# Date 2008-01-16 Time 04:59:31 PST -0800 (1200488371.49 s)
#phil __OFF__

Command line arguments: "../545.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15409
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 545

-------------------------------------------------------------------------------
  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: (69.8988, 46.93, 86.822, 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: 3.33, 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: (69.8988, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99058
Completeness in resolution range: 0.972497
Completeness with d_max=infinity: 0.969417

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9906

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: (69.8988, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99058
Completeness in resolution range: 0.972497
Completeness with d_max=infinity: 0.969417

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2587 [2117/2141]  1903   214  10.1%
  bin  2:  4.2587 -  3.3932 [2037/2056]  1836   201   9.9%
  bin  3:  3.3932 -  2.9681 [2007/2026]  1808   199   9.9%
  bin  4:  2.9681 -  2.6985 [1983/2013]  1778   205  10.3%
  bin  5:  2.6985 -  2.5060 [1981/2000]  1786   195   9.8%
  bin  6:  2.5060 -  2.3589 [1964/1989]  1769   195   9.9%
  bin  7:  2.3589 -  2.2411 [1953/1981]  1758   195  10.0%
  bin  8:  2.2411 -  2.1439 [1946/1982]  1751   195  10.0%
  bin  9:  2.1439 -  2.0615 [1929/1971]  1735   194  10.1%
  bin 10:  2.0615 -  1.9906 [1672/1984]  1506   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2206
        3.04 -     3.66: 4634
        3.66 -     4.28: 9075
        4.28 -     4.90: 12326
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.096 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.240 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28247 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_545/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/model_refine_001.geo

CPU time processing inputs: 9.02


============================ 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 = 69.89875 46.93 86.82195 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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1962   r_free= 0.1943   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.549434                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.2379 0.2358      6.2157      6.1731|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.1501 0.1375      5.9438      5.9122|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.1616 0.1590      5.8333      5.8685|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.1649 0.1871      5.6911       5.746|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.1935 0.1696      5.6096      5.5345|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.1789 0.1906      5.4965      5.4632|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.1927 0.1894      5.4679      5.4694|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.1982 0.1806      5.4572      5.4131|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.1937 0.2066       5.374      5.3635|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.1956 0.2044      5.3708      5.3262|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.1985 0.1864      5.3263      5.2835|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.2073 0.2015      5.3174      5.3895|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.2066 0.1877      5.2232      5.1485|
| 14:  2.0402 -  1.9906 0.78    990  112 0.2112 0.1958      5.1917       5.073|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1380   153  0.82  22.82   0.88     0.83      32795.11|
|  2:  4.7496 -  3.7901  1312   149  0.91  14.50   1.01     0.96      21241.70|
|  3:  3.7901 -  3.3169  1305   145  0.92  13.49   1.03     1.01      14181.24|
|  4:  3.3169 -  3.0164  1290   136  0.92  14.15   1.03     1.02      11507.18|
|  5:  3.0164 -  2.8017  1268   144  0.89  17.06   1.06     1.01       9532.34|
|  6:  2.8017 -  2.6374  1276   145  0.90  16.29   1.05     1.01       7875.71|
|  7:  2.6374 -  2.5060  1280   142  0.90  16.77   1.06     1.03       6956.10|
|  8:  2.5060 -  2.3974  1261   136  0.90  16.76   1.07     1.05       6455.83|
|  9:  2.3974 -  2.3054  1253   143  0.90  16.82   1.10     1.07       6101.88|
| 10:  2.3054 -  2.2261  1261   136  0.89  17.70   1.12     1.08       5727.19|
| 11:  2.2261 -  2.1567  1263   142  0.89  17.54   1.10     1.10       5403.43|
| 12:  2.1567 -  2.0953  1228   139  0.90  17.16   1.13     1.12       4990.13|
| 13:  2.0953 -  2.0402  1263   137  0.90  17.08   1.12     1.12       4263.01|
| 14:  2.0402 -  1.9906   990   112  0.90  16.79   1.12     1.08       3281.77|
|alpha:            min =        0.83 max =            1.12 mean =         1.03|
|beta:             min =     3281.77 max =        32795.11 mean =     10329.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.80|
|phase err.(test): min =        0.00 max =           89.66 mean =        16.80|
|-----------------------------------------------------------------------------|

