# Date 2008-01-16 Time 04:55:10 PST -0800 (1200488110.36 s)
#phil __OFF__

Command line arguments: "../511.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5042
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 511

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.97229
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9723

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.97229
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2202 [2132/2156]  1918   214  10.0%
  bin  2:  4.2202 -  3.3623 [2038/2058]  1836   202   9.9%
  bin  3:  3.3623 -  2.9410 [2031/2050]  1824   207  10.2%
  bin  4:  2.9410 -  2.6737 [1999/2029]  1802   197   9.9%
  bin  5:  2.6737 -  2.4830 [2008/2027]  1807   201  10.0%
  bin  6:  2.4830 -  2.3372 [1957/1982]  1762   195  10.0%
  bin  7:  2.3372 -  2.2206 [1979/2007]  1778   201  10.2%
  bin  8:  2.2206 -  2.1242 [1978/2014]  1784   194   9.8%
  bin  9:  2.1242 -  2.0426 [1928/1970]  1734   194  10.1%
  bin 10:  2.0426 -  1.9723 [1539/2020]  1385   154  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/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: 0.14 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: 32
        2.42 -     3.04: 2213
        3.04 -     3.66: 4755
        3.66 -     4.28: 9151
        4.28 -     4.90: 12400
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.968 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.156 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28546 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_511/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.22605 86.39 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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3368   r_free= 0.3296   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.100661                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.2960 0.2877      6.3858       6.344|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.2683 0.2415      6.5081      6.4083|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.2899 0.2689      6.4248      6.5002|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.3059 0.3280      6.2947      6.3567|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.3502 0.2951      6.1816       6.056|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.3466 0.3695      6.0915      6.0332|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.3555 0.3418      6.0468      6.0042|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.3692 0.4048      6.0301      6.0816|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.3664 0.3848      5.9777      5.9978|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.3739 0.3376      5.9622       5.872|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.3737 0.3913      5.8937       5.963|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.3942 0.3672      5.8888      5.8591|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.3921 0.3694      5.7576      5.7282|
| 14:  2.0215 -  1.9723 0.66    839   97 0.4279 0.4043      5.8071      5.7053|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7070  1389   153  0.79  26.23   0.86     0.82      43998.26|
|  2:  4.7070 -  3.7557  1328   152  0.83  23.10   0.97     0.93      50658.71|
|  3:  3.7557 -  3.2867  1304   140  0.79  27.12   1.00     0.96      50887.36|
|  4:  3.2867 -  2.9888  1297   149  0.76  30.16   0.99     0.94      45468.35|
|  5:  2.9888 -  2.7760  1293   145  0.70  35.04   0.98     0.91      36517.58|
|  6:  2.7760 -  2.6133  1297   138  0.70  35.35   0.98     0.89      32245.03|
|  7:  2.6133 -  2.4830  1279   144  0.68  37.66   1.01     0.89      31061.90|
|  8:  2.4830 -  2.3754  1269   142  0.66  38.94   1.01     0.87      30315.22|
|  9:  2.3754 -  2.2843  1257   140  0.67  38.79   1.01     0.88      28030.80|
| 10:  2.2843 -  2.2057  1283   143  0.66  39.45   1.03     0.89      25226.67|
| 11:  2.2057 -  2.1369  1254   137  0.65  39.87   1.04     0.92      24294.98|
| 12:  2.1369 -  2.0760  1249   138  0.63  41.44   1.04     0.89      22681.98|
| 13:  2.0760 -  2.0215  1292   141  0.60  44.12   1.03     0.86      20638.52|
| 14:  2.0215 -  1.9723   839    97  0.61  43.64   1.05     0.81      17769.49|
|alpha:            min =        0.81 max =            0.96 mean =         0.89|
