " C   ASN A 285 " =    2.408
peak=   -3.505 closest distance to " O   HOH Z  77 " =    1.686
peak=   -3.505 closest distance to " O   HOH Z 276 " =    1.020
peak=   -3.490 closest distance to " O   HOH Z 368 " =    1.744
peak=   -3.480 closest distance to " OG BSER A 134 " =    1.695
peak=   -3.476 closest distance to " O   HOH Z 134 " =    1.497
peak=   -3.462 closest distance to " CB  HIS A  86 " =    1.257
peak=   -3.460 closest distance to " O   HOH Z 165 " =    1.855
peak=   -3.457 closest distance to " O   HOH Z  24 " =    0.956
peak=   -3.443 closest distance to " CD2 TYR A 169 " =    2.273
peak=   -3.438 closest distance to " O   HOH Z 198 " =    1.724
peak=   -3.436 closest distance to " CG2BVAL A  41 " =    1.213
peak=   -3.434 closest distance to " O   ASP A 162 " =    2.151
peak=   -3.434 closest distance to " O   HOH Z 128 " =    2.564
peak=   -3.429 closest distance to " O   HOH Z  37 " =    1.314
peak=   -3.422 closest distance to " CB  ALA A 160 " =    2.139
peak=   -3.418 closest distance to " CB  ALA A 161 " =    1.533
peak=   -3.417 closest distance to " CA  ARG A  56 " =    1.025
peak=   -3.409 closest distance to " CB  PRO A  54 " =    2.382
peak=   -3.406 closest distance to " CB  ASP A 171 " =    2.358
peak=   -3.402 closest distance to " CG1 VAL A  78 " =    2.418
peak=   -3.400 closest distance to " O   HOH Z 404 " =    1.188
peak=   -3.397 closest distance to " NH2AARG A 275 " =    5.685
peak=   -3.389 closest distance to " CD  LYS A 289 " =    2.283
peak=   -3.387 closest distance to " NE2 GLN A 240 " =    1.110
peak=   -3.386 closest distance to " C   VAL A  72 " =    0.907
peak=   -3.384 closest distance to " CE3 TRP A  70 " =    1.747
peak=   -3.383 closest distance to " CG2 THR A 221 " =    2.344
peak=   -3.381 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.381 closest distance to " O   GLU A 152 " =    1.531
peak=   -3.380 closest distance to " CD  LYS A 166 " =    2.574
peak=   -3.379 closest distance to " CA  GLY A  91 " =    2.353
peak=   -3.377 closest distance to " O   ILE A  49 " =    1.671
peak=   -3.374 closest distance to " CG  LEU A  83 " =    2.357
peak=   -3.374 closest distance to " O   HOH Z 385 " =    1.329
peak=   -3.374 closest distance to " O   HOH Z 277 " =    1.635
peak=   -3.371 closest distance to " CB  TYR A  68 " =    1.094
peak=   -3.370 closest distance to " CA  GLY A 241 " =    2.324
peak=   -3.363 closest distance to " O   HOH Z 286 " =    1.760
peak=   -3.348 closest distance to " O   HOH Z 300 " =    2.249
peak=   -3.348 closest distance to " O   ASP A  27 " =    1.802
peak=   -3.336 closest distance to " CH2 TRP A 179 " =    1.324
peak=   -3.332 closest distance to " OG  SER A  87 " =    1.587
peak=   -3.327 closest distance to " OE2 GLU A 152 " =    1.150
peak=   -3.325 closest distance to " O   ALA A  51 " =    1.336
peak=   -3.324 closest distance to " N   GLN A  58 " =    1.449
peak=   -3.323 closest distance to " O   HOH Z 188 " =    0.847
peak=   -3.319 closest distance to " CG  LEU A 282 " =    2.566
peak=   -3.318 closest distance to " O   HOH Z 348 " =    2.063
peak=   -3.317 closest distance to " O   HOH Z 357 " =    1.706
