# Date 2008-01-16 Time 05:13:08 PST -0800 (1200489188.38 s)
#phil __OFF__

Command line arguments: "../642.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19262
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 642

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.98157
Completeness in resolution range: 0.973463
Completeness with d_max=infinity: 0.970425

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9735
                             d_min =   1.9816

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.98157
Completeness in resolution range: 0.973463
Completeness with d_max=infinity: 0.970425

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9740 -  4.2399 [2108/2132]  1898   210  10.0%
  bin  2:  4.2399 -  3.3780 [2034/2054]  1829   205  10.1%
  bin  3:  3.3780 -  2.9548 [2003/2022]  1802   201  10.0%
  bin  4:  2.9548 -  2.6863 [1987/2017]  1792   195   9.8%
  bin  5:  2.6863 -  2.4947 [1980/1999]  1782   198  10.0%
  bin  6:  2.4947 -  2.3482 [1961/1986]  1759   202  10.3%
  bin  7:  2.3482 -  2.2310 [1950/1978]  1757   193   9.9%
  bin  8:  2.2310 -  2.1342 [1953/1989]  1760   193   9.9%
  bin  9:  2.1342 -  2.0522 [1927/1969]  1735   192  10.0%
  bin 10:  2.0522 -  1.9816 [1686/1977]  1516   170  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2212
        3.04 -     3.66: 4722
        3.66 -     4.28: 9130
        4.28 -     4.90: 12401
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.286 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  2.286 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  ... (remaining 28479 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_642/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/model_refine_001.geo

CPU time processing inputs: 9.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2821   r_free= 0.2801   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.940246                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7288 0.99   1378  152 0.2717 0.2656      6.3123      6.2539|
|  2:  4.7288 -  3.7732 0.99   1314  147 0.2208 0.2109      6.3189      6.2621|
|  3:  3.7732 -  3.3021 0.99   1294  143 0.2319 0.2288      6.2046      6.3137|
|  4:  3.3021 -  3.0028 0.99   1279  146 0.2496 0.2777      6.1064      6.1596|
|  5:  3.0028 -  2.7891 0.99   1288  142 0.2786 0.2528      5.9869       5.905|
|  6:  2.7891 -  2.6256 0.99   1275  140 0.2841 0.2914      5.9289      5.8798|
|  7:  2.6256 -  2.4947 0.99   1275  139 0.2973 0.2651      5.8923      5.8264|
|  8:  2.4947 -  2.3866 0.98   1246  142 0.3025 0.3197      5.8702      5.9202|
|  9:  2.3866 -  2.2950 0.98   1265  139 0.2980 0.3094      5.8051      5.7813|
| 10:  2.2950 -  2.2161 1.00   1253  143 0.3084 0.2869      5.7994      5.7027|
| 11:  2.2161 -  2.1470 0.97   1254  133 0.3244 0.3154      5.7857      5.7877|
| 12:  2.1470 -  2.0858 0.98   1243  142 0.3218 0.3302      5.7383      5.7542|
| 13:  2.0858 -  2.0310 0.99   1267  140 0.3297 0.3258        5.64      5.6317|
| 14:  2.0310 -  1.9816 0.79    999  111 0.3449 0.3343      5.6505      5.5145|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9740 -  4.7288  1378   152  0.81  24.48   0.87     0.83      37827.92|
|  2:  4.7288 -  3.7732  1314   147  0.87  19.64   0.99     0.94      37377.13|
|  3:  3.7732 -  3.3021  1294   143  0.85  22.01   1.02     1.00      34456.23|
|  4:  3.3021 -  3.0028  1279   146  0.83  23.60   1.02     0.99      29346.91|
|  5:  3.0028 -  2.7891  1288   142  0.80  26.52   1.01     0.98      23108.03|
|  6:  2.7891 -  2.6256  1275   140  0.80  26.64   1.02     0.98      19717.80|
|  7:  2.6256 -  2.4947  1275   139  0.79  27.91   1.03     0.99      18218.85|
|  8:  2.4947 -  2.3866  1246   142  0.79  28.22   1.05     0.98      17596.07|
|  9:  2.3866 -  2.2950  1265   139  0.79  28.31   1.05     0.99      16370.11|
| 10:  2.2950 -  2.2161  1253   143  0.77  29.57   1.07     1.01      15569.88|
| 11:  2.2161 -  2.1470  1254   133  0.75  31.31   1.07     1.02      15439.16|
| 12:  2.1470 -  2.0858  1243   142  0.75  31.92   1.09     1.00      14903.66|
| 13:  2.0858 -  2.0310  1267   140  0.72  33.98   1.07     0.97      13330.81|
| 14:  2.0310 -  1.9816   999   111  0.75  32.07   1.08     0.95      10596.95|
|alpha:            min =        0.83 max =            1.02 mean =         0.97|
|beta:             min =    10596.95 max =        37827.92 mean =     22064.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.94 mean =        27.45|
|phase err.(test): min =        0.00 max =           89.81 mean =        27.42|
|-----------------------------------------------------------------------------|

============================== 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 = 3.238692              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.342   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.010   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      211 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2001 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2859 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4686 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4444 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5644 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6757 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.162 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2821   r_free= 0.2801   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.940246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2647   r_free= 0.2622   ksol= 0.33   Bsol= 44.20   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,0.31,-1.40,0.00,-0.00,-0.00); trace/3= -1.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.914114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.897894              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.449   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262209              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.946   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2647      final r-factor (work) = 0.1575          |
| start r-factor (free) = 0.2622      final r-factor (free) = 0.1799          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7567 = 2.90 * 0.50 * 5.9327 + 1.00 * 0.1605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1527 = 2.90 * 0.50 * 5.5869 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1575      final r-factor (work) = 0.1462          |
| start r-factor (free) = 0.1799      final r-factor (free) = 0.1864          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4710 = 0.26 * 1.00 * 5.5869 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4205 = 0.26 * 1.00 * 5.3397 + 1.00 * 0.0204                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.32   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    62.32   16.48    None  None   None       |
|    Sol.    : 438    0      7.74    62.32   37.36    None  None   None       |
|    Mac.    : 2385   0      0.00    51.67   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.232:  187   |   5:    31.161 -  37.394:  103        |
|      1:     6.232 -  12.465: 1281   |   6:    37.394 -  43.626:  103        |
|      2:    12.465 -  18.697:  664   |   7:    43.626 -  49.858:   71        |
|      3:    18.697 -  24.929:  220   |   8:    49.858 -  56.090:   54        |
