# Date 2008-01-16 Time 05:28:20 PST -0800 (1200490100.22 s)
#phil __OFF__

Command line arguments: "../745.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22105
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 745

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.9914, 87.6859, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.96344
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.931036

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9634

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.96344
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.931036

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2026 [2203/2229]  1982   221  10.0%
  bin  2:  4.2026 -  3.3477 [2124/2144]  1912   212  10.0%
  bin  3:  3.3477 -  2.9280 [2084/2103]  1878   206   9.9%
  bin  4:  2.9280 -  2.6619 [2068/2098]  1854   214  10.3%
  bin  5:  2.6619 -  2.4720 [2063/2082]  1866   197   9.5%
  bin  6:  2.4720 -  2.3268 [2055/2080]  1844   211  10.3%
  bin  7:  2.3268 -  2.2106 [2009/2037]  1804   205  10.2%
  bin  8:  2.2106 -  2.1147 [2064/2100]  1856   208  10.1%
  bin  9:  2.1147 -  2.0335 [2021/2063]  1828   193   9.5%
  bin 10:  2.0335 -  1.9634 [ 898/2043]   806    92  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/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: 0.11 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: 39
        2.42 -     3.04: 2204
        3.04 -     3.66: 4702
        3.66 -     4.28: 9028
        4.28 -     4.90: 12331
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.966 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28299 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_745/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/model_refine_001.geo

CPU time processing inputs: 8.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4316   r_free= 0.4316   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.246794                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.3516 0.3334      6.5324      6.4737|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.3591 0.3509      6.7419      6.6755|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.3879 0.3794         6.6       6.609|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.4239 0.4516      6.4866      6.5224|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.4589 0.4164      6.3219      6.3144|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.4586 0.4872      6.2186      6.1765|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.4607 0.4577      6.2042      6.1617|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.4900 0.4885      6.1526      6.1467|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.4715 0.5165       6.091      6.1726|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.4929 0.4888      6.0654      6.0421|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.4828 0.5189      6.0132      6.0189|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.4873 0.4694      5.9267      5.9531|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.4811 0.4715      5.8581      5.7855|
| 14:  2.0124 -  1.9634 0.27    352   42 0.5436 0.5715      5.8929      5.8917|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.6880  1426   157  0.76  28.74   0.83     0.81      53900.26|
|  2:  4.6880 -  3.7396  1385   156  0.76  30.01   0.92     0.86      84072.99|
|  3:  3.7396 -  3.2723  1352   147  0.65  39.44   0.95     0.84      92499.14|
|  4:  3.2723 -  2.9756  1337   151  0.57  45.91   0.92     0.77      87579.42|
|  5:  2.9756 -  2.7638  1335   151  0.50  51.70   0.91     0.70      68350.03|
|  6:  2.7638 -  2.6017  1325   145  0.48  53.96   0.91     0.65      60707.72|
|  7:  2.6017 -  2.4720  1332   143  0.45  55.96   0.93     0.61      56428.60|
|  8:  2.4720 -  2.3648  1296   151  0.41  58.84   0.92     0.59      52927.05|
|  9:  2.3648 -  2.2741  1313   145  0.42  58.33   0.94     0.60      49526.25|
| 10:  2.2741 -  2.1958  1324   150  0.42  58.69   0.95     0.60      43882.48|
| 11:  2.1958 -  2.1274  1306   139  0.40  60.31   0.97     0.60      44546.30|
| 12:  2.1274 -  2.0667  1298   143  0.37  61.95   0.94     0.58      40419.87|
| 13:  2.0667 -  2.0124  1249   139  0.36  63.47   0.97     0.59      35808.48|
| 14:  2.0124 -  1.9634   352    42  0.44  57.14   0.95     0.62      26971.82|
|alpha:            min =        0.58 max =            0.86 mean =         0.68|
|beta:             min =    26971.82 max =        92499.14 mean =     58927.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.13|
|phase err.(test): min =        0.00 max =           89.84 mean =        51.64|
|-----------------------------------------------------------------------------|

============================== 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 = 10.199894             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.999050              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.797   (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:       13 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2010 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1869 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2833 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4638 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4390 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5627 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6704 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.331 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4316   r_free= 0.4316   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.246794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4205   r_free= 0.4250   ksol= 0.34   Bsol= 50.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,2.56,1.66,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.237707                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.407473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.011229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.507   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4205      final r-factor (work) = 0.3021          |
| start r-factor (free) = 0.4250      final r-factor (free) = 0.3412          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3692 = 8.41 * 0.50 * 6.2317 + 1.00 * 0.1729                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.6894 = 8.41 * 0.50 * 6.0826 + 1.00 * 0.1199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3021      final r-factor (work) = 0.2733          |
| start r-factor (free) = 0.3412      final r-factor (free) = 0.3547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1570 = 1.01 * 1.00 * 6.0826 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0101 = 1.01 * 1.00 * 5.9262 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.20  18.30    None  None   None       |
|    all(noH): 2823   0      0.00    101.20  18.30    None  None   None       |
|    Sol.    : 438    0      0.83    101.20  40.26    None  None   None       |
|    Mac.    : 2385   0      0.00    69.87   14.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.120:  957   |   5:    50.599 -  60.719:   76        |
|      1:    10.120 -  20.240:  982   |   6:    60.719 -  70.839:   42        |
|      2:    20.240 -  30.360:  417   |   7:    70.839 -  80.959:   14        |
|      3:    30.360 -  40.480:  199   |   8:    80.959 -  91.079:    5        |
|      4:    40.480 -  50.599:  130   |   9:    91.079 - 101.199:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2733 r_free = 0.3547             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2730 r_free = 0.3556             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2730   r_free= 0.3556   ksol= 0.34   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,2.56,1.66,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.940140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2714   r_free= 0.3522   ksol= 0.34   Bsol= 68.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.14,0.30,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.937921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.532284              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.970   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2714      final r-factor (work) = 0.2084          |