peak=   -3.314 closest distance to " OD1 ASN A 148 " =    1.476
peak=   -3.313 closest distance to " CZ  PHE A 225 " =    1.247
peak=   -3.311 closest distance to " O   ARG A  56 " =    4.462
peak=   -3.311 closest distance to " O   SER A 141 " =    1.777
peak=   -3.307 closest distance to " O   HOH Z 364 " =    2.984
peak=   -3.307 closest distance to " O   HOH Z  49 " =    1.591
peak=   -3.305 closest distance to " N   ARG A 159 " =    2.037
peak=   -3.298 closest distance to " O   HOH Z  67 " =    1.531
peak=   -3.291 closest distance to " O   HOH Z 118 " =    0.954
peak=   -3.288 closest distance to " O   HOH Z 231 " =    2.093
peak=   -3.285 closest distance to " CD2 PHE A  61 " =    2.052
peak=   -3.282 closest distance to " O   HOH Z 290 " =    1.168
peak=   -3.281 closest distance to " O   SER A  28 " =    1.125
peak=   -3.279 closest distance to " CG2BVAL A  72 " =    1.933
peak=   -3.276 closest distance to " OD2 ASP A 171 " =    1.664
peak=   -3.273 closest distance to " ND2 ASN A 285 " =    2.187
peak=   -3.271 closest distance to " CB  ALA A 100 " =    2.287
peak=   -3.270 closest distance to " N   TRP A 274 " =    1.098
peak=   -3.265 closest distance to " NE2 GLN A 122 " =    1.020
peak=   -3.264 closest distance to " O   HOH Z 278 " =    1.082
peak=   -3.262 closest distance to " O   HOH Z  76 " =    1.606
peak=   -3.259 closest distance to " O   HOH Z 378 " =    1.442
peak=   -3.258 closest distance to " O   HOH Z 181 " =    2.105
peak=   -3.252 closest distance to " CD  GLN A 223 " =    1.252
peak=   -3.248 closest distance to " O   HOH Z 251 " =    0.819
peak=   -3.248 closest distance to " O   HOH Z 434 " =    1.826
peak=   -3.247 closest distance to " OE1 GLN A 278 " =    1.260
peak=   -3.246 closest distance to " CG  PRO A 213 " =    1.986
peak=   -3.244 closest distance to " NH2 ARG A  56 " =    1.115
peak=   -3.243 closest distance to " CE1 PHE A  16 " =    2.727
peak=   -3.231 closest distance to " O   HOH Z  32 " =    1.572
peak=   -3.227 closest distance to " N   GLN A 122 " =    1.383
peak=   -3.226 closest distance to " O   HOH Z   5 " =    1.654
peak=   -3.224 closest distance to " O   HOH Z 201 " =    1.900
peak=   -3.221 closest distance to " O   HOH Z 189 " =    1.199
peak=   -3.220 closest distance to " O   MET A  47 " =    2.734
peak=   -3.218 closest distance to " NH2 ARG A  79 " =    2.177
peak=   -3.212 closest distance to " O   THR A  52 " =    1.504
peak=   -3.211 closest distance to " O   HOH Z 318 " =    1.358
peak=   -3.210 closest distance to " CG  MET A 185 " =    2.739
peak=   -3.210 closest distance to " CA  GLY A 133 " =    2.203
peak=   -3.209 closest distance to " CD1 LEU A 101 " =    2.373
peak=   -3.209 closest distance to " CZ  PHE A  38 " =    2.501
peak=   -3.208 closest distance to " O   HOH Z 337 " =    1.374
peak=   -3.205 closest distance to " CA  GLY A 203 " =    2.514
peak=   -3.203 closest distance to " CG1BVAL A  41 " =    2.768
peak=   -3.200 closest distance to " O   HOH Z 285 " =    1.704
peak=   -3.199 closest distance to " CG1 VAL A 126 " =    2.551
peak=   -3.197 closest distance to " CB  PHE A  61 " =    1.174