============================== 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 = 2.403819              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.697   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259722              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.084   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      189 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2017 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1829 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4402 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5613 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6713 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.143 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1962   r_free= 0.1943   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.549434                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1750   r_free= 0.1729   ksol= 0.33   Bsol= 50.00   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.87,-1.03,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.496045                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.202374              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.648   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.005   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3452 = 2.20 * 0.50 * 5.6166 + 1.00 * 0.1603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8453 = 2.20 * 0.50 * 5.2488 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1464      final r-factor (free) = 0.1469          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7765 = 0.15 * 1.00 * 5.2488 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7742 = 0.15 * 1.00 * 5.1211 + 1.00 * 0.0225                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.77   16.39    None  None   None       |
|    all(noH): 2823   0      0.00    62.77   16.39    None  None   None       |
|    Sol.    : 438    0      4.72    62.77   36.81    None  None   None       |
|    Mac.    : 2385   0      0.00    58.96   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 -   6.277:  130   |   5:    31.386 -  37.663:   99        |
|      1:     6.277 -  12.554: 1381   |   6:    37.663 -  43.940:  105        |
|      2:    12.554 -  18.831:  653   |   7:    43.940 -  50.217:   72        |
|      3:    18.831 -  25.108:  197   |   8:    50.217 -  56.494:   50        |
|      4:    25.108 -  31.386:  113   |   9:    56.494 -  62.771:   23        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1469             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1467             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1467   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.87,-1.03,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1466   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.70,-1.26,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.856583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.700  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.143599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.794   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1466      final r-factor (free) = 0.1487          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3794 = 2.86 * 0.50 * 5.1208 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3527 = 2.86 * 0.50 * 5.0950 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1487      final r-factor (free) = 0.1489          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7565 = 0.14 * 1.00 * 5.0950 + 1.00 * 0.0248                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7374 = 0.14 * 1.00 * 5.0907 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.20    65.36   16.36    None  None   None       |
|    all(noH): 2823   0      2.20    65.36   16.36    None  None   None       |
|    Sol.    : 438    0      5.09    64.73   36.13    None  None   None       |
|    Mac.    : 2385   0      2.20    65.36   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.195 -   8.511:  583   |   5:    33.776 -  40.092:  123        |
|      1:     8.511 -  14.827: 1274   |   6:    40.092 -  46.408:   89        |
|      2:    14.827 -  21.144:  394   |   7:    46.408 -  52.725:   83        |
|      3:    21.144 -  27.460:  139   |   8:    52.725 -  59.041:   33        |
|      4:    27.460 -  33.776:   98   |   9:    59.041 -  65.357:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1489             target_work(ml) = 5.094         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1489             target_work(ml) = 5.094         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1489   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.70,-1.26,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093674                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1489   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.42,-1.12,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093702                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.625466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.505  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1489      final r-factor (free) = 0.1507          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7593 = 2.63 * 0.50 * 5.0918 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7563 = 2.63 * 0.50 * 5.0944 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1507      final r-factor (free) = 0.1511          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9746 = 0.19 * 1.00 * 5.0944 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9755 = 0.19 * 1.00 * 5.0979 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.72    66.98   16.29    None  None   None       |
|    all(noH): 2823   0      1.72    66.98   16.29    None  None   None       |
|    Sol.    : 438    0      5.79    64.83   36.28    None  None   None       |
|    Mac.    : 2385   0      1.72    66.98   12.61    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:     1.717 -   8.244:  550   |   5:    34.350 -  40.877:  127        |
|      1:     8.244 -  14.770: 1306   |   6:    40.877 -  47.404:   89        |
|      2:    14.770 -  21.297:  400   |   7:    47.404 -  53.930:   80        |
|      3:    21.297 -  27.824:  141   |   8:    53.930 -  60.457:   28        |
|      4:    27.824 -  34.350:   97   |   9:    60.457 -  66.984:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1511             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1512             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1512   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.42,-1.12,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.100343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1512   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.26,-0.99,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.100426                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.426750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663114              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.276  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7059 = 1.43 * 0.50 * 5.0986 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7028 = 1.43 * 0.50 * 5.1135 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3975 = 0.66 * 1.00 * 5.1135 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3982 = 0.66 * 1.00 * 5.1118 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    76.20   16.59    None  None   None       |
|    all(noH): 2823   0      0.58    76.20   16.59    None  None   None       |
|    Sol.    : 438    0      6.10    68.43   38.23    None  None   None       |
|    Mac.    : 2385   0      0.58    76.20   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.579 -   8.142:  614   |   5:    38.391 -  45.953:  113        |
|      1:     8.142 -  15.704: 1321   |   6:    45.953 -  53.516:   87        |
|      2:    15.704 -  23.266:  366   |   7:    53.516 -  61.078:   56        |
|      3:    23.266 -  30.829:  128   |   8:    61.078 -  68.640:   25        |
|      4:    30.829 -  38.391:  109   |   9:    68.640 -  76.203:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1534             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1534             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1534   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.26,-0.99,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116673                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1533   ksol= 0.32   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.04,-0.82,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116545                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.066542              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.212  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.181715              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.866  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3376 = 2.07 * 0.50 * 5.1126 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3399 = 2.07 * 0.50 * 5.1099 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0469 = 1.18 * 1.00 * 5.1099 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0460 = 1.18 * 1.00 * 5.1086 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.12    78.10   16.47    None  None   None       |
|    all(noH): 2823   0      0.12    78.10   16.47    None  None   None       |
|    Sol.    : 438    0      5.78    69.95   38.42    None  None   None       |
|    Mac.    : 2385   0      0.12    78.10   12.44    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:     0.115 -   7.914:  611   |   5:    39.107 -  46.906:  108        |
|      1:     7.914 -  15.712: 1335   |   6:    46.906 -  54.704:   86        |
|      2:    15.712 -  23.510:  358   |   7:    54.704 -  62.502:   54        |
|      3:    23.510 -  31.309:  132   |   8:    62.502 -  70.301:   21        |
|      4:    31.309 -  39.107:  114   |   9:    70.301 -  78.099:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1546             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1545             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1545   ksol= 0.32   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.04,-0.82,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112181                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.0979 0.1282      5.3825      5.5164|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.0835 0.1109      5.4278      5.6349|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.1015 0.1496      5.4523      5.8506|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.1142 0.1478      5.4134      5.5504|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.1257 0.1702      5.2946       5.535|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.1131 0.1835      5.1784       5.445|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.1184 0.1603      5.1233      5.3261|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.1101 0.1678      5.0389      5.3309|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.1098 0.1753      4.9891      5.2704|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.1050 0.1669      4.9299      5.1905|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.1076 0.1676      4.9112      5.1973|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.1070 0.1636      4.8519      5.2056|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.1044 0.1721      4.7665      5.0526|
| 14:  2.0402 -  1.9906 0.78    990  112 0.0988 0.1797      4.6445      4.9536|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1380   153  0.94   9.30   0.97     0.94       7316.16|
|  2:  4.7496 -  3.7901  1312   149  0.95   7.81   1.01     1.00       8986.32|
|  3:  3.7901 -  3.3169  1305   145  0.94  10.83   1.02     1.01      10004.67|
|  4:  3.3169 -  3.0164  1290   136  0.93  12.85   1.00     0.99       9646.56|
|  5:  3.0164 -  2.8017  1268   144  0.90  15.35   1.00     0.97       7912.54|
|  6:  2.8017 -  2.6374  1276   145  0.91  15.42   0.98     0.95       6780.63|
|  7:  2.6374 -  2.5060  1280   142  0.91  15.14   0.98     0.95       5857.00|
|  8:  2.5060 -  2.3974  1261   136  0.92  14.11   0.99     0.97       4977.54|
|  9:  2.3974 -  2.3054  1253   143  0.91  14.70   0.99     0.96       4680.98|
| 10:  2.3054 -  2.2261  1261   136  0.90  15.22   0.99     0.94       4159.59|
| 11:  2.2261 -  2.1567  1263   142  0.91  15.44   0.99     0.96       4225.04|
| 12:  2.1567 -  2.0953  1228   139  0.91  15.00   1.00     0.98       3800.23|
| 13:  2.0953 -  2.0402  1263   137  0.91  15.22   0.98     0.97       3260.82|
| 14:  2.0402 -  1.9906   990   112  0.92  14.18   0.96     0.92       2491.80|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2491.80 max =        10004.67 mean =      6100.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1545   ksol= 0.32   Bsol= 48.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.78,-0.58,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1545   ksol= 0.32   Bsol= 48.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.78,-0.58,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.0979 0.1283       5.383      5.5175|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.0834 0.1108      5.4275      5.6337|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.1015 0.1497      5.4519      5.8511|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.1142 0.1479      5.4138       5.551|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.1258 0.1702      5.2952      5.5353|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.1132 0.1838      5.1791      5.4458|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.1185 0.1604      5.1239      5.3266|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.1101 0.1678      5.0393      5.3309|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.1098 0.1753      4.9893      5.2701|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.1050 0.1670      4.9301      5.1906|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.1076 0.1676      4.9112       5.197|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.1070 0.1636      4.8518      5.2055|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.1044 0.1720      4.7666      5.0525|
| 14:  2.0402 -  1.9906 0.78    990  112 0.0987 0.1797      4.6449      4.9541|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1380   153  0.94   9.31   0.98     0.95       7326.47|
|  2:  4.7496 -  3.7901  1312   149  0.95   7.81   1.01     1.00       8988.04|
|  3:  3.7901 -  3.3169  1305   145  0.94  10.82   1.03     1.02       9999.54|
|  4:  3.3169 -  3.0164  1290   136  0.93  12.86   1.01     0.99       9653.86|
|  5:  3.0164 -  2.8017  1268   144  0.90  15.36   1.00     0.97       7921.46|
|  6:  2.8017 -  2.6374  1276   145  0.91  15.43   0.99     0.96       6788.02|
|  7:  2.6374 -  2.5060  1280   142  0.91  15.15   0.99     0.96       5864.80|
|  8:  2.5060 -  2.3974  1261   136  0.92  14.12   1.00     0.98       4981.87|
|  9:  2.3974 -  2.3054  1253   143  0.91  14.70   1.01     0.97       4683.54|
| 10:  2.3054 -  2.2261  1261   136  0.90  15.22   1.00     0.95       4159.10|
| 11:  2.2261 -  2.1567  1263   142  0.91  15.44   1.00     0.97       4224.68|
| 12:  2.1567 -  2.0953  1228   139  0.91  15.00   1.01     1.00       3800.21|
| 13:  2.0953 -  2.0402  1263   137  0.91  15.22   1.00     0.98       3262.05|
| 14:  2.0402 -  1.9906   990   112  0.92  14.18   0.98     0.94       2493.88|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2493.88 max =         9999.54 mean =      6103.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.11    78.10   16.47    None  None   None       |
|    all(noH): 2823   0      0.11    78.10   16.47    None  None   None       |
|    Sol.    : 438    0      5.78    69.94   38.41    None  None   None       |
|    Mac.    : 2385   0      0.11    78.10   12.44    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:     0.114 -   7.912:  611   |   5:    39.106 -  46.904:  108        |
|      1:     7.912 -  15.711: 1335   |   6:    46.904 -  54.702:   86        |
|      2:    15.711 -  23.509:  358   |   7:    54.702 -  62.501:   54        |
|      3:    23.509 -  31.307:  132   |   8:    62.501 -  70.299:   21        |
|      4:    31.307 -  39.106:  114   |   9:    70.299 -  78.098:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.449 - 4.786
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 272 from: 279
   mapped sites are within: 0.715 - 4.786

