# Date 2008-01-16 Time 05:06:27 PST -0800 (1200488787.38 s)
#phil __OFF__

Command line arguments: "../590.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10716
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 590

-------------------------------------------------------------------------------
  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, 47.8686, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.99069
Completeness in resolution range: 0.950138
Completeness with d_max=infinity: 0.947198

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9854
                             d_min =   1.9907

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, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.99069
Completeness in resolution range: 0.950138
Completeness with d_max=infinity: 0.947198

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9858 -  4.2591 [2178/2206]  1957   221  10.1%
  bin  2:  4.2591 -  3.3935 [2061/2084]  1857   204   9.9%
  bin  3:  3.3935 -  2.9683 [2062/2084]  1856   206  10.0%
  bin  4:  2.9683 -  2.6986 [2030/2049]  1830   200   9.9%
  bin  5:  2.6986 -  2.5062 [2023/2052]  1810   213  10.5%
  bin  6:  2.5062 -  2.3590 [2008/2050]  1814   194   9.7%
  bin  7:  2.3590 -  2.2413 [1998/2034]  1803   195   9.8%
  bin  8:  2.2413 -  2.1440 [1999/2036]  1795   204  10.2%
  bin  9:  2.1440 -  2.0617 [1985/2016]  1789   196   9.9%
  bin 10:  2.0617 -  1.9907 [1245/2006]  1119   126  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/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: 0.15 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: 25
        2.42 -     3.04: 2160
        3.04 -     3.66: 4632
        3.66 -     4.28: 8873
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.026 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  2.130 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.132 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.156 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27977 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_590/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 47.8686 87.2539 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4073   r_free= 0.3944   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.214411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7501 0.99   1403  157 0.3250 0.3444      6.4578      6.4636|
|  2:  4.7501 -  3.7904 0.99   1362  151 0.3429 0.3445      6.7187      6.7149|
|  3:  3.7904 -  3.3172 0.99   1327  149 0.3751 0.3489      6.5786      6.5155|
|  4:  3.3172 -  3.0166 0.99   1314  136 0.3960 0.3666      6.4369      6.3333|
|  5:  3.0166 -  2.8019 0.99   1305  149 0.4301 0.3687      6.3006      6.2721|
|  6:  2.8019 -  2.6376 0.98   1305  149 0.4353 0.4285      6.2135      6.1052|
|  7:  2.6376 -  2.5062 0.99   1294  153 0.4332 0.3963      6.1812      6.0872|
|  8:  2.5062 -  2.3975 0.99   1308  131 0.4400 0.4482      6.1173      6.1089|
|  9:  2.3975 -  2.3056 0.98   1293  147 0.4462 0.4113       6.053      6.0661|
| 10:  2.3056 -  2.2263 0.98   1275  143 0.4647 0.4082      6.0722      6.0132|
| 11:  2.2263 -  2.1569 0.98   1286  147 0.4584 0.4411      5.9903      5.9761|
| 12:  2.1569 -  2.0954 0.99   1286  137 0.4596 0.5141      5.9218      6.0134|
| 13:  2.0954 -  2.0404 0.97   1266  137 0.4772 0.4491      5.8629      5.8131|
| 14:  2.0404 -  1.9907 0.48    606   73 0.4277 0.5069      5.8089      5.7552|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7501  1403   157  0.73  31.26   0.84     0.76      59516.61|
|  2:  4.7501 -  3.7904  1362   151  0.77  28.80   0.93     0.85      74383.25|
|  3:  3.7904 -  3.3172  1327   149  0.72  33.74   0.93     0.87      73962.47|
|  4:  3.3172 -  3.0166  1314   136  0.67  37.89   0.93     0.83      62766.21|
|  5:  3.0166 -  2.8019  1305   149  0.61  43.14   0.92     0.77      51122.98|
|  6:  2.8019 -  2.6376  1305   149  0.58  45.56   0.92     0.74      45072.15|
|  7:  2.6376 -  2.5062  1294   153  0.58  45.62   0.96     0.73      41264.72|
|  8:  2.5062 -  2.3975  1308   131  0.57  46.57   0.94     0.75      39409.01|
|  9:  2.3975 -  2.3056  1293   147  0.56  47.52   0.94     0.77      36564.32|
| 10:  2.3056 -  2.2263  1275   143  0.56  47.62   0.96     0.77      34025.39|
| 11:  2.2263 -  2.1569  1286   147  0.53  49.97   0.96     0.76      33690.88|
| 12:  2.1569 -  2.0954  1286   137  0.46  55.18   0.96     0.68      35375.49|
| 13:  2.0954 -  2.0404  1266   137  0.39  60.71   0.94     0.57      33736.29|
| 14:  2.0404 -  1.9907   606    73  0.34  64.29   1.01     0.45      28091.88|
|alpha:            min =        0.45 max =            0.87 mean =         0.75|
|beta:             min =    28091.88 max =        74383.25 mean =     47369.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           90.00 mean =        44.61|
|phase err.(test): min =        0.00 max =           89.57 mean =        44.93|
|-----------------------------------------------------------------------------|

============================== 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 = 5.033697              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.996   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.171180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.003   (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:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      176 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1984 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1834 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2798 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4566 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4307 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5617 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6675 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4073   r_free= 0.3944   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.214411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3951   r_free= 0.3812   ksol= 0.29   Bsol= 37.62   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.56,4.76,-0.06,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.199356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.553072              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.650   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.648711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.828   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3951      final r-factor (work) = 0.2953          |
| start r-factor (free) = 0.3812      final r-factor (free) = 0.3177          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2767 = 4.55 * 0.50 * 6.1993 + 1.00 * 0.1637                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8219 = 4.55 * 0.50 * 6.0267 + 1.00 * 0.1018                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2953      final r-factor (work) = 0.2707          |
| start r-factor (free) = 0.3177      final r-factor (free) = 0.3301          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9155 = 0.65 * 1.00 * 6.0267 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8482 = 0.65 * 1.00 * 5.9115 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.08   17.50    None  None   None       |
|    all(noH): 2823   0      0.00    91.08   17.50    None  None   None       |
|    Sol.    : 438    0      1.44    91.08   36.94    None  None   None       |
|    Mac.    : 2385   0      0.00    72.89   13.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.108:  858   |   5:    45.540 -  54.648:   94        |
|      1:     9.108 -  18.216: 1038   |   6:    54.648 -  63.756:   53        |
|      2:    18.216 -  27.324:  418   |   7:    63.756 -  72.864:   25        |
|      3:    27.324 -  36.432:  216   |   8:    72.864 -  81.972:    7        |
|      4:    36.432 -  45.540:  110   |   9:    81.972 -  91.080:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2707 r_free = 0.3301             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2707 r_free = 0.3303             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2707   r_free= 0.3303   ksol= 0.29   Bsol= 37.62   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.56,4.76,-0.06,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.919085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2694   r_free= 0.3272   ksol= 0.32   Bsol= 64.09   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,2.04,-0.12,0.00,-0.00,-0.00); trace/3= -0.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.917243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.296816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.074   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.901  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2694      final r-factor (work) = 0.1874          |