peak=   -3.195 closest distance to " CA  HIS A  86 " =    2.098
peak=   -3.195 closest distance to " O   ALA A   1 " =    1.751
peak=   -3.187 closest distance to " C   LEU A 101 " =    1.307
peak=   -3.184 closest distance to " CD2 HIS A 207 " =    1.421
peak=   -3.179 closest distance to " O   HOH Z 166 " =    1.780
peak=   -3.178 closest distance to " O   HOH Z 179 " =    1.595
peak=   -3.172 closest distance to " CB  TRP A  85 " =    1.978
peak=   -3.170 closest distance to " CB  PRO A 163 " =    2.393
peak=   -3.170 closest distance to " OD1 ASN A  60 " =    0.925
peak=   -3.165 closest distance to " O   HOH Z 417 " =    3.440
peak=   -3.165 closest distance to " CZ  TYR A 169 " =    1.724
peak=   -3.155 closest distance to " N   ASP A 191 " =    1.212
peak=   -3.151 closest distance to " O   HOH Z  11 " =    1.711
peak=   -3.149 closest distance to " O   HOH Z  37 " =    2.044
peak=   -3.144 closest distance to " CD  GLU A 277 " =    0.964
peak=   -3.138 closest distance to " O   HOH Z 131 " =    1.619
peak=   -3.136 closest distance to " CB  PRO A  90 " =    1.372
peak=   -3.132 closest distance to " O   HOH Z   4 " =    1.555
peak=   -3.129 closest distance to " O   HOH Z 138 " =    0.875
peak=   -3.125 closest distance to " C   LYS A  76 " =    1.331
peak=   -3.115 closest distance to " O   HOH Z 351 " =    1.723
peak=   -3.115 closest distance to " O   HOH Z 286 " =    1.539
peak=   -3.107 closest distance to " CG2 THR A  52 " =    3.183
peak=   -3.107 closest distance to " O   ASP A 171 " =    0.914
peak=   -3.107 closest distance to " OG  SER A  28 " =    2.163
peak=   -3.099 closest distance to " O   HOH Z 389 " =    1.190
peak=   -3.079 closest distance to " OG  SER A 245 " =    1.622
peak=   -3.078 closest distance to " NE2 GLN A  77 " =    1.843
peak=   -3.076 closest distance to " O   HOH Z 131 " =    3.881
peak=   -3.059 closest distance to " O   LYS A  76 " =    1.940
peak=   -3.057 closest distance to " O   PRO A 243 " =    2.414
peak=   -3.036 closest distance to " NH1 ARG A 195 " =    2.387
peak=   -3.007 closest distance to " O   HOH Z 364 " =    2.059

================= 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    :  0.4968 0.4997   6.304897e+00   6.293920e+00
   1_bss:  0.4900 0.4975   6.302927e+00   6.291067e+00
   1_xyz:  0.3980 0.4378   6.173702e+00   6.225133e+00
   1_adp:  0.3604 0.4504   6.135947e+00   6.236789e+00
   1_occ:  0.3598 0.4516   6.135865e+00   6.237101e+00
   2_bss:  0.3602 0.4501   6.137467e+00   6.236758e+00
   2_xyz:  0.2986 0.3721   5.982098e+00   6.124079e+00
   2_adp:  0.2794 0.3609   5.948049e+00   6.103636e+00
   2_occ:  0.2794 0.3611   5.947933e+00   6.104094e+00
   3_bss:  0.2795 0.3609   5.947959e+00   6.103243e+00
   3_xyz:  0.2355 0.3107   5.806436e+00   5.993562e+00
   3_adp:  0.2140 0.2955   5.744895e+00   5.951000e+00
   3_occ:  0.2140 0.2951   5.744163e+00   5.950698e+00
   4_bss:  0.2142 0.2951   5.743827e+00   5.950571e+00
   4_xyz:  0.1786 0.2490   5.574024e+00   5.810780e+00
   4_adp:  0.1682 0.2312   5.518505e+00   5.744106e+00
   4_occ:  0.1682 0.2311   5.518020e+00   5.743768e+00
   5_bss:  0.1685 0.2308   5.517300e+00   5.742603e+00