| start r-factor (free) = 0.3522      final r-factor (free) = 0.2671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5133 = 5.53 * 0.50 * 5.9266 + 1.00 * 0.1195                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2271 = 5.53 * 0.50 * 5.8394 + 1.00 * 0.0744                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2084      final r-factor (work) = 0.1922          |
| start r-factor (free) = 0.2671      final r-factor (free) = 0.2491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9143 = 0.32 * 1.00 * 5.8394 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9129 = 0.32 * 1.00 * 5.6543 + 1.00 * 0.0758                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.09  17.88    None  None   None       |
|    all(noH): 2823   0      0.00    100.09  17.88    None  None   None       |
|    Sol.    : 438    0      4.66    100.09  40.88    None  None   None       |
|    Mac.    : 2385   0      0.00    73.46   13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.009:  965   |   5:    50.045 -  60.054:   72        |
|      1:    10.009 -  20.018: 1087   |   6:    60.054 -  70.064:   41        |
|      2:    20.018 -  30.027:  319   |   7:    70.064 -  80.073:   15        |
|      3:    30.027 -  40.036:  173   |   8:    80.073 -  90.082:    3        |
|      4:    40.036 -  50.045:  147   |   9:    90.082 - 100.091:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1922 r_free = 0.2491             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1920 r_free = 0.2485             target_work(ml) = 5.623         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1920   r_free= 0.2485   ksol= 0.34   Bsol= 68.39   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.14,0.30,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.623011                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1917   r_free= 0.2479   ksol= 0.33   Bsol= 62.37   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.49,-0.23,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.620670                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.058517              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.535  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.730593              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.106   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1917      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2479      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7206 = 3.06 * 0.50 * 5.6538 + 1.00 * 0.0744                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4938 = 3.06 * 0.50 * 5.5169 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1514      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0459 = 0.73 * 1.00 * 5.5169 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9277 = 0.73 * 1.00 * 5.3606 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.13  17.97    None  None   None       |
|    all(noH): 2823   0      0.00    100.13  17.97    None  None   None       |
|    Sol.    : 438    0      6.05    100.13  44.56    None  None   None       |
|    Mac.    : 2385   0      0.00    82.31   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.013: 1049   |   5:    50.066 -  60.080:  116        |
|      1:    10.013 -  20.027: 1082   |   6:    60.080 -  70.093:   65        |
|      2:    20.027 -  30.040:  251   |   7:    70.093 -  80.106:   30        |
|      3:    30.040 -  40.053:  120   |   8:    80.106 -  90.120:    7        |
|      4:    40.053 -  50.066:  102   |   9:    90.120 - 100.133:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1896             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1895             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1895   ksol= 0.33   Bsol= 62.37   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.49,-0.23,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.332779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1891   ksol= 0.32   Bsol= 62.37   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.26,-0.54,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.263396              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.127699              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1256 = 2.26 * 0.50 * 5.3623 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0402 = 2.26 * 0.50 * 5.2885 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6864 = 0.13 * 1.00 * 5.2885 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6771 = 0.13 * 1.00 * 5.2446 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    87.54   16.80    None  None   None       |
|    all(noH): 2823   0      1.54    87.54   16.80    None  None   None       |
|    Sol.    : 438    0      6.06    87.54   39.18    None  None   None       |
|    Mac.    : 2385   0      1.54    81.72   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.542 -  10.142: 1065   |   5:    44.543 -  53.143:   99        |
|      1:    10.142 -  18.742: 1068   |   6:    53.143 -  61.743:   63        |
|      2:    18.742 -  27.342:  242   |   7:    61.743 -  70.344:   20        |
|      3:    27.342 -  35.943:  141   |   8:    70.344 -  78.944:   12        |
|      4:    35.943 -  44.543:  109   |   9:    78.944 -  87.544:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1690             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1689             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1689   ksol= 0.32   Bsol= 62.37   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.26,-0.54,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1690   ksol= 0.32   Bsol= 52.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.48,-0.62,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227641                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.091022              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.215307              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.941  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5378 = 2.09 * 0.50 * 5.2438 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4970 = 2.09 * 0.50 * 5.2020 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1273 = 0.22 * 1.00 * 5.2020 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1218 = 0.22 * 1.00 * 5.1749 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    85.06   16.68    None  None   None       |
|    all(noH): 2823   0      0.93    85.06   16.68    None  None   None       |
|    Sol.    : 438    0      5.99    85.06   38.98    None  None   None       |
|    Mac.    : 2385   0      0.93    83.60   12.58    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:     0.935 -   9.347:  909   |   5:    42.998 -  51.411:  103        |
|      1:     9.347 -  17.760: 1181   |   6:    51.411 -  59.823:   69        |
|      2:    17.760 -  26.173:  271   |   7:    59.823 -  68.236:   23        |
|      3:    26.173 -  34.585:  133   |   8:    68.236 -  76.649:   14        |