| start r-factor (free) = 0.3272      final r-factor (free) = 0.2276          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6259 = 8.30 * 0.50 * 5.9117 + 1.00 * 0.1018                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0633 = 8.30 * 0.50 * 5.7773 + 1.00 * 0.0967                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1874      final r-factor (work) = 0.1642          |
| start r-factor (free) = 0.2276      final r-factor (free) = 0.2058          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1711 = 0.37 * 1.00 * 5.7773 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0669 = 0.37 * 1.00 * 5.5068 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.10   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    90.10   17.23    None  None   None       |
|    Sol.    : 438    0      4.61    90.10   39.96    None  None   None       |
|    Mac.    : 2385   0      0.00    76.45   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.010:  916   |   5:    45.051 -  54.061:  114        |
|      1:     9.010 -  18.020: 1115   |   6:    54.061 -  63.072:   58        |
|      2:    18.020 -  27.031:  299   |   7:    63.072 -  72.082:   29        |
|      3:    27.031 -  36.041:  145   |   8:    72.082 -  81.092:   14        |
|      4:    36.041 -  45.051:  130   |   9:    81.092 -  90.102:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1642 r_free = 0.2058             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1640 r_free = 0.2057             target_work(ml) = 5.463         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1640   r_free= 0.2057   ksol= 0.32   Bsol= 64.09   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,2.04,-0.12,0.00,-0.00,-0.00); trace/3= -0.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.463302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2048   ksol= 0.33   Bsol= 68.15   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.22,-0.39,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.458898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.981891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.261  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.601  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1346          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3091 = 2.98 * 0.50 * 5.5082 + 1.00 * 0.0967                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0793 = 2.98 * 0.50 * 5.3756 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1346      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5348 = 0.28 * 1.00 * 5.3756 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5045 = 0.28 * 1.00 * 5.2712 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    87.70   16.82    None  None   None       |
|    all(noH): 2823   0      0.94    87.70   16.82    None  None   None       |
|    Sol.    : 438    0      5.19    87.70   40.07    None  None   None       |
|    Mac.    : 2385   0      0.94    80.85   12.55    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:     0.944 -   9.620: 1050   |   5:    44.322 -  52.997:  105        |
|      1:     9.620 -  18.295: 1057   |   6:    52.997 -  61.673:   74        |
|      2:    18.295 -  26.971:  247   |   7:    61.673 -  70.348:   34        |
|      3:    26.971 -  35.646:  133   |   8:    70.348 -  79.024:   14        |
|      4:    35.646 -  44.322:  105   |   9:    79.024 -  87.699:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1289 r_free = 0.1711             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1288 r_free = 0.1711             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1288   r_free= 0.1711   ksol= 0.33   Bsol= 68.15   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.22,-0.39,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.255655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1710   ksol= 0.33   Bsol= 66.64   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-0.88,-0.47,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.256673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.577264              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.944  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.493960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.488  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4956 = 3.58 * 0.50 * 5.2727 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3981 = 3.58 * 0.50 * 5.2092 + 1.00 * 0.0809                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5824 = 0.49 * 1.00 * 5.2092 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5618 = 0.49 * 1.00 * 5.1665 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.84   16.64    None  None   None       |
|    all(noH): 2823   0      0.00    88.84   16.64    None  None   None       |
|    Sol.    : 438    0      1.64    84.96   40.23    None  None   None       |
|    Mac.    : 2385   0      0.00    88.84   12.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.884:  930   |   5:    44.421 -  53.306:   96        |
|      1:     8.884 -  17.769: 1176   |   6:    53.306 -  62.190:   80        |
|      2:    17.769 -  26.653:  247   |   7:    62.190 -  71.074:   35        |
|      3:    26.653 -  35.537:  129   |   8:    71.074 -  79.958:   11        |
|      4:    35.537 -  44.421:  114   |   9:    79.958 -  88.842:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1617             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1618             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1618   ksol= 0.33   Bsol= 66.64   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-0.88,-0.47,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.163370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1617   ksol= 0.32   Bsol= 63.15   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.92,-0.28,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.163319                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.539781              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.128  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.907195              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.465  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0586 = 1.54 * 0.50 * 5.1666 + 1.00 * 0.0809                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0439 = 1.54 * 0.50 * 5.1798 + 1.00 * 0.0561                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7089 = 0.91 * 1.00 * 5.1798 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7116 = 0.91 * 1.00 * 5.1817 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.75   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    94.75   16.57    None  None   None       |
|    Sol.    : 438    0      1.91    86.35   40.52    None  None   None       |
|    Mac.    : 2385   0      0.00    94.75   12.18    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 -   9.475: 1117   |   5:    47.377 -  56.852:   92        |
|      1:     9.475 -  18.951: 1048   |   6:    56.852 -  66.328:   71        |
|      2:    18.951 -  28.426:  217   |   7:    66.328 -  75.803:   19        |
|      3:    28.426 -  37.902:  127   |   8:    75.803 -  85.279:    8        |
|      4:    37.902 -  47.377:  119   |   9:    85.279 -  94.754:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1637             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1637             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1637   ksol= 0.32   Bsol= 63.15   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.92,-0.28,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186493                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7501 0.99   1403  157 0.0994 0.1293      5.3891      5.5505|
|  2:  4.7501 -  3.7904 0.99   1362  151 0.0865 0.1035      5.4342       5.607|
|  3:  3.7904 -  3.3172 0.99   1327  149 0.1077 0.1516      5.4814      5.8537|
|  4:  3.3172 -  3.0166 0.99   1314  136 0.1274 0.1652      5.4849      5.6271|
|  5:  3.0166 -  2.8019 0.99   1305  149 0.1430 0.1836      5.3918      5.5691|
|  6:  2.8019 -  2.6376 0.98   1305  149 0.1349 0.2204      5.2824      5.5581|