|beta:             min =    17769.49 max =        50887.36 mean =     33404.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.96 mean =        35.45|
|phase err.(test): min =        0.00 max =           89.92 mean =        35.34|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.195727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.382   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.831785              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.237   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       29 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      209 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2870 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4694 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4457 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5674 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6726 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.224 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3368   r_free= 0.3296   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.100661                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3201   r_free= 0.3144   ksol= 0.34   Bsol= 42.02   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,2.58,-1.70,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.078537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.811315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.344   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.166   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3201      final r-factor (work) = 0.2271          |
| start r-factor (free) = 0.3144      final r-factor (free) = 0.2544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7131 = 2.81 * 0.50 * 6.0816 + 1.00 * 0.1644                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2932 = 2.81 * 0.50 * 5.8453 + 1.00 * 0.0767                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2271      final r-factor (work) = 0.2076          |
| start r-factor (free) = 0.2544      final r-factor (free) = 0.2645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5660 = 0.44 * 1.00 * 5.8453 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4999 = 0.44 * 1.00 * 5.6843 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.18   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    82.18   17.22    None  None   None       |
|    Sol.    : 438    0      6.06    82.18   38.50    None  None   None       |
|    Mac.    : 2385   0      0.00    74.19   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.218:  624   |   5:    41.090 -  49.308:  120        |
|      1:     8.218 -  16.436: 1218   |   6:    49.308 -  57.526:   72        |
|      2:    16.436 -  24.654:  434   |   7:    57.526 -  65.744:   29        |
|      3:    24.654 -  32.872:  175   |   8:    65.744 -  73.962:   13        |
|      4:    32.872 -  41.090:  134   |   9:    73.962 -  82.180:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2076 r_free = 0.2645             target_work(ml) = 5.697         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2073 r_free = 0.2641             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2073   r_free= 0.2641   ksol= 0.34   Bsol= 42.02   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,2.58,-1.70,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.696113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2055   r_free= 0.2599   ksol= 0.33   Bsol= 47.29   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-0.76,-1.40,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.686846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.106065              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.141737              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.760  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2055      final r-factor (work) = 0.1530          |
| start r-factor (free) = 0.2599      final r-factor (free) = 0.1973          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0618 = 2.11 * 0.50 * 5.6837 + 1.00 * 0.0767                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9000 = 2.11 * 0.50 * 5.5523 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1530      final r-factor (work) = 0.1445          |