|      4:    24.929 -  31.161:  108   |   9:    56.090 -  62.322:   32        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1462 r_free = 0.1864             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.1864             target_work(ml) = 5.352         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1864   ksol= 0.33   Bsol= 44.20   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,0.31,-1.40,0.00,-0.00,-0.00); trace/3= -1.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.351878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1835   ksol= 0.33   Bsol= 45.53   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.07,-1.74,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.343040                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.038738              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.072  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.159920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.077   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1835      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5079 = 2.04 * 0.50 * 5.3468 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4084 = 2.04 * 0.50 * 5.2534 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0008 = 0.16 * 1.00 * 5.2534 + 1.00 * 0.1606                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8317 = 0.16 * 1.00 * 5.1588 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.91    65.59   16.51    None  None   None       |
|    all(noH): 2823   0      1.91    65.59   16.51    None  None   None       |
|    Sol.    : 438    0      4.17    65.59   37.08    None  None   None       |
|    Mac.    : 2385   0      1.91    58.04   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.909 -   8.277:  532   |   5:    33.748 -  40.115:  114        |
|      1:     8.277 -  14.645: 1289   |   6:    40.115 -  46.483:   84        |
|      2:    14.645 -  21.012:  423   |   7:    46.483 -  52.850:   86        |
|      3:    21.012 -  27.380:  139   |   8:    52.850 -  59.218:   49        |
|      4:    27.380 -  33.748:  102   |   9:    59.218 -  65.586:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1535             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1535             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1535   ksol= 0.33   Bsol= 45.53   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.07,-1.74,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1533   ksol= 0.33   Bsol= 45.53   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.37,-1.46,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141716                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.258389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.074  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.467484              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2981 = 1.26 * 0.50 * 5.1581 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2766 = 1.26 * 0.50 * 5.1329 + 1.00 * 0.0470                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5392 = 1.47 * 1.00 * 5.1329 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5178 = 1.47 * 1.00 * 5.1168 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    79.21   17.07    None  None   None       |
|    all(noH): 2823   0      0.54    79.21   17.07    None  None   None       |
|    Sol.    : 438    0      4.15    75.74   39.75    None  None   None       |
|    Mac.    : 2385   0      0.54    79.21   12.90    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:     0.539 -   8.406:  642   |   5:    39.876 -  47.743:  114        |
|      1:     8.406 -  16.274: 1321   |   6:    47.743 -  55.611:   76        |
|      2:    16.274 -  24.141:  341   |   7:    55.611 -  63.478:   66        |
|      3:    24.141 -  32.008:  133   |   8:    63.478 -  71.345:   24        |
|      4:    32.008 -  39.876:   98   |   9:    71.345 -  79.213:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1525             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1525             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1525   ksol= 0.33   Bsol= 45.53   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.37,-1.46,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122007                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1527   ksol= 0.32   Bsol= 46.58   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.34,-1.31,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122372                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.946922              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.102705              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.424  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1046          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5867 = 2.95 * 0.50 * 5.1170 + 1.00 * 0.0470                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5755 = 2.95 * 0.50 * 5.0964 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1046      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5324 = 0.10 * 1.00 * 5.0964 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5304 = 0.10 * 1.00 * 5.1037 + 1.00 * 0.0063                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.25    75.04   16.14    None  None   None       |
|    all(noH): 2823   0      2.25    75.04   16.14    None  None   None       |
|    Sol.    : 438    0      5.83    75.04   35.76    None  None   None       |
|    Mac.    : 2385   0      2.25    74.22   12.54    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:     2.253 -   9.532:  911   |   5:    38.648 -  45.927:   95        |
|      1:     9.532 -  16.811: 1128   |   6:    45.927 -  53.206:   81        |
|      2:    16.811 -  24.090:  294   |   7:    53.206 -  60.485:   27        |
|      3:    24.090 -  31.369:  129   |   8:    60.485 -  67.764:   11        |
|      4:    31.369 -  38.648:  142   |   9:    67.764 -  75.043:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1510             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1510             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1510   ksol= 0.32   Bsol= 46.58   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.34,-1.31,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1512   ksol= 0.32   Bsol= 41.17   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.29,-1.14,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.098221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.245365              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.472  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.239758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1067      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2443 = 1.25 * 0.50 * 5.1040 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2325 = 1.25 * 0.50 * 5.1140 + 1.00 * 0.0482                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2324 = 0.24 * 1.00 * 5.1140 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2330 = 0.24 * 1.00 * 5.1129 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    75.51   16.23    None  None   None       |
|    all(noH): 2823   0      1.34    75.51   16.23    None  None   None       |
|    Sol.    : 438    0      6.46    74.91   36.68    None  None   None       |
|    Mac.    : 2385   0      1.34    75.51   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.343 -   8.759:  757   |   5:    38.425 -  45.842:  114        |
|      1:     8.759 -  16.176: 1231   |   6:    45.842 -  53.258:   96        |
|      2:    16.176 -  23.592:  329   |   7:    53.258 -  60.675:   32        |
|      3:    23.592 -  31.009:  126   |   8:    60.675 -  68.092:   13        |
|      4:    31.009 -  38.425:  120   |   9:    68.092 -  75.508:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1528             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1528             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1528   ksol= 0.32   Bsol= 41.17   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.29,-1.14,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116167                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7288 0.99   1378  152 0.1006 0.1265      5.3857      5.4978|