|      4:    34.585 -  42.998:  114   |   9:    76.649 -  85.061:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1608             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1609             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1609   ksol= 0.32   Bsol= 52.73   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.48,-0.62,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174140                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.0990 0.1274      5.3891      5.5842|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.0869 0.1170      5.4594      5.6769|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.1131 0.1588      5.5148      5.8194|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.1284 0.1724      5.4854      5.6226|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.1415 0.1783      5.3637      5.5894|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.1293 0.1986      5.2303      5.4991|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.1337 0.1574      5.2092      5.3336|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.1221 0.1754      5.0822       5.364|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.1215 0.1837      5.0487      5.3372|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.1135 0.1687      4.9403      5.1857|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.1123 0.1883      4.9455      5.3223|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.1198 0.1707      4.8927      5.1407|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.1084 0.1609      4.7674      4.9973|
| 14:  2.0124 -  1.9634 0.27    352   42 0.0953 0.1505      4.6421       4.854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.6880  1426   157  0.94   8.94   0.98     0.94       6950.23|
|  2:  4.6880 -  3.7396  1385   156  0.95   8.07   1.01     1.00       9409.84|
|  3:  3.7396 -  3.2723  1352   147  0.93  12.11   1.02     1.02      11159.68|
|  4:  3.2723 -  2.9756  1337   151  0.91  14.50   1.01     0.98      10865.80|
|  5:  2.9756 -  2.7638  1335   151  0.90  16.34   0.99     0.98       8646.72|
|  6:  2.7638 -  2.6017  1325   145  0.89  16.64   0.98     0.95       7172.82|
|  7:  2.6017 -  2.4720  1332   143  0.90  16.09   0.99     0.96       6618.43|
|  8:  2.4720 -  2.3648  1296   151  0.90  15.84   0.99     0.97       5389.20|
|  9:  2.3648 -  2.2741  1313   145  0.90  15.75   0.99     0.96       5077.88|
| 10:  2.2741 -  2.1958  1324   150  0.90  15.66   1.01     0.98       4264.62|
| 11:  2.1958 -  2.1274  1306   139  0.90  15.96   0.99     0.93       4327.48|
| 12:  2.1274 -  2.0667  1298   143  0.90  16.23   1.01     1.01       4034.03|
| 13:  2.0667 -  2.0124  1249   139  0.90  16.65   1.00     0.98       3339.59|
| 14:  2.0124 -  1.9634   352    42  0.93  12.99   0.99     0.96       2495.87|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2495.87 max =        11159.68 mean =      6673.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.42|
|phase err.(test): min =        0.00 max =           87.79 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1601   ksol= 0.32   Bsol= 52.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.45,-0.59,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.171668                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1601   ksol= 0.32   Bsol= 52.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.45,-0.59,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.171668                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.0986 0.1232      5.3662      5.5491|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.0871 0.1140      5.4497      5.6659|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.1136 0.1579      5.5143      5.8132|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.1283 0.1724      5.4854       5.623|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.1416 0.1776      5.3645      5.5907|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.1294 0.1989      5.2312      5.4996|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.1338 0.1580      5.2093      5.3353|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.1218 0.1754      5.0817      5.3633|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.1216 0.1835      5.0486      5.3372|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.1135 0.1689      4.9405      5.1867|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.1123 0.1883      4.9455      5.3223|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.1198 0.1709      4.8929      5.1418|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.1083 0.1613      4.7681      4.9992|
| 14:  2.0124 -  1.9634 0.27    352   42 0.0953 0.1499      4.6428      4.8526|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.6880  1426   157  0.94   8.46   0.97     0.94       6358.73|
|  2:  4.6880 -  3.7396  1385   156  0.95   7.78   1.01     1.00       8931.82|
|  3:  3.7396 -  3.2723  1352   147  0.93  12.00   1.02     1.02      11020.63|
|  4:  3.2723 -  2.9756  1337   151  0.91  14.53   1.01     0.98      10860.09|
|  5:  2.9756 -  2.7638  1335   151  0.90  16.35   0.99     0.98       8660.63|
|  6:  2.7638 -  2.6017  1325   145  0.89  16.64   0.98     0.95       7184.51|
|  7:  2.6017 -  2.4720  1332   143  0.90  16.10   0.99     0.96       6624.08|
|  8:  2.4720 -  2.3648  1296   151  0.90  15.86   0.99     0.97       5397.47|
|  9:  2.3648 -  2.2741  1313   145  0.90  15.75   0.99     0.96       5077.73|
| 10:  2.2741 -  2.1958  1324   150  0.90  15.66   1.01     0.98       4268.15|
| 11:  2.1958 -  2.1274  1306   139  0.90  15.98   0.99     0.93       4331.31|
| 12:  2.1274 -  2.0667  1298   143  0.90  16.25   1.01     1.01       4040.99|
| 13:  2.0667 -  2.0124  1249   139  0.90  16.67   1.00     0.98       3347.50|
| 14:  2.0124 -  1.9634   352    42  0.93  13.03   0.99     0.96       2503.31|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2503.31 max =        11020.63 mean =      6581.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.36|
|phase err.(test): min =        0.00 max =           87.44 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    85.03   16.65    None  None   None       |
|    all(noH): 2823   0      0.90    85.03   16.65    None  None   None       |
|    Sol.    : 438    0      5.96    85.03   38.94    None  None   None       |
|    Mac.    : 2385   0      0.90    83.57   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:     0.903 -   9.315:  909   |   5:    42.966 -  51.379:  103        |
|      1:     9.315 -  17.728: 1181   |   6:    51.379 -  59.791:   69        |
|      2:    17.728 -  26.141:  271   |   7:    59.791 -  68.204:   23        |
|      3:    26.141 -  34.553:  133   |   8:    68.204 -  76.616:   14        |
|      4:    34.553 -  42.966:  114   |   9:    76.616 -  85.029:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.614 - 4.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 300
   mapped sites are within: 0.719 - 4.777

peak=    5.980 closest distance to " NE2 GLN A  11 " =    1.277
peak=    5.577 closest distance to " O   HOH Z 144 " =    1.974
peak=    5.490 closest distance to " CG  PRO A  54 " =    1.396
peak=    5.304 closest distance to " NH2 ARG A  56 " =    2.055
peak=    5.284 closest distance to " O   HOH Z  63 " =    1.635
peak=    5.240 closest distance to " O   HOH Z 126 " =    2.015
peak=    5.228 closest distance to " O   HOH Z 423 " =    1.967
peak=    5.189 closest distance to " O   HOH Z 287 " =    2.119
peak=    5.155 closest distance to " CB  GLN A 223 " =    1.491
peak=    5.093 closest distance to " O   HOH Z 417 " =    2.140
peak=    5.048 closest distance to " O   HOH Z   7 " =    1.504
peak=    4.934 closest distance to " O   HOH Z 369 " =    2.191
peak=    4.908 closest distance to " O   HOH Z 232 " =    2.279
peak=    4.750 closest distance to " O   HOH Z   9 " =    1.685
peak=    4.660 closest distance to " O   HOH Z  57 " =    2.296
peak=    4.657 closest distance to " O   HOH Z  78 " =    1.594
peak=    4.641 closest distance to " O   HOH Z 380 " =    1.880
peak=    4.630 closest distance to " CB  PRO A  54 " =    1.037
peak=    4.586 closest distance to " CB  ASN A 148 " =    1.395
peak=    4.570 closest distance to " CB  SER A  63 " =    1.255
peak=    4.563 closest distance to " O   HOH Z 298 " =    1.967
peak=    4.488 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.455 closest distance to " O   HOH Z 427 " =    2.559
peak=    4.325 closest distance to " CB  ARG A 190 " =    1.452
peak=    4.324 closest distance to " ND2 ASN A 187 " =    1.597
peak=    4.292 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.260 closest distance to " O   HOH Z   1 " =    1.889
peak=    4.238 closest distance to " O   HOH Z 403 " =    1.460
peak=    4.222 closest distance to " CG  PRO A 198 " =    1.306