| start r-factor (free) = 0.1973      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7973 = 0.14 * 1.00 * 5.5523 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7693 = 0.14 * 1.00 * 5.3812 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.42   16.71    None  None   None       |
|    all(noH): 2823   0      0.00    74.42   16.71    None  None   None       |
|    Sol.    : 438    0      6.55    74.42   36.97    None  None   None       |
|    Mac.    : 2385   0      0.00    72.48   12.99    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 -   7.442:  378   |   5:    37.209 -  44.651:  114        |
|      1:     7.442 -  14.884: 1438   |   6:    44.651 -  52.093:   92        |
|      2:    14.884 -  22.326:  451   |   7:    52.093 -  59.535:   40        |
|      3:    22.326 -  29.767:  146   |   8:    59.535 -  66.976:   15        |
|      4:    29.767 -  37.209:  144   |   9:    66.976 -  74.418:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1445 r_free = 0.1866             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1444 r_free = 0.1867             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1867   ksol= 0.33   Bsol= 47.29   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-0.76,-1.40,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.355124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1856   ksol= 0.33   Bsol= 47.29   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.07,-1.22,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.349881                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.586202              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.229178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.145  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1856      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3197 = 1.59 * 0.50 * 5.3795 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2281 = 1.59 * 0.50 * 5.2716 + 1.00 * 0.0472                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2147 = 0.23 * 1.00 * 5.2716 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1971 = 0.23 * 1.00 * 5.1915 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    77.45   16.80    None  None   None       |
|    all(noH): 2823   0      0.93    77.45   16.80    None  None   None       |
|    Sol.    : 438    0      3.02    75.09   38.27    None  None   None       |
|    Mac.    : 2385   0      0.93    77.45   12.85    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:     0.929 -   8.581:  641   |   5:    39.189 -  46.841:  105        |
|      1:     8.581 -  16.233: 1332   |   6:    46.841 -  54.493:   91        |
|      2:    16.233 -  23.885:  343   |   7:    54.493 -  62.145:   49        |
|      3:    23.885 -  31.537:  120   |   8:    62.145 -  69.797:   11        |
|      4:    31.537 -  39.189:  124   |   9:    69.797 -  77.449:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1604             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1606             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1606   ksol= 0.33   Bsol= 47.29   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.07,-1.22,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179968                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1604   ksol= 0.33   Bsol= 47.29   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.45,-1.23,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179083                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.945761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.928  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0975 = 1.95 * 0.50 * 5.1911 + 1.00 * 0.0472                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0629 = 1.95 * 0.50 * 5.1483 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3069 = 0.45 * 1.00 * 5.1483 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2938 = 0.45 * 1.00 * 5.1176 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    79.32   16.77    None  None   None       |
|    all(noH): 2823   0      0.77    79.32   16.77    None  None   None       |
|    Sol.    : 438    0      4.28    75.82   38.64    None  None   None       |
|    Mac.    : 2385   0      0.77    79.32   12.75    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:     0.767 -   8.623:  690   |   5:    40.046 -  47.901:  108        |