|  2:  4.7288 -  3.7732 0.99   1314  147 0.0867 0.1118      5.4462       5.626|
|  3:  3.7732 -  3.3021 0.99   1294  143 0.1054 0.1481      5.4723      5.8466|
|  4:  3.3021 -  3.0028 0.99   1279  146 0.1191 0.1520      5.4355      5.5682|
|  5:  3.0028 -  2.7891 0.99   1288  142 0.1280 0.1703      5.3076      5.5412|
|  6:  2.7891 -  2.6256 0.99   1275  140 0.1152 0.1725      5.1793      5.3999|
|  7:  2.6256 -  2.4947 0.99   1275  139 0.1252 0.1480      5.1443      5.3224|
|  8:  2.4947 -  2.3866 0.98   1246  142 0.1114 0.1748      5.0215      5.3418|
|  9:  2.3866 -  2.2950 0.98   1265  139 0.1106 0.1653      4.9888      5.2163|
| 10:  2.2950 -  2.2161 1.00   1253  143 0.1076 0.1681      4.9238      5.2196|
| 11:  2.2161 -  2.1470 0.97   1254  133 0.1114 0.1663      4.9137      5.2139|
| 12:  2.1470 -  2.0858 0.98   1243  142 0.1063 0.1638      4.8398      5.1843|
| 13:  2.0858 -  2.0310 0.99   1267  140 0.1062 0.1666      4.7593      5.0406|
| 14:  2.0310 -  1.9816 0.79    999  111 0.1017 0.1663      4.6478      4.8886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9740 -  4.7288  1378   152  0.94   8.88   0.98     0.95       6788.99|
|  2:  4.7288 -  3.7732  1314   147  0.95   7.71   1.02     1.01       8817.61|
|  3:  3.7732 -  3.3021  1294   143  0.94  10.98   1.02     1.02      10168.36|
|  4:  3.3021 -  3.0028  1279   146  0.92  12.95   1.00     0.99       9789.62|
|  5:  3.0028 -  2.7891  1288   142  0.91  15.21   0.99     0.96       7895.29|
|  6:  2.7891 -  2.6256  1275   140  0.91  15.10   0.98     0.96       6605.71|
|  7:  2.6256 -  2.4947  1275   139  0.91  15.18   0.99     0.96       5817.05|
|  8:  2.4947 -  2.3866  1246   142  0.92  13.68   0.99     0.97       4632.03|
|  9:  2.3866 -  2.2950  1265   139  0.92  14.26   1.01     0.98       4536.52|
| 10:  2.2950 -  2.2161  1253   143  0.91  14.23   1.00     0.96       3943.70|
| 11:  2.2161 -  2.1470  1254   133  0.90  15.94   1.00     0.96       4145.68|
| 12:  2.1470 -  2.0858  1243   142  0.92  14.16   1.01     0.99       3606.90|
| 13:  2.0858 -  2.0310  1267   140  0.91  14.95   1.00     1.00       3134.14|
| 14:  2.0310 -  1.9816   999   111  0.92  13.88   0.98     0.94       2442.41|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2442.41 max =        10168.36 mean =      5965.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.31|
|phase err.(test): min =        0.00 max =           89.04 mean =        12.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1528   ksol= 0.32   Bsol= 41.12   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.17,-1.00,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1528   ksol= 0.32   Bsol= 41.12   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.17,-1.00,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116190                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7288 0.99   1378  152 0.1006 0.1266      5.3862      5.4984|
|  2:  4.7288 -  3.7732 0.99   1314  147 0.0867 0.1118      5.4465      5.6259|
|  3:  3.7732 -  3.3021 0.99   1294  143 0.1054 0.1482      5.4723      5.8468|
|  4:  3.3021 -  3.0028 0.99   1279  146 0.1191 0.1520      5.4355      5.5683|
|  5:  3.0028 -  2.7891 0.99   1288  142 0.1280 0.1703      5.3075       5.541|
|  6:  2.7891 -  2.6256 0.99   1275  140 0.1152 0.1725      5.1792      5.3998|
|  7:  2.6256 -  2.4947 0.99   1275  139 0.1252 0.1481      5.1444      5.3227|
|  8:  2.4947 -  2.3866 0.98   1246  142 0.1114 0.1748      5.0215      5.3417|
|  9:  2.3866 -  2.2950 0.98   1265  139 0.1106 0.1653      4.9888      5.2162|
| 10:  2.2950 -  2.2161 1.00   1253  143 0.1076 0.1682      4.9239        5.22|
| 11:  2.2161 -  2.1470 0.97   1254  133 0.1114 0.1663      4.9138      5.2138|
| 12:  2.1470 -  2.0858 0.98   1243  142 0.1062 0.1638      4.8397      5.1843|
| 13:  2.0858 -  2.0310 0.99   1267  140 0.1062 0.1666      4.7592      5.0403|
| 14:  2.0310 -  1.9816 0.79    999  111 0.1017 0.1662      4.6476      4.8884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9740 -  4.7288  1378   152  0.94   8.88   0.98     0.95       6797.67|
|  2:  4.7288 -  3.7732  1314   147  0.95   7.72   1.02     1.01       8823.66|
|  3:  3.7732 -  3.3021  1294   143  0.94  10.98   1.02     1.02      10169.59|
|  4:  3.3021 -  3.0028  1279   146  0.92  12.95   1.01     0.99       9788.55|
|  5:  3.0028 -  2.7891  1288   142  0.91  15.20   1.00     0.96       7893.17|
|  6:  2.7891 -  2.6256  1275   140  0.91  15.10   0.99     0.96       6604.69|
|  7:  2.6256 -  2.4947  1275   139  0.91  15.18   0.99     0.96       5816.96|
|  8:  2.4947 -  2.3866  1246   142  0.92  13.68   0.99     0.98       4631.44|
|  9:  2.3866 -  2.2950  1265   139  0.92  14.26   1.01     0.99       4537.04|
| 10:  2.2950 -  2.2161  1253   143  0.91  14.23   1.00     0.96       3943.47|
| 11:  2.2161 -  2.1470  1254   133  0.90  15.94   1.00     0.97       4146.40|
| 12:  2.1470 -  2.0858  1243   142  0.92  14.16   1.01     1.00       3606.31|
| 13:  2.0858 -  2.0310  1267   140  0.91  14.95   1.01     1.00       3132.99|
| 14:  2.0310 -  1.9816   999   111  0.92  13.87   0.99     0.95       2440.55|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2440.55 max =        10169.59 mean =      5966.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.31|
|phase err.(test): min =        0.00 max =           89.04 mean =        12.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    75.46   16.18    None  None   None       |
|    all(noH): 2823   0      1.30    75.46   16.18    None  None   None       |
|    Sol.    : 438    0      6.41    74.86   36.63    None  None   None       |
|    Mac.    : 2385   0      1.30    75.46   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.295 -   8.712:  757   |   5:    38.378 -  45.795:  114        |
|      1:     8.712 -  16.128: 1231   |   6:    45.795 -  53.211:   96        |
|      2:    16.128 -  23.545:  329   |   7:    53.211 -  60.628:   32        |
|      3:    23.545 -  30.961:  126   |   8:    60.628 -  68.044:   13        |
|      4:    30.961 -  38.378:  120   |   9:    68.044 -  75.461:    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)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 4.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 287
   mapped sites are within: 0.718 - 4.639

peak=    5.812 closest distance to " NH2 ARG A  56 " =    2.187
peak=    5.578 closest distance to " CG  PRO A  54 " =    1.324
peak=    5.567 closest distance to " NE2 GLN A  11 " =    1.192
peak=    5.544 closest distance to " O   HOH Z 126 " =    1.900
peak=    5.462 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.220 closest distance to " O   HOH Z 232 " =    2.345
peak=    5.187 closest distance to " CG  PRO A 213 " =    1.276
peak=    5.177 closest distance to " CB  GLN A 223 " =    1.435
peak=    5.092 closest distance to " O   HOH Z 144 " =    1.779
peak=    4.892 closest distance to " CB  SER A  63 " =    1.197
peak=    4.887 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.714 closest distance to " O   HOH Z  78 " =    1.796
peak=    4.632 closest distance to " CB  GLN A 183 " =    1.181
peak=    4.622 closest distance to " CG  PRO A  90 " =    1.124
peak=    4.608 closest distance to " CG2 VAL A 257 " =    0.929
peak=    4.496 closest distance to " O   HOH Z 236 " =    2.080
peak=    4.486 closest distance to " C   PRO A 198 " =    1.486
peak=    4.439 closest distance to " O   HOH Z 209 " =    2.264
peak=    4.417 closest distance to " CB  GLU A 152 " =    1.233
peak=    4.405 closest distance to " O   HOH Z 303 " =    2.109