   5_xyz:  0.1460 0.1999   5.379243e+00   5.614562e+00
   5_adp:  0.1396 0.1932   5.339244e+00   5.571653e+00
   5_occ:  0.1395 0.1931   5.338938e+00   5.571423e+00
   5_bss:  0.1397 0.1932   5.338336e+00   5.570050e+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:  0.318  64.465  -0.695  -0.099   2.952  -0.000   0.000   0.000
   1_xyz:  0.318  64.465  -0.695  -0.099   2.952  -0.000   0.000   0.000
   1_adp:  0.318  64.465  -0.695  -0.099   2.952  -0.000   0.000   0.000
   1_occ:  0.318  64.465  -0.695  -0.099   2.952  -0.000   0.000   0.000
   2_bss:  0.367  96.556  -0.302  -0.688   2.078  -0.000   0.000   0.000
   2_xyz:  0.367  96.556  -0.302  -0.688   2.078  -0.000   0.000   0.000
   2_adp:  0.367  96.556  -0.302  -0.688   2.078  -0.000   0.000   0.000
   2_occ:  0.367  96.556  -0.302  -0.688   2.078  -0.000   0.000   0.000
   3_bss:  0.354  85.989  -0.950  -1.355   0.801  -0.000   0.000   0.000
   3_xyz:  0.354  85.989  -0.950  -1.355   0.801  -0.000   0.000   0.000
   3_adp:  0.354  85.989  -0.950  -1.355   0.801  -0.000   0.000   0.000
   3_occ:  0.354  85.989  -0.950  -1.355   0.801  -0.000   0.000   0.000
   4_bss:  0.350  97.869  -1.852  -2.333  -0.038  -0.000  -0.000  -0.000
   4_xyz:  0.350  97.869  -1.852  -2.333  -0.038  -0.000  -0.000  -0.000
   4_adp:  0.350  97.869  -1.852  -2.333  -0.038  -0.000  -0.000  -0.000
   4_occ:  0.350  97.869  -1.852  -2.333  -0.038  -0.000  -0.000  -0.000
   5_bss:  0.339  87.466  -2.034  -2.731  -0.475  -0.000  -0.000  -0.000
   5_xyz:  0.339  87.466  -2.034  -2.731  -0.475  -0.000  -0.000  -0.000
   5_adp:  0.339  87.466  -2.034  -2.731  -0.475  -0.000  -0.000  -0.000
   5_occ:  0.339  87.466  -2.034  -2.731  -0.475  -0.000  -0.000  -0.000
   5_bss:  0.329  77.024  -2.401  -3.111  -0.865  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.157 0.3256  0.4455    83808.465
   1_bss:  64.833 0.3291  0.4715    83394.057
   1_xyz:  51.464 0.5014  0.6982    58480.416
   1_adp:  52.444 0.4886  0.7003    61032.108
   1_occ:  52.548 0.4872  0.6979    61185.336
   2_bss:  52.432 0.4887  0.6922    61040.607
   2_xyz:  41.227 0.6261  0.8644    39570.211
   2_adp:  39.527 0.6469  0.8872    37242.827
   2_occ:  39.549 0.6466  0.8865    37283.097
   3_bss:  39.486 0.6472  0.8613    37148.017
   3_xyz:  32.697 0.7264  0.9449    26493.662
   3_adp:  30.558 0.7505  0.9443    23371.163
   3_occ:  30.541 0.7506  0.9441    23310.477
   4_bss:  30.476 0.7513  0.9160    23265.368
   4_xyz:  25.150 0.8080  0.9624    16124.780
   4_adp:  22.907 0.8321  0.9694    14097.922
   4_occ:  22.893 0.8323  0.9693    14072.797
   5_bss:  22.838 0.8327  0.9585    14008.588
   5_xyz:  19.176 0.8688  0.9801    10299.151
   5_adp:  18.065 0.8798  0.9803     9532.984
   5_occ:  18.058 0.8799  0.9802     9522.887
   5_bss:  18.029 0.8801  0.9672     9489.653
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7197e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7197e-01
   1_xyz:   1.632  0.012  0.111 16.577  0.006  4.107   1.5604e-01
   1_adp:   1.632  0.012  0.111 16.577  0.006  4.107   1.5604e-01
   1_occ:   1.632  0.012  0.111 16.577  0.006  4.107   1.5604e-01