|      1:     8.623 -  16.478: 1300   |   6:    47.901 -  55.757:   89        |
|      2:    16.478 -  24.334:  330   |   7:    55.757 -  63.613:   47        |
|      3:    24.334 -  32.190:  121   |   8:    63.613 -  71.469:   12        |
|      4:    32.190 -  40.046:  120   |   9:    71.469 -  79.324:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1527             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1094 r_free = 0.1527             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1527   ksol= 0.33   Bsol= 47.29   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.45,-1.23,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1533   ksol= 0.33   Bsol= 47.29   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.45,-1.11,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118842                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.678241              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.854697              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.922  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9084 = 2.68 * 0.50 * 5.1184 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8970 = 2.68 * 0.50 * 5.1035 + 1.00 * 0.0628                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.6802 = 3.85 * 1.00 * 5.1035 + 1.00 * 0.0080                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.6632 = 3.85 * 1.00 * 5.0986 + 1.00 * 0.0095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.82   16.98    None  None   None       |
|    all(noH): 2823   0      0.00    89.82   16.98    None  None   None       |
|    Sol.    : 438    0      6.02    82.75   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    89.82   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.982:  841   |   5:    44.910 -  53.892:   96        |
|      1:     8.982 -  17.964: 1263   |   6:    53.892 -  62.874:   74        |
|      2:    17.964 -  26.946:  252   |   7:    62.874 -  71.856:   29        |
|      3:    26.946 -  35.928:  135   |   8:    71.856 -  80.838:   11        |
|      4:    35.928 -  44.910:  118   |   9:    80.838 -  89.820:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1538             target_work(ml) = 5.103         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1051 r_free = 0.1538             target_work(ml) = 5.103         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1538   ksol= 0.33   Bsol= 47.29   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.45,-1.11,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.103047                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.0956 0.1258      5.3572      5.5158|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.0809 0.1094      5.4024      5.5934|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.1013 0.1511      5.4432      5.8591|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.1134 0.1608      5.4103      5.5748|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.1242 0.1691      5.2908      5.5433|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.1103 0.1816      5.1625       5.426|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.1216 0.1528      5.1319      5.3229|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.1076 0.1675      5.0204       5.306|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.1082 0.1637      4.9863      5.2388|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.1036 0.1672      4.9112      5.1985|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.1056 0.1678      4.9029      5.2384|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.1053 0.1638      4.8416      5.1852|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.1028 0.1787      4.7391      5.0466|
| 14:  2.0215 -  1.9723 0.66    839   97 0.0929 0.1568      4.6219       4.851|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7070  1389   153  0.94   8.93   0.98     0.95       6838.54|
|  2:  4.7070 -  3.7557  1328   152  0.95   7.62   1.02     1.01       8692.08|
|  3:  3.7557 -  3.2867  1304   140  0.94  10.88   1.03     1.03       9878.15|
|  4:  3.2867 -  2.9888  1297   149  0.92  13.04   1.01     0.99       9726.65|
|  5:  2.9888 -  2.7760  1293   145  0.90  15.44   1.00     0.98       8017.56|