peak=    4.402 closest distance to " O   HOH Z 369 " =    2.108
peak=    4.392 closest distance to " ND2 ASN A 187 " =    1.514
peak=    4.383 closest distance to " CB  SER A   3 " =    1.294
peak=    4.380 closest distance to " O   HOH Z 298 " =    1.917
peak=    4.377 closest distance to " O   HOH Z   9 " =    2.320
peak=    4.345 closest distance to " CB  ASN A 148 " =    1.446
peak=    4.338 closest distance to " CG  PRO A 243 " =    1.066
peak=    4.330 closest distance to " O   HOH Z 427 " =    2.823
peak=    4.318 closest distance to " CB  GLU A 128 " =    1.006
peak=    4.316 closest distance to " CG  PRO A 198 " =    1.291
peak=    4.239 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.231 closest distance to " O   HOH Z 234 " =    3.691
peak=    4.220 closest distance to " O   HOH Z  78 " =    2.120
peak=    4.213 closest distance to " CB  ARG A  79 " =    1.321
peak=    4.199 closest distance to " O   HOH Z  61 " =    1.647
peak=    4.199 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.190 closest distance to " CA  ASN A 215 " =    1.099
peak=    4.184 closest distance to " O   HOH Z 193 " =    1.768
peak=    4.184 closest distance to " O   HOH Z 158 " =    3.035
peak=    4.173 closest distance to " O   HOH Z 419 " =    2.120
peak=    4.160 closest distance to " CB  VAL A 265 " =    1.267
peak=    4.084 closest distance to " O   HOH Z  66 " =    2.237
peak=    4.051 closest distance to " O   HOH Z 316 " =    3.109
peak=    4.048 closest distance to " O   HOH Z 250 " =    1.467
peak=    4.042 closest distance to " O   HOH Z 272 " =    1.836
peak=    3.997 closest distance to " O   HOH Z 144 " =    2.229
peak=    3.989 closest distance to " O   HOH Z 203 " =    1.780
peak=    3.986 closest distance to " OD1 ASN A  69 " =    2.607
peak=    3.956 closest distance to " O   HOH Z 346 " =    1.711
peak=    3.931 closest distance to " CB  ARG A 190 " =    1.622
peak=    3.917 closest distance to " CB  SER A 216 " =    0.792
peak=    3.915 closest distance to " O   SER A  87 " =    2.202
peak=    3.902 closest distance to " CE  LYS A  76 " =    0.917
peak=    3.895 closest distance to " NZ  LYS A 117 " =    3.174
peak=    3.875 closest distance to " O   HOH Z 189 " =    2.232
peak=    3.873 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.849 closest distance to " O   HOH Z  44 " =    1.765
peak=    3.837 closest distance to " O   HOH Z 344 " =    3.140
peak=    3.827 closest distance to " O   HOH Z   9 " =    1.988
peak=    3.817 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.816 closest distance to " O   HOH Z   1 " =    1.977
peak=    3.803 closest distance to " O   HOH Z 132 " =    2.399
peak=    3.801 closest distance to " O   HOH Z  10 " =    1.831
peak=    3.797 closest distance to " CZ  PHE A 218 " =    1.025
peak=    3.786 closest distance to " O   HOH Z 368 " =    3.587
peak=    3.785 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.779 closest distance to " O   HOH Z  21 " =    1.748
peak=    3.744 closest distance to " O   HOH Z 402 " =    1.432
peak=    3.733 closest distance to " O  BHOH Z  74 " =    1.273
peak=    3.727 closest distance to " O   HOH Z 368 " =    1.851
peak=    3.718 closest distance to " O   HOH Z 245 " =    1.305
peak=    3.717 closest distance to " CD  ARG A 159 " =    0.718
peak=    3.716 closest distance to " CA  THR A 264 " =    0.853
peak=    3.714 closest distance to " CB  ASN A  39 " =    0.868
peak=    3.703 closest distance to " OD2 ASP A 286 " =    2.800
peak=    3.703 closest distance to " O   HOH Z 389 " =    1.822
peak=    3.700 closest distance to " NH1BARG A 145 " =    1.297
peak=    3.697 closest distance to " O   HOH Z  40 " =    1.614
peak=    3.694 closest distance to " NH1AARG A 145 " =    1.160
peak=    3.693 closest distance to " O   HOH Z  43 " =    1.891
peak=    3.689 closest distance to " O   HOH Z 425 " =    2.033
peak=    3.686 closest distance to " O   HOH Z 403 " =    1.671
peak=    3.683 closest distance to " O   HOH Z 265 " =    2.482
peak=    3.681 closest distance to " CG  ARG A  66 " =    2.463
peak=    3.675 closest distance to " O   HOH Z 305 " =    3.594
peak=    3.671 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.668 closest distance to " O   HOH Z 371 " =    1.690
peak=    3.662 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.658 closest distance to " O   HOH Z  64 " =    2.256
peak=    3.658 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.656 closest distance to " N   ARG A 156 " =    1.278
peak=    3.639 closest distance to " O   HOH Z 248 " =    1.633
peak=    3.633 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.628 closest distance to " CB  ALA A  34 " =    1.082
peak=    3.627 closest distance to " CD BLYS A 290 " =    1.216
peak=    3.621 closest distance to " CG2 ILE A 120 " =    1.190
peak=    3.618 closest distance to " CB  THR A 157 " =    1.108
peak=    3.616 closest distance to " O   HOH Z   1 " =    1.753
peak=    3.614 closest distance to " CB  ALA A 291 " =    1.312
peak=    3.610 closest distance to " CB  TRP A 179 " =    1.328
peak=    3.599 closest distance to " NH2AARG A 190 " =    1.951
peak=    3.597 closest distance to " O   HOH Z 291 " =    1.525
peak=    3.593 closest distance to " O   HOH Z 219 " =    2.242
peak=    3.590 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.589 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.586 closest distance to " N   PHE A 130 " =    1.235
peak=    3.585 closest distance to " O   HOH Z 386 " =    3.201
peak=    3.584 closest distance to " NH2BARG A 145 " =    2.030
peak=    3.581 closest distance to " CG  LEU A 167 " =    1.224
peak=    3.579 closest distance to " CD1 ILE A 106 " =    0.835
peak=    3.572 closest distance to " CB  SER A 212 " =    1.148
peak=    3.566 closest distance to " CA  ALA A  21 " =    1.135
peak=    3.563 closest distance to " CG1BVAL A  72 " =    1.494
peak=    3.556 closest distance to " CB  LEU A 143 " =    1.103
peak=    3.542 closest distance to " O   HOH Z 261 " =    2.244
peak=    3.534 closest distance to " CG1 VAL A 153 " =    0.926
peak=    3.531 closest distance to " CB  ASN A 142 " =    0.960
peak=    3.527 closest distance to " O   HOH Z 371 " =    2.964
peak=    3.524 closest distance to " CG2 THR A 221 " =    1.107
peak=    3.523 closest distance to " CB  ILE A 120 " =    1.200
peak=    3.520 closest distance to " O   HOH Z 327 " =    1.696
peak=    3.519 closest distance to " CG  GLN A  11 " =    1.951
peak=    3.510 closest distance to " O   HOH Z  93 " =    2.412
peak=    3.506 closest distance to " CA  ALA A  84 " =    1.272
peak=    3.503 closest distance to " O   HOH Z 148 " =    3.363
peak=    3.497 closest distance to " O   HOH Z 407 " =    2.202
peak=    3.494 closest distance to " O   HOH Z 207 " =    1.768
peak=    3.493 closest distance to " O   HOH Z 437 " =    1.563
peak=    3.485 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.479 closest distance to " O   HOH Z 147 " =    1.751
peak=    3.479 closest distance to " O   HOH Z  97 " =    2.001
peak=    3.477 closest distance to " CB  TYR A 116 " =    0.822
peak=    3.477 closest distance to " O   HOH Z 417 " =    3.225
peak=    3.475 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.473 closest distance to " O   HOH Z  40 " =    1.894
peak=    3.470 closest distance to " N   ASN A  39 " =    1.162
peak=    3.463 closest distance to " CB  ASP A 140 " =    0.860
peak=    3.462 closest distance to " O   HOH Z 180 " =    2.176
peak=    3.461 closest distance to " O   HOH Z 133 " =    1.516
peak=    3.461 closest distance to " O   HOH Z 433 " =    1.787
peak=    3.459 closest distance to " ND1 HIS A  86 " =    1.655
peak=    3.454 closest distance to " CA  SER A  87 " =    1.019
peak=    3.453 closest distance to " CD  PRO A 243 " =    1.496