peak=    5.372 closest distance to " NH2 ARG A  56 " =    2.239
peak=    5.361 closest distance to " CB  ARG A 275 " =    0.947
peak=    5.293 closest distance to " O   HOH Z 232 " =    2.350
peak=    5.123 closest distance to " CB  GLN A 223 " =    1.403
peak=    4.933 closest distance to " CG  PRO A 213 " =    1.202
peak=    4.908 closest distance to " O   HOH Z 126 " =    1.866
peak=    4.892 closest distance to " O   HOH Z 142 " =    1.660
peak=    4.834 closest distance to " CB  SER A  63 " =    1.164
peak=    4.811 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.737 closest distance to " NE2 GLN A  11 " =    1.068
peak=    4.528 closest distance to " CB  GLU A 152 " =    1.212
peak=    4.520 closest distance to " CA  TYR A  30 " =    0.931
peak=    4.512 closest distance to " C   PRO A 198 " =    1.446
peak=    4.504 closest distance to " CB  ARG A  79 " =    1.297
peak=    4.495 closest distance to " O   HOH Z  15 " =    2.229
peak=    4.473 closest distance to " O   HOH Z  78 " =    1.686
peak=    4.462 closest distance to " O   HOH Z 298 " =    1.852
peak=    4.399 closest distance to " O   HOH Z 236 " =    2.028
peak=    4.374 closest distance to " O   HOH Z 427 " =    2.936
peak=    4.350 closest distance to " CB  ARG A 190 " =    1.688
peak=    4.309 closest distance to " O   HOH Z 250 " =    1.483
peak=    4.281 closest distance to " CB  TYR A 169 " =    0.764
peak=    4.279 closest distance to " OD1 ASN A  69 " =    2.541
peak=    4.243 closest distance to " O   HOH Z 303 " =    2.114
peak=    4.236 closest distance to " O   HOH Z 189 " =    2.385
peak=    4.223 closest distance to " O   HOH Z  61 " =    1.643
peak=    4.208 closest distance to " CB  LEU A 228 " =    1.108
peak=    4.202 closest distance to " O   HOH Z 272 " =    1.883
peak=    4.201 closest distance to " CG  PRO A 198 " =    1.283
peak=    4.160 closest distance to " ND2 ASN A 187 " =    1.444
peak=    4.159 closest distance to " O   HOH Z 234 " =    3.660
peak=    4.139 closest distance to " CZ  PHE A 218 " =    1.086
peak=    4.127 closest distance to " O   HOH Z 158 " =    3.064
peak=    4.119 closest distance to " CG2 VAL A 257 " =    0.869
peak=    4.112 closest distance to " O   HOH Z 369 " =    2.183
peak=    4.093 closest distance to " O   HOH Z 203 " =    1.694
peak=    4.091 closest distance to " CB  VAL A 265 " =    1.265
peak=    4.090 closest distance to " CB  ASN A 148 " =    1.422
peak=    4.070 closest distance to " O   HOH Z 209 " =    2.330
peak=    4.028 closest distance to " O   HOH Z  40 " =    1.771
peak=    4.026 closest distance to " NZ  LYS A 117 " =    3.261
peak=    4.019 closest distance to " O   HOH Z 392 " =    3.107
peak=    4.007 closest distance to " O   HOH Z 193 " =    1.849
peak=    4.004 closest distance to " CB  TRP A 266 " =    1.008
peak=    4.003 closest distance to " O   HOH Z 346 " =    1.656
peak=    4.002 closest distance to " CD2 TRP A 179 " =    1.362
peak=    3.998 closest distance to " O   HOH Z 389 " =    1.885
peak=    3.998 closest distance to " O   SER A  87 " =    2.210
peak=    3.994 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.992 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.984 closest distance to " O   HOH Z  19 " =    2.448
peak=    3.981 closest distance to " CB  ASP A 140 " =    1.001
peak=    3.962 closest distance to " O   HOH Z  43 " =    1.905
peak=    3.952 closest distance to " OG ASER A 258 " =    3.109
peak=    3.917 closest distance to " O   HOH Z 423 " =    1.916
peak=    3.916 closest distance to " CG  ARG A  66 " =    2.540
peak=    3.888 closest distance to " CB  GLU A 128 " =    1.035
peak=    3.866 closest distance to " O   HOH Z 368 " =    2.090
peak=    3.860 closest distance to " CA  ARG A  36 " =    1.029
peak=    3.853 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.848 closest distance to " O   HOH Z 402 " =    1.381
peak=    3.821 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.809 closest distance to " CB  SER A   3 " =    1.303
peak=    3.779 closest distance to " CG  PRO A 243 " =    1.020
peak=    3.779 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.776 closest distance to " O   HOH Z 403 " =    1.621
peak=    3.769 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.749 closest distance to " CB  GLU A 277 " =    3.572
peak=    3.741 closest distance to " CG2 ILE A 120 " =    1.137
peak=    3.715 closest distance to " O   HOH Z  66 " =    2.144
peak=    3.713 closest distance to " CA  ARG A 195 " =    1.202
peak=    3.703 closest distance to " O   HOH Z   1 " =    1.907
peak=    3.703 closest distance to " CB  ASN A  39 " =    0.899
peak=    3.700 closest distance to " O   HOH Z  10 " =    1.789
peak=    3.678 closest distance to " O   HOH Z 417 " =    3.125
peak=    3.676 closest distance to " NH1AARG A 145 " =    1.224
peak=    3.676 closest distance to " O   HOH Z 126 " =    2.107
peak=    3.674 closest distance to " O   HOH Z 172 " =    3.383
peak=    3.664 closest distance to " CD2 LEU A 297 " =    0.861
peak=    3.658 closest distance to " O   HOH Z 280 " =    2.977
peak=    3.653 closest distance to " O   HOH Z   9 " =    2.114
peak=    3.647 closest distance to " CG1BVAL A  72 " =    1.626
peak=    3.643 closest distance to " O   HOH Z 141 " =    1.725
peak=    3.639 closest distance to " O   HOH Z  97 " =    2.542
peak=    3.636 closest distance to " CB  SER A 212 " =    1.079
peak=    3.629 closest distance to " O   HOH Z 371 " =    3.162
peak=    3.629 closest distance to " O   HOH Z 305 " =    3.674
peak=    3.618 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.614 closest distance to " O   HOH Z 180 " =    2.214
peak=    3.607 closest distance to " CB  TYR A 169 " =    0.784
peak=    3.603 closest distance to " O   HOH Z 344 " =    3.209
peak=    3.593 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.592 closest distance to " N   ARG A 156 " =    1.352
peak=    3.590 closest distance to " O   HOH Z 147 " =    1.777
peak=    3.584 closest distance to " O   HOH Z 265 " =    2.377
peak=    3.577 closest distance to " O   HOH Z 403 " =    1.363
peak=    3.570 closest distance to " O   HOH Z  59 " =    1.953
peak=    3.567 closest distance to " O   HOH Z 425 " =    2.008
peak=    3.566 closest distance to " O   HOH Z  97 " =    1.962
peak=    3.564 closest distance to " O   HOH Z 128 " =    2.098
peak=    3.559 closest distance to " CG1 ILE A  33 " =    1.223
peak=    3.557 closest distance to " O   HOH Z 214 " =    2.127
peak=    3.555 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.550 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.548 closest distance to " CA  ALA A  51 " =    0.910
peak=    3.548 closest distance to " CB  ASN A 110 " =    1.092
peak=    3.546 closest distance to " CB  TRP A 179 " =    1.314
peak=    3.544 closest distance to " C   ILE A 106 " =    1.905
peak=    3.542 closest distance to " O   HOH Z 291 " =    1.555
peak=    3.540 closest distance to " O   HOH Z 248 " =    1.579
peak=    3.540 closest distance to " O   HOH Z 359 " =    1.471
peak=    3.534 closest distance to " NH2BARG A 145 " =    2.086
peak=    3.532 closest distance to " O   HOH Z 213 " =    1.728
peak=    3.528 closest distance to " O   HOH Z 407 " =    2.411
peak=    3.526 closest distance to " O   HOH Z 185 " =    1.798
peak=    3.524 closest distance to " O   HOH Z 148 " =    3.366
peak=    3.511 closest distance to " OG1 THR A 294 " =    2.430
peak=    3.511 closest distance to " CA  THR A 221 " =    1.001
peak=    3.509 closest distance to " CG2 ILE A  20 " =    1.435
peak=    3.507 closest distance to " CB  THR A  31 " =    1.698
peak=    3.497 closest distance to " CD BLYS A 290 " =    1.040
peak=    3.494 closest distance to " CB  ALA A 291 " =    1.319
peak=    3.493 closest distance to " O   HOH Z 298 " =    2.569
peak=    3.492 closest distance to " O   HOH Z 406 " =    1.519
peak=    3.481 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.479 closest distance to " CD1 ILE A 106 " =    0.803
peak=    3.477 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.473 closest distance to " CB  ALA A 248 " =    1.330
peak=    3.467 closest distance to " CA  ALA A  21 " =    1.160
peak=    3.463 closest distance to " O   HOH Z 353 " =    2.668
peak=    3.462 closest distance to " O   HOH Z 175 " =    2.136
peak=    3.458 closest distance to " O   HOH Z 133 " =    2.599
peak=    3.456 closest distance to " OD2 ASP A 286 " =    2.820
peak=    3.454 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.452 closest distance to " O   HOH Z 132 " =    2.500
peak=    3.451 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.444 closest distance to " NE2 GLN A  77 " =    3.148