|  7:  2.6376 -  2.5062 0.99   1294  153 0.1303 0.1645      5.2113      5.3719|
|  8:  2.5062 -  2.3975 0.99   1308  131 0.1225 0.1785      5.1349      5.3606|
|  9:  2.3975 -  2.3056 0.98   1293  147 0.1220 0.1974      5.0622      5.3732|
| 10:  2.3056 -  2.2263 0.98   1275  143 0.1192 0.1729      5.0174      5.2105|
| 11:  2.2263 -  2.1569 0.98   1286  147 0.1206 0.1882      4.9627      5.2708|
| 12:  2.1569 -  2.0954 0.99   1286  137 0.1155 0.1725      4.8941      5.1935|
| 13:  2.0954 -  2.0404 0.97   1266  137 0.1164 0.1737      4.8274      5.0619|
| 14:  2.0404 -  1.9907 0.48    606   73 0.1132 0.1946      4.7444       5.019|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7501  1403   157  0.94   9.11   0.96     0.94       7174.49|
|  2:  4.7501 -  3.7904  1362   151  0.95   7.99   1.00     0.99       8812.09|
|  3:  3.7904 -  3.3172  1327   149  0.94  11.16   1.02     1.01      10370.33|
|  4:  3.3172 -  3.0166  1314   136  0.91  14.37   1.00     0.98      10918.83|
|  5:  3.0166 -  2.8019  1305   149  0.89  17.02   0.99     0.97       9364.67|
|  6:  2.8019 -  2.6376  1305   149  0.89  17.51   0.97     0.94       8006.91|
|  7:  2.6376 -  2.5062  1294   153  0.90  16.20   0.98     0.95       6781.24|
|  8:  2.5062 -  2.3975  1308   131  0.90  16.17   0.98     0.94       6090.59|
|  9:  2.3975 -  2.3056  1293   147  0.90  16.82   0.99     0.94       5434.82|
| 10:  2.3056 -  2.2263  1275   143  0.89  16.68   0.98     0.93       4904.90|
| 11:  2.2263 -  2.1569  1286   147  0.90  16.43   0.98     0.93       4474.45|
| 12:  2.1569 -  2.0954  1286   137  0.91  15.88   0.99     0.98       4082.93|
| 13:  2.0954 -  2.0404  1266   137  0.90  16.60   0.97     0.95       3623.04|
| 14:  2.0404 -  1.9907   606    73  0.90  16.68   0.94     0.89       3012.56|
|alpha:            min =        0.89 max =            1.01 mean =         0.96|
|beta:             min =     3012.56 max =        10918.83 mean =      6822.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.76|
|phase err.(test): min =        0.00 max =           87.17 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1636   ksol= 0.32   Bsol= 64.69   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.83,-0.09,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186573                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1636   ksol= 0.32   Bsol= 64.69   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.83,-0.09,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7501 0.99   1403  157 0.0994 0.1293      5.3896      5.5527|
|  2:  4.7501 -  3.7904 0.99   1362  151 0.0867 0.1036      5.4359      5.6082|
|  3:  3.7904 -  3.3172 0.99   1327  149 0.1077 0.1518      5.4821       5.854|
|  4:  3.3172 -  3.0166 0.99   1314  136 0.1273 0.1651      5.4846      5.6268|
|  5:  3.0166 -  2.8019 0.99   1305  149 0.1429 0.1836      5.3911      5.5684|
|  6:  2.8019 -  2.6376 0.98   1305  149 0.1348 0.2201      5.2818      5.5568|
|  7:  2.6376 -  2.5062 0.99   1294  153 0.1303 0.1646      5.2109      5.3719|
|  8:  2.5062 -  2.3975 0.99   1308  131 0.1225 0.1785      5.1348      5.3605|
|  9:  2.3975 -  2.3056 0.98   1293  147 0.1219 0.1973      5.0623      5.3732|
| 10:  2.3056 -  2.2263 0.98   1275  143 0.1192 0.1730      5.0177      5.2116|
| 11:  2.2263 -  2.1569 0.98   1286  147 0.1206 0.1882      4.9626      5.2706|
| 12:  2.1569 -  2.0954 0.99   1286  137 0.1155 0.1726       4.894       5.194|
| 13:  2.0954 -  2.0404 0.97   1266  137 0.1164 0.1733      4.8273      5.0608|
| 14:  2.0404 -  1.9907 0.48    606   73 0.1132 0.1947      4.7444       5.019|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7501  1403   157  0.94   9.12   0.96     0.94       7185.50|
|  2:  4.7501 -  3.7904  1362   151  0.95   8.00   1.00     0.99       8836.05|
|  3:  3.7904 -  3.3172  1327   149  0.94  11.19   1.02     1.01      10396.49|
|  4:  3.3172 -  3.0166  1314   136  0.91  14.37   1.00     0.98      10914.53|
|  5:  3.0166 -  2.8019  1305   149  0.89  17.01   1.00     0.97       9349.54|
|  6:  2.8019 -  2.6376  1305   149  0.89  17.50   0.98     0.95       7994.29|
|  7:  2.6376 -  2.5062  1294   153  0.90  16.19   0.99     0.96       6773.90|
|  8:  2.5062 -  2.3975  1308   131  0.90  16.17   0.99     0.95       6089.75|
|  9:  2.3975 -  2.3056  1293   147  0.90  16.83   1.00     0.95       5436.99|
| 10:  2.3056 -  2.2263  1275   143  0.89  16.68   0.98     0.94       4906.56|
| 11:  2.2263 -  2.1569  1286   147  0.90  16.44   0.98     0.94       4476.08|
| 12:  2.1569 -  2.0954  1286   137  0.91  15.88   1.00     0.99       4083.35|
| 13:  2.0954 -  2.0404  1266   137  0.90  16.60   0.98     0.96       3621.15|
| 14:  2.0404 -  1.9907   606    73  0.90  16.68   0.95     0.90       3008.80|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     3008.80 max =        10914.53 mean =      6824.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.76|
|phase err.(test): min =        0.00 max =           87.17 mean =        14.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.76   16.58    None  None   None       |
|    all(noH): 2823   0      0.00    94.76   16.58    None  None   None       |
|    Sol.    : 438    0      1.91    86.35   40.52    None  None   None       |
|    Mac.    : 2385   0      0.00    94.76   12.18    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:     0.003 -   9.478: 1117   |   5:    47.380 -  56.855:   92        |
|      1:     9.478 -  18.954: 1048   |   6:    56.855 -  66.331:   71        |
|      2:    18.954 -  28.429:  217   |   7:    66.331 -  75.806:   19        |
|      3:    28.429 -  37.905:  127   |   8:    75.806 -  85.282:    8        |
|      4:    37.905 -  47.380:  119   |   9:    85.282 -  94.757:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.711
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 330
   mapped sites are within: 0.700 - 5.711

peak=    5.636 closest distance to " O   HOH Z 113 " =    2.303
peak=    5.479 closest distance to " CB  GLN A 223 " =    1.379
peak=    5.242 closest distance to " CG  PRO A  54 " =    1.342
peak=    5.240 closest distance to " O   HOH Z 210 " =    1.142
peak=    5.018 closest distance to " CB  ARG A 190 " =    1.763
peak=    4.916 closest distance to " CG  PRO A  90 " =    1.210
peak=    4.848 closest distance to " CG  PRO A 198 " =    1.212
peak=    4.831 closest distance to " CA  TYR A  30 " =    0.919
peak=    4.703 closest distance to " O   PRO A 198 " =    1.527
peak=    4.699 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.660 closest distance to " CB  SER A  63 " =    1.175
peak=    4.660 closest distance to " CB  ARG A 275 " =    0.883
peak=    4.607 closest distance to " O   HOH Z 403 " =    1.771
peak=    4.595 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.538 closest distance to " O   HOH Z 234 " =    3.836
peak=    4.502 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.488 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.452 closest distance to " CZ  PHE A 218 " =    1.107
peak=    4.451 closest distance to " O   HOH Z  43 " =    2.127
peak=    4.395 closest distance to " CD  ARG A 269 " =    1.031
peak=    4.330 closest distance to " CB  GLU A 128 " =    1.173
peak=    4.301 closest distance to " O   HOH Z 298 " =    1.850
peak=    4.262 closest distance to " O   HOH Z 209 " =    2.362
peak=    4.233 closest distance to " CG  PRO A 243 " =    1.085
peak=    4.206 closest distance to " CA  ARG A  36 " =    1.084
peak=    4.192 closest distance to " O   HOH Z 423 " =    1.894
peak=    4.190 closest distance to " CB  TYR A 169 " =    0.802
peak=    4.188 closest distance to " CD2 TRP A 179 " =    1.339
peak=    4.175 closest distance to " O   HOH Z  15 " =    2.299
peak=    4.172 closest distance to " O   HOH Z 189 " =    2.569
peak=    4.160 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.160 closest distance to " O   HOH Z 369 " =    2.389
peak=    4.141 closest distance to " O   HOH Z 402 " =    1.560
peak=    4.141 closest distance to " CA  ALA A  51 " =    0.946
peak=    4.121 closest distance to " CB  ARG A  79 " =    1.340
peak=    4.072 closest distance to " O   HOH Z  44 " =    1.927
peak=    3.996 closest distance to " O   HOH Z 134 " =    1.481
peak=    3.991 closest distance to " O   SER A  87 " =    2.236
peak=    3.980 closest distance to " O   HOH Z  97 " =    2.057
peak=    3.980 closest distance to " CA  ARG A 195 " =    1.227
peak=    3.972 closest distance to " O   HOH Z 368 " =    2.173