peak=    3.452 closest distance to " CA  ALA A 233 " =    1.295
peak=    3.447 closest distance to " CA  ALA A  51 " =    0.879
peak=    3.445 closest distance to " O   HOH Z 172 " =    3.126
peak=    3.438 closest distance to " CB  SER A  62 " =    1.239
peak=    3.434 closest distance to " CG  MET A 113 " =    1.128
peak=    3.430 closest distance to " O   HOH Z 353 " =    2.618
peak=    3.418 closest distance to " O   HOH Z 234 " =    1.847
peak=    3.415 closest distance to " OG BSER A 164 " =    2.338
peak=    3.414 closest distance to " NZ  LYS A  76 " =    1.527
peak=    3.409 closest distance to " O   HOH Z 214 " =    2.091
peak=    3.408 closest distance to " CA  PHE A 283 " =    1.206
peak=    3.407 closest distance to " O   HOH Z  44 " =    3.073
peak=    3.404 closest distance to " O   HOH Z  59 " =    1.695
peak=    3.404 closest distance to " CG  LYS A  76 " =    0.967
peak=    3.402 closest distance to " O   HOH Z 273 " =    2.722
peak=    3.398 closest distance to " O   HOH Z 423 " =    1.474
peak=    3.396 closest distance to " CD2 LEU A 255 " =    1.475
peak=    3.395 closest distance to " O   HOH Z 213 " =    1.889
peak=    3.392 closest distance to " CD1 LEU A 300 " =    1.248
peak=    3.387 closest distance to " O   HOH Z  96 " =    2.131
peak=    3.386 closest distance to " OD1BASN A 224 " =    2.262
peak=    3.386 closest distance to " NE2 GLN A  73 " =    3.674
peak=    3.381 closest distance to " O   HOH Z 263 " =    1.653
peak=    3.380 closest distance to " CA  ARG A  36 " =    1.017
peak=    3.377 closest distance to " O   HOH Z 271 " =    2.292
peak=    3.367 closest distance to " O   HOH Z 345 " =    3.397
peak=    3.366 closest distance to " CB  GLU A 277 " =    3.513
peak=    3.364 closest distance to " O   HOH Z   6 " =    1.999
peak=    3.360 closest distance to " O   HOH Z 411 " =    3.798
peak=    3.359 closest distance to " CB  MET A  40 " =    0.814
peak=    3.356 closest distance to " CA  ASP A 162 " =    1.060
peak=    3.349 closest distance to " O   HOH Z 173 " =    1.860
peak=    3.343 closest distance to " CG2AVAL A 121 " =    2.407
peak=    3.342 closest distance to " O   HOH Z 284 " =    3.062
peak=    3.339 closest distance to " CB  LYS A 117 " =    1.219
peak=    3.338 closest distance to " O   HOH Z 357 " =    1.837
peak=    3.335 closest distance to " O   HOH Z 426 " =    1.852
peak=    3.333 closest distance to " O   HOH Z  88 " =    2.718
peak=    3.332 closest distance to " O   HOH Z 227 " =    2.127
peak=    3.325 closest distance to " O   HOH Z 409 " =    2.616
peak=    3.325 closest distance to " O   HOH Z  53 " =    2.546
peak=    3.321 closest distance to " CB  SER A 273 " =    0.855
peak=    3.320 closest distance to " O   HOH Z 257 " =    2.157
peak=    3.320 closest distance to " CA  ASN A 127 " =    1.063
peak=    3.313 closest distance to " N   GLN A 278 " =    1.190
peak=    3.310 closest distance to " CA  THR A 221 " =    0.971
peak=    3.304 closest distance to " CA  MET A  40 " =    1.093
peak=    3.303 closest distance to " O   HOH Z 163 " =    1.888
peak=    3.299 closest distance to " CB  ASN A 110 " =    1.055
peak=    3.299 closest distance to " CB  ASN A 224 " =    1.031
peak=    3.293 closest distance to " O   HOH Z 135 " =    1.621
peak=    3.291 closest distance to " O   MET A 105 " =    1.789
peak=    3.291 closest distance to " O   HOH Z 329 " =    3.764
peak=    3.284 closest distance to " CB  ALA A 242 " =    0.859
peak=    3.278 closest distance to " O   HOH Z 236 " =    1.465
peak=    3.277 closest distance to " O   HOH Z 435 " =    1.959
peak=    3.275 closest distance to " CB  SER A  26 " =    1.571
peak=    3.265 closest distance to " O   HOH Z 133 " =    2.521
peak=    3.265 closest distance to " CA  ILE A 234 " =    0.909
peak=    3.257 closest distance to " CA  ALA A 158 " =    1.206
peak=    3.254 closest distance to " O   HOH Z 406 " =    1.621
peak=    3.254 closest distance to " CZ2 TRP A 179 " =    1.755
peak=    3.253 closest distance to " CG  ARG A 159 " =    0.822
peak=    3.250 closest distance to " O   HOH Z  88 " =    2.544
peak=    3.247 closest distance to " CB  ALA A   1 " =    4.639
peak=    3.246 closest distance to " CB  VAL A 126 " =    0.969
peak=    3.246 closest distance to " O   HOH Z  88 " =    1.967
peak=    3.244 closest distance to " O   HOH Z 146 " =    1.647
peak=    3.244 closest distance to " CB  ALA A 114 " =    1.103
peak=    3.241 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.240 closest distance to " CD  LYS A 166 " =    1.226
peak=    3.235 closest distance to " O  BHOH Z 338 " =    2.353
peak=    3.229 closest distance to " CD  ARG A  36 " =    1.033
peak=    3.226 closest distance to " O   GLN A 278 " =    1.439
peak=    3.225 closest distance to " O   HOH Z 163 " =    1.847
peak=    3.223 closest distance to " CB  THR A 294 " =    1.721
peak=    3.223 closest distance to " O   HOH Z  85 " =    2.271
peak=    3.220 closest distance to " O   HOH Z 193 " =    1.868
peak=    3.218 closest distance to " NH1 ARG A 138 " =    1.148
peak=    3.217 closest distance to " OG  SER A 206 " =    1.295
peak=    3.216 closest distance to " CB  ALA A  21 " =    1.893
peak=    3.212 closest distance to " O   HOH Z 337 " =    3.673
peak=    3.211 closest distance to " O   HOH Z 183 " =    1.326
peak=    3.206 closest distance to " CB  MET A  47 " =    1.078
peak=    3.203 closest distance to " O   THR A 220 " =    1.306
peak=    3.202 closest distance to " OG  SER A  22 " =    2.707
peak=    3.198 closest distance to " CG1 ILE A 151 " =    0.987
peak=    3.193 closest distance to " CD1 LEU A  96 " =    0.857
peak=    3.188 closest distance to " O   HOH Z 188 " =    1.994
peak=    3.188 closest distance to " CA  ARG A 195 " =    1.166
peak=    3.187 closest distance to " O   HOH Z 234 " =    2.299
peak=    3.184 closest distance to " CA  ASN A 217 " =    1.234
peak=    3.181 closest distance to " CA  ALA A 291 " =    0.900
peak=    3.181 closest distance to " O   HOH Z  71 " =    2.260
peak=    3.177 closest distance to " CB  ALA A 248 " =    1.414
peak=    3.174 closest distance to " CD1 ILE A 263 " =    1.322
peak=    3.173 closest distance to " CB  GLN A 278 " =    0.816
peak=    3.164 closest distance to " O   HOH Z 336 " =    1.974
peak=    3.160 closest distance to " CG2 ILE A  20 " =    1.487
peak=    3.158 closest distance to " CG1 VAL A 189 " =    2.015
peak=    3.149 closest distance to " O   HOH Z 295 " =    1.564
peak=    3.142 closest distance to " CD  ARG A 219 " =    1.130
peak=    3.136 closest distance to " O   HOH Z 365 " =    2.949
peak=    3.136 closest distance to " NE2 HIS A 207 " =    1.368
peak=    3.136 closest distance to " O   ALA A   1 " =    1.727
peak=    3.136 closest distance to " N   ASN A 127 " =    1.230
peak=    3.131 closest distance to " ND1 HIS A  81 " =    1.648
peak=    3.128 closest distance to " O   HOH Z 423 " =    1.758
peak=    3.125 closest distance to " CA  ALA A 248 " =    1.227
peak=    3.123 closest distance to " N   TYR A  15 " =    0.743
peak=    3.122 closest distance to " CG BARG A 102 " =    1.760
peak=    3.121 closest distance to " CE AMET A  47 " =    1.387
peak=    3.120 closest distance to " O   HOH Z  49 " =    2.126
peak=    3.120 closest distance to " O   HOH Z 423 " =    2.711
peak=    3.120 closest distance to " CB  ARG A 138 " =    0.950
peak=    3.120 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.119 closest distance to " O   HOH Z 391 " =    2.929
peak=    3.117 closest distance to " CB  VAL A 268 " =    0.865
peak=    3.112 closest distance to " CB  ASP A 171 " =    0.826
peak=    3.108 closest distance to " CA  LYS A 290 " =    1.240
peak=    3.107 closest distance to " CZ  PHE A  38 " =    1.317