|  6:  2.7760 -  2.6133  1297   138  0.91  15.31   0.99     0.96       6652.62|
|  7:  2.6133 -  2.4830  1279   144  0.91  15.51   0.98     0.95       5926.19|
|  8:  2.4830 -  2.3754  1269   142  0.91  14.33   0.99     0.97       4874.70|
|  9:  2.3754 -  2.2843  1257   140  0.92  14.58   1.00     0.97       4710.19|
| 10:  2.2843 -  2.2057  1283   143  0.91  14.90   1.00     0.96       4089.17|
| 11:  2.2057 -  2.1369  1254   137  0.90  15.87   0.99     0.96       4209.94|
| 12:  2.1369 -  2.0760  1249   138  0.91  14.77   1.01     1.00       3745.15|
| 13:  2.0760 -  2.0215  1292   141  0.91  15.49   0.99     0.97       3119.67|
| 14:  2.0215 -  1.9723   839    97  0.93  13.22   0.98     0.95       2441.33|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2441.33 max =         9878.15 mean =      6040.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.52|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1537   ksol= 0.32   Bsol= 46.95   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.28,-0.88,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1537   ksol= 0.32   Bsol= 46.95   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.28,-0.88,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102790                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.0954 0.1257      5.3547      5.5141|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.0810 0.1095      5.4028      5.5938|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.1014 0.1511      5.4436      5.8596|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.1134 0.1607      5.4102      5.5746|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.1241 0.1690      5.2904      5.5427|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.1102 0.1815      5.1622      5.4255|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.1215 0.1530      5.1319      5.3234|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.1076 0.1674      5.0204      5.3054|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.1083 0.1637      4.9863      5.2385|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.1035 0.1674      4.9113      5.1997|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.1056 0.1678       4.903      5.2382|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.1052 0.1637      4.8413      5.1851|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.1028 0.1785      4.7387      5.0458|
| 14:  2.0215 -  1.9723 0.66    839   97 0.0929 0.1566      4.6213      4.8502|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7070  1389   153  0.94   8.90   0.98     0.95       6795.13|
|  2:  4.7070 -  3.7557  1328   152  0.95   7.62   1.03     1.02       8679.38|
|  3:  3.7557 -  3.2867  1304   140  0.94  10.88   1.04     1.03       9886.79|
|  4:  3.2867 -  2.9888  1297   149  0.92  13.04   1.02     1.00       9723.68|
|  5:  2.9888 -  2.7760  1293   145  0.90  15.43   1.01     0.98       8010.55|
|  6:  2.7760 -  2.6133  1297   138  0.91  15.31   0.99     0.97       6647.86|
|  7:  2.6133 -  2.4830  1279   144  0.91  15.51   0.99     0.96       5924.63|
|  8:  2.4830 -  2.3754  1269   142  0.91  14.33   1.00     0.98       4872.63|
|  9:  2.3754 -  2.2843  1257   140  0.92  14.58   1.01     0.98       4711.21|
| 10:  2.2843 -  2.2057  1283   143  0.91  14.91   1.01     0.97       4089.31|
| 11:  2.2057 -  2.1369  1254   137  0.90  15.87   1.00     0.97       4211.61|
| 12:  2.1369 -  2.0760  1249   138  0.91  14.77   1.02     1.01       3743.84|
| 13:  2.0760 -  2.0215  1292   141  0.91  15.48   1.01     0.98       3116.32|
| 14:  2.0215 -  1.9723   839    97  0.93  13.20   0.99     0.97       2436.58|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2436.58 max =         9886.79 mean =      6035.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.52|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.82   16.98    None  None   None       |
|    all(noH): 2823   0      0.00    89.82   16.98    None  None   None       |
|    Sol.    : 438    0      6.03    82.76   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    89.82   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.985:  841   |   5:    44.913 -  53.895:   96        |
|      1:     8.985 -  17.967: 1263   |   6:    53.895 -  62.877:   74        |