peak=    3.962 closest distance to " CG1 ILE A  33 " =    1.261
peak=    3.954 closest distance to " O   HOH Z 412 " =    3.659
peak=    3.943 closest distance to " CB  LEU A 228 " =    1.113
peak=    3.934 closest distance to " CG  ARG A  66 " =    2.639
peak=    3.923 closest distance to " CZ  PHE A  38 " =    1.250
peak=    3.913 closest distance to " O   HOH Z  63 " =    1.955
peak=    3.911 closest distance to " O   HOH Z 261 " =    1.993
peak=    3.902 closest distance to " O   HOH Z 132 " =    2.744
peak=    3.896 closest distance to " CA  ALA A 160 " =    0.896
peak=    3.895 closest distance to " CB  TRP A 266 " =    1.039
peak=    3.869 closest distance to " CB  GLU A 277 " =    3.734
peak=    3.864 closest distance to " CB  ASN A 148 " =    1.475
peak=    3.851 closest distance to " N   HIS A 108 " =    1.869
peak=    3.850 closest distance to " CB  ARG A  79 " =    0.934
peak=    3.843 closest distance to " CB  ASN A  39 " =    0.859
peak=    3.826 closest distance to " O   HOH Z 203 " =    1.760
peak=    3.824 closest distance to " O   HOH Z 265 " =    2.024
peak=    3.823 closest distance to " O   HOH Z 128 " =    2.057
peak=    3.817 closest distance to " O   ASN A  74 " =    1.776
peak=    3.812 closest distance to " CD2 LEU A 297 " =    0.908
peak=    3.810 closest distance to " O   HOH Z  40 " =    1.851
peak=    3.805 closest distance to " O   HOH Z  80 " =    1.909
peak=    3.804 closest distance to " O   HOH Z  21 " =    1.857
peak=    3.788 closest distance to " CD  LYS A 166 " =    1.371
peak=    3.782 closest distance to " CB  TRP A 179 " =    1.323
peak=    3.781 closest distance to " O   HOH Z 346 " =    1.603
peak=    3.771 closest distance to " O   HOH Z 158 " =    3.012
peak=    3.770 closest distance to " OD1 ASN A  69 " =    2.439
peak=    3.768 closest distance to " O   HOH Z 291 " =    1.467
peak=    3.763 closest distance to " CG2 ILE A 120 " =    1.117
peak=    3.761 closest distance to " CE  LYS A  76 " =    0.829
peak=    3.761 closest distance to " CG2BVAL A  41 " =    0.901
peak=    3.760 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.750 closest distance to " CB  VAL A 202 " =    1.507
peak=    3.749 closest distance to " NZ  LYS A 117 " =    3.012
peak=    3.748 closest distance to " O   HOH Z 142 " =    1.552
peak=    3.747 closest distance to " O   HOH Z 126 " =    2.027
peak=    3.745 closest distance to " O   HOH Z  59 " =    2.377
peak=    3.745 closest distance to " N   ASN A  39 " =    1.314
peak=    3.742 closest distance to " O   HOH Z 345 " =    1.683
peak=    3.741 closest distance to " CB  SER A  62 " =    0.865
peak=    3.738 closest distance to " O   HOH Z  78 " =    1.761
peak=    3.733 closest distance to " O   HOH Z 284 " =    2.958
peak=    3.728 closest distance to " O   HOH Z 389 " =    1.991
peak=    3.728 closest distance to " O   HOH Z 245 " =    1.301
peak=    3.728 closest distance to " O   THR A 220 " =    1.109
peak=    3.722 closest distance to " CB  ALA A 291 " =    1.129
peak=    3.717 closest distance to " CD1 LEU A  96 " =    0.795
peak=    3.715 closest distance to " O   HOH Z 336 " =    1.785
peak=    3.712 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.704 closest distance to " O   HOH Z 214 " =    2.531
peak=    3.699 closest distance to " O   HOH Z 285 " =    2.865
peak=    3.697 closest distance to " CB  ASP A 140 " =    0.998
peak=    3.695 closest distance to " O   HOH Z 316 " =    3.070
peak=    3.694 closest distance to " NH1AARG A 145 " =    1.333
peak=    3.689 closest distance to " CB  ASP A 124 " =    0.710
peak=    3.677 closest distance to " O   HOH Z 258 " =    2.138
peak=    3.672 closest distance to " CG  GLN A  11 " =    1.359
peak=    3.670 closest distance to " O   HOH Z  20 " =    1.480
peak=    3.663 closest distance to " O   HOH Z 102 " =    1.294
peak=    3.663 closest distance to " CB  SER A 141 " =    1.028
peak=    3.656 closest distance to " O   HOH Z 287 " =    1.864
peak=    3.654 closest distance to " O   THR A 251 " =    1.108
peak=    3.648 closest distance to " NH2BARG A 145 " =    2.113
peak=    3.643 closest distance to " O   HOH Z  61 " =    1.566
peak=    3.643 closest distance to " O   ALA A 165 " =    1.430
peak=    3.638 closest distance to " CA  ALA A 295 " =    1.110
peak=    3.632 closest distance to " O   HOH Z 303 " =    2.243
peak=    3.621 closest distance to " CG2 VAL A 197 " =    1.133
peak=    3.619 closest distance to " NZ  LYS A  48 " =    1.195
peak=    3.617 closest distance to " CA  ALA A  21 " =    1.314
peak=    3.617 closest distance to " O   HOH Z 247 " =    1.439
peak=    3.613 closest distance to " ND2 ASN A 187 " =    1.576
peak=    3.599 closest distance to " O   HOH Z 362 " =    3.531
peak=    3.598 closest distance to " CA  ASN A 215 " =    1.044
peak=    3.595 closest distance to " O   HOH Z 433 " =    1.482
peak=    3.592 closest distance to " CB  SER A   3 " =    1.322
peak=    3.592 closest distance to " N   CYS A 260 " =    0.782
peak=    3.592 closest distance to " O   HOH Z 421 " =    1.998
peak=    3.590 closest distance to " CB  VAL A 265 " =    1.190
peak=    3.589 closest distance to " NE2 GLN A  77 " =    3.268
peak=    3.581 closest distance to " O   HOH Z 327 " =    1.620
peak=    3.578 closest distance to " CB  MET A  47 " =    0.932
peak=    3.577 closest distance to " O   HOH Z 417 " =    2.923
peak=    3.571 closest distance to " CA  GLU A 152 " =    0.863
peak=    3.571 closest distance to " CG2AVAL A  72 " =    1.869
peak=    3.565 closest distance to " CA  SER A  87 " =    1.068
peak=    3.556 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.544 closest distance to " O   HOH Z 180 " =    2.332
peak=    3.541 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    3.541 closest distance to " CG2 VAL A 257 " =    0.829
peak=    3.541 closest distance to " CG1 VAL A 153 " =    1.017
peak=    3.535 closest distance to " CA  VAL A 125 " =    1.286
peak=    3.534 closest distance to " CA  ASN A 176 " =    1.487
peak=    3.531 closest distance to " O   HOH Z 427 " =    2.949
peak=    3.531 closest distance to " O   HOH Z 279 " =    2.130
peak=    3.524 closest distance to " CB  LEU A  83 " =    0.859
peak=    3.524 closest distance to " O   HOH Z 357 " =    2.142
peak=    3.523 closest distance to " O   HOH Z 374 " =    2.734
peak=    3.523 closest distance to " O   HOH Z 109 " =    2.475
peak=    3.519 closest distance to " O   HOH Z 250 " =    1.384
peak=    3.516 closest distance to " ND2 ASN A 249 " =    0.911
peak=    3.513 closest distance to " O   TYR A 116 " =    1.405
peak=    3.511 closest distance to " O   HOH Z 214 " =    1.438
peak=    3.509 closest distance to " O   HOH Z  49 " =    0.887
peak=    3.508 closest distance to " O   HOH Z 383 " =    2.195
peak=    3.502 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.501 closest distance to " O   HOH Z 403 " =    1.441
peak=    3.498 closest distance to " O   HOH Z 193 " =    2.215
peak=    3.497 closest distance to " CG  GLU A  37 " =    0.934
peak=    3.491 closest distance to " CB  ALA A 248 " =    1.252
peak=    3.490 closest distance to " OG BSER A 134 " =    2.836
peak=    3.479 closest distance to " CG  GLN A  58 " =    2.675
peak=    3.471 closest distance to " NE2 GLN A  11 " =    1.005
peak=    3.470 closest distance to " CB  ASN A 142 " =    1.185
peak=    3.467 closest distance to " O   HOH Z 185 " =    1.753
peak=    3.458 closest distance to " O   HOH Z 271 " =    2.711
peak=    3.454 closest distance to " O   HOH Z 126 " =    1.510
peak=    3.449 closest distance to " CG AARG A 275 " =    1.147
peak=    3.443 closest distance to " OG BSER A 164 " =    2.304
peak=    3.441 closest distance to " CG2 ILE A  20 " =    1.366
peak=    3.438 closest distance to " OH  TYR A 116 " =    1.126
peak=    3.434 closest distance to " O   HOH Z 393 " =    3.276
peak=    3.433 closest distance to " O   HOH Z 132 " =    2.777
peak=    3.432 closest distance to " O   HOH Z 147 " =    1.837
peak=    3.430 closest distance to " CG  MET A 185 " =    1.148
peak=    3.428 closest distance to " O   ASP A 124 " =    1.375
peak=    3.425 closest distance to " CB  ASN A 285 " =    0.937
peak=    3.418 closest distance to " O   HOH Z 371 " =    3.100
peak=    3.416 closest distance to " O   HOH Z 227 " =    1.638
peak=    3.413 closest distance to " O   HOH Z 173 " =    2.253
peak=    3.408 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.407 closest distance to " CA  ASP A 191 " =    0.929
peak=    3.405 closest distance to " N   SER A 164 " =    1.027