peak=    3.106 closest distance to " ND2 ASN A 249 " =    0.853
peak=    3.106 closest distance to " N   SER A 135 " =    1.168
peak=    3.103 closest distance to " CA  MET A 105 " =    0.935
peak=    3.097 closest distance to " N   ALA A   1 " =    2.038
peak=    3.097 closest distance to " CB  LEU A 300 " =    0.946
peak=    3.096 closest distance to " CB  ALA A 248 " =    0.878
peak=    3.095 closest distance to " O   HOH Z 359 " =    1.408
peak=    3.087 closest distance to " O   HOH Z 203 " =    1.219
peak=    3.085 closest distance to " O   HOH Z 411 " =    1.706
peak=    3.073 closest distance to " CB  GLU A  46 " =    1.101
peak=    3.072 closest distance to " O   HOH Z 151 " =    1.784
peak=    3.063 closest distance to " O   HOH Z 303 " =    1.618
peak=    3.061 closest distance to " O   HOH Z 291 " =    1.836
peak=    3.054 closest distance to " CB  ASN A 215 " =    1.055
peak=    3.049 closest distance to " NH2AARG A 190 " =    1.169
peak=    3.043 closest distance to " O   TRP A 274 " =    1.858
peak=    3.018 closest distance to " CA  ALA A 299 " =    0.946

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.505 - 5.248
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 185
   mapped sites are within: 0.724 - 5.248

peak=   -4.705 closest distance to " CB  PRO A 243 " =    2.626
peak=   -4.501 closest distance to " O   HOH Z 266 " =    4.911
peak=   -4.489 closest distance to " O   HOH Z 290 " =    1.060
peak=   -4.386 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.307 closest distance to " O   HOH Z 435 " =    2.832
peak=   -4.251 closest distance to " CG  GLN A 223 " =    1.767
peak=   -4.146 closest distance to " C   HIS A 108 " =    1.091
peak=   -4.120 closest distance to " CG1 VAL A 112 " =    2.880
peak=   -4.109 closest distance to " O   VAL A  67 " =    2.647
peak=   -4.102 closest distance to " CD  GLN A  58 " =    0.983
peak=   -4.089 closest distance to " ND2 ASN A  45 " =    1.484
peak=   -4.076 closest distance to " O   PRO A 198 " =    1.239
peak=   -4.066 closest distance to " CZ3 TRP A 179 " =    1.161
peak=   -4.057 closest distance to " SG  CYS A 254 " =    3.519
peak=   -4.051 closest distance to " O   HOH Z 377 " =    2.041
peak=   -4.050 closest distance to " CA  VAL A  67 " =    2.873
peak=   -4.036 closest distance to " O   HOH Z 389 " =    1.947
peak=   -4.018 closest distance to " O   HOH Z 372 " =    2.392
peak=   -3.981 closest distance to " O   HOH Z 351 " =    1.483
peak=   -3.944 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.941 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.918 closest distance to " OG BSER A 134 " =    1.220
peak=   -3.915 closest distance to " CD2 PHE A 192 " =    2.023
peak=   -3.914 closest distance to " CE2 PHE A 218 " =    2.500
peak=   -3.907 closest distance to " CG  PHE A 283 " =    2.713
peak=   -3.905 closest distance to " O   HOH Z 313 " =    1.899
peak=   -3.897 closest distance to " CE  MET A 105 " =    2.278
peak=   -3.871 closest distance to " O   ILE A 109 " =    2.565
peak=   -3.845 closest distance to " CE2 TYR A  30 " =    2.828
peak=   -3.834 closest distance to " O   HOH Z 185 " =    2.257
peak=   -3.801 closest distance to " O   HOH Z 407 " =    3.092
peak=   -3.786 closest distance to " O   HOH Z 231 " =    2.139
peak=   -3.775 closest distance to " CB  ALA A 248 " =    2.059
peak=   -3.768 closest distance to " N   GLN A  58 " =    1.788
peak=   -3.764 closest distance to " N   ALA A  43 " =    2.451
peak=   -3.755 closest distance to " CD  ARG A 139 " =    1.503
peak=   -3.754 closest distance to " CZ  PHE A  59 " =    1.473
peak=   -3.743 closest distance to " C   ALA A 158 " =    1.361
peak=   -3.724 closest distance to " CZ  TYR A 169 " =    1.670
peak=   -3.722 closest distance to " O   HOH Z 114 " =    3.014
peak=   -3.702 closest distance to " O   ARG A 145 " =    1.535
peak=   -3.700 closest distance to " O   HOH Z 353 " =    2.119
peak=   -3.692 closest distance to " CA  GLY A 203 " =    2.278
peak=   -3.682 closest distance to " O   HOH Z 198 " =    1.940
peak=   -3.681 closest distance to " CB  ASN A  39 " =    2.253
peak=   -3.670 closest distance to " CB  ALA A  43 " =    2.479
peak=   -3.660 closest distance to " CA  GLY A  98 " =    1.849
peak=   -3.645 closest distance to " OD1 ASN A 187 " =    1.527
peak=   -3.645 closest distance to " O   HOH Z 211 " =    1.664
peak=   -3.625 closest distance to " OD1 ASP A 171 " =    1.590
peak=   -3.594 closest distance to " O   HOH Z 298 " =    1.216
peak=   -3.577 closest distance to " O   PRO A 163 " =    1.959
peak=   -3.569 closest distance to " O   HOH Z 395 " =    5.188
peak=   -3.564 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.563 closest distance to " CG2 ILE A 263 " =    2.317
peak=   -3.562 closest distance to " OXT GLY A 302 " =    2.772
peak=   -3.559 closest distance to " O   ALA A 161 " =    1.540
peak=   -3.557 closest distance to " OG  SER A  97 " =    2.148
peak=   -3.549 closest distance to " O   VAL A 189 " =    2.530
peak=   -3.543 closest distance to " N   ASP A 286 " =    2.447
peak=   -3.539 closest distance to " C   LEU A 143 " =    1.113
peak=   -3.539 closest distance to " CD1 PHE A  59 " =    1.888
peak=   -3.538 closest distance to " O   HOH Z  43 " =    1.770
peak=   -3.533 closest distance to " O   HOH Z 198 " =    1.394
peak=   -3.531 closest distance to " OD2 ASP A 171 " =    2.319
peak=   -3.513 closest distance to " NH2AARG A 275 " =    5.248
peak=   -3.511 closest distance to " CB  CYS A 201 " =    2.592
peak=   -3.504 closest distance to " NE2 GLN A 278 " =    1.708
peak=   -3.498 closest distance to " O   HOH Z 126 " =    1.877
peak=   -3.485 closest distance to " ND2 ASN A 249 " =    2.112
peak=   -3.481 closest distance to " O   HOH Z 102 " =    1.619
peak=   -3.474 closest distance to " CB  PRO A 163 " =    2.535
peak=   -3.439 closest distance to " NH2BARG A 275 " =    1.827
peak=   -3.435 closest distance to " CD1 LEU A 228 " =    2.168
peak=   -3.430 closest distance to " O   TRP A  70 " =    1.474
peak=   -3.428 closest distance to " O   HOH Z 266 " =    4.646
peak=   -3.427 closest distance to " O   HOH Z 244 " =    2.100
peak=   -3.424 closest distance to " CB  PHE A 208 " =    2.250
peak=   -3.422 closest distance to " O   HOH Z  13 " =    1.460
peak=   -3.412 closest distance to " CD1 ILE A 239 " =    2.553
peak=   -3.408 closest distance to " O   GLN A 240 " =    2.061
peak=   -3.407 closest distance to " OD2 ASP A 191 " =    1.420
peak=   -3.404 closest distance to " O   HOH Z  63 " =    1.729
peak=   -3.404 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.402 closest distance to " N   THR A 157 " =    1.477
peak=   -3.401 closest distance to " CG  MET A 105 " =    0.950
peak=   -3.397 closest distance to " O   SER A 135 " =    1.468
peak=   -3.397 closest distance to " CG  GLU A 152 " =    0.724
peak=   -3.395 closest distance to " CG  GLU A 277 " =    1.254
peak=   -3.393 closest distance to " CE3 TRP A 274 " =    1.110
peak=   -3.390 closest distance to " OD1 ASN A 148 " =    1.566
peak=   -3.387 closest distance to " O   SER A  95 " =    1.495
peak=   -3.384 closest distance to " O   HOH Z  60 " =    2.427
peak=   -3.382 closest distance to " CG2 THR A 178 " =    2.261
peak=   -3.378 closest distance to " OD2 ASP A  50 " =    1.594
peak=   -3.378 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.377 closest distance to " O   SER A  22 " =    2.426
peak=   -3.377 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.375 closest distance to " N   ALA A 248 " =    1.602
peak=   -3.370 closest distance to " CD1 LEU A 101 " =    2.245
peak=   -3.370 closest distance to " O   HOH Z 385 " =    2.015
peak=   -3.369 closest distance to " O   HOH Z 322 " =    1.561