   2_bss:   1.632  0.012  0.111 16.577  0.006  4.107   1.5604e-01
   2_xyz:   1.377  0.010  0.098 15.221  0.006  4.109   1.0134e-01
   2_adp:   1.377  0.010  0.098 15.221  0.006  4.109   1.0134e-01
   2_occ:   1.377  0.010  0.098 15.221  0.006  4.109   1.0134e-01
   3_bss:   1.377  0.010  0.098 15.221  0.006  4.109   1.0134e-01
   3_xyz:   1.031  0.008  0.070 14.816  0.004  4.120   6.5528e-02
   3_adp:   1.031  0.008  0.070 14.816  0.004  4.120   6.5528e-02
   3_occ:   1.031  0.008  0.070 14.816  0.004  4.120   6.5528e-02
   4_bss:   1.031  0.008  0.070 14.816  0.004  4.120   6.5528e-02
   4_xyz:   0.982  0.007  0.075 14.412  0.004  4.110   5.8708e-02
   4_adp:   0.982  0.007  0.075 14.412  0.004  4.110   5.8708e-02
   4_occ:   0.982  0.007  0.075 14.412  0.004  4.110   5.8708e-02
   5_bss:   0.982  0.007  0.075 14.412  0.004  4.110   5.8708e-02
   5_xyz:   1.026  0.008  0.074 14.499  0.003  4.121   6.2611e-02
   5_adp:   1.026  0.008  0.074 14.499  0.003  4.121   6.2611e-02
   5_occ:   1.026  0.008  0.074 14.499  0.003  4.121   6.2611e-02
   5_bss:   1.026  0.008  0.074 14.499  0.003  4.121   6.2611e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4297e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4297e-01
   1_xyz:   9.358  0.069  0.378 83.628  0.039  1.977   1.0924e-01
   1_adp:   9.358  0.069  0.378 83.628  0.039  1.977   1.0924e-01
   1_occ:   9.358  0.069  0.378 83.628  0.039  1.977   1.0924e-01
   2_bss:   9.358  0.069  0.378 83.628  0.039  1.977   1.0924e-01
   2_xyz:  10.899  0.051  0.323 80.524  0.050  2.039   1.0857e-01
   2_adp:  10.899  0.051  0.323 80.524  0.050  2.039   1.0857e-01
   2_occ:  10.899  0.051  0.323 80.524  0.050  2.039   1.0857e-01
   3_bss:  10.899  0.051  0.323 80.524  0.050  2.039   1.0857e-01
   3_xyz:   8.698  0.046  0.245 80.000  0.029  2.279   7.0032e-02
   3_adp:   8.698  0.046  0.245 80.000  0.029  2.279   7.0032e-02
   3_occ:   8.698  0.046  0.245 80.000  0.029  2.279   7.0032e-02
   4_bss:   8.698  0.046  0.245 80.000  0.029  2.279   7.0032e-02
   4_xyz:   7.132  0.049  0.264 80.716  0.041  2.313   4.9434e-02
   4_adp:   7.132  0.049  0.264 80.716  0.041  2.313   4.9434e-02
   4_occ:   7.132  0.049  0.264 80.716  0.041  2.313   4.9434e-02
   5_bss:   7.132  0.049  0.264 80.716  0.041  2.313   4.9434e-02
   5_xyz:   8.958  0.039  0.233 82.248  0.035  2.354   4.6311e-02
   5_adp:   8.958  0.039  0.233 82.248  0.035  2.354   4.6311e-02
   5_occ:   8.958  0.039  0.233 82.248  0.035  2.354   4.6311e-02
   5_bss:   8.958  0.039  0.233 82.248  0.035  2.354   4.6311e-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:  86.11   0.00  20.62  81.12   0.00  17.20  86.11   0.00  39.23
   1_occ:  86.11   0.00  20.62  81.12   0.00  17.20  86.11   0.00  39.23
   2_bss:  86.11   0.00  20.62  81.12   0.00  17.20  86.11   0.00  39.23
   2_xyz:  86.11   0.00  20.62  81.12   0.00  17.20  86.11   0.00  39.23
   2_adp:  85.47   0.00  20.47  78.84   0.00  16.81  85.47   0.00  40.42
   2_occ:  85.47   0.00  20.47  78.84   0.00  16.81  85.47   0.00  40.42
   3_bss:  85.47   0.00  20.47  78.84   0.00  16.81  85.47   0.00  40.42
   3_xyz:  85.47   0.00  20.47  78.84   0.00  16.81  85.47   0.00  40.42