|      2:    17.967 -  26.949:  252   |   7:    62.877 -  71.859:   29        |
|      3:    26.949 -  35.931:  135   |   8:    71.859 -  80.841:   11        |
|      4:    35.931 -  44.913:  118   |   9:    80.841 -  89.823:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.418 - 4.718
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 275 from: 278
   mapped sites are within: 0.734 - 4.718

peak=    6.218 closest distance to " NE2 GLN A  11 " =    1.218
peak=    5.707 closest distance to " O   HOH Z 144 " =    1.755
peak=    5.651 closest distance to " O   HOH Z 126 " =    1.935
peak=    5.569 closest distance to " NH2 ARG A  56 " =    2.170
peak=    5.131 closest distance to " CG  PRO A  54 " =    1.195
peak=    5.052 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.841 closest distance to " O   HOH Z 232 " =    2.378
peak=    4.790 closest distance to " O   HOH Z 427 " =    2.766
peak=    4.789 closest distance to " CB  GLN A 223 " =    1.488
peak=    4.783 closest distance to " O   HOH Z  78 " =    1.799
peak=    4.758 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.649 closest distance to " CG  PRO A 213 " =    1.230
peak=    4.600 closest distance to " CB  ARG A  79 " =    1.432
peak=    4.581 closest distance to " CB  SER A  63 " =    1.180
peak=    4.562 closest distance to " O   HOH Z 369 " =    2.245
peak=    4.486 closest distance to " O   HOH Z 287 " =    2.117
peak=    4.472 closest distance to " O   HOH Z 298 " =    1.901
peak=    4.459 closest distance to " C   PRO A 198 " =    1.418
peak=    4.435 closest distance to " O   HOH Z 303 " =    2.161
peak=    4.358 closest distance to " O   HOH Z 193 " =    1.760
peak=    4.328 closest distance to " CB  GLU A 152 " =    1.309
peak=    4.319 closest distance to " O   HOH Z   9 " =    2.171
peak=    4.318 closest distance to " O   HOH Z  78 " =    2.116
peak=    4.314 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.270 closest distance to " O   HOH Z 158 " =    3.047
peak=    4.266 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.263 closest distance to " O   HOH Z 209 " =    2.244
peak=    4.251 closest distance to " ND2 ASN A 187 " =    1.380
peak=    4.216 closest distance to " CB  ARG A 190 " =    1.613
peak=    4.216 closest distance to " O   HOH Z  57 " =    2.342
peak=    4.208 closest distance to " O   HOH Z 371 " =    1.923
peak=    4.204 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.203 closest distance to " CG  ARG A  66 " =    2.466
peak=    4.187 closest distance to " O   HOH Z 272 " =    1.791
peak=    4.168 closest distance to " CB  ASN A 187 " =    1.374
peak=    4.095 closest distance to " NZ  LYS A 117 " =    3.207
peak=    4.085 closest distance to " CB  ASN A 148 " =    1.399
peak=    4.078 closest distance to " O   HOH Z 234 " =    3.589
peak=    4.058 closest distance to " O   HOH Z  61 " =    1.641
peak=    4.051 closest distance to " O   HOH Z 316 " =    3.081
peak=    4.023 closest distance to " O   HOH Z 133 " =    2.585
peak=    4.022 closest distance to " O   HOH Z   1 " =    1.939
peak=    3.986 closest distance to " O   HOH Z 346 " =    1.659
peak=    3.972 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.967 closest distance to " OD1 ASN A  69 " =    2.613
peak=    3.959 closest distance to " O   SER A  87 " =    2.200
peak=    3.957 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.955 closest distance to " O   HOH Z 144 " =    2.229
peak=    3.952 closest distance to " CG2 VAL A 257 " =    0.827
peak=    3.950 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.929 closest distance to " CA  ASN A 215 " =    1.174
peak=    3.925 closest distance to " CB  GLU A 128 " =    1.032
peak=    3.921 closest distance to " OG BSER A 164 " =    2.211
peak=    3.919 closest distance to " CB  TRP A 266 " =    1.055
peak=    3.916 closest distance to " CB  SER A   3 " =    1.314
peak=    3.906 closest distance to " O   HOH Z  63 " =    1.368
peak=    3.903 closest distance to " CD  ARG A 159 " =    0.734
peak=    3.901 closest distance to " CZ  PHE A 218 " =    1.017
peak=    3.891 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.881 closest distance to " O   HOH Z 132 " =    2.361
peak=    3.863 closest distance to " O   HOH Z   1 " =    1.682
peak=    3.846 closest distance to " O   HOH Z  44 " =    1.696