peak=    3.440 closest distance to " CD  LYS A 166 " =    1.232
peak=    3.438 closest distance to " OG BSER A 164 " =    2.290
peak=    3.436 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.435 closest distance to " O   HOH Z 261 " =    1.619
peak=    3.434 closest distance to " O   HOH Z 337 " =    3.650
peak=    3.433 closest distance to " O   HOH Z 313 " =    1.935
peak=    3.431 closest distance to " NE2 GLN A  73 " =    3.853
peak=    3.422 closest distance to " CB  MET A  47 " =    0.969
peak=    3.414 closest distance to " O   HOH Z 193 " =    2.064
peak=    3.411 closest distance to " OG  SER A  22 " =    2.629
peak=    3.408 closest distance to " O   HOH Z 193 " =    1.610
peak=    3.406 closest distance to " CB  ASN A 142 " =    1.098
peak=    3.403 closest distance to " O   HOH Z 411 " =    3.906
peak=    3.403 closest distance to " N   ASN A  39 " =    1.267
peak=    3.398 closest distance to " O   HOH Z 421 " =    1.809
peak=    3.395 closest distance to " O   HOH Z 426 " =    1.670
peak=    3.394 closest distance to " CD  LYS A 119 " =    1.338
peak=    3.390 closest distance to " CB  PRO A  54 " =    0.748
peak=    3.386 closest distance to " O   HOH Z  88 " =    2.659
peak=    3.386 closest distance to " NH2 ARG A 156 " =    1.192
peak=    3.383 closest distance to " O   HOH Z 173 " =    1.881
peak=    3.379 closest distance to " O   HOH Z 419 " =    1.981
peak=    3.378 closest distance to " O   HOH Z 219 " =    1.899
peak=    3.377 closest distance to " CA  ALA A 291 " =    0.790
peak=    3.374 closest distance to " O   HOH Z 329 " =    3.923
peak=    3.372 closest distance to " O   HOH Z 234 " =    1.910
peak=    3.371 closest distance to " CA  ALA A 158 " =    1.285
peak=    3.365 closest distance to " CB  ILE A 120 " =    1.279
peak=    3.362 closest distance to " CA  MET A 105 " =    0.992
peak=    3.359 closest distance to " O   HOH Z  21 " =    1.779
peak=    3.350 closest distance to " O   HOH Z  44 " =    1.768
peak=    3.348 closest distance to " CG  LEU A 167 " =    1.265
peak=    3.344 closest distance to " CA  SER A  87 " =    1.034
peak=    3.342 closest distance to " CZ2 TRP A 179 " =    1.739
peak=    3.341 closest distance to " ND2 ASN A 249 " =    0.860
peak=    3.340 closest distance to " CB  GLN A  89 " =    1.353
peak=    3.337 closest distance to " O   HOH Z 128 " =    2.280
peak=    3.335 closest distance to " CE1 TYR A 186 " =    1.324
peak=    3.331 closest distance to " OE1 GLU A   2 " =    2.209
peak=    3.328 closest distance to " CG2 THR A 221 " =    1.164
peak=    3.323 closest distance to " CB  SER A  26 " =    1.659
peak=    3.323 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.322 closest distance to " O   HOH Z 273 " =    2.798
peak=    3.322 closest distance to " O   HOH Z 285 " =    2.754
peak=    3.320 closest distance to " CD1 LEU A  96 " =    0.715
peak=    3.318 closest distance to " O   HOH Z 383 " =    1.787
peak=    3.315 closest distance to " CB  LYS A 290 " =    0.912
peak=    3.309 closest distance to " O   HOH Z  61 " =    1.420
peak=    3.304 closest distance to " CD2 LEU A 255 " =    1.448
peak=    3.304 closest distance to " O   HOH Z 325 " =    2.490
peak=    3.299 closest distance to " CG  LYS A  76 " =    0.945
peak=    3.299 closest distance to " O   HOH Z 279 " =    2.173
peak=    3.293 closest distance to " CB  ASN A 215 " =    1.119
peak=    3.291 closest distance to " O   HOH Z 371 " =    1.711
peak=    3.287 closest distance to " CA  ALA A 233 " =    1.160
peak=    3.287 closest distance to " CA  PHE A 283 " =    1.316
peak=    3.286 closest distance to " CB  ASN A 224 " =    1.008
peak=    3.283 closest distance to " O   HOH Z 435 " =    1.953
peak=    3.281 closest distance to " CB  SER A  62 " =    1.290
peak=    3.277 closest distance to " CG  MET A 185 " =    1.141
peak=    3.270 closest distance to " N   TYR A 116 " =    1.560
peak=    3.270 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.270 closest distance to " CB  ALA A  34 " =    1.000
peak=    3.270 closest distance to " O   HOH Z 187 " =    2.252
peak=    3.264 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.261 closest distance to " CA  MET A  40 " =    1.115
peak=    3.260 closest distance to " N   ASN A 127 " =    1.213
peak=    3.255 closest distance to " CB  PRO A  90 " =    1.192
peak=    3.254 closest distance to " O   HOH Z 391 " =    2.893
peak=    3.253 closest distance to " CA  ALA A  84 " =    1.252
peak=    3.253 closest distance to " O   THR A 251 " =    1.134
peak=    3.248 closest distance to " CA  THR A 264 " =    0.904
peak=    3.246 closest distance to " O   HOH Z  44 " =    3.126
peak=    3.245 closest distance to " O   HOH Z 433 " =    1.827
peak=    3.242 closest distance to " CA  ASN A 217 " =    1.192
peak=    3.230 closest distance to " O   HOH Z 188 " =    2.080
peak=    3.227 closest distance to " CB  MET A  40 " =    0.805
peak=    3.224 closest distance to " O   HOH Z  62 " =    1.988
peak=    3.223 closest distance to " O   THR A 220 " =    1.280
peak=    3.222 closest distance to " CG  LYS A  76 " =    1.563
peak=    3.216 closest distance to " O   HOH Z 299 " =    4.458
peak=    3.210 closest distance to " O   HOH Z  88 " =    1.989
peak=    3.209 closest distance to " O   HOH Z  35 " =    2.569
peak=    3.207 closest distance to " ND2 ASN A 110 " =    1.651
peak=    3.207 closest distance to " CD1AILE A 234 " =    0.911
peak=    3.206 closest distance to " CB  ALA A   9 " =    1.538
peak=    3.203 closest distance to " O   ALA A   1 " =    1.640
peak=    3.202 closest distance to " CB  SER A 141 " =    1.028
peak=    3.201 closest distance to " CA  TYR A 116 " =    1.341
peak=    3.200 closest distance to " CA  ASN A 176 " =    1.225
peak=    3.197 closest distance to " NZ  LYS A  76 " =    1.578
peak=    3.195 closest distance to " O   HOH Z 345 " =    3.316
peak=    3.194 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.193 closest distance to " O   HOH Z 357 " =    1.879
peak=    3.193 closest distance to " CB  SER A  62 " =    0.871
peak=    3.193 closest distance to " CA  ALA A 248 " =    1.228
peak=    3.187 closest distance to " O   HOH Z 365 " =    2.906
peak=    3.185 closest distance to " ND1 HIS A  86 " =    1.800
peak=    3.178 closest distance to " CG  GLN A  11 " =    1.611
peak=    3.173 closest distance to " CG2 VAL A 197 " =    1.100
peak=    3.167 closest distance to " CD  ARG A  66 " =    2.390
peak=    3.167 closest distance to " CG1 ILE A  49 " =    1.460
peak=    3.151 closest distance to " CB  LYS A 117 " =    1.211
peak=    3.149 closest distance to " CB  LEU A 255 " =    0.751
peak=    3.146 closest distance to " CG  GLN A  77 " =    2.064
peak=    3.141 closest distance to " O   SER A 164 " =    1.185
peak=    3.140 closest distance to " O   TRP A 274 " =    1.824
peak=    3.134 closest distance to " NZ  LYS A  48 " =    1.222
peak=    3.133 closest distance to " O   HOH Z 302 " =    2.000
peak=    3.118 closest distance to " CE  LYS A  48 " =    1.083
peak=    3.117 closest distance to " CG2 ILE A 234 " =    0.773
peak=    3.115 closest distance to " CB  LEU A 300 " =    0.906
peak=    3.114 closest distance to " O   HOH Z 327 " =    1.576
peak=    3.110 closest distance to " CB  ALA A 248 " =    0.895
peak=    3.100 closest distance to " CE AMET A  47 " =    1.410
peak=    3.099 closest distance to " NH1BARG A 145 " =    1.156
peak=    3.099 closest distance to " O   HOH Z  85 " =    2.319
peak=    3.095 closest distance to " CG BARG A 275 " =    1.453
peak=    3.093 closest distance to " O   HOH Z 271 " =    2.362
peak=    3.093 closest distance to " N   PHE A 130 " =    1.305
peak=    3.088 closest distance to " CB  ALA A   1 " =    4.786
peak=    3.087 closest distance to " O   HOH Z 201 " =    3.172
peak=    3.083 closest distance to " CB  SER A 216 " =    0.810
peak=    3.079 closest distance to " O   HOH Z 336 " =    1.702
peak=    3.078 closest distance to " CA  ALA A 154 " =    0.963
peak=    3.076 closest distance to " CA  GLY A  80 " =    0.846
peak=    3.073 closest distance to " CA  SER A 146 " =    1.722
peak=    3.063 closest distance to " CD  ARG A 156 " =    1.531
peak=    3.058 closest distance to " NE2 HIS A 207 " =    1.299
peak=    3.056 closest distance to " CB  VAL A 126 " =    1.050
peak=    3.049 closest distance to " ND1 HIS A  81 " =    1.657
peak=    3.045 closest distance to " O   HOH Z 409 " =    3.028
peak=    3.015 closest distance to " O   HOH Z 258 " =    1.989
peak=    3.015 closest distance to " NH1AARG A 145 " =    0.890
peak=    3.010 closest distance to " OG BSER A  99 " =    2.260