peak=    3.400 closest distance to " CB  PRO A 198 " =    1.141
peak=    3.400 closest distance to " O   ALA A 158 " =    1.162
peak=    3.399 closest distance to " N   GLY A  98 " =    1.147
peak=    3.399 closest distance to " CA  TYR A 116 " =    1.318
peak=    3.392 closest distance to " O   HOH Z 411 " =    1.727
peak=    3.392 closest distance to " CB  TYR A 247 " =    0.989
peak=    3.390 closest distance to " CD  ARG A 159 " =    0.839
peak=    3.385 closest distance to " NH2AARG A 275 " =    3.543
peak=    3.384 closest distance to " O   HOH Z  66 " =    2.192
peak=    3.383 closest distance to " O   HOH Z 250 " =    1.648
peak=    3.377 closest distance to " O   HOH Z 422 " =    2.624
peak=    3.369 closest distance to " O   HOH Z 365 " =    2.790
peak=    3.364 closest distance to " O   HOH Z 183 " =    1.565
peak=    3.361 closest distance to " CB  MET A  40 " =    0.961
peak=    3.359 closest distance to " CB  SER A  28 " =    1.042
peak=    3.354 closest distance to " O   HOH Z 402 " =    2.956
peak=    3.353 closest distance to " CB  GLN A  89 " =    1.298
peak=    3.351 closest distance to " C   GLY A  80 " =    1.055
peak=    3.349 closest distance to " CB  ASN A 148 " =    2.046
peak=    3.347 closest distance to " O   HOH Z 361 " =    2.566
peak=    3.347 closest distance to " CE1 TYR A 186 " =    1.256
peak=    3.346 closest distance to " CG  LEU A 167 " =    1.092
peak=    3.345 closest distance to " O   HOH Z 418 " =    1.473
peak=    3.344 closest distance to " O   TRP A 274 " =    1.796
peak=    3.342 closest distance to " CA  ASP A 132 " =    1.219
peak=    3.340 closest distance to " O   HOH Z  19 " =    1.544
peak=    3.335 closest distance to " O   HOH Z 298 " =    2.387
peak=    3.331 closest distance to " CA  ALA A 100 " =    1.085
peak=    3.329 closest distance to " CA  ASP A 162 " =    1.168
peak=    3.325 closest distance to " O   HOH Z 272 " =    1.870
peak=    3.319 closest distance to " O   HOH Z 299 " =    4.484
peak=    3.319 closest distance to " O   HOH Z 156 " =    2.650
peak=    3.317 closest distance to " CD  PRO A  54 " =    1.053
peak=    3.316 closest distance to " CE1 HIS A 108 " =    1.140
peak=    3.314 closest distance to " O   HOH Z 325 " =    2.125
peak=    3.313 closest distance to " O   HOH Z 353 " =    2.800
peak=    3.311 closest distance to " O   HOH Z 427 " =    3.078
peak=    3.311 closest distance to " O   HOH Z 359 " =    1.489
peak=    3.309 closest distance to " O   HOH Z 437 " =    1.362
peak=    3.306 closest distance to " CG2 VAL A  78 " =    0.882
peak=    3.303 closest distance to " CB  ARG A 269 " =    0.808
peak=    3.302 closest distance to " CB  ASN A 187 " =    1.252
peak=    3.299 closest distance to " OE1 GLN A  11 " =    1.978
peak=    3.295 closest distance to " O   HOH Z  68 " =    1.936
peak=    3.294 closest distance to " O   HOH Z 248 " =    1.574
peak=    3.294 closest distance to " CA  LEU A  83 " =    1.262
peak=    3.292 closest distance to " OD2 ASP A 298 " =    3.819
peak=    3.292 closest distance to " O   HOH Z 240 " =    2.706
peak=    3.287 closest distance to " CA  MET A 105 " =    1.093
peak=    3.287 closest distance to " O   HOH Z 305 " =    3.745
peak=    3.286 closest distance to " O   HOH Z 435 " =    2.931
peak=    3.282 closest distance to " CA  MET A 188 " =    0.947
peak=    3.279 closest distance to " O   HOH Z 380 " =    1.854
peak=    3.278 closest distance to " N   ILE A  33 " =    1.043
peak=    3.278 closest distance to " CA  GLY A 241 " =    0.929
peak=    3.278 closest distance to " N   TYR A 116 " =    1.548
peak=    3.273 closest distance to " CB  PHE A  16 " =    0.996
peak=    3.270 closest distance to " O   HOH Z 139 " =    4.772
peak=    3.270 closest distance to " O   HOH Z  97 " =    2.293
peak=    3.268 closest distance to " CA  LYS A 117 " =    1.252
peak=    3.262 closest distance to " O   HOH Z 426 " =    1.497
peak=    3.259 closest distance to " CB  GLN A  88 " =    1.156
peak=    3.259 closest distance to " O   HOH Z 171 " =    1.962
peak=    3.259 closest distance to " O   HOH Z 163 " =    1.546
peak=    3.258 closest distance to " CA  ALA A 233 " =    1.761
peak=    3.252 closest distance to " CB  PRO A 243 " =    1.399
peak=    3.248 closest distance to " CB  ALA A 114 " =    0.747
peak=    3.247 closest distance to " CA  ASP A 191 " =    1.170
peak=    3.246 closest distance to " O   HOH Z 141 " =    1.696
peak=    3.246 closest distance to " O   HOH Z  48 " =    1.695
peak=    3.245 closest distance to " CD1 ILE A 199 " =    1.123
peak=    3.240 closest distance to " O   HOH Z 375 " =    2.181
peak=    3.238 closest distance to " CA  ALA A  84 " =    1.178
peak=    3.235 closest distance to " CB  THR A  52 " =    0.811
peak=    3.233 closest distance to " O   HOH Z 394 " =    1.623
peak=    3.233 closest distance to " OE1 GLN A  58 " =    3.572
peak=    3.233 closest distance to " O   HOH Z 130 " =    2.240
peak=    3.229 closest distance to " OE1 GLU A   2 " =    1.943
peak=    3.228 closest distance to " ND1 HIS A  81 " =    1.713
peak=    3.227 closest distance to " OG  SER A  62 " =    2.849
peak=    3.227 closest distance to " CA  ALA A 248 " =    1.186
peak=    3.226 closest distance to " CB  SER A 273 " =    0.892
peak=    3.226 closest distance to " O   HOH Z 128 " =    2.285
peak=    3.221 closest distance to " CG2 THR A 221 " =    1.176
peak=    3.221 closest distance to " O   HOH Z 193 " =    1.697
peak=    3.220 closest distance to " CB  SER A  26 " =    1.781
peak=    3.219 closest distance to " CG  ARG A 219 " =    1.228
peak=    3.216 closest distance to " CA  ILE A 106 " =    0.803
peak=    3.216 closest distance to " O   HOH Z 219 " =    5.173
peak=    3.214 closest distance to " CZ3 TRP A  85 " =    0.921
peak=    3.213 closest distance to " CB  PHE A 204 " =    0.700
peak=    3.212 closest distance to " O   HOH Z 197 " =    2.478
peak=    3.210 closest distance to " CB  GLN A 103 " =    0.884
peak=    3.208 closest distance to " O  BHOH Z 338 " =    2.182
peak=    3.206 closest distance to " O   HOH Z 345 " =    2.932
peak=    3.206 closest distance to " NH1 ARG A 269 " =    0.751
peak=    3.204 closest distance to " CD1 LEU A 222 " =    0.742
peak=    3.202 closest distance to " CB  THR A  31 " =    1.633
peak=    3.197 closest distance to " C   TYR A 214 " =    1.555
peak=    3.196 closest distance to " O  BHOH Z  74 " =    1.277
peak=    3.189 closest distance to " NE2 HIS A 115 " =    1.015
peak=    3.185 closest distance to " CA  SER A  12 " =    1.561
peak=    3.182 closest distance to " CA  THR A 221 " =    1.558
peak=    3.181 closest distance to " CB  ASN A 215 " =    1.209
peak=    3.178 closest distance to " CA  GLU A  46 " =    0.860
peak=    3.176 closest distance to " O   HOH Z 313 " =    1.855
peak=    3.176 closest distance to " CA  ASN A 217 " =    1.264
peak=    3.170 closest distance to " CD  PRO A 213 " =    1.347
peak=    3.169 closest distance to " O   HOH Z 419 " =    1.674
peak=    3.164 closest distance to " CA  GLY A 196 " =    0.990
peak=    3.163 closest distance to " CB  TYR A 116 " =    0.859
peak=    3.158 closest distance to " CA  VAL A  41 " =    0.888
peak=    3.155 closest distance to " CB  HIS A 108 " =    0.757
peak=    3.154 closest distance to " CB  PHE A 204 " =    0.773
peak=    3.152 closest distance to " O   HOH Z 420 " =    5.711
peak=    3.151 closest distance to " CA  THR A 221 " =    0.944
peak=    3.151 closest distance to " O   HOH Z  88 " =    1.741
peak=    3.149 closest distance to " OH  TYR A  30 " =    1.231
peak=    3.145 closest distance to " CG  ARG A 138 " =    1.215
peak=    3.140 closest distance to " CE  LYS A 119 " =    1.094
peak=    3.137 closest distance to " N   ARG A 156 " =    1.554
peak=    3.136 closest distance to " CA  GLN A  88 " =    1.346
peak=    3.134 closest distance to " CD  LYS A 119 " =    1.731
peak=    3.133 closest distance to " CB  PRO A  90 " =    1.126
peak=    3.130 closest distance to " CA  ALA A 154 " =    0.987
peak=    3.128 closest distance to " CA  ASN A 249 " =    1.401
peak=    3.125 closest distance to " CB  ASN A 110 " =    1.154
peak=    3.125 closest distance to " CB  ILE A 120 " =    1.351
peak=    3.120 closest distance to " O   HOH Z 294 " =    1.550
peak=    3.119 closest distance to " CA  SER A  32 " =    1.598
peak=    3.119 closest distance to " CB  PHE A 283 " =    0.724
peak=    3.118 closest distance to " O   HOH Z 162 " =    1.690
peak=    3.113 closest distance to " OG  SER A 245 " =    1.557