peak=    3.846 closest distance to " CG  PRO A  90 " =    1.103
peak=    3.812 closest distance to " CG  PRO A 198 " =    1.196
peak=    3.810 closest distance to " O   HOH Z 189 " =    2.253
peak=    3.808 closest distance to " O   HOH Z 403 " =    1.632
peak=    3.790 closest distance to " O   HOH Z 362 " =    2.574
peak=    3.789 closest distance to " O   HOH Z 368 " =    2.025
peak=    3.783 closest distance to " CG1 ILE A  33 " =    1.189
peak=    3.780 closest distance to " O   HOH Z 344 " =    3.248
peak=    3.778 closest distance to " O   HOH Z 423 " =    1.405
peak=    3.774 closest distance to " CB  ARG A 139 " =    1.010
peak=    3.772 closest distance to " O   HOH Z  10 " =    1.825
peak=    3.764 closest distance to " O   HOH Z 368 " =    3.608
peak=    3.756 closest distance to " ND1 HIS A  86 " =    1.756
peak=    3.755 closest distance to " O   HOH Z 180 " =    2.213
peak=    3.748 closest distance to " CB  GLU A 277 " =    3.512
peak=    3.748 closest distance to " O   HOH Z 380 " =    1.600
peak=    3.745 closest distance to " O   HOH Z 389 " =    1.830
peak=    3.745 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.731 closest distance to " O   HOH Z 327 " =    1.635
peak=    3.727 closest distance to " O   HOH Z 392 " =    3.097
peak=    3.725 closest distance to " O   HOH Z 214 " =    2.161
peak=    3.724 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.720 closest distance to " CG1BVAL A  72 " =    1.489
peak=    3.718 closest distance to " O   HOH Z 405 " =    1.176
peak=    3.706 closest distance to " CD2 TRP A 179 " =    1.358
peak=    3.705 closest distance to " CB  LYS A 117 " =    1.211
peak=    3.698 closest distance to " O   HOH Z  66 " =    2.131
peak=    3.687 closest distance to " O   HOH Z  61 " =    1.458
peak=    3.674 closest distance to " O   HOH Z 365 " =    2.774
peak=    3.673 closest distance to " O   HOH Z 245 " =    1.307
peak=    3.668 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.653 closest distance to " O   HOH Z 371 " =    3.006
peak=    3.640 closest distance to " O   HOH Z 213 " =    1.882
peak=    3.625 closest distance to " N   PHE A 130 " =    1.235
peak=    3.621 closest distance to " O   HOH Z 437 " =    1.608
peak=    3.619 closest distance to " CB  THR A 157 " =    1.132
peak=    3.608 closest distance to " CB  TYR A 169 " =    0.819
peak=    3.607 closest distance to " O   HOH Z 357 " =    1.893
peak=    3.603 closest distance to " CD BLYS A 290 " =    1.230
peak=    3.592 closest distance to " O   HOH Z 425 " =    1.265
peak=    3.588 closest distance to " OD2 ASP A 286 " =    2.756
peak=    3.580 closest distance to " CB  SER A 216 " =    0.810
peak=    3.571 closest distance to " CA  ALA A 233 " =    0.964
peak=    3.571 closest distance to " CD  PRO A 243 " =    1.553
peak=    3.567 closest distance to " NH1AARG A 145 " =    1.187
peak=    3.566 closest distance to " O   HOH Z 175 " =    2.101
peak=    3.560 closest distance to " CD2 LEU A 297 " =    0.934
peak=    3.559 closest distance to " O   HOH Z 286 " =    2.340
peak=    3.554 closest distance to " O   HOH Z 147 " =    1.767
peak=    3.549 closest distance to " NH2AARG A 190 " =    1.927
peak=    3.548 closest distance to " NH2AARG A 275 " =    3.587
peak=    3.546 closest distance to " O   HOH Z 305 " =    3.566
peak=    3.545 closest distance to " CG  LEU A 167 " =    1.239
peak=    3.543 closest distance to " O   HOH Z 219 " =    2.258
peak=    3.536 closest distance to " CB  SER A 212 " =    1.052
peak=    3.533 closest distance to " O   HOH Z 193 " =    1.989
peak=    3.530 closest distance to " CG  PRO A 243 " =    1.067
peak=    3.520 closest distance to " O   HOH Z  64 " =    2.361
peak=    3.519 closest distance to " CB  GLN A  89 " =    1.462
peak=    3.512 closest distance to " CB  ILE A 120 " =    1.358
peak=    3.509 closest distance to " O   HOH Z 172 " =    2.964
peak=    3.507 closest distance to " CB  ASP A 140 " =    0.981
peak=    3.505 closest distance to " O   HOH Z  93 " =    2.305
peak=    3.496 closest distance to " CB  TRP A 179 " =    1.374
peak=    3.496 closest distance to " O   HOH Z 265 " =    2.264
peak=    3.495 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.494 closest distance to " O   HOH Z 343 " =    3.369
peak=    3.485 closest distance to " O   HOH Z 391 " =    2.841