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.820 - 5.220
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.820 - 5.220

peak=   -4.842 closest distance to " O   HOH Z 266 " =    5.114
peak=   -4.642 closest distance to " CD  GLN A  58 " =    1.025
peak=   -4.511 closest distance to " CD  ARG A 156 " =    2.061
peak=   -4.496 closest distance to " C   HIS A 108 " =    1.111
peak=   -4.474 closest distance to " SG  CYS A 254 " =    3.483
peak=   -4.428 closest distance to " O   VAL A  67 " =    2.719
peak=   -4.409 closest distance to " CB  PRO A 243 " =    2.679
peak=   -4.246 closest distance to " CG  GLN A 223 " =    1.996
peak=   -4.232 closest distance to " O   HOH Z 377 " =    2.043
peak=   -4.192 closest distance to " OG BSER A 134 " =    1.260
peak=   -4.176 closest distance to " O   HOH Z 231 " =    2.261
peak=   -4.171 closest distance to " CG1 VAL A 112 " =    2.806
peak=   -4.128 closest distance to " CA  VAL A  67 " =    2.887
peak=   -4.115 closest distance to " CZ3 TRP A 179 " =    1.170
peak=   -4.098 closest distance to " O   HOH Z 198 " =    2.049
peak=   -4.058 closest distance to " CD2 PHE A 192 " =    2.044
peak=   -4.002 closest distance to " O   HOH Z 372 " =    2.287
peak=   -3.995 closest distance to " CA  ASN A 110 " =    2.548
peak=   -3.961 closest distance to " CB  ASN A  39 " =    2.344
peak=   -3.950 closest distance to " O   HOH Z 114 " =    3.059
peak=   -3.933 closest distance to " CE  MET A 105 " =    2.457
peak=   -3.904 closest distance to " CG2 ILE A 263 " =    2.286
peak=   -3.898 closest distance to " CB  ALA A 291 " =    2.280
peak=   -3.879 closest distance to " N   ALA A  43 " =    2.637
peak=   -3.875 closest distance to " O   HOH Z 389 " =    1.891
peak=   -3.870 closest distance to " O   HOH Z 290 " =    1.204
peak=   -3.855 closest distance to " O   HOH Z 435 " =    2.821
peak=   -3.844 closest distance to " ND2 ASN A  45 " =    1.763
peak=   -3.836 closest distance to " OXT GLY A 302 " =    2.790
peak=   -3.832 closest distance to " CB  ALA A  43 " =    2.521
peak=   -3.818 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -3.792 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.783 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.774 closest distance to " CD  ARG A 139 " =    1.508
peak=   -3.771 closest distance to " O   HOH Z  10 " =    1.485
peak=   -3.740 closest distance to " CD1 PHE A  59 " =    1.985
peak=   -3.738 closest distance to " O   HOH Z  73 " =    2.277
peak=   -3.735 closest distance to " O   HOH Z 196 " =    2.021
peak=   -3.730 closest distance to " O   HOH Z 407 " =    2.984
peak=   -3.723 closest distance to " OD1 ASP A 171 " =    1.619
peak=   -3.694 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.686 closest distance to " O   PRO A 163 " =    2.092
peak=   -3.664 closest distance to " O   HOH Z 185 " =    2.346
peak=   -3.639 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.627 closest distance to " CA  GLY A 203 " =    2.395
peak=   -3.612 closest distance to " CB  ALA A 248 " =    2.309
peak=   -3.610 closest distance to " CG1 VAL A 112 " =    2.603
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.393
peak=   -3.595 closest distance to " O   HOH Z 313 " =    1.878
peak=   -3.593 closest distance to " O   HOH Z 353 " =    2.172
peak=   -3.583 closest distance to " CD1 LEU A 101 " =    2.273
peak=   -3.570 closest distance to " O   HOH Z  44 " =    2.263
peak=   -3.567 closest distance to " O   HOH Z 351 " =    1.506
peak=   -3.564 closest distance to " CG  PHE A 283 " =    2.619
peak=   -3.563 closest distance to " O   HOH Z 126 " =    1.921
peak=   -3.557 closest distance to " CA  GLY A 133 " =    1.998
peak=   -3.557 closest distance to " CB  TYR A  15 " =    2.196
peak=   -3.552 closest distance to " N   ALA A 248 " =    1.708
peak=   -3.547 closest distance to " OD1 ASN A 148 " =    1.513
peak=   -3.533 closest distance to " CE2 PHE A 218 " =    2.434
peak=   -3.532 closest distance to " O   HOH Z 193 " =    2.086
peak=   -3.530 closest distance to " NH2AARG A 275 " =    5.220
peak=   -3.529 closest distance to " O   PHE A 218 " =    1.551
peak=   -3.525 closest distance to " CA  GLY A 241 " =    3.088
peak=   -3.523 closest distance to " O   HOH Z 311 " =    3.702
peak=   -3.521 closest distance to " ND2 ASN A  45 " =    1.107
peak=   -3.497 closest distance to " NE2 GLN A 278 " =    1.777
peak=   -3.489 closest distance to " O   HOH Z 166 " =    2.021
peak=   -3.475 closest distance to " CD1 LEU A 228 " =    2.165
peak=   -3.475 closest distance to " CG  ARG A  66 " =    2.430
peak=   -3.469 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.467 closest distance to " O   SER A  95 " =    1.564
peak=   -3.466 closest distance to " O   ALA A 161 " =    1.714
peak=   -3.465 closest distance to " O   HOH Z 198 " =    1.373
peak=   -3.465 closest distance to " OD2 ASP A 191 " =    1.442
peak=   -3.463 closest distance to " CZ  PHE A  59 " =    1.542
peak=   -3.459 closest distance to " CG  ARG A 269 " =    2.389
peak=   -3.453 closest distance to " NE2 GLN A  88 " =    1.839
peak=   -3.448 closest distance to " CG  GLN A  11 " =    1.813
peak=   -3.440 closest distance to " CB  ALA A 248 " =    2.216
peak=   -3.437 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.437 closest distance to " CG1 VAL A 250 " =    2.641
peak=   -3.430 closest distance to " CB  PHE A 208 " =    2.249
peak=   -3.429 closest distance to " O   HOH Z  13 " =    1.613
peak=   -3.429 closest distance to " O   HOH Z 394 " =    1.499
peak=   -3.428 closest distance to " O   HOH Z 385 " =    2.075
peak=   -3.425 closest distance to " OD1 ASN A 187 " =    1.639
peak=   -3.420 closest distance to " O   HOH Z  38 " =    1.575
peak=   -3.419 closest distance to " O   HOH Z  43 " =    1.655
peak=   -3.416 closest distance to " O   SER A 135 " =    1.449
peak=   -3.416 closest distance to " OG  SER A  62 " =    1.697
peak=   -3.416 closest distance to " CZ  TYR A 169 " =    1.798
peak=   -3.409 closest distance to " CG  GLU A 277 " =    1.187