peak=    4.203 closest distance to " CG  PRO A 213 " =    1.295
peak=    4.195 closest distance to " CG  TRP A 179 " =    2.133
peak=    4.177 closest distance to " CD  ARG A 159 " =    0.792
peak=    4.174 closest distance to " CG2 VAL A 257 " =    0.876
peak=    4.158 closest distance to " CB  ASN A 187 " =    1.044
peak=    4.122 closest distance to " O   HOH Z   2 " =    1.686
peak=    4.096 closest distance to " CB  ARG A  79 " =    1.359
peak=    4.095 closest distance to " CB  VAL A 265 " =    1.317
peak=    4.088 closest distance to " O   HOH Z 362 " =    1.970
peak=    4.086 closest distance to " O   HOH Z 133 " =    2.532
peak=    4.085 closest distance to " CA  TYR A  30 " =    1.038
peak=    4.061 closest distance to " CZ  PHE A 218 " =    1.104
peak=    4.026 closest distance to " CB  GLU A 128 " =    0.936
peak=    4.024 closest distance to " CD  ARG A  66 " =    2.139
peak=    4.023 closest distance to " O   HOH Z  68 " =    2.092
peak=    3.996 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.996 closest distance to " NE2 HIS A 207 " =    1.157
peak=    3.991 closest distance to " CB  SER A   3 " =    1.389
peak=    3.990 closest distance to " CB  SER A 216 " =    0.907
peak=    3.988 closest distance to " O   HOH Z 425 " =    1.427
peak=    3.970 closest distance to " O   HOH Z 116 " =    3.108
peak=    3.956 closest distance to " CE  LYS A  76 " =    0.861
peak=    3.945 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.944 closest distance to " O   HOH Z 183 " =    1.462
peak=    3.942 closest distance to " O   HOH Z   1 " =    1.797
peak=    3.931 closest distance to " CB  TYR A 169 " =    0.817
peak=    3.929 closest distance to " O   HOH Z  61 " =    1.668
peak=    3.907 closest distance to " CB  GLU A 277 " =    3.598
peak=    3.901 closest distance to " O   HOH Z  44 " =    1.793
peak=    3.901 closest distance to " O   HOH Z 145 " =    2.193
peak=    3.898 closest distance to " O   HOH Z 158 " =    2.919
peak=    3.898 closest distance to " CG  PRO A  90 " =    1.405
peak=    3.898 closest distance to " O   HOH Z 437 " =    1.767
peak=    3.897 closest distance to " CB  TRP A 266 " =    1.012
peak=    3.893 closest distance to " O   HOH Z 225 " =    1.597
peak=    3.885 closest distance to " CB  SER A 212 " =    1.314
peak=    3.879 closest distance to " CA  ARG A 195 " =    1.236
peak=    3.878 closest distance to " O   HOH Z 405 " =    1.468
peak=    3.870 closest distance to " CG  PRO A 243 " =    1.114
peak=    3.858 closest distance to " OG ASER A 258 " =    3.112
peak=    3.856 closest distance to " O   SER A  87 " =    2.424
peak=    3.854 closest distance to " O   HOH Z 214 " =    2.262
peak=    3.840 closest distance to " O   PRO A 198 " =    1.578
peak=    3.833 closest distance to " CG  LEU A 167 " =    1.265
peak=    3.828 closest distance to " O   HOH Z  69 " =    2.193
peak=    3.808 closest distance to " NH1AARG A 145 " =    1.216
peak=    3.806 closest distance to " CB  GLU A 152 " =    1.276
peak=    3.800 closest distance to " NH2AARG A 190 " =    1.841
peak=    3.796 closest distance to " CB  ASN A 142 " =    0.950
peak=    3.795 closest distance to " CB  LEU A 228 " =    1.051
peak=    3.779 closest distance to " O   HOH Z  24 " =    1.857
peak=    3.774 closest distance to " N   PHE A 130 " =    1.271
peak=    3.762 closest distance to " O   HOH Z  44 " =    2.707
peak=    3.753 closest distance to " ND1 HIS A  86 " =    1.666
peak=    3.743 closest distance to " O   HOH Z 145 " =    1.448
peak=    3.742 closest distance to " CA  SER A  87 " =    0.988
peak=    3.733 closest distance to " O   HOH Z 368 " =    3.609
peak=    3.708 closest distance to " CB  SER A 210 " =    0.773
peak=    3.702 closest distance to " N   CYS A 260 " =    0.826
peak=    3.697 closest distance to " CB  GLN A  88 " =    1.259
peak=    3.687 closest distance to " OD1 ASN A  69 " =    2.612
peak=    3.684 closest distance to " O   HOH Z  40 " =    2.120
peak=    3.681 closest distance to " O   HOH Z 375 " =    1.078
peak=    3.680 closest distance to " O   HOH Z  10 " =    1.710
peak=    3.668 closest distance to " CG2 THR A 221 " =    1.037
peak=    3.663 closest distance to " O   HOH Z 128 " =    1.932
peak=    3.662 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.658 closest distance to " O   HOH Z  21 " =    1.686
peak=    3.650 closest distance to " CA  ASN A 127 " =    1.054
peak=    3.645 closest distance to " CA  VAL A 125 " =    1.105
peak=    3.644 closest distance to " CE  LYS A 119 " =    1.233
peak=    3.640 closest distance to " O   HOH Z 327 " =    1.732
peak=    3.637 closest distance to " O   HOH Z 189 " =    2.530
peak=    3.636 closest distance to " O   HOH Z 180 " =    2.159
peak=    3.635 closest distance to " O   HOH Z 394 " =    1.726
peak=    3.632 closest distance to " O   HOH Z 272 " =    1.774
peak=    3.626 closest distance to " O   HOH Z 352 " =    1.735
peak=    3.617 closest distance to " CA  ALA A 233 " =    1.148
peak=    3.616 closest distance to " CD2 TRP A 179 " =    1.234
peak=    3.606 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.605 closest distance to " O   ASN A  74 " =    1.477
peak=    3.603 closest distance to " O   HOH Z  49 " =    1.036
peak=    3.601 closest distance to " CG1BVAL A  72 " =    1.495
peak=    3.577 closest distance to " O   HOH Z 257 " =    2.254
peak=    3.575 closest distance to " CA  ALA A  51 " =    0.979
peak=    3.564 closest distance to " CB  ALA A 114 " =    1.077
peak=    3.561 closest distance to " O   TYR A 116 " =    1.317
peak=    3.560 closest distance to " CB  ASN A 110 " =    1.037
peak=    3.553 closest distance to " N   SER A  97 " =    0.905
peak=    3.549 closest distance to " CB  ILE A 120 " =    1.301
peak=    3.548 closest distance to " O   HOH Z 250 " =    1.472
peak=    3.546 closest distance to " CB  SER A 276 " =    1.171
peak=    3.543 closest distance to " O   HOH Z 305 " =    3.534
peak=    3.542 closest distance to " O   HOH Z 195 " =    1.368
peak=    3.541 closest distance to " O   HOH Z 172 " =    2.425
peak=    3.537 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.537 closest distance to " O   HOH Z 126 " =    1.478
peak=    3.533 closest distance to " O   HOH Z 406 " =    1.649
peak=    3.532 closest distance to " O   HOH Z 236 " =    1.551
peak=    3.528 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.528 closest distance to " CB  ARG A 138 " =    0.966
peak=    3.521 closest distance to " CA  ILE A 234 " =    0.976
peak=    3.519 closest distance to " CB  THR A 157 " =    1.165
peak=    3.503 closest distance to " CA  THR A 264 " =    0.850
peak=    3.500 closest distance to " CZ3 TRP A 266 " =    1.130
peak=    3.489 closest distance to " CB  TYR A  30 " =    1.360
peak=    3.488 closest distance to " NZ  LYS A 117 " =    3.006
peak=    3.480 closest distance to " N   ARG A 156 " =    1.289
peak=    3.480 closest distance to " CB  LYS A 117 " =    1.253
peak=    3.475 closest distance to " CB  GLU A  46 " =    1.041
peak=    3.473 closest distance to " O   HOH Z 346 " =    1.761
peak=    3.472 closest distance to " O   GLY A 302 " =    1.711
peak=    3.470 closest distance to " O   HOH Z 215 " =    1.400
peak=    3.467 closest distance to " O   HOH Z 392 " =    1.279
peak=    3.465 closest distance to " O   HOH Z 394 " =    3.902
peak=    3.465 closest distance to " N   GLN A 278 " =    1.229
peak=    3.458 closest distance to " CA  ASN A 215 " =    1.129
peak=    3.453 closest distance to " O   HOH Z 294 " =    1.499
peak=    3.449 closest distance to " O   HOH Z  97 " =    2.023
peak=    3.448 closest distance to " CD  PRO A 243 " =    1.705
peak=    3.447 closest distance to " O   HOH Z 368 " =    1.751
peak=    3.442 closest distance to " CD1 LEU A 300 " =    1.130
peak=    3.439 closest distance to " O   HOH Z 188 " =    2.050
peak=    3.434 closest distance to " O   HOH Z 286 " =    2.144
peak=    3.432 closest distance to " O   HOH Z 272 " =    2.082
peak=    3.425 closest distance to " CE3 TRP A 150 " =    1.058