peak=    3.111 closest distance to " CG2 THR A   4 " =    1.078
peak=    3.106 closest distance to " O   HOH Z 261 " =    2.466
peak=    3.103 closest distance to " CB  ALA A 100 " =    1.272
peak=    3.103 closest distance to " CB  ALA A  43 " =    0.815
peak=    3.098 closest distance to " CD1AILE A 234 " =    0.846
peak=    3.092 closest distance to " CA  ALA A 299 " =    0.932
peak=    3.089 closest distance to " O   HOH Z  28 " =    2.082
peak=    3.087 closest distance to " O   HOH Z  35 " =    2.272
peak=    3.085 closest distance to " CA  ASP A 140 " =    1.247
peak=    3.072 closest distance to " O   HOH Z 414 " =    1.720
peak=    3.072 closest distance to " O   HOH Z 425 " =    1.347
peak=    3.060 closest distance to " CD  ARG A  66 " =    2.543
peak=    3.054 closest distance to " CB  ALA A 242 " =    0.966
peak=    3.051 closest distance to " O   HOH Z 301 " =    1.990
peak=    3.034 closest distance to " O   HOH Z  47 " =    2.371
peak=    3.033 closest distance to " O   HOH Z 141 " =    1.667
peak=    3.031 closest distance to " CB  ASP A 298 " =    1.254

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.854 - 5.985
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 218
   mapped sites are within: 0.854 - 5.985

peak=   -4.681 closest distance to " CD  GLN A  58 " =    0.967
peak=   -4.593 closest distance to " O   HOH Z 266 " =    5.190
peak=   -4.351 closest distance to " CB  PRO A 243 " =    2.774
peak=   -4.290 closest distance to " CD  ARG A 156 " =    2.092
peak=   -4.269 closest distance to " C   HIS A 108 " =    1.072
peak=   -4.265 closest distance to " O   HOH Z   5 " =    1.654
peak=   -4.191 closest distance to " CG1 VAL A 112 " =    2.622
peak=   -4.147 closest distance to " O   HOH Z 166 " =    1.617
peak=   -4.121 closest distance to " CD  ARG A  14 " =    3.474
peak=   -4.092 closest distance to " CD1 LEU A 101 " =    2.456
peak=   -4.081 closest distance to " O   PRO A 198 " =    1.303
peak=   -4.077 closest distance to " CD2 LEU A 237 " =    2.654
peak=   -4.074 closest distance to " OXT GLY A 302 " =    2.938
peak=   -3.995 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.945 closest distance to " CB  PHE A 192 " =    2.048
peak=   -3.934 closest distance to " CH2 TRP A 179 " =    1.251
peak=   -3.931 closest distance to " CD  GLN A  58 " =    1.036
peak=   -3.920 closest distance to " O   VAL A  67 " =    2.681
peak=   -3.906 closest distance to " O   HOH Z  13 " =    1.782
peak=   -3.869 closest distance to " OG  SER A  97 " =    2.256
peak=   -3.866 closest distance to " O   HOH Z 394 " =    1.527
peak=   -3.861 closest distance to " O   HOH Z 348 " =    2.365
peak=   -3.846 closest distance to " O   HOH Z 210 " =    0.894
peak=   -3.844 closest distance to " CE2 PHE A  61 " =    2.605
peak=   -3.837 closest distance to " ND2 ASN A  45 " =    1.894
peak=   -3.828 closest distance to " CG  ASP A 132 " =    2.364
peak=   -3.821 closest distance to " O   HOH Z 283 " =    2.101
peak=   -3.813 closest distance to " O   HOH Z 231 " =    2.408
peak=   -3.803 closest distance to " N   ALA A  43 " =    2.755
peak=   -3.798 closest distance to " CD1 LEU A  25 " =    2.496
peak=   -3.796 closest distance to " CD  GLN A 223 " =    1.278
peak=   -3.788 closest distance to " O   ALA A  34 " =    2.371
peak=   -3.779 closest distance to " OD1 ASN A 148 " =    1.446
peak=   -3.771 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.771 closest distance to " CZ  TYR A 169 " =    1.801
peak=   -3.749 closest distance to " O   HOH Z 196 " =    2.161
peak=   -3.744 closest distance to " CB  ALA A 161 " =    2.629
peak=   -3.741 closest distance to " CA  VAL A  67 " =    3.020
peak=   -3.724 closest distance to " CG2 ILE A  49 " =    2.746
peak=   -3.716 closest distance to " CE2 TYR A  30 " =    2.661
peak=   -3.699 closest distance to " CE3 TRP A 150 " =    2.255
peak=   -3.684 closest distance to " O   HOH Z 165 " =    1.910
peak=   -3.680 closest distance to " CG  GLU A  53 " =    1.424
peak=   -3.679 closest distance to " O   HOH Z 377 " =    2.079
peak=   -3.676 closest distance to " C   SER A 206 " =    1.548
peak=   -3.668 closest distance to " ND2 ASN A 187 " =    1.580
peak=   -3.662 closest distance to " CD2 TYR A 293 " =    1.894
peak=   -3.645 closest distance to " O   HOH Z 372 " =    2.357
peak=   -3.629 closest distance to " CB  ALA A  10 " =    2.201
peak=   -3.629 closest distance to " OE1 GLN A 223 " =    2.193
peak=   -3.627 closest distance to " O   SER A 210 " =    1.904
peak=   -3.621 closest distance to " CD  ARG A 139 " =    1.582
peak=   -3.612 closest distance to " O   HOH Z 171 " =    2.244
peak=   -3.609 closest distance to " C   THR A 279 " =    1.126
peak=   -3.608 closest distance to " O   HOH Z 374 " =    1.968
peak=   -3.595 closest distance to " O   HOH Z 351 " =    1.548
peak=   -3.587 closest distance to " O   HOH Z 290 " =    1.099
peak=   -3.587 closest distance to " O   HOH Z  71 " =    1.993
peak=   -3.576 closest distance to " CG2 ILE A 263 " =    2.306
peak=   -3.568 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.567 closest distance to " O   HOH Z 185 " =    2.507
peak=   -3.560 closest distance to " O   HOH Z 301 " =    2.398
peak=   -3.559 closest distance to " O   HOH Z 197 " =    2.128
peak=   -3.559 closest distance to " ND2BASN A 224 " =    1.837
peak=   -3.558 closest distance to " O   PRO A 163 " =    2.089
peak=   -3.555 closest distance to " O   HOH Z   6 " =    1.481
peak=   -3.553 closest distance to " O   HOH Z 292 " =    4.668
peak=   -3.550 closest distance to " CD  ARG A  79 " =    1.220
peak=   -3.536 closest distance to " O   PHE A 218 " =    1.493
peak=   -3.530 closest distance to " CG  PRO A 243 " =    1.717
peak=   -3.525 closest distance to " CB  ALA A 291 " =    2.449
peak=   -3.524 closest distance to " CE BMET A  47 " =    1.887
peak=   -3.523 closest distance to " NE2 GLN A  88 " =    1.826
peak=   -3.514 closest distance to " ND2 ASN A 249 " =    2.274
peak=   -3.507 closest distance to " CG1 VAL A  78 " =    2.734
peak=   -3.488 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.486 closest distance to " N   THR A  52 " =    1.677
peak=   -3.482 closest distance to " O   HOH Z 150 " =    1.091
peak=   -3.479 closest distance to " O   ALA A  10 " =    1.774
peak=   -3.474 closest distance to " O   HOH Z 106 " =    1.956
peak=   -3.469 closest distance to " C   ASN A 285 " =    2.275
peak=   -3.461 closest distance to " O   HOH Z 353 " =    2.286
peak=   -3.453 closest distance to " O   HOH Z  15 " =    1.487
peak=   -3.452 closest distance to " NE  ARG A  66 " =    4.363
peak=   -3.450 closest distance to " CB  ALA A  43 " =    2.585
peak=   -3.443 closest distance to " OG BSER A 134 " =    1.346
peak=   -3.438 closest distance to " CA  GLY A 241 " =    2.352
peak=   -3.431 closest distance to " O   HOH Z 234 " =    4.328
peak=   -3.429 closest distance to " OD1 ASP A 191 " =    1.424
peak=   -3.429 closest distance to " O   HOH Z 198 " =    2.034
peak=   -3.419 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.419 closest distance to " CB  ALA A 248 " =    2.252
peak=   -3.415 closest distance to " CD  LYS A 289 " =    2.409
peak=   -3.414 closest distance to " O   HOH Z 366 " =    1.904
peak=   -3.412 closest distance to " O   HOH Z 150 " =    2.214
peak=   -3.411 closest distance to " CB  PHE A  16 " =    2.488
peak=   -3.411 closest distance to " ND2 ASN A  69 " =    1.656
peak=   -3.408 closest distance to " O   HOH Z 264 " =    1.784
peak=   -3.408 closest distance to " O   HOH Z   6 " =    1.948
peak=   -3.407 closest distance to " O   HOH Z 102 " =    1.560
peak=   -3.405 closest distance to " O   HOH Z 422 " =    1.435
peak=   -3.404 closest distance to " N   ALA A 226 " =    1.991
peak=   -3.404 closest distance to " CG1 VAL A 112 " =    2.776
peak=   -3.390 closest distance to " CH2 TRP A 150 " =    1.106
peak=   -3.389 closest distance to " CA  GLY A 133 " =    2.392
peak=   -3.388 closest distance to " N   SER A 276 " =    1.493
peak=   -3.383 closest distance to " CA  GLY A 203 " =    2.380
peak=   -3.383 closest distance to " CD  ARG A 195 " =    5.072
peak=   -3.377 closest distance to " O   ALA A  34 " =    2.093
peak=   -3.373 closest distance to " CG2 VAL A 189 " =    2.247
peak=   -3.370 closest distance to " NH2 ARG A  66 " =    2.070
peak=   -3.367 closest distance to " ND2 ASN A  45 " =    1.082
peak=   -3.366 closest distance to " CG  GLU A 277 " =    1.242
peak=   -3.363 closest distance to " O   VAL A 189 " =    2.600