peak=   -3.404 closest distance to " CD2 PHE A  61 " =    2.546
peak=   -3.399 closest distance to " CG  ASP A 231 " =    0.820
peak=   -3.396 closest distance to " O   HOH Z 253 " =    3.905
peak=   -3.389 closest distance to " O   HOH Z 292 " =    4.591
peak=   -3.387 closest distance to " CD  ARG A 195 " =    5.190
peak=   -3.384 closest distance to " O   HOH Z  51 " =    1.672
peak=   -3.380 closest distance to " CB  ASP A 286 " =    1.797
peak=   -3.376 closest distance to " N   MET A 105 " =    2.657
peak=   -3.376 closest distance to " N   SER A 212 " =    2.021
peak=   -3.370 closest distance to " CD2 TYR A 293 " =    2.043
peak=   -3.366 closest distance to " O   HOH Z 298 " =    1.306
peak=   -3.353 closest distance to " NH2 ARG A  79 " =    1.548
peak=   -3.346 closest distance to " O   ALA A  10 " =    1.674
peak=   -3.343 closest distance to " ND2 ASN A 187 " =    1.536
peak=   -3.342 closest distance to " SG ACYS A 201 " =    1.822
peak=   -3.332 closest distance to " CD1 ILE A 239 " =    2.296
peak=   -3.331 closest distance to " CB  PRO A  54 " =    2.389
peak=   -3.327 closest distance to " NH2BARG A 275 " =    2.022
peak=   -3.326 closest distance to " OD2 ASP A 171 " =    2.381
peak=   -3.326 closest distance to " CD2 LEU A 237 " =    2.715
peak=   -3.321 closest distance to " O   HOH Z 243 " =    1.999
peak=   -3.318 closest distance to " C   MET A 188 " =    1.343
peak=   -3.316 closest distance to " CG1 VAL A 197 " =    2.332
peak=   -3.313 closest distance to " O   HOH Z  11 " =    1.727
peak=   -3.308 closest distance to " OE1 GLN A  88 " =    1.147
peak=   -3.307 closest distance to " O   ALA A  51 " =    1.313
peak=   -3.302 closest distance to " CD1 LEU A   5 " =    2.512
peak=   -3.296 closest distance to " O   HOH Z 134 " =    3.038
peak=   -3.289 closest distance to " O   VAL A 189 " =    2.622
peak=   -3.288 closest distance to " O   HOH Z  52 " =    1.325
peak=   -3.270 closest distance to " CB  PRO A 163 " =    2.491
peak=   -3.259 closest distance to " CG1 VAL A 125 " =    1.975
peak=   -3.256 closest distance to " O   HOH Z   6 " =    2.157
peak=   -3.256 closest distance to " O   HOH Z 123 " =    2.304
peak=   -3.255 closest distance to " O   ARG A 145 " =    1.548
peak=   -3.253 closest distance to " N   ALA A 226 " =    2.047
peak=   -3.248 closest distance to " CA  GLY A 241 " =    2.821
peak=   -3.230 closest distance to " O   PRO A 198 " =    1.741
peak=   -3.228 closest distance to " CD2 HIS A 207 " =    2.416
peak=   -3.225 closest distance to " O   HOH Z 265 " =    2.175
peak=   -3.223 closest distance to " NE2 GLN A 194 " =    1.744
peak=   -3.220 closest distance to " CD1 LEU A 297 " =    2.437
peak=   -3.215 closest distance to " CD  GLU A 236 " =    1.056
peak=   -3.212 closest distance to " CE3 TRP A 150 " =    2.204
peak=   -3.212 closest distance to " O   HOH Z   6 " =    1.456
peak=   -3.208 closest distance to " N   ASP A 286 " =    2.375
peak=   -3.206 closest distance to " O   VAL A 174 " =    2.138
peak=   -3.206 closest distance to " O   GLU A 152 " =    1.369
peak=   -3.205 closest distance to " O   HOH Z 166 " =    1.628
peak=   -3.203 closest distance to " O   HOH Z 317 " =    1.553
peak=   -3.198 closest distance to " CG1 VAL A  67 " =    3.172
peak=   -3.191 closest distance to " O   PRO A 198 " =    1.320
peak=   -3.188 closest distance to " C   ALA A 158 " =    1.290
peak=   -3.187 closest distance to " CA  GLY A  98 " =    1.933
peak=   -3.184 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.184 closest distance to " O   HOH Z 295 " =    1.637
peak=   -3.173 closest distance to " CG1AVAL A  41 " =    2.873
peak=   -3.171 closest distance to " NH2 ARG A  79 " =    2.044
peak=   -3.163 closest distance to " ND2BASN A 224 " =    1.747
peak=   -3.163 closest distance to " OG BSER A 210 " =    2.422
peak=   -3.157 closest distance to " O   TRP A  70 " =    1.470
peak=   -3.154 closest distance to " CG  GLU A 152 " =    1.279
peak=   -3.152 closest distance to " CB  TRP A  85 " =    2.524
peak=   -3.151 closest distance to " CG  ASN A 252 " =    1.750
peak=   -3.149 closest distance to " NH1 ARG A  36 " =    2.069
peak=   -3.148 closest distance to " O   HOH Z 377 " =    1.738
peak=   -3.146 closest distance to " CG  PRO A 163 " =    2.536
peak=   -3.136 closest distance to " O   HOH Z  60 " =    2.217
peak=   -3.134 closest distance to " O   HOH Z  37 " =    1.797
peak=   -3.132 closest distance to " CZ  PHE A 192 " =    2.853
peak=   -3.125 closest distance to " O   HOH Z 210 " =    1.248
peak=   -3.119 closest distance to " O   HOH Z 421 " =    3.086
peak=   -3.112 closest distance to " O   ALA A 292 " =    2.064
peak=   -3.110 closest distance to " N   SER A 276 " =    1.236
peak=   -3.106 closest distance to " CG1 VAL A 125 " =    2.358
peak=   -3.104 closest distance to " CE1 TYR A 247 " =    2.751
peak=   -3.102 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.097 closest distance to " O   HOH Z  41 " =    2.440
peak=   -3.097 closest distance to " O   HOH Z 174 " =    4.290
peak=   -3.092 closest distance to " C   TRP A 274 " =    1.425
peak=   -3.092 closest distance to " O   HOH Z 357 " =    2.219
peak=   -3.079 closest distance to " CA  SER A  62 " =    2.629
peak=   -3.065 closest distance to " C   GLN A  58 " =    1.974
peak=   -3.060 closest distance to " CB  ALA A 100 " =    2.160
peak=   -3.060 closest distance to " CG2 VAL A 189 " =    2.107
peak=   -3.059 closest distance to " CG  GLU A   2 " =    1.912
peak=   -3.052 closest distance to " CD2 LEU A 300 " =    2.909
peak=   -3.052 closest distance to " O   HOH Z 357 " =    2.066
peak=   -3.039 closest distance to " OD1AASN A 224 " =    1.791
peak=   -3.039 closest distance to " ND2 ASN A  60 " =    1.379
peak=   -3.036 closest distance to " OD1 ASP A 200 " =    1.462
peak=   -3.030 closest distance to " CG2 THR A 221 " =    2.276
peak=   -3.009 closest distance to " CD1 TRP A  70 " =    1.091
peak=   -3.008 closest distance to " CG1BVAL A  72 " =    2.983