peak=    3.423 closest distance to " CB  ASP A 124 " =    0.756
peak=    3.423 closest distance to " CG AARG A 275 " =    1.231
peak=    3.422 closest distance to " CA  SER A  95 " =    1.023
peak=    3.421 closest distance to " O   HOH Z 234 " =    3.829
peak=    3.421 closest distance to " OG  SER A  62 " =    2.937
peak=    3.419 closest distance to " O   HOH Z 148 " =    3.434
peak=    3.409 closest distance to " CB  VAL A 202 " =    1.590
peak=    3.406 closest distance to " O   HOH Z 213 " =    2.209
peak=    3.405 closest distance to " CA  ARG A 102 " =    1.146
peak=    3.403 closest distance to " O   HOH Z  88 " =    3.973
peak=    3.403 closest distance to " O   HOH Z 132 " =    2.587
peak=    3.393 closest distance to " NH1BARG A 145 " =    1.291
peak=    3.386 closest distance to " O   HOH Z 184 " =    1.530
peak=    3.384 closest distance to " O   PHE A 192 " =    1.354
peak=    3.376 closest distance to " O   HOH Z 371 " =    2.810
peak=    3.374 closest distance to " O   HOH Z 154 " =    1.943
peak=    3.373 closest distance to " O   HOH Z 222 " =    2.383
peak=    3.366 closest distance to " O   HOH Z 219 " =    1.952
peak=    3.363 closest distance to " CB  THR A  31 " =    1.644
peak=    3.361 closest distance to " CA  TYR A  30 " =    1.073
peak=    3.359 closest distance to " O   HOH Z 434 " =    1.388
peak=    3.354 closest distance to " O   HOH Z 193 " =    1.620
peak=    3.349 closest distance to " CD  LYS A  76 " =    1.820
peak=    3.347 closest distance to " O   HOH Z 175 " =    2.188
peak=    3.347 closest distance to " CB  ALA A   1 " =    4.777
peak=    3.345 closest distance to " O   HOH Z 345 " =    1.779
peak=    3.345 closest distance to " N   ALA A   1 " =    2.032
peak=    3.337 closest distance to " CB  TYR A 116 " =    0.886
peak=    3.334 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.333 closest distance to " O   HOH Z 218 " =    1.752
peak=    3.330 closest distance to " CB  ALA A 114 " =    0.983
peak=    3.328 closest distance to " CB  MET A  40 " =    0.775
peak=    3.326 closest distance to " CA  ALA A 180 " =    1.373
peak=    3.325 closest distance to " O   CYS A 168 " =    1.350
peak=    3.323 closest distance to " O   HOH Z 402 " =    1.563
peak=    3.321 closest distance to " ND2AASN A 224 " =    0.882
peak=    3.315 closest distance to " CE3 TRP A  85 " =    0.974
peak=    3.312 closest distance to " O   HOH Z 421 " =    2.118
peak=    3.311 closest distance to " O   HOH Z 156 " =    2.571
peak=    3.308 closest distance to " O   HOH Z 193 " =    1.804
peak=    3.306 closest distance to " CD2 TYR A 186 " =    1.187
peak=    3.304 closest distance to " O   HOH Z 344 " =    3.125
peak=    3.304 closest distance to " O   HOH Z 171 " =    2.932
peak=    3.294 closest distance to " O   HOH Z 411 " =    3.804
peak=    3.288 closest distance to " O   HOH Z 181 " =    2.139
peak=    3.285 closest distance to " CA  ALA A 158 " =    1.182
peak=    3.285 closest distance to " CD  LYS A 166 " =    1.276
peak=    3.279 closest distance to " O   HOH Z  85 " =    2.127
peak=    3.277 closest distance to " O   HOH Z 357 " =    1.997
peak=    3.276 closest distance to " O   HOH Z 201 " =    1.445
peak=    3.276 closest distance to " CG1 ILE A 151 " =    1.052
peak=    3.275 closest distance to " O   HOH Z 368 " =    4.302
peak=    3.275 closest distance to " O   HOH Z   3 " =    1.914
peak=    3.275 closest distance to " O   HOH Z 425 " =    1.888
peak=    3.270 closest distance to " CD1 ILE A 263 " =    1.288
peak=    3.269 closest distance to " O   HOH Z  58 " =    1.801
peak=    3.269 closest distance to " O   HOH Z 274 " =    2.094
peak=    3.267 closest distance to " OG BSER A 134 " =    2.956
peak=    3.266 closest distance to " O   HOH Z 130 " =    3.733
peak=    3.265 closest distance to " O   HOH Z 248 " =    1.553
peak=    3.262 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.261 closest distance to " O   HOH Z 238 " =    3.903
peak=    3.261 closest distance to " O   HOH Z 260 " =    2.387
peak=    3.260 closest distance to " O   HOH Z 414 " =    1.293
peak=    3.257 closest distance to " O   HOH Z 389 " =    1.863
peak=    3.251 closest distance to " O   HOH Z 244 " =    1.665
peak=    3.249 closest distance to " CZ3 TRP A 123 " =    1.543
peak=    3.248 closest distance to " CZ  PHE A  38 " =    1.245
peak=    3.248 closest distance to " CB  ALA A 160 " =    1.413
peak=    3.243 closest distance to " O   HOH Z 371 " =    1.982
peak=    3.241 closest distance to " N   TYR A  15 " =    0.803
peak=    3.228 closest distance to " CG1 ILE A  33 " =    1.297
peak=    3.224 closest distance to " O   ASN A 209 " =    1.422
peak=    3.222 closest distance to " CD  ARG A 269 " =    0.864
peak=    3.221 closest distance to " N   VAL A 296 " =    1.630
peak=    3.221 closest distance to " O   HOH Z 325 " =    2.268
peak=    3.220 closest distance to " O   HOH Z   3 " =    2.646
peak=    3.217 closest distance to " CD2 LEU A 297 " =    0.962
peak=    3.215 closest distance to " CB  ARG A 139 " =    1.139
peak=    3.211 closest distance to " NE2 GLN A  73 " =    3.886
peak=    3.210 closest distance to " NH1 ARG A 138 " =    1.027
peak=    3.208 closest distance to " CG2 ILE A  20 " =    1.496
peak=    3.202 closest distance to " OG BSER A 164 " =    2.326
peak=    3.202 closest distance to " CA  GLY A 136 " =    0.937
peak=    3.201 closest distance to " CB  PRO A 243 " =    1.182
peak=    3.199 closest distance to " CG  LYS A 119 " =    1.147
peak=    3.195 closest distance to " CB  PHE A 130 " =    0.889
peak=    3.185 closest distance to " CA  ALA A 299 " =    0.882
peak=    3.184 closest distance to " O   HOH Z  42 " =    1.647
peak=    3.184 closest distance to " N   GLU A   2 " =    1.397
peak=    3.180 closest distance to " ND2 ASN A 249 " =    0.854
peak=    3.180 closest distance to " CE1 TYR A 186 " =    1.416
peak=    3.179 closest distance to " O   HOH Z 153 " =    1.717
peak=    3.175 closest distance to " O   HOH Z 285 " =    2.222
peak=    3.174 closest distance to " CG1 VAL A 153 " =    0.907
peak=    3.173 closest distance to " CG2 VAL A 197 " =    1.004
peak=    3.170 closest distance to " NH2BARG A 190 " =    1.405
peak=    3.169 closest distance to " CE3 TRP A 274 " =    1.314
peak=    3.169 closest distance to " CG2 ILE A 120 " =    1.358
peak=    3.166 closest distance to " CB  LEU A 300 " =    0.912
peak=    3.162 closest distance to " CG  GLN A 278 " =    1.289
peak=    3.161 closest distance to " CA  ALA A 291 " =    0.854
peak=    3.160 closest distance to " OG BSER A  99 " =    2.350
peak=    3.160 closest distance to " CB  TRP A 150 " =    1.206
peak=    3.158 closest distance to " CB  ASN A 215 " =    1.074
peak=    3.154 closest distance to " CD BLYS A 290 " =    1.153
peak=    3.153 closest distance to " O   HOH Z 135 " =    1.792
peak=    3.151 closest distance to " CB  PHE A 204 " =    0.720
peak=    3.151 closest distance to " NH2 ARG A 219 " =    1.755
peak=    3.148 closest distance to " CA  ILE A 106 " =    0.759
peak=    3.145 closest distance to " CG2 ILE A 151 " =    0.824
peak=    3.145 closest distance to " O   HOH Z 415 " =    3.886
peak=    3.139 closest distance to " O   HOH Z 153 " =    3.695
peak=    3.139 closest distance to " O   HOH Z 217 " =    1.557
peak=    3.132 closest distance to " CA  THR A 221 " =    0.969
peak=    3.132 closest distance to " CD  ARG A 138 " =    0.824
peak=    3.130 closest distance to " O   HOH Z 109 " =    2.447
peak=    3.123 closest distance to " CB  SER A  62 " =    0.981
peak=    3.120 closest distance to " CB  ALA A  10 " =    0.742
peak=    3.119 closest distance to " CA  ALA A 129 " =    1.237
peak=    3.119 closest distance to " CG BARG A 102 " =    1.883
peak=    3.117 closest distance to " O   HOH Z 432 " =    1.793
peak=    3.116 closest distance to " N   TYR A 116 " =    1.301
peak=    3.111 closest distance to " CB  MET A 188 " =    1.765
peak=    3.107 closest distance to " O   HOH Z  50 " =    1.672
peak=    3.107 closest distance to " NZ  LYS A 119 " =    1.335