peak=   -3.359 closest distance to " CB  CYS A 254 " =    2.339
peak=   -3.357 closest distance to " O   HOH Z 282 " =    1.097
peak=   -3.349 closest distance to " CB  ASP A 286 " =    2.132
peak=   -3.336 closest distance to " O   HOH Z  51 " =    1.200
peak=   -3.322 closest distance to " CA  GLY A 241 " =    2.248
peak=   -3.314 closest distance to " CD2 LEU A 237 " =    2.811
peak=   -3.298 closest distance to " O   HOH Z  38 " =    1.607
peak=   -3.297 closest distance to " O   HOH Z  10 " =    1.465
peak=   -3.294 closest distance to " O   HOH Z  11 " =    1.827
peak=   -3.286 closest distance to " OG BSER A 134 " =    1.658
peak=   -3.281 closest distance to " O   HOH Z 388 " =    2.151
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    1.993
peak=   -3.277 closest distance to " CZ  PHE A 155 " =    1.233
peak=   -3.277 closest distance to " O   ALA A 180 " =    1.151
peak=   -3.275 closest distance to " O   GLY A 211 " =    1.279
peak=   -3.272 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.269 closest distance to " CG1 VAL A 230 " =    2.043
peak=   -3.269 closest distance to " N   SER A 212 " =    1.846
peak=   -3.268 closest distance to " NH1 ARG A 195 " =    2.545
peak=   -3.265 closest distance to " CA  GLY A 133 " =    1.999
peak=   -3.261 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.260 closest distance to " O   HOH Z 140 " =    1.594
peak=   -3.259 closest distance to " CD2 PHE A  61 " =    2.551
peak=   -3.257 closest distance to " OD1 ASP A 191 " =    1.522
peak=   -3.253 closest distance to " CG  LEU A  83 " =    1.807
peak=   -3.252 closest distance to " ND2BASN A 224 " =    1.800
peak=   -3.249 closest distance to " O   HOH Z 377 " =    0.826
peak=   -3.247 closest distance to " O   HOH Z  24 " =    1.393
peak=   -3.244 closest distance to " C   MET A 188 " =    1.438
peak=   -3.241 closest distance to " O   HOH Z  52 " =    1.150
peak=   -3.241 closest distance to " O   HOH Z 298 " =    2.352
peak=   -3.241 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.241 closest distance to " SG ACYS A 201 " =    1.839
peak=   -3.235 closest distance to " CD1 LEU A 297 " =    2.460
peak=   -3.233 closest distance to " CA  TRP A 274 " =    1.416
peak=   -3.231 closest distance to " CD  GLU A 236 " =    1.022
peak=   -3.231 closest distance to " OXT GLY A 302 " =    3.454
peak=   -3.231 closest distance to " O   PHE A 218 " =    1.558
peak=   -3.231 closest distance to " CB  ASP A 132 " =    2.228
peak=   -3.221 closest distance to " NH2 ARG A  79 " =    1.593
peak=   -3.214 closest distance to " ND2 ASN A 187 " =    1.550
peak=   -3.213 closest distance to " O   GLY A  80 " =    2.391
peak=   -3.210 closest distance to " CE1 TYR A 169 " =    2.526
peak=   -3.207 closest distance to " O   HOH Z 359 " =    3.283
peak=   -3.205 closest distance to " CG  TRP A 266 " =    1.960
peak=   -3.203 closest distance to " CA  GLY A 241 " =    3.215
peak=   -3.200 closest distance to " OG1 THR A 246 " =    1.387
peak=   -3.197 closest distance to " O   VAL A 189 " =    1.604
peak=   -3.196 closest distance to " OD1 ASN A 176 " =    1.336
peak=   -3.192 closest distance to " O   HOH Z 311 " =    3.531
peak=   -3.184 closest distance to " N   THR A 235 " =    1.284
peak=   -3.180 closest distance to " O   ASN A 249 " =    1.399
peak=   -3.179 closest distance to " O   ALA A  51 " =    1.415
peak=   -3.167 closest distance to " O   ALA A  34 " =    2.567
peak=   -3.163 closest distance to " O   VAL A 174 " =    2.096
peak=   -3.162 closest distance to " O   HOH Z 250 " =    1.422
peak=   -3.149 closest distance to " CG  GLN A  88 " =    0.825
peak=   -3.148 closest distance to " CD2 TYR A 293 " =    1.963
peak=   -3.144 closest distance to " CG  ARG A 269 " =    2.599
peak=   -3.140 closest distance to " O   HOH Z 281 " =    3.146
peak=   -3.139 closest distance to " O   HOH Z 423 " =    1.149
peak=   -3.137 closest distance to " CG1 VAL A 197 " =    2.145
peak=   -3.131 closest distance to " O   HOH Z 394 " =    1.419
peak=   -3.131 closest distance to " OE1 GLN A 223 " =    1.802
peak=   -3.122 closest distance to " O   HOH Z 175 " =    4.344
peak=   -3.120 closest distance to " OG  SER A 206 " =    1.728
peak=   -3.113 closest distance to " CE  LYS A  76 " =    2.837
peak=   -3.106 closest distance to " O   LYS A 289 " =    2.976
peak=   -3.106 closest distance to " OD2 ASP A 171 " =    1.744
peak=   -3.104 closest distance to " O   ALA A  10 " =    1.600
peak=   -3.104 closest distance to " O   ALA A 292 " =    1.975
peak=   -3.100 closest distance to " O   HOH Z 288 " =    1.437
peak=   -3.098 closest distance to " CB  ILE A  33 " =    2.934
peak=   -3.078 closest distance to " O   HOH Z 423 " =    2.119
peak=   -3.076 closest distance to " O   HOH Z 417 " =    2.498
peak=   -3.059 closest distance to " O   HOH Z 281 " =    2.685
peak=   -3.057 closest distance to " O   HOH Z 263 " =    2.989
peak=   -3.053 closest distance to " N   GLN A  77 " =    1.664
peak=   -3.017 closest distance to " CD2 LEU A 300 " =    2.873

================= 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    :  0.2821 0.2801   5.940246e+00   5.917296e+00
   1_bss:  0.2647 0.2622   5.914114e+00   5.879571e+00
   1_xyz:  0.1575 0.1799   5.398768e+00   5.509061e+00
   1_adp:  0.1462 0.1864   5.353717e+00   5.543117e+00
   1_occ:  0.1459 0.1864   5.351878e+00   5.542222e+00
   2_bss:  0.1447 0.1835   5.343040e+00   5.529528e+00
   2_xyz:  0.1196 0.1589   5.176264e+00   5.392851e+00
   2_adp:  0.1156 0.1535   5.143599e+00   5.363006e+00
   2_occ:  0.1155 0.1535   5.143394e+00   5.363170e+00
   3_bss:  0.1153 0.1533   5.141716e+00   5.361862e+00
   3_xyz:  0.1129 0.1513   5.128284e+00   5.352844e+00
   3_adp:  0.1106 0.1525   5.121985e+00   5.358741e+00
   3_occ:  0.1106 0.1525   5.122007e+00   5.358961e+00
   4_bss:  0.1106 0.1527   5.122372e+00   5.358938e+00
   4_xyz:  0.1046 0.1523   5.093066e+00   5.354666e+00
   4_adp:  0.1069 0.1510   5.097510e+00   5.345751e+00
   4_occ:  0.1068 0.1510   5.097532e+00   5.346101e+00
   5_bss:  0.1067 0.1512   5.098221e+00   5.347241e+00
   5_xyz:  0.1104 0.1525   5.119485e+00   5.357076e+00
   5_adp:  0.1092 0.1528   5.116184e+00   5.361054e+00
   5_occ:  0.1092 0.1528   5.116167e+00   5.361055e+00
   5_bss:  0.1091 0.1528   5.116190e+00   5.361080e+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:  0.334  44.203  -3.030   0.312  -1.400   0.000  -0.000  -0.000
   1_xyz:  0.334  44.203  -3.030   0.312  -1.400   0.000  -0.000  -0.000
   1_adp:  0.334  44.203  -3.030   0.312  -1.400   0.000  -0.000  -0.000
   1_occ:  0.334  44.203  -3.030   0.312  -1.400   0.000  -0.000  -0.000
   2_bss:  0.326  45.525  -3.055  -2.068  -1.744  -0.000  -0.000  -0.000
   2_xyz:  0.326  45.525  -3.055  -2.068  -1.744  -0.000  -0.000  -0.000
   2_adp:  0.326  45.525  -3.055  -2.068  -1.744  -0.000  -0.000  -0.000
   2_occ:  0.326  45.525  -3.055  -2.068  -1.744  -0.000  -0.000  -0.000
   3_bss:  0.326  45.525  -2.738  -2.371  -1.459  -0.000  -0.000  -0.000
   3_xyz:  0.326  45.525  -2.738  -2.371  -1.459  -0.000  -0.000  -0.000
   3_adp:  0.326  45.525  -2.738  -2.371  -1.459  -0.000  -0.000  -0.000
   3_occ:  0.326  45.525  -2.738  -2.371  -1.459  -0.000  -0.000  -0.000
   4_bss:  0.321  46.577  -2.518  -2.345  -1.314  -0.000  -0.000  -0.000
   4_xyz:  0.321  46.577  -2.518  -2.345  -1.314  -0.000  -0.000  -0.000
   4_adp:  0.321  46.577  -2.518  -2.345  -1.314  -0.000  -0.000  -0.000
   4_occ:  0.321  46.577  -2.518  -2.345  -1.314  -0.000  -0.000  -0.000
   5_bss:  0.321  41.171  -2.386  -2.290  -1.144  -0.000  -0.000  -0.000
   5_xyz:  0.321  41.171  -2.386  -2.290  -1.144  -0.000  -0.000  -0.000
   5_adp:  0.321  41.171  -2.386  -2.290  -1.144  -0.000  -0.000  -0.000