================= 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    :  0.1962 0.1943   5.549434e+00   5.525280e+00
   1_bss:  0.1750 0.1729   5.496045e+00   5.465754e+00
   1_xyz:  0.1259 0.1464   5.180866e+00   5.304260e+00
   1_adp:  0.1159 0.1469   5.127274e+00   5.318503e+00
   1_occ:  0.1154 0.1467   5.125577e+00   5.317964e+00
   2_bss:  0.1158 0.1466   5.127373e+00   5.317626e+00
   2_xyz:  0.1089 0.1487   5.100249e+00   5.331516e+00
   2_adp:  0.1069 0.1489   5.093876e+00   5.335619e+00
   2_occ:  0.1067 0.1489   5.093674e+00   5.335962e+00
   3_bss:  0.1066 0.1489   5.093702e+00   5.335863e+00
   3_xyz:  0.1070 0.1507   5.101021e+00   5.348571e+00
   3_adp:  0.1065 0.1511   5.100170e+00   5.350927e+00
   3_occ:  0.1065 0.1512   5.100343e+00   5.351409e+00
   4_bss:  0.1064 0.1512   5.100426e+00   5.351435e+00
   4_xyz:  0.1094 0.1524   5.118746e+00   5.360536e+00
   4_adp:  0.1083 0.1534   5.116629e+00   5.365463e+00
   4_occ:  0.1083 0.1534   5.116673e+00   5.365664e+00
   5_bss:  0.1082 0.1533   5.116545e+00   5.365424e+00
   5_xyz:  0.1066 0.1539   5.110807e+00   5.367722e+00
   5_adp:  0.1065 0.1546   5.112168e+00   5.371427e+00
   5_occ:  0.1065 0.1545   5.112181e+00   5.371536e+00
   5_bss:  0.1064 0.1545   5.112411e+00   5.371721e+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:  0.329  50.001  -3.019  -2.872  -1.034  -0.000  -0.000  -0.000
   1_xyz:  0.329  50.001  -3.019  -2.872  -1.034  -0.000  -0.000  -0.000
   1_adp:  0.329  50.001  -3.019  -2.872  -1.034  -0.000  -0.000  -0.000
   1_occ:  0.329  50.001  -3.019  -2.872  -1.034  -0.000  -0.000  -0.000
   2_bss:  0.329  50.001  -3.084  -2.704  -1.258  -0.000  -0.000  -0.000
   2_xyz:  0.329  50.001  -3.084  -2.704  -1.258  -0.000  -0.000  -0.000
   2_adp:  0.329  50.001  -3.084  -2.704  -1.258  -0.000  -0.000  -0.000
   2_occ:  0.329  50.001  -3.084  -2.704  -1.258  -0.000  -0.000  -0.000
   3_bss:  0.327  50.001  -2.861  -2.424  -1.123  -0.000  -0.000  -0.000
   3_xyz:  0.327  50.001  -2.861  -2.424  -1.123  -0.000  -0.000  -0.000
   3_adp:  0.327  50.001  -2.861  -2.424  -1.123  -0.000  -0.000  -0.000
   3_occ:  0.327  50.001  -2.861  -2.424  -1.123  -0.000  -0.000  -0.000
   4_bss:  0.327  50.001  -2.699  -2.259  -0.989  -0.000  -0.000  -0.000
   4_xyz:  0.327  50.001  -2.699  -2.259  -0.989  -0.000  -0.000  -0.000
   4_adp:  0.327  50.001  -2.699  -2.259  -0.989  -0.000  -0.000  -0.000
   4_occ:  0.327  50.001  -2.699  -2.259  -0.989  -0.000  -0.000  -0.000
   5_bss:  0.322  50.001  -2.489  -2.042  -0.816  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.001  -2.489  -2.042  -0.816  -0.000  -0.000  -0.000
   5_adp:  0.322  50.001  -2.489  -2.042  -0.816  -0.000  -0.000  -0.000
   5_occ:  0.322  50.001  -2.489  -2.042  -0.816  -0.000  -0.000  -0.000
   5_bss:  0.321  48.767  -2.226  -1.778  -0.577  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  16.801 0.8942  1.0326    10330.269
   1_bss:  15.193 0.9073  0.9648     7441.597
   1_xyz:  12.284 0.9288  0.9780     5438.052
   1_adp:  12.594 0.9260  0.9762     5532.476
   1_occ:  12.583 0.9261  0.9760     5514.987
   2_bss:  12.582 0.9261  0.9745     5513.800
   2_xyz:  12.728 0.9253  0.9729     5689.594
   2_adp:  12.812 0.9246  0.9679     5696.024
   2_occ:  12.818 0.9245  0.9678     5697.061
   3_bss:  12.819 0.9245  0.9752     5697.345
   3_xyz:  13.042 0.9229  0.9750     5878.715
   3_adp:  13.082 0.9226  0.9695     5893.544
   3_occ:  13.092 0.9225  0.9694     5899.668
   4_bss:  13.093 0.9225  0.9748     5901.103
   4_xyz:  13.239 0.9215  0.9740     5993.137
   4_adp:  13.375 0.9204  0.9669     6029.641
   4_occ:  13.379 0.9204  0.9668     6032.956
   5_bss:  13.376 0.9204  0.9738     6028.287
   5_xyz:  13.428 0.9199  0.9738     6072.632
   5_adp:  13.502 0.9193  0.9661     6097.580
   5_occ:  13.504 0.9193  0.9661     6099.613
   5_bss:  13.510 0.9193  0.9750     6103.080
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6028e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6028e-01
   1_xyz:   1.015  0.008  0.076 15.640  0.004  4.112   6.5390e-02
   1_adp:   1.015  0.008  0.076 15.640  0.004  4.112   6.5390e-02
   1_occ:   1.015  0.008  0.076 15.640  0.004  4.112   6.5390e-02
   2_bss:   1.015  0.008  0.076 15.640  0.004  4.112   6.5390e-02
   2_xyz:   1.098  0.010  0.086 15.478  0.005  4.115   7.5512e-02
   2_adp:   1.098  0.010  0.086 15.478  0.005  4.115   7.5512e-02
   2_occ:   1.098  0.010  0.086 15.478  0.005  4.115   7.5512e-02
   3_bss:   1.098  0.010  0.086 15.478  0.005  4.115   7.5512e-02
   3_xyz:   1.046  0.009  0.081 15.327  0.004  4.119   6.8744e-02
   3_adp:   1.046  0.009  0.081 15.327  0.004  4.119   6.8744e-02
   3_occ:   1.046  0.009  0.081 15.327  0.004  4.119   6.8744e-02
   4_bss:   1.046  0.009  0.081 15.327  0.004  4.119   6.8744e-02
   4_xyz:   0.925  0.006  0.073 15.124  0.004  4.118   5.4946e-02
   4_adp:   0.925  0.006  0.073 15.124  0.004  4.118   5.4946e-02
   4_occ:   0.925  0.006  0.073 15.124  0.004  4.118   5.4946e-02
   5_bss:   0.925  0.006  0.073 15.124  0.004  4.118   5.4946e-02
   5_xyz:   0.979  0.007  0.077 15.164  0.004  4.119   6.0009e-02
   5_adp:   0.979  0.007  0.077 15.164  0.004  4.119   6.0009e-02