peak=    3.106 closest distance to " CG1 VAL A 189 " =    1.777
peak=    3.102 closest distance to " CB  TRP A 179 " =    1.472
peak=    3.091 closest distance to " CA  ARG A  36 " =    1.060
peak=    3.091 closest distance to " CB  SER A  99 " =    0.912
peak=    3.091 closest distance to " O   PRO A  90 " =    1.628
peak=    3.086 closest distance to " N   VAL A  72 " =    1.440
peak=    3.085 closest distance to " O   HOH Z 227 " =    1.954
peak=    3.079 closest distance to " CD2 LEU A 255 " =    1.587
peak=    3.079 closest distance to " OD1BASN A 224 " =    2.390
peak=    3.073 closest distance to " CB  LEU A  83 " =    0.719
peak=    3.062 closest distance to " OE2 GLU A  53 " =    1.992
peak=    3.059 closest distance to " CD2 LEU A   5 " =    1.429
peak=    3.057 closest distance to " N   ASN A 127 " =    1.388
peak=    3.043 closest distance to " O   HOH Z 213 " =    1.934
peak=    3.036 closest distance to " O   HOH Z 386 " =    3.027

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.456 - 5.450
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 197
   mapped sites are within: 0.709 - 5.450

peak=   -4.456 closest distance to " CB  PRO A 243 " =    2.602
peak=   -4.359 closest distance to " CD  ARG A  14 " =    3.306
peak=   -4.315 closest distance to " O   HOH Z 290 " =    1.007
peak=   -4.241 closest distance to " O   HOH Z 351 " =    1.526
peak=   -4.227 closest distance to " O   HOH Z 377 " =    1.954
peak=   -4.219 closest distance to " CD  ARG A 156 " =    2.080
peak=   -4.188 closest distance to " CA  GLY A  98 " =    1.790
peak=   -4.159 closest distance to " CB  ALA A  43 " =    2.431
peak=   -4.096 closest distance to " O   HOH Z 185 " =    2.111
peak=   -4.088 closest distance to " O   PRO A 198 " =    1.173
peak=   -4.076 closest distance to " O   HOH Z 131 " =    4.039
peak=   -4.055 closest distance to " O   VAL A  67 " =    2.613
peak=   -4.052 closest distance to " CD1 LEU A 255 " =    2.913
peak=   -4.019 closest distance to " O   HOH Z 231 " =    0.931
peak=   -3.985 closest distance to " OG BSER A 134 " =    1.380
peak=   -3.931 closest distance to " O   SER A  22 " =    2.612
peak=   -3.911 closest distance to " ND2 ASN A 249 " =    2.218
peak=   -3.893 closest distance to " O   HOH Z 298 " =    2.533
peak=   -3.892 closest distance to " N   THR A 157 " =    1.509
peak=   -3.888 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.884 closest distance to " CZ3 TRP A 179 " =    1.243
peak=   -3.881 closest distance to " CB  ALA A 291 " =    2.223
peak=   -3.878 closest distance to " O   HOH Z 211 " =    1.258
peak=   -3.863 closest distance to " O   HOH Z  60 " =    1.521
peak=   -3.839 closest distance to " O   HOH Z 266 " =    5.113
peak=   -3.803 closest distance to " CE BMET A  47 " =    1.340
peak=   -3.798 closest distance to " O   ALA A  10 " =    1.635
peak=   -3.763 closest distance to " O   HOH Z 231 " =    1.950
peak=   -3.757 closest distance to " CB  ALA A 248 " =    2.131
peak=   -3.742 closest distance to " CA  GLY A 241 " =    2.294
peak=   -3.737 closest distance to " O   HOH Z  65 " =    1.082
peak=   -3.719 closest distance to " O   HOH Z 372 " =    2.462
peak=   -3.696 closest distance to " CD2 LEU A 237 " =    2.897
peak=   -3.690 closest distance to " O   SER A 135 " =    1.438
peak=   -3.679 closest distance to " O   HOH Z 389 " =    2.079
peak=   -3.675 closest distance to " C   HIS A 108 " =    1.139
peak=   -3.673 closest distance to " O   HOH Z  11 " =    1.754
peak=   -3.669 closest distance to " CD2 TYR A 293 " =    1.944
peak=   -3.650 closest distance to " CG1 VAL A 112 " =    3.015
peak=   -3.647 closest distance to " CG2 THR A  18 " =    2.726
peak=   -3.645 closest distance to " CB  PHE A 192 " =    1.947
peak=   -3.638 closest distance to " CE2 PHE A 218 " =    2.458
peak=   -3.629 closest distance to " O   HOH Z  52 " =    1.120
peak=   -3.611 closest distance to " CB  ALA A 158 " =    1.715
peak=   -3.605 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.602 closest distance to " CD  GLN A  58 " =    0.885
peak=   -3.602 closest distance to " O   HOH Z 282 " =    4.594
peak=   -3.599 closest distance to " CD  GLN A  88 " =    0.848
peak=   -3.591 closest distance to " CE  MET A 105 " =    2.551
peak=   -3.589 closest distance to " CE2 TYR A  30 " =    2.610
peak=   -3.588 closest distance to " OD1 ASP A 191 " =    1.864
peak=   -3.585 closest distance to " CA  GLY A 203 " =    2.347
peak=   -3.584 closest distance to " OG  SER A  97 " =    2.190
peak=   -3.582 closest distance to " CD1 LEU A 101 " =    2.225
peak=   -3.574 closest distance to " O   PRO A 243 " =    2.432
peak=   -3.554 closest distance to " CD  GLU A 277 " =    1.219
peak=   -3.554 closest distance to " O   HOH Z   1 " =    1.395
peak=   -3.552 closest distance to " CB  ASN A  39 " =    2.283
peak=   -3.545 closest distance to " O   HOH Z  60 " =    0.890
peak=   -3.543 closest distance to " O   HOH Z 313 " =    1.757
peak=   -3.543 closest distance to " CG  MET A 105 " =    0.967
peak=   -3.537 closest distance to " CG  GLN A 223 " =    1.888
peak=   -3.530 closest distance to " O   HOH Z  39 " =    1.101
peak=   -3.526 closest distance to " O   HOH Z  24 " =    1.189
peak=   -3.508 closest distance to " CA  GLY A 133 " =    2.042
peak=   -3.506 closest distance to " N   ALA A  43 " =    2.559
peak=   -3.501 closest distance to " CG  PHE A 283 " =    2.651
peak=   -3.500 closest distance to " O   HOH Z 317 " =    1.384
peak=   -3.498 closest distance to " CZ2 TRP A 274 " =    0.968
peak=   -3.495 closest distance to " O   HOH Z  38 " =    1.596
peak=   -3.492 closest distance to " O   ILE A  49 " =    1.684
peak=   -3.487 closest distance to " CE1 PHE A  59 " =    2.136
peak=   -3.486 closest distance to " CB  ALA A 114 " =    2.469
peak=   -3.486 closest distance to " O   PRO A 198 " =    1.371
peak=   -3.485 closest distance to " O   PRO A 163 " =    1.856
peak=   -3.477 closest distance to " CB  ASP A 132 " =    2.381
peak=   -3.461 closest distance to " CA  ASP A  27 " =    2.366
peak=   -3.457 closest distance to " O   HOH Z 111 " =    1.784
peak=   -3.453 closest distance to " ND2 ASN A  45 " =    2.155
peak=   -3.451 closest distance to " O   HOH Z 140 " =    1.283
peak=   -3.446 closest distance to " CG  ASN A  39 " =    1.658
peak=   -3.445 closest distance to " O   HOH Z 407 " =    3.136
peak=   -3.441 closest distance to " OG BSER A 134 " =    1.773
peak=   -3.440 closest distance to " O   HOH Z  60 " =    1.062
peak=   -3.438 closest distance to " CB  TRP A  85 " =    2.419
peak=   -3.436 closest distance to " O   ALA A   1 " =    1.682
peak=   -3.428 closest distance to " O   HOH Z 385 " =    2.143
peak=   -3.427 closest distance to " O   HOH Z  15 " =    1.525
peak=   -3.425 closest distance to " O   HOH Z 174 " =    2.746
peak=   -3.424 closest distance to " CG  GLN A 223 " =    1.004
peak=   -3.418 closest distance to " NE2 GLN A 278 " =    1.673
peak=   -3.416 closest distance to " N   GLN A  58 " =    1.703
peak=   -3.415 closest distance to " CG2 ILE A  49 " =    2.802
peak=   -3.414 closest distance to " O   VAL A  67 " =    2.935
peak=   -3.407 closest distance to " O   HOH Z  90 " =    2.693
peak=   -3.406 closest distance to " O   ARG A 145 " =    1.323
peak=   -3.406 closest distance to " O   VAL A 189 " =    2.589
peak=   -3.402 closest distance to " O   HOH Z 359 " =    3.317
peak=   -3.400 closest distance to " O   HOH Z 412 " =    4.208
peak=   -3.399 closest distance to " CG2 THR A 178 " =    2.197
peak=   -3.389 closest distance to " ND2 ASN A  60 " =    4.061
peak=   -3.389 closest distance to " CB  PRO A  54 " =    2.473
peak=   -3.382 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.380 closest distance to " CG2 ILE A 263 " =    2.392
peak=   -3.378 closest distance to " O   HOH Z 191 " =    5.450
peak=   -3.375 closest distance to " N   ASP A 171 " =    2.556
peak=   -3.375 closest distance to " O   GLN A 240 " =    1.998
peak=   -3.375 closest distance to " CE  LYS A  76 " =    2.733