peak=   -3.351 closest distance to " CD  GLU A 236 " =    1.094
peak=   -3.350 closest distance to " O   HOH Z  52 " =    1.743
peak=   -3.349 closest distance to " O   HOH Z 177 " =    1.784
peak=   -3.347 closest distance to " O   HOH Z 196 " =    1.871
peak=   -3.345 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.343 closest distance to " CA  VAL A 197 " =    1.003
peak=   -3.342 closest distance to " O   HOH Z 111 " =    1.646
peak=   -3.342 closest distance to " NE2 GLN A 103 " =    1.722
peak=   -3.340 closest distance to " CG  GLN A  11 " =    1.635
peak=   -3.338 closest distance to " O   ALA A   1 " =    1.950
peak=   -3.337 closest distance to " CZ  PHE A 155 " =    1.171
peak=   -3.336 closest distance to " CA  GLY A 241 " =    3.271
peak=   -3.335 closest distance to " O   HOH Z 193 " =    2.472
peak=   -3.334 closest distance to " O   HOH Z 136 " =    2.068
peak=   -3.323 closest distance to " CB  ALA A 291 " =    2.189
peak=   -3.318 closest distance to " O   TRP A  92 " =    1.955
peak=   -3.318 closest distance to " O   HOH Z  63 " =    1.183
peak=   -3.316 closest distance to " CG1 VAL A  78 " =    3.245
peak=   -3.315 closest distance to " O   SER A 276 " =    1.773
peak=   -3.313 closest distance to " O   HOH Z 145 " =    2.599
peak=   -3.305 closest distance to " CG  ASP A 231 " =    0.854
peak=   -3.300 closest distance to " CB  TRP A  85 " =    2.445
peak=   -3.299 closest distance to " OG BSER A 210 " =    1.386
peak=   -3.297 closest distance to " OG BSER A 210 " =    2.295
peak=   -3.295 closest distance to " O   HOH Z 128 " =    2.631
peak=   -3.285 closest distance to " O   HOH Z  30 " =    0.887
peak=   -3.284 closest distance to " O   HOH Z  56 " =    1.633
peak=   -3.283 closest distance to " O   HOH Z 407 " =    3.305
peak=   -3.277 closest distance to " NE2 GLN A 223 " =    1.266
peak=   -3.276 closest distance to " O   HOH Z 191 " =    5.985
peak=   -3.274 closest distance to " O   HOH Z 149 " =    1.999
peak=   -3.273 closest distance to " CD2 HIS A 207 " =    2.443
peak=   -3.261 closest distance to " N   ALA A 248 " =    1.759
peak=   -3.259 closest distance to " NE2 GLN A 223 " =    1.160
peak=   -3.253 closest distance to " O   HOH Z 377 " =    1.516
peak=   -3.249 closest distance to " O   HOH Z 252 " =    3.961
peak=   -3.246 closest distance to " CD2 LEU A 237 " =    2.842
peak=   -3.246 closest distance to " O   GLY A 196 " =    1.121
peak=   -3.243 closest distance to " NE2 GLN A  88 " =    1.036
peak=   -3.233 closest distance to " NH2 ARG A  79 " =    2.188
peak=   -3.232 closest distance to " O   HOH Z 392 " =    1.402
peak=   -3.231 closest distance to " CB  PRO A 213 " =    1.720
peak=   -3.229 closest distance to " CG1 VAL A 112 " =    2.764
peak=   -3.223 closest distance to " O   HOH Z 114 " =    3.403
peak=   -3.223 closest distance to " N   SER A 134 " =    1.224
peak=   -3.211 closest distance to " CB  ALA A   9 " =    2.585
peak=   -3.206 closest distance to " NH2 ARG A 159 " =    2.321
peak=   -3.205 closest distance to " O   HOH Z 275 " =    1.807
peak=   -3.202 closest distance to " CD1 ILE A 263 " =    1.946
peak=   -3.200 closest distance to " CZ  PHE A  38 " =    1.936
peak=   -3.198 closest distance to " O   SER A  26 " =    1.626
peak=   -3.196 closest distance to " CG  ARG A 219 " =    2.601
peak=   -3.196 closest distance to " O   ASN A 187 " =    1.630
peak=   -3.195 closest distance to " O   GLY A  75 " =    1.967
peak=   -3.193 closest distance to " CB  ASP A 286 " =    1.903
peak=   -3.190 closest distance to " O   GLY A  80 " =    2.508
peak=   -3.187 closest distance to " CD1 ILE A 106 " =    2.188
peak=   -3.185 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.184 closest distance to " OG BSER A 134 " =    1.958
peak=   -3.181 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.177 closest distance to " OD1 ASP A 171 " =    1.447
peak=   -3.175 closest distance to " O   HOH Z  78 " =    1.819
peak=   -3.173 closest distance to " O   HOH Z  37 " =    1.817
peak=   -3.172 closest distance to " O   HOH Z 200 " =    1.315
peak=   -3.169 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.169 closest distance to " O   ALA A 160 " =    1.574
peak=   -3.168 closest distance to " O   HOH Z 252 " =    3.855
peak=   -3.167 closest distance to " OG1 THR A  82 " =    1.463
peak=   -3.163 closest distance to " O   HOH Z 240 " =    3.873
peak=   -3.160 closest distance to " CB  SER A 210 " =    1.048
peak=   -3.159 closest distance to " CD2 TYR A 247 " =    2.352
peak=   -3.157 closest distance to " O   HOH Z 154 " =    1.673
peak=   -3.150 closest distance to " CE3 TRP A 274 " =    2.490
peak=   -3.140 closest distance to " CG2BVAL A  41 " =    1.519
peak=   -3.136 closest distance to " O   HOH Z 426 " =    1.705
peak=   -3.132 closest distance to " O  BHOH Z 338 " =    1.166
peak=   -3.131 closest distance to " NH1 ARG A 195 " =    2.348
peak=   -3.130 closest distance to " O   HOH Z 350 " =    2.356
peak=   -3.124 closest distance to " CB  ASP A 162 " =    2.624
peak=   -3.120 closest distance to " O   HOH Z 171 " =    1.970
peak=   -3.114 closest distance to " O   HOH Z 357 " =    2.100
peak=   -3.114 closest distance to " O   HOH Z 418 " =    1.383
peak=   -3.113 closest distance to " O   HOH Z 134 " =    2.563
peak=   -3.111 closest distance to " CA  GLY A 241 " =    2.886
peak=   -3.102 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.102 closest distance to " CD1 ILE A 151 " =    2.365
peak=   -3.101 closest distance to " O   HOH Z 285 " =    1.281
peak=   -3.101 closest distance to " CD2 PHE A  61 " =    2.152
peak=   -3.097 closest distance to " O   HOH Z 389 " =    1.827
peak=   -3.097 closest distance to " O   HOH Z  19 " =    2.171
peak=   -3.096 closest distance to " CE  MET A 105 " =    2.322
peak=   -3.095 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.094 closest distance to " CD2 LEU A 237 " =    2.309
peak=   -3.089 closest distance to " O   TYR A 186 " =    1.731
peak=   -3.088 closest distance to " O   HOH Z 135 " =    1.550
peak=   -3.081 closest distance to " NE1 TRP A 266 " =    2.470
peak=   -3.080 closest distance to " O   HOH Z  91 " =    2.116
peak=   -3.072 closest distance to " C   GLY A 262 " =    2.022
peak=   -3.072 closest distance to " OG  SER A 273 " =    2.215
peak=   -3.070 closest distance to " O   HOH Z 434 " =    2.530
peak=   -3.059 closest distance to " O   HOH Z 166 " =    1.658
peak=   -3.041 closest distance to " O   HOH Z  77 " =    2.112
peak=   -3.040 closest distance to " O   HOH Z 156 " =    3.555

================= 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    :  0.4073 0.3944   6.214411e+00   6.180274e+00
   1_bss:  0.3951 0.3812   6.199356e+00   6.160692e+00
   1_xyz:  0.2953 0.3177   5.970476e+00   6.023036e+00
   1_adp:  0.2707 0.3301   5.919543e+00   6.044461e+00
   1_occ:  0.2707 0.3303   5.919085e+00   6.044669e+00
   2_bss:  0.2694 0.3272   5.917243e+00   6.043377e+00
   2_xyz:  0.1874 0.2276   5.569967e+00   5.739271e+00
   2_adp:  0.1642 0.2058   5.464318e+00   5.652290e+00
   2_occ:  0.1640 0.2057   5.463302e+00   5.651644e+00
   3_bss:  0.1627 0.2048   5.458898e+00   5.645745e+00
   3_xyz:  0.1346 0.1767   5.292359e+00   5.499208e+00
   3_adp:  0.1289 0.1711   5.255743e+00   5.466570e+00
   3_occ:  0.1288 0.1711   5.255655e+00   5.466625e+00
   4_bss:  0.1293 0.1710   5.256673e+00   5.465770e+00
   4_xyz:  0.1159 0.1621   5.176828e+00   5.411061e+00
   4_adp:  0.1135 0.1617   5.163568e+00   5.404291e+00
   4_occ:  0.1134 0.1618   5.163370e+00   5.404281e+00
   5_bss:  0.1133 0.1617   5.163319e+00   5.404343e+00
   5_xyz:  0.1172 0.1628   5.185602e+00   5.414499e+00
   5_adp:  0.1167 0.1637   5.186598e+00   5.420587e+00
   5_occ:  0.1166 0.1637   5.186493e+00   5.420524e+00
   5_bss:  0.1166 0.1636   5.186573e+00   5.420659e+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:  0.293  37.615  -3.561   4.761  -0.059   0.000  -0.000  -0.000
   1_xyz:  0.293  37.615  -3.561   4.761  -0.059   0.000  -0.000  -0.000
   1_adp:  0.293  37.615  -3.561   4.761  -0.059   0.000  -0.000  -0.000
   1_occ:  0.293  37.615  -3.561   4.761  -0.059   0.000  -0.000  -0.000
   2_bss:  0.321  64.086  -2.299   2.040  -0.118   0.000  -0.000  -0.000
   2_xyz:  0.321  64.086  -2.299   2.040  -0.118   0.000  -0.000  -0.000
   2_adp:  0.321  64.086  -2.299   2.040  -0.118   0.000  -0.000  -0.000
   2_occ:  0.321  64.086  -2.299   2.040  -0.118   0.000  -0.000  -0.000