   5_occ:   0.979  0.007  0.077 15.164  0.004  4.119   6.0009e-02
   5_bss:   0.979  0.007  0.077 15.164  0.004  4.119   6.0009e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_xyz:   7.389  0.043  0.229 83.715  0.039  2.289   6.0747e-02
   1_adp:   7.389  0.043  0.229 83.715  0.039  2.289   6.0747e-02
   1_occ:   7.389  0.043  0.229 83.715  0.039  2.289   6.0747e-02
   2_bss:   7.389  0.043  0.229 83.715  0.039  2.289   6.0747e-02
   2_xyz:   7.259  0.048  0.289 83.568  0.038  2.272   6.7875e-02
   2_adp:   7.259  0.048  0.289 83.568  0.038  2.272   6.7875e-02
   2_occ:   7.259  0.048  0.289 83.568  0.038  2.272   6.7875e-02
   3_bss:   7.259  0.048  0.289 83.568  0.038  2.272   6.7875e-02
   3_xyz:   7.046  0.049  0.268 83.408  0.036  2.298   5.6408e-02
   3_adp:   7.046  0.049  0.268 83.408  0.036  2.298   5.6408e-02
   3_occ:   7.046  0.049  0.268 83.408  0.036  2.298   5.6408e-02
   4_bss:   7.046  0.049  0.268 83.408  0.036  2.298   5.6408e-02
   4_xyz:   6.352  0.042  0.225 83.349  0.032  2.351   3.2552e-02
   4_adp:   6.352  0.042  0.225 83.349  0.032  2.351   3.2552e-02
   4_occ:   6.352  0.042  0.225 83.349  0.032  2.351   3.2552e-02
   5_bss:   6.352  0.042  0.225 83.349  0.032  2.351   3.2552e-02
   5_xyz:   6.667  0.045  0.245 82.962  0.034  2.341   4.1141e-02
   5_adp:   6.667  0.045  0.245 82.962  0.034  2.341   4.1141e-02
   5_occ:   6.667  0.045  0.245 82.962  0.034  2.341   4.1141e-02
   5_bss:   6.667  0.045  0.245 82.962  0.034  2.341   4.1141e-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:  62.77   0.00  16.39  58.96   0.00  12.64  62.77   4.72  36.81
   1_occ:  62.77   0.00  16.39  58.96   0.00  12.64  62.77   4.72  36.81
   2_bss:  62.77   0.00  16.39  58.96   0.00  12.64  62.77   4.72  36.81
   2_xyz:  62.77   0.00  16.39  58.96   0.00  12.64  62.77   4.72  36.81
   2_adp:  65.36   2.20  16.36  65.36   2.20  12.72  64.73   5.09  36.13
   2_occ:  65.36   2.20  16.36  65.36   2.20  12.72  64.73   5.09  36.13
   3_bss:  65.36   2.20  16.36  65.36   2.20  12.72  64.73   5.09  36.13
   3_xyz:  65.36   2.20  16.36  65.36   2.20  12.72  64.73   5.09  36.13
   3_adp:  66.98   1.72  16.29  66.98   1.72  12.61  64.83   5.79  36.28
   3_occ:  66.98   1.72  16.29  66.98   1.72  12.61  64.83   5.79  36.28
   4_bss:  66.98   1.72  16.29  66.98   1.72  12.61  64.83   5.79  36.28
   4_xyz:  66.98   1.72  16.29  66.98   1.72  12.61  64.83   5.79  36.28
   4_adp:  76.20   0.58  16.59  76.20   0.58  12.62  68.43   6.10  38.23
   4_occ:  76.20   0.58  16.59  76.20   0.58  12.62  68.43   6.10  38.23
   5_bss:  76.20   0.58  16.59  76.20   0.58  12.62  68.43   6.10  38.23
   5_xyz:  76.20   0.58  16.59  76.20   0.58  12.62  68.43   6.10  38.23
   5_adp:  78.10   0.12  16.47  78.10   0.12  12.44  69.95   5.78  38.42
   5_occ:  78.10   0.12  16.47  78.10   0.12  12.44  69.95   5.78  38.42
   5_bss:  78.10   0.11  16.47  78.10   0.11  12.44  69.94   5.78  38.41
------------------------------------------------------------------------
 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:    0.487    0.006    0.138
   1_adp:    0.487    0.006    0.138
   1_occ:    0.487    0.006    0.138
   2_bss:    0.487    0.006    0.138
   2_xyz:    0.825    0.009    0.157
   2_adp:    0.825    0.009    0.157
   2_occ:    0.825    0.009    0.157
   3_bss:    0.825    0.009    0.157
   3_xyz:    0.978    0.002    0.163
   3_adp:    0.978    0.002    0.163
   3_occ:    0.978    0.002    0.163
   4_bss:    0.978    0.002    0.163
   4_xyz:    1.035    0.012    0.165
   4_adp:    1.035    0.012    0.165
   4_occ:    1.035    0.012    0.165
   5_bss:    1.035    0.012    0.165
   5_xyz:    1.104    0.007    0.168
   5_adp:    1.104    0.007    0.168
   5_occ:    1.104    0.007    0.168
   5_bss:    1.104    0.007    0.168
------------------------------------------------------------------------

CPU time actual refinement: 326.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/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_545/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_545/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.73 
  Macro-tasks:
    bulk solvent and scale       = 38.23  
    individual site refinement   = 138.82 
    weights calculation          = 29.82  
    collect and process          = 6.65   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 213.61 
  Micro-tasks:
    mask                            = 0.56   
    f_calc                          = 104.68 
    alpha_beta                      = 8.30   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 110.72 
    fmodel                         = 7.09   
    r_factors                      = 0.11   
    phase_errors                   = 12.30  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 245.23 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.559 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    654 calls, 104.28 s
gradients_fft:          599 calls,  98.16 s

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

# Date 2008-01-16 Time 05:05:12 PST -0800 (1200488712.91 s)
Start R-work = 0.1962, R-free = 0.1943 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.1750, R-free = 0.1729
Final R-work = 0.1064, R-free = 0.1545