peak=   -3.367 closest distance to " OD2 ASP A 171 " =    2.211
peak=   -3.365 closest distance to " O   GLU A 152 " =    1.382
peak=   -3.365 closest distance to " ND2 ASN A 285 " =    2.144
peak=   -3.364 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.353 closest distance to " O   HOH Z  49 " =    1.285
peak=   -3.352 closest distance to " O   HOH Z  51 " =    0.935
peak=   -3.346 closest distance to " O   HOH Z 152 " =    4.726
peak=   -3.346 closest distance to " CE1 PHE A  59 " =    2.109
peak=   -3.344 closest distance to " O   HOH Z 282 " =    0.709
peak=   -3.340 closest distance to " OD1 ASN A 148 " =    1.462
peak=   -3.329 closest distance to " O   HOH Z 198 " =    1.470
peak=   -3.320 closest distance to " CG1 VAL A  78 " =    2.587
peak=   -3.318 closest distance to " CZ  PHE A 155 " =    1.177
peak=   -3.313 closest distance to " OG  SER A  87 " =    1.310
peak=   -3.312 closest distance to " O   HOH Z  60 " =    2.548
peak=   -3.311 closest distance to " CB  PRO A 163 " =    2.456
peak=   -3.307 closest distance to " O   HOH Z 275 " =    1.738
peak=   -3.299 closest distance to " CD  LYS A 166 " =    2.542
peak=   -3.299 closest distance to " CG  LEU A  83 " =    2.012
peak=   -3.297 closest distance to " NH2 ARG A  79 " =    2.097
peak=   -3.291 closest distance to " CB  TYR A  15 " =    2.237
peak=   -3.290 closest distance to " C   GLU A 236 " =    0.820
peak=   -3.285 closest distance to " O   HOH Z  73 " =    2.265
peak=   -3.282 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.278 closest distance to " ND2 ASN A 187 " =    1.323
peak=   -3.270 closest distance to " ND2 ASN A  45 " =    1.228
peak=   -3.266 closest distance to " NZ  LYS A 166 " =    1.038
peak=   -3.261 closest distance to " CG2 THR A  42 " =    1.920
peak=   -3.261 closest distance to " O   HOH Z 298 " =    1.175
peak=   -3.261 closest distance to " O   HOH Z 286 " =    1.607
peak=   -3.255 closest distance to " CE3 TRP A 274 " =    2.408
peak=   -3.252 closest distance to " CE2 PHE A  61 " =    2.659
peak=   -3.248 closest distance to " OD1 ASP A 171 " =    1.671
peak=   -3.246 closest distance to " CG  GLN A 240 " =    2.415
peak=   -3.240 closest distance to " CB  ALA A 291 " =    2.003
peak=   -3.235 closest distance to " O   ASP A 162 " =    2.219
peak=   -3.234 closest distance to " O   HOH Z 292 " =    1.494
peak=   -3.226 closest distance to " NH2AARG A 275 " =    5.405
peak=   -3.225 closest distance to " OH  TYR A 172 " =    1.904
peak=   -3.224 closest distance to " ND2BASN A 224 " =    1.666
peak=   -3.222 closest distance to " O   HOH Z 318 " =    1.774
peak=   -3.221 closest distance to " CB  GLN A  55 " =    1.313
peak=   -3.216 closest distance to " O   HOH Z 346 " =    1.658
peak=   -3.216 closest distance to " CG  LEU A 167 " =    0.980
peak=   -3.215 closest distance to " O   HOH Z 134 " =    3.713
peak=   -3.214 closest distance to " O   HOH Z 281 " =    2.709
peak=   -3.210 closest distance to " CG2 ILE A 151 " =    2.556
peak=   -3.209 closest distance to " O   HOH Z 176 " =    0.711
peak=   -3.209 closest distance to " O   HOH Z  28 " =    1.685
peak=   -3.208 closest distance to " OD1 ASN A 187 " =    1.547
peak=   -3.197 closest distance to " OG1 THR A  82 " =    1.987
peak=   -3.191 closest distance to " N   GLN A 122 " =    1.372
peak=   -3.187 closest distance to " CE3 TRP A 123 " =    1.306
peak=   -3.185 closest distance to " N   SER A 212 " =    1.972
peak=   -3.184 closest distance to " C   ASP A 270 " =    1.337
peak=   -3.183 closest distance to " NE2 GLN A 194 " =    1.800
peak=   -3.182 closest distance to " O   PHE A 218 " =    1.469
peak=   -3.179 closest distance to " OD2 ASP A  27 " =    1.608
peak=   -3.174 closest distance to " CB  ALA A 180 " =    1.618
peak=   -3.174 closest distance to " O   HOH Z 377 " =    0.892
peak=   -3.172 closest distance to " CG1 VAL A 230 " =    2.145
peak=   -3.172 closest distance to " CG1 VAL A 250 " =    2.745
peak=   -3.168 closest distance to " CB  ALA A   9 " =    2.344
peak=   -3.168 closest distance to " O   GLY A  17 " =    1.139
peak=   -3.165 closest distance to " O   HOH Z 171 " =    1.486
peak=   -3.164 closest distance to " O   ALA A 161 " =    1.605
peak=   -3.160 closest distance to " O   HOH Z 218 " =    3.885
peak=   -3.149 closest distance to " CG  ARG A 269 " =    2.460
peak=   -3.147 closest distance to " CD2 PHE A 130 " =    3.036
peak=   -3.142 closest distance to " CB  ALA A 131 " =    2.030
peak=   -3.139 closest distance to " CB  GLN A  11 " =    1.735
peak=   -3.130 closest distance to " CA  GLY A  57 " =    2.090
peak=   -3.122 closest distance to " CD1 ILE A 199 " =    2.586
peak=   -3.121 closest distance to " O   HOH Z   2 " =    1.643
peak=   -3.120 closest distance to " CD1 ILE A 263 " =    2.643
peak=   -3.107 closest distance to " O   HOH Z 414 " =    1.982
peak=   -3.101 closest distance to " O   HOH Z 152 " =    0.825
peak=   -3.097 closest distance to " O   ASN A 127 " =    1.541
peak=   -3.093 closest distance to " O   HOH Z 253 " =    3.912
peak=   -3.082 closest distance to " O   HOH Z 364 " =    2.285
peak=   -3.080 closest distance to " CD1 TRP A 179 " =    0.982
peak=   -3.075 closest distance to " CZ  PHE A  16 " =    2.289
peak=   -3.072 closest distance to " O   HOH Z 281 " =    2.937
peak=   -3.056 closest distance to " N   VAL A 232 " =    2.178
peak=   -3.055 closest distance to " CZ  TYR A 169 " =    1.654
peak=   -3.054 closest distance to " OG  SER A 245 " =    1.255
peak=   -3.041 closest distance to " O   HOH Z  68 " =    1.322

================= 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    :  0.4316 0.4316   6.246794e+00   6.234518e+00
   1_bss:  0.4205 0.4250   6.237707e+00   6.224070e+00
   1_xyz:  0.3021 0.3412   5.988664e+00   6.063345e+00
   1_adp:  0.2733 0.3547   5.940096e+00   6.090754e+00
   1_occ:  0.2730 0.3556   5.940140e+00   6.091567e+00
   2_bss:  0.2714 0.3522   5.937921e+00   6.088922e+00
   2_xyz:  0.2084 0.2671   5.688183e+00   5.873142e+00
   2_adp:  0.1922 0.2491   5.623928e+00   5.813594e+00
   2_occ:  0.1920 0.2485   5.623011e+00   5.812578e+00
   3_bss:  0.1917 0.2479   5.620670e+00   5.809792e+00
   3_xyz:  0.1514 0.2006   5.403347e+00   5.618144e+00
   3_adp:  0.1381 0.1896   5.333189e+00   5.561745e+00
   3_occ:  0.1380 0.1895   5.332779e+00   5.561379e+00
   4_bss:  0.1383 0.1891   5.330615e+00   5.557818e+00
   4_xyz:  0.1246 0.1742   5.239882e+00   5.477688e+00
   4_adp:  0.1245 0.1690   5.228489e+00   5.451291e+00
   4_occ:  0.1244 0.1689   5.227898e+00   5.450460e+00
   5_bss:  0.1243 0.1690   5.227641e+00   5.450070e+00
   5_xyz:  0.1173 0.1617   5.181266e+00   5.416164e+00
   5_adp:  0.1158 0.1608   5.174367e+00   5.414276e+00
   5_occ:  0.1157 0.1609   5.174140e+00   5.413978e+00
   5_bss:  0.1158 0.1601   5.171668e+00   5.410325e+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:  0.340  50.000  -2.879   2.558   1.656   0.000   0.000   0.000
   1_xyz:  0.340  50.000  -2.879   2.558   1.656   0.000   0.000   0.000
   1_adp:  0.340  50.000  -2.879   2.558   1.656   0.000   0.000   0.000
   1_occ:  0.340  50.000  -2.879   2.558   1.656   0.000   0.000   0.000
   2_bss:  0.341  68.394  -2.043  -0.142   0.304  -0.000   0.000   0.000
   2_xyz:  0.341  68.394  -2.043  -0.142   0.304  -0.000   0.000   0.000
   2_adp:  0.341  68.394  -2.043  -0.142   0.304  -0.000   0.000   0.000
   2_occ:  0.341  68.394  -2.043  -0.142   0.304  -0.000   0.000   0.000
   3_bss:  0.332  62.367  -2.223  -1.485  -0.229  -0.000  -0.000  -0.000
   3_xyz:  0.332  62.367  -2.223  -1.485  -0.229  -0.000  -0.000  -0.000
   3_adp:  0.332  62.367  -2.223  -1.485  -0.229  -0.000  -0.000  -0.000
   3_occ:  0.332  62.367  -2.223  -1.485  -0.229  -0.000  -0.000  -0.000
   4_bss:  0.324  62.367  -2.336  -2.260  -0.542  -0.000  -0.000  -0.000
   4_xyz:  0.324  62.367  -2.336  -2.260  -0.542  -0.000  -0.000  -0.000
   4_adp:  0.324  62.367  -2.336  -2.260  -0.542  -0.000  -0.000  -0.000
   4_occ:  0.324  62.367  -2.336  -2.260  -0.542  -0.000  -0.000  -0.000
   5_bss:  0.318  52.735  -2.392  -2.481  -0.623  -0.000  -0.000  -0.000