   3_adp: 101.65   0.00  20.65  91.77   0.00  15.57 101.65   1.90  48.30
   3_occ: 101.65   0.00  20.65  91.77   0.00  15.57 101.65   1.90  48.30
   4_bss: 101.65   0.00  20.65  91.77   0.00  15.57 101.65   1.90  48.30
   4_xyz: 101.65   0.00  20.65  91.77   0.00  15.57 101.65   1.90  48.30
   4_adp: 107.02   0.00  19.78  95.70   0.00  14.39 107.02   4.97  49.11
   4_occ: 107.02   0.00  19.78  95.70   0.00  14.39 107.02   4.97  49.11
   5_bss: 107.02   0.00  19.78  95.70   0.00  14.39 107.02   4.97  49.11
   5_xyz: 107.02   0.00  19.78  95.70   0.00  14.39 107.02   4.97  49.11
   5_adp: 105.10   0.43  19.36  93.86   0.43  13.90 105.10   6.97  49.12
   5_occ: 105.10   0.43  19.36  93.86   0.43  13.90 105.10   6.97  49.12
   5_bss: 105.09   0.42  19.35  93.84   0.42  13.88 105.09   6.96  49.10
------------------------------------------------------------------------
 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:    1.573    0.027    0.413
   1_adp:    1.573    0.027    0.413
   1_occ:    1.573    0.027    0.413
   2_bss:    1.573    0.027    0.413
   2_xyz:    1.428    0.058    0.595
   2_adp:    1.428    0.058    0.595
   2_occ:    1.428    0.058    0.595
   3_bss:    1.428    0.058    0.595
   3_xyz:    1.378    0.056    0.711
   3_adp:    1.378    0.056    0.711
   3_occ:    1.378    0.056    0.711
   4_bss:    1.378    0.056    0.711
   4_xyz:    1.476    0.065    0.795
   4_adp:    1.476    0.065    0.795
   4_occ:    1.476    0.065    0.795
   5_bss:    1.476    0.065    0.795
   5_xyz:    1.566    0.090    0.857
   5_adp:    1.566    0.090    0.857
   5_occ:    1.566    0.090    0.857
   5_bss:    1.566    0.090    0.857
------------------------------------------------------------------------

CPU time actual refinement: 376.46


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/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_1110/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1110/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 376.33 
  Macro-tasks:
    bulk solvent and scale       = 64.63  
    individual site refinement   = 151.01 
    weights calculation          = 30.79  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 253.03 
  Micro-tasks:
    mask                            = 2.91   
    f_calc                          = 116.88 
    alpha_beta                      = 8.48   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 120.00 
    fmodel                         = 9.99   
    r_factors                      = 0.29   
    phase_errors                   = 10.85  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 270.88 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.290 micro seconds
Total CPU time: 6.49 minutes
from_scatterers_fft:    615 calls, 116.45 s
gradients_fft:          560 calls, 108.80 s

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

# Date 2008-01-16 Time 06:27:59 PST -0800 (1200493679.93 s)
Start R-work = 0.4968, R-free = 0.4997 (no bulk solvent and anisotropic scale)
Final R-work = 0.1615, R-free = 0.2110 (no bulk solvent and anisotropic scale)

Start R-work = 0.4900, R-free = 0.4975
Final R-work = 0.1397, R-free = 0.1932