   3_bss:  0.329  68.149  -2.291  -0.218  -0.388  -0.000  -0.000  -0.000
   3_xyz:  0.329  68.149  -2.291  -0.218  -0.388  -0.000  -0.000  -0.000
   3_adp:  0.329  68.149  -2.291  -0.218  -0.388  -0.000  -0.000  -0.000
   3_occ:  0.329  68.149  -2.291  -0.218  -0.388  -0.000  -0.000  -0.000
   4_bss:  0.328  66.636  -2.313  -0.876  -0.471  -0.000  -0.000  -0.000
   4_xyz:  0.328  66.636  -2.313  -0.876  -0.471  -0.000  -0.000  -0.000
   4_adp:  0.328  66.636  -2.313  -0.876  -0.471  -0.000  -0.000  -0.000
   4_occ:  0.328  66.636  -2.313  -0.876  -0.471  -0.000  -0.000  -0.000
   5_bss:  0.322  63.147  -2.099  -0.922  -0.283  -0.000  -0.000  -0.000
   5_xyz:  0.322  63.147  -2.099  -0.922  -0.283  -0.000  -0.000  -0.000
   5_adp:  0.322  63.147  -2.099  -0.922  -0.283  -0.000  -0.000  -0.000
   5_occ:  0.322  63.147  -2.099  -0.922  -0.283  -0.000  -0.000  -0.000
   5_bss:  0.321  64.687  -1.908  -0.826  -0.094  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.646 0.5884  0.7479    47362.299
   1_bss:  43.609 0.5994  0.7715    44064.488
   1_xyz:  34.571 0.7068  0.8842    28840.242
   1_adp:  35.685 0.6933  0.8622    30594.929
   1_occ:  35.727 0.6927  0.8612    30612.580
   2_bss:  35.245 0.6985  0.8576    30163.242
   2_xyz:  23.133 0.8292  0.9779    13414.199
   2_adp:  20.481 0.8563  0.9848    11097.959
   2_occ:  20.459 0.8565  0.9848    11079.768
   3_bss:  20.240 0.8586  0.9594    10901.735
   3_xyz:  16.563 0.8930  0.9760     7902.636
   3_adp:  15.795 0.9001  0.9716     7506.583
   3_occ:  15.797 0.9001  0.9715     7514.595
   4_bss:  15.779 0.9002  0.9634     7494.100
   4_xyz:  14.630 0.9097  0.9689     6700.388
   4_adp:  14.452 0.9114  0.9624     6634.392
   4_occ:  14.449 0.9114  0.9623     6633.014
   5_bss:  14.449 0.9114  0.9665     6631.761
   5_xyz:  14.592 0.9105  0.9650     6746.159
   5_adp:  14.714 0.9095  0.9563     6821.401
   5_occ:  14.712 0.9096  0.9562     6821.723
   5_bss:  14.713 0.9096  0.9617     6823.603
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6367e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6367e-01
   1_xyz:   1.356  0.011  0.082 15.046  0.005  4.111   1.0181e-01
   1_adp:   1.356  0.011  0.082 15.046  0.005  4.111   1.0181e-01
   1_occ:   1.356  0.011  0.082 15.046  0.005  4.111   1.0181e-01
   2_bss:   1.356  0.011  0.082 15.046  0.005  4.111   1.0181e-01
   2_xyz:   1.358  0.011  0.090 14.978  0.005  4.112   9.6667e-02
   2_adp:   1.358  0.011  0.090 14.978  0.005  4.112   9.6667e-02
   2_occ:   1.358  0.011  0.090 14.978  0.005  4.112   9.6667e-02
   3_bss:   1.358  0.011  0.090 14.978  0.005  4.112   9.6667e-02
   3_xyz:   1.050  0.008  0.073 14.645  0.004  4.122   6.4632e-02
   3_adp:   1.050  0.008  0.073 14.645  0.004  4.122   6.4632e-02
   3_occ:   1.050  0.008  0.073 14.645  0.004  4.122   6.4632e-02
   4_bss:   1.050  0.008  0.073 14.645  0.004  4.122   6.4632e-02
   4_xyz:   1.164  0.011  0.087 14.900  0.005  4.116   8.0863e-02
   4_adp:   1.164  0.011  0.087 14.900  0.005  4.116   8.0863e-02
   4_occ:   1.164  0.011  0.087 14.900  0.005  4.116   8.0863e-02
   5_bss:   1.164  0.011  0.087 14.900  0.005  4.116   8.0863e-02
   5_xyz:   0.964  0.007  0.074 14.481  0.004  4.115   5.6072e-02
   5_adp:   0.964  0.007  0.074 14.481  0.004  4.115   5.6072e-02
   5_occ:   0.964  0.007  0.074 14.481  0.004  4.115   5.6072e-02
   5_bss:   0.964  0.007  0.074 14.481  0.004  4.115   5.6072e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4305e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4305e-01
   1_xyz:   9.140  0.063  0.409 85.793  0.028  2.092   1.8850e-01
   1_adp:   9.140  0.063  0.409 85.793  0.028  2.092   1.8850e-01
   1_occ:   9.140  0.063  0.409 85.793  0.028  2.092   1.8850e-01
   2_bss:   9.140  0.063  0.409 85.793  0.028  2.092   1.8850e-01
   2_xyz:   8.541  0.049  0.284 87.168  0.044  2.138   8.4972e-02
   2_adp:   8.541  0.049  0.284 87.168  0.044  2.138   8.4972e-02
   2_occ:   8.541  0.049  0.284 87.168  0.044  2.138   8.4972e-02
   3_bss:   8.541  0.049  0.284 87.168  0.044  2.138   8.4972e-02
   3_xyz:   7.708  0.051  0.242 80.986  0.037  2.350   4.3436e-02
   3_adp:   7.708  0.051  0.242 80.986  0.037  2.350   4.3436e-02
   3_occ:   7.708  0.051  0.242 80.986  0.037  2.350   4.3436e-02
   4_bss:   7.708  0.051  0.242 80.986  0.037  2.350   4.3436e-02
   4_xyz:   8.524  0.053  0.298 82.546  0.040  2.294   6.1307e-02
   4_adp:   8.524  0.053  0.298 82.546  0.040  2.294   6.1307e-02
   4_occ:   8.524  0.053  0.298 82.546  0.040  2.294   6.1307e-02
   5_bss:   8.524  0.053  0.298 82.546  0.040  2.294   6.1307e-02
   5_xyz:   7.295  0.044  0.234 81.562  0.034  2.407   3.4177e-02
   5_adp:   7.295  0.044  0.234 81.562  0.034  2.407   3.4177e-02
   5_occ:   7.295  0.044  0.234 81.562  0.034  2.407   3.4177e-02
   5_bss:   7.295  0.044  0.234 81.562  0.034  2.407   3.4177e-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:  91.08   0.00  17.50  72.89   0.00  13.93  91.08   1.44  36.94
   1_occ:  91.08   0.00  17.50  72.89   0.00  13.93  91.08   1.44  36.94
   2_bss:  91.08   0.00  17.50  72.89   0.00  13.93  91.08   1.44  36.94
   2_xyz:  91.08   0.00  17.50  72.89   0.00  13.93  91.08   1.44  36.94
   2_adp:  90.10   0.00  17.23  76.45   0.00  13.05  90.10   4.61  39.96
   2_occ:  90.10   0.00  17.23  76.45   0.00  13.05  90.10   4.61  39.96
   3_bss:  90.10   0.00  17.23  76.45   0.00  13.05  90.10   4.61  39.96
   3_xyz:  90.10   0.00  17.23  76.45   0.00  13.05  90.10   4.61  39.96
   3_adp:  87.70   0.94  16.82  80.85   0.94  12.55  87.70   5.19  40.07
   3_occ:  87.70   0.94  16.82  80.85   0.94  12.55  87.70   5.19  40.07
   4_bss:  87.70   0.94  16.82  80.85   0.94  12.55  87.70   5.19  40.07
   4_xyz:  87.70   0.94  16.82  80.85   0.94  12.55  87.70   5.19  40.07
   4_adp:  88.84   0.00  16.64  88.84   0.00  12.31  84.96   1.64  40.23
   4_occ:  88.84   0.00  16.64  88.84   0.00  12.31  84.96   1.64  40.23
   5_bss:  88.84   0.00  16.64  88.84   0.00  12.31  84.96   1.64  40.23
   5_xyz:  88.84   0.00  16.64  88.84   0.00  12.31  84.96   1.64  40.23
   5_adp:  94.75   0.00  16.57  94.75   0.00  12.18  86.35   1.91  40.52
   5_occ:  94.75   0.00  16.57  94.75   0.00  12.18  86.35   1.91  40.52
   5_bss:  94.76   0.00  16.58  94.76   0.00  12.18  86.35   1.91  40.52
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.739    0.005    0.323
   1_adp:    1.739    0.005    0.323
   1_occ:    1.739    0.005    0.323
   2_bss:    1.739    0.005    0.323
   2_xyz:    1.277    0.022    0.547
   2_adp:    1.277    0.022    0.547
   2_occ:    1.277    0.022    0.547
   3_bss:    1.277    0.022    0.547
   3_xyz:    1.253    0.069    0.607
   3_adp:    1.253    0.069    0.607
   3_occ:    1.253    0.069    0.607
   4_bss:    1.253    0.069    0.607
   4_xyz:    1.278    0.046    0.646
   4_adp:    1.278    0.046    0.646
   4_occ:    1.278    0.046    0.646
   5_bss:    1.278    0.046    0.646
   5_xyz:    1.261    0.082    0.650
   5_adp:    1.261    0.082    0.650
   5_occ:    1.261    0.082    0.650
   5_bss:    1.261    0.082    0.650
------------------------------------------------------------------------

CPU time actual refinement: 328.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/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_590/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_590/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.66 
  Macro-tasks:
    bulk solvent and scale       = 37.91  
    individual site refinement   = 136.63 
    weights calculation          = 29.20  
    collect and process          = 6.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.51 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 104.98 
    alpha_beta                      = 8.30   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.78 
    fmodel                         = 6.24   
    r_factors                      = 0.19   
    phase_errors                   = 10.97  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 247.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.665 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    639 calls, 104.58 s
gradients_fft:          584 calls, 100.36 s

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

# Date 2008-01-16 Time 05:12:08 PST -0800 (1200489128.71 s)
Start R-work = 0.4073, R-free = 0.3944 (no bulk solvent and anisotropic scale)
Final R-work = 0.1356, R-free = 0.1789 (no bulk solvent and anisotropic scale)

Start R-work = 0.3951, R-free = 0.3812
Final R-work = 0.1166, R-free = 0.1636