   5_xyz:  0.318  52.735  -2.392  -2.481  -0.623  -0.000  -0.000  -0.000
   5_adp:  0.318  52.735  -2.392  -2.481  -0.623  -0.000  -0.000  -0.000
   5_occ:  0.318  52.735  -2.392  -2.481  -0.623  -0.000  -0.000  -0.000
   5_bss:  0.318  52.703  -2.359  -2.449  -0.591  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.181 0.5060  0.6779    58926.778
   1_bss:  50.409 0.5143  0.7038    56741.112
   1_xyz:  35.764 0.6932  0.9041    31911.957
   1_adp:  37.653 0.6699  0.8788    34693.847
   1_occ:  37.775 0.6684  0.8762    34800.198
   2_bss:  37.342 0.6735  0.8519    34272.722
   2_xyz:  27.083 0.7881  0.9620    18638.114
   2_adp:  24.699 0.8143  0.9777    16179.879
   2_occ:  24.661 0.8147  0.9778    16135.040
   3_bss:  24.537 0.8158  0.9551    15990.939
   3_xyz:  19.276 0.8679  0.9864    10237.932
   3_adp:  17.917 0.8810  0.9830     9180.882
   3_occ:  17.908 0.8811  0.9829     9169.724
   4_bss:  17.817 0.8818  0.9696     9075.085
   4_xyz:  15.922 0.8987  0.9789     7589.331
   4_adp:  15.245 0.9050  0.9783     7273.053
   4_occ:  15.231 0.9051  0.9782     7252.757
   5_bss:  15.234 0.9050  0.9739     7247.310
   5_xyz:  14.450 0.9115  0.9770     6717.798
   5_adp:  14.370 0.9123  0.9734     6681.245
   5_occ:  14.366 0.9123  0.9733     6673.514
   5_bss:  14.305 0.9127  0.9738     6581.762
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7290e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7290e-01
   1_xyz:   1.475  0.011  0.098 16.014  0.006  4.109   1.1987e-01
   1_adp:   1.475  0.011  0.098 16.014  0.006  4.109   1.1987e-01
   1_occ:   1.475  0.011  0.098 16.014  0.006  4.109   1.1987e-01
   2_bss:   1.475  0.011  0.098 16.014  0.006  4.109   1.1987e-01
   2_xyz:   1.182  0.008  0.086 14.821  0.004  4.108   7.4450e-02
   2_adp:   1.182  0.008  0.086 14.821  0.004  4.108   7.4450e-02
   2_occ:   1.182  0.008  0.086 14.821  0.004  4.108   7.4450e-02
   3_bss:   1.182  0.008  0.086 14.821  0.004  4.108   7.4450e-02
   3_xyz:   0.973  0.007  0.070 14.777  0.004  4.115   5.7069e-02
   3_adp:   0.973  0.007  0.070 14.777  0.004  4.115   5.7069e-02
   3_occ:   0.973  0.007  0.070 14.777  0.004  4.115   5.7069e-02
   4_bss:   0.973  0.007  0.070 14.777  0.004  4.115   5.7069e-02
   4_xyz:   0.960  0.006  0.072 14.567  0.004  4.110   5.5286e-02
   4_adp:   0.960  0.006  0.072 14.567  0.004  4.110   5.5286e-02
   4_occ:   0.960  0.006  0.072 14.567  0.004  4.110   5.5286e-02
   5_bss:   0.960  0.006  0.072 14.567  0.004  4.110   5.5286e-02
   5_xyz:   0.970  0.007  0.075 14.524  0.004  4.113   5.8301e-02
   5_adp:   0.970  0.007  0.075 14.524  0.004  4.113   5.8301e-02
   5_occ:   0.970  0.007  0.075 14.524  0.004  4.113   5.8301e-02
   5_bss:   0.970  0.007  0.075 14.524  0.004  4.113   5.8301e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4113e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4113e-01
   1_xyz:   8.841  0.071  0.316 82.446  0.048  2.056   9.0202e-02
   1_adp:   8.841  0.071  0.316 82.446  0.048  2.056   9.0202e-02
   1_occ:   8.841  0.071  0.316 82.446  0.048  2.056   9.0202e-02
   2_bss:   8.841  0.071  0.316 82.446  0.048  2.056   9.0202e-02
   2_xyz:   6.653  0.057  0.303 84.619  0.039  2.220   7.5657e-02
   2_adp:   6.653  0.057  0.303 84.619  0.039  2.220   7.5657e-02
   2_occ:   6.653  0.057  0.303 84.619  0.039  2.220   7.5657e-02
   3_bss:   6.653  0.057  0.303 84.619  0.039  2.220   7.5657e-02
   3_xyz:   6.988  0.042  0.213 80.927  0.032  2.329   4.8863e-02
   3_adp:   6.988  0.042  0.213 80.927  0.032  2.329   4.8863e-02
   3_occ:   6.988  0.042  0.213 80.927  0.032  2.329   4.8863e-02
   4_bss:   6.988  0.042  0.213 80.927  0.032  2.329   4.8863e-02
   4_xyz:   7.481  0.041  0.216 81.531  0.035  2.367   3.8592e-02
   4_adp:   7.481  0.041  0.216 81.531  0.035  2.367   3.8592e-02
   4_occ:   7.481  0.041  0.216 81.531  0.035  2.367   3.8592e-02
   5_bss:   7.481  0.041  0.216 81.531  0.035  2.367   3.8592e-02
   5_xyz:   6.894  0.050  0.246 84.296  0.035  2.311   4.3591e-02
   5_adp:   6.894  0.050  0.246 84.296  0.035  2.311   4.3591e-02
   5_occ:   6.894  0.050  0.246 84.296  0.035  2.311   4.3591e-02
   5_bss:   6.894  0.050  0.246 84.296  0.035  2.311   4.3591e-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: 101.20   0.00  18.30  69.87   0.00  14.27 101.20   0.83  40.26
   1_occ: 101.20   0.00  18.30  69.87   0.00  14.27 101.20   0.83  40.26
   2_bss: 101.20   0.00  18.30  69.87   0.00  14.27 101.20   0.83  40.26
   2_xyz: 101.20   0.00  18.30  69.87   0.00  14.27 101.20   0.83  40.26
   2_adp: 100.09   0.00  17.88  73.46   0.00  13.65 100.09   4.66  40.88
   2_occ: 100.09   0.00  17.88  73.46   0.00  13.65 100.09   4.66  40.88
   3_bss: 100.09   0.00  17.88  73.46   0.00  13.65 100.09   4.66  40.88
   3_xyz: 100.09   0.00  17.88  73.46   0.00  13.65 100.09   4.66  40.88
   3_adp: 100.13   0.00  17.97  82.31   0.00  13.09 100.13   6.05  44.56
   3_occ: 100.13   0.00  17.97  82.31   0.00  13.09 100.13   6.05  44.56
   4_bss: 100.13   0.00  17.97  82.31   0.00  13.09 100.13   6.05  44.56
   4_xyz: 100.13   0.00  17.97  82.31   0.00  13.09 100.13   6.05  44.56
   4_adp:  87.54   1.54  16.80  81.72   1.54  12.69  87.54   6.06  39.18
   4_occ:  87.54   1.54  16.80  81.72   1.54  12.69  87.54   6.06  39.18
   5_bss:  87.54   1.54  16.80  81.72   1.54  12.69  87.54   6.06  39.18
   5_xyz:  87.54   1.54  16.80  81.72   1.54  12.69  87.54   6.06  39.18
   5_adp:  85.06   0.93  16.68  83.60   0.93  12.58  85.06   5.99  38.98
   5_occ:  85.06   0.93  16.68  83.60   0.93  12.58  85.06   5.99  38.98
   5_bss:  85.03   0.90  16.65  83.57   0.90  12.55  85.03   5.96  38.94
------------------------------------------------------------------------
 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:    1.679    0.015    0.409
   1_adp:    1.679    0.015    0.409
   1_occ:    1.679    0.015    0.409
   2_bss:    1.679    0.015    0.409
   2_xyz:    1.347    0.031    0.536
   2_adp:    1.347    0.031    0.536
   2_occ:    1.347    0.031    0.536
   3_bss:    1.347    0.031    0.536
   3_xyz:    1.323    0.023    0.647
   3_adp:    1.323    0.023    0.647
   3_occ:    1.323    0.023    0.647
   4_bss:    1.323    0.023    0.647
   4_xyz:    1.394    0.038    0.671
   4_adp:    1.394    0.038    0.671
   4_occ:    1.394    0.038    0.671
   5_bss:    1.394    0.038    0.671
   5_xyz:    1.576    0.047    0.696
   5_adp:    1.576    0.047    0.696
   5_occ:    1.576    0.047    0.696
   5_bss:    1.576    0.047    0.696
------------------------------------------------------------------------

CPU time actual refinement: 279.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/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_745/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_745/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.49 
  Macro-tasks:
    bulk solvent and scale       = 31.84  
    individual site refinement   = 117.77 
    weights calculation          = 24.65  
    collect and process          = 5.45   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 179.81 
  Micro-tasks:
    mask                            = 2.01   
    f_calc                          = 89.14  
    alpha_beta                      = 6.76   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 97.16  
    fmodel                         = 5.41   
    r_factors                      = 0.19   
    phase_errors                   = 8.85   
    foms                           = 0.29   
    TOTAL for micro-tasks          = 210.76 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.946 micro seconds
Total CPU time: 4.85 minutes
from_scatterers_fft:    649 calls, 88.79 s
gradients_fft:          594 calls, 85.38 s

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

# Date 2008-01-16 Time 05:33:09 PST -0800 (1200490389.96 s)
Start R-work = 0.4316, R-free = 0.4316 (no bulk solvent and anisotropic scale)
Final R-work = 0.1395, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4205, R-free = 0.4250
Final R-work = 0.1158, R-free = 0.1601