   5_occ:  0.321  41.171  -2.386  -2.290  -1.144  -0.000  -0.000  -0.000
   5_bss:  0.321  41.124  -2.237  -2.172  -1.004  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.447 0.7900  0.9723    22065.523
   1_bss:  26.031 0.8028  0.9382    18726.272
   1_xyz:  16.292 0.8970  1.0018     8254.549
   1_adp:  17.110 0.8895  0.9969     8770.189
   1_occ:  17.100 0.8895  0.9968     8730.584
   2_bss:  16.761 0.8924  0.9680     8456.974
   2_xyz:  13.986 0.9150  0.9797     6318.890
   2_adp:  13.417 0.9195  0.9783     5995.677
   2_occ:  13.423 0.9195  0.9781     5994.387
   3_bss:  13.388 0.9198  0.9823     5979.465
   3_xyz:  13.139 0.9220  0.9820     5866.585
   3_adp:  13.255 0.9211  0.9756     5899.525
   3_occ:  13.261 0.9210  0.9755     5904.234
   4_bss:  13.259 0.9211  0.9803     5903.835
   4_xyz:  13.190 0.9215  0.9808     5869.744
   4_adp:  12.998 0.9230  0.9779     5803.979
   4_occ:  13.008 0.9229  0.9778     5806.692
   5_bss:  13.031 0.9227  0.9818     5817.670
   5_xyz:  13.186 0.9217  0.9811     5932.395
   5_adp:  13.267 0.9211  0.9764     5964.738
   5_occ:  13.270 0.9211  0.9764     5965.839
   5_bss:  13.270 0.9211  0.9796     5966.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6051e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6051e-01
   1_xyz:   0.959  0.007  0.068 14.955  0.004  4.107   5.7539e-02
   1_adp:   0.959  0.007  0.068 14.955  0.004  4.107   5.7539e-02
   1_occ:   0.959  0.007  0.068 14.955  0.004  4.107   5.7539e-02
   2_bss:   0.959  0.007  0.068 14.955  0.004  4.107   5.7539e-02
   2_xyz:   0.930  0.006  0.071 14.645  0.004  4.105   5.3252e-02
   2_adp:   0.930  0.006  0.071 14.645  0.004  4.105   5.3252e-02
   2_occ:   0.930  0.006  0.071 14.645  0.004  4.105   5.3252e-02
   3_bss:   0.930  0.006  0.071 14.645  0.004  4.105   5.3252e-02
   3_xyz:   0.854  0.005  0.068 14.434  0.004  4.115   4.6955e-02
   3_adp:   0.854  0.005  0.068 14.434  0.004  4.115   4.6955e-02
   3_occ:   0.854  0.005  0.068 14.434  0.004  4.115   4.6955e-02
   4_bss:   0.854  0.005  0.068 14.434  0.004  4.115   4.6955e-02
   4_xyz:   1.045  0.008  0.080 14.903  0.005  4.117   6.6069e-02
   4_adp:   1.045  0.008  0.080 14.903  0.005  4.117   6.6069e-02
   4_occ:   1.045  0.008  0.080 14.903  0.005  4.117   6.6069e-02
   5_bss:   1.045  0.008  0.080 14.903  0.005  4.117   6.6069e-02
   5_xyz:   0.866  0.005  0.068 14.455  0.004  4.116   4.8160e-02
   5_adp:   0.866  0.005  0.068 14.455  0.004  4.116   4.8160e-02
   5_occ:   0.866  0.005  0.068 14.455  0.004  4.116   4.8160e-02
   5_bss:   0.866  0.005  0.068 14.455  0.004  4.116   4.8160e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3961e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3961e-01
   1_xyz:   7.169  0.049  0.285 85.250  0.039  2.266   5.7790e-02
   1_adp:   7.169  0.049  0.285 85.250  0.039  2.266   5.7790e-02
   1_occ:   7.169  0.049  0.285 85.250  0.039  2.266   5.7790e-02
   2_bss:   7.169  0.049  0.285 85.250  0.039  2.266   5.7790e-02
   2_xyz:   7.428  0.038  0.201 83.839  0.041  2.339   5.2970e-02
   2_adp:   7.428  0.038  0.201 83.839  0.041  2.339   5.2970e-02
   2_occ:   7.428  0.038  0.201 83.839  0.041  2.339   5.2970e-02
   3_bss:   7.428  0.038  0.201 83.839  0.041  2.339   5.2970e-02
   3_xyz:   6.734  0.036  0.218 84.534  0.037  2.376   2.9625e-02
   3_adp:   6.734  0.036  0.218 84.534  0.037  2.376   2.9625e-02
   3_occ:   6.734  0.036  0.218 84.534  0.037  2.376   2.9625e-02
   4_bss:   6.734  0.036  0.218 84.534  0.037  2.376   2.9625e-02
   4_xyz:   6.325  0.047  0.262 83.566  0.036  2.271   5.7909e-02
   4_adp:   6.325  0.047  0.262 83.566  0.036  2.271   5.7909e-02
   4_occ:   6.325  0.047  0.262 83.566  0.036  2.271   5.7909e-02
   5_bss:   6.325  0.047  0.262 83.566  0.036  2.271   5.7909e-02
   5_xyz:   6.520  0.039  0.215 83.999  0.039  2.340   3.0606e-02
   5_adp:   6.520  0.039  0.215 83.999  0.039  2.340   3.0606e-02
   5_occ:   6.520  0.039  0.215 83.999  0.039  2.340   3.0606e-02
   5_bss:   6.520  0.039  0.215 83.999  0.039  2.340   3.0606e-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:  62.32   0.00  16.48  51.67   0.00  12.64  62.32   7.74  37.36
   1_occ:  62.32   0.00  16.48  51.67   0.00  12.64  62.32   7.74  37.36
   2_bss:  62.32   0.00  16.48  51.67   0.00  12.64  62.32   7.74  37.36
   2_xyz:  62.32   0.00  16.48  51.67   0.00  12.64  62.32   7.74  37.36
   2_adp:  65.59   1.91  16.51  58.04   1.91  12.74  65.59   4.17  37.08
   2_occ:  65.59   1.91  16.51  58.04   1.91  12.74  65.59   4.17  37.08
   3_bss:  65.59   1.91  16.51  58.04   1.91  12.74  65.59   4.17  37.08
   3_xyz:  65.59   1.91  16.51  58.04   1.91  12.74  65.59   4.17  37.08
   3_adp:  79.21   0.54  17.07  79.21   0.54  12.90  75.74   4.15  39.75
   3_occ:  79.21   0.54  17.07  79.21   0.54  12.90  75.74   4.15  39.75
   4_bss:  79.21   0.54  17.07  79.21   0.54  12.90  75.74   4.15  39.75
   4_xyz:  79.21   0.54  17.07  79.21   0.54  12.90  75.74   4.15  39.75
   4_adp:  75.04   2.25  16.14  74.22   2.25  12.54  75.04   5.83  35.76
   4_occ:  75.04   2.25  16.14  74.22   2.25  12.54  75.04   5.83  35.76
   5_bss:  75.04   2.25  16.14  74.22   2.25  12.54  75.04   5.83  35.76
   5_xyz:  75.04   2.25  16.14  74.22   2.25  12.54  75.04   5.83  35.76
   5_adp:  75.51   1.34  16.23  75.51   1.34  12.48  74.91   6.46  36.68
   5_occ:  75.51   1.34  16.23  75.51   1.34  12.48  74.91   6.46  36.68
   5_bss:  75.46   1.30  16.18  75.46   1.30  12.43  74.86   6.41  36.63
------------------------------------------------------------------------
 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:    0.934    0.005    0.263
   1_adp:    0.934    0.005    0.263
   1_occ:    0.934    0.005    0.263
   2_bss:    0.934    0.005    0.263
   2_xyz:    0.661    0.024    0.304
   2_adp:    0.661    0.024    0.304
   2_occ:    0.661    0.024    0.304
   3_bss:    0.661    0.024    0.304
   3_xyz:    0.760    0.027    0.323
   3_adp:    0.760    0.027    0.323
   3_occ:    0.760    0.027    0.323
   4_bss:    0.760    0.027    0.323
   4_xyz:    0.860    0.031    0.336
   4_adp:    0.860    0.031    0.336
   4_occ:    0.860    0.031    0.336
   5_bss:    0.860    0.031    0.336
   5_xyz:    0.950    0.043    0.338
   5_adp:    0.950    0.043    0.338
   5_occ:    0.950    0.043    0.338
   5_bss:    0.950    0.043    0.338
------------------------------------------------------------------------

CPU time actual refinement: 324.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/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_642/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_642/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.43 
  Macro-tasks:
    bulk solvent and scale       = 42.34  
    individual site refinement   = 127.62 
    weights calculation          = 29.94  
    collect and process          = 6.81   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 206.80 
  Micro-tasks:
    mask                            = 1.10   
    f_calc                          = 102.89 
    alpha_beta                      = 8.70   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 106.27 
    fmodel                         = 6.85   
    r_factors                      = 0.18   
    phase_errors                   = 12.18  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 239.66 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.631 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    640 calls, 102.40 s
gradients_fft:          585 calls,  94.99 s

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

# Date 2008-01-16 Time 05:18:46 PST -0800 (1200489526.13 s)
Start R-work = 0.2821, R-free = 0.2801 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.2647, R-free = 0.2622
Final R-work = 0.1091, R-free = 0.1528