peak=    3.484 closest distance to " O   HOH Z 291 " =    1.529
peak=    3.480 closest distance to " O   HOH Z 193 " =    1.670
peak=    3.479 closest distance to " NH1BARG A 145 " =    1.234
peak=    3.478 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.476 closest distance to " CB  ALA A  34 " =    1.131
peak=    3.476 closest distance to " OD1BASN A 224 " =    2.287
peak=    3.473 closest distance to " O   HOH Z 116 " =    2.934
peak=    3.471 closest distance to " O   HOH Z 236 " =    1.452
peak=    3.469 closest distance to " O   HOH Z   3 " =    1.918
peak=    3.469 closest distance to " O   HOH Z 359 " =    1.408
peak=    3.468 closest distance to " NH2BARG A 145 " =    2.009
peak=    3.451 closest distance to " CD2 LEU A 255 " =    1.424
peak=    3.441 closest distance to " O   HOH Z  59 " =    1.561
peak=    3.439 closest distance to " O   HOH Z 373 " =    1.419
peak=    3.439 closest distance to " CA  ALA A  21 " =    1.128
peak=    3.436 closest distance to " CA  ALA A  84 " =    1.367
peak=    3.435 closest distance to " O   HOH Z  21 " =    1.718
peak=    3.432 closest distance to " O   HOH Z 402 " =    1.396
peak=    3.430 closest distance to " O  BHOH Z 338 " =    2.375
peak=    3.426 closest distance to " CG2 ILE A 120 " =    1.059
peak=    3.424 closest distance to " CB  SER A  62 " =    1.336
peak=    3.424 closest distance to " O   HOH Z   2 " =    1.274
peak=    3.424 closest distance to " CB  ASN A 142 " =    1.014
peak=    3.419 closest distance to " OE1 GLN A  11 " =    2.183
peak=    3.418 closest distance to " O   HOH Z 257 " =    2.231
peak=    3.418 closest distance to " O   HOH Z 417 " =    3.542
peak=    3.417 closest distance to " CB  SER A  26 " =    1.633
peak=    3.416 closest distance to " O   HOH Z  88 " =    2.628
peak=    3.409 closest distance to " O   HOH Z  43 " =    1.972
peak=    3.408 closest distance to " O   HOH Z 325 " =    3.800
peak=    3.406 closest distance to " N   TYR A 116 " =    1.567
peak=    3.396 closest distance to " CA  ALA A 291 " =    0.837
peak=    3.394 closest distance to " CE1 TYR A 186 " =    1.287
peak=    3.394 closest distance to " CB  GLN A  88 " =    1.223
peak=    3.385 closest distance to " NE2 GLN A  73 " =    3.709
peak=    3.385 closest distance to " O   HOH Z  40 " =    1.985
peak=    3.376 closest distance to " CD1 ILE A 263 " =    1.355
peak=    3.375 closest distance to " O   HOH Z 261 " =    2.331
peak=    3.374 closest distance to " CA  ASP A 162 " =    1.044
peak=    3.372 closest distance to " O   HOH Z 426 " =    1.935
peak=    3.367 closest distance to " CB  THR A  31 " =    1.686
peak=    3.366 closest distance to " O   HOH Z 126 " =    1.497
peak=    3.364 closest distance to " OG  SER A  62 " =    2.872
peak=    3.357 closest distance to " O   HOH Z  44 " =    2.949
peak=    3.356 closest distance to " CB  ALA A   1 " =    4.718
peak=    3.355 closest distance to " O   HOH Z 422 " =    2.591
peak=    3.352 closest distance to " O   HOH Z  97 " =    2.015
peak=    3.350 closest distance to " O   HOH Z 280 " =    3.009
peak=    3.349 closest distance to " N   ASN A  39 " =    1.238
peak=    3.347 closest distance to " O   HOH Z 411 " =    3.787
peak=    3.344 closest distance to " CB  TYR A 116 " =    0.796
peak=    3.343 closest distance to " CD1 ILE A 106 " =    0.847
peak=    3.342 closest distance to " OG  SER A  22 " =    2.779
peak=    3.340 closest distance to " O   HOH Z 213 " =    1.713
peak=    3.339 closest distance to " O   HOH Z  85 " =    2.265
peak=    3.339 closest distance to " O   HOH Z 298 " =    2.472
peak=    3.335 closest distance to " O   HOH Z  89 " =    2.056
peak=    3.334 closest distance to " O   HOH Z 407 " =    2.237
peak=    3.334 closest distance to " O   HOH Z 423 " =    2.526
peak=    3.330 closest distance to " O   HOH Z   6 " =    1.951
peak=    3.330 closest distance to " CA  SER A 146 " =    1.749
peak=    3.327 closest distance to " CB  MET A  47 " =    1.119
peak=    3.321 closest distance to " CG  LYS A  76 " =    0.993
peak=    3.320 closest distance to " CA  ALA A 158 " =    1.184
peak=    3.319 closest distance to " CB  ALA A 114 " =    1.450
peak=    3.317 closest distance to " CA  THR A 264 " =    0.870
peak=    3.307 closest distance to " CD  ARG A  79 " =    2.312
peak=    3.303 closest distance to " O   HOH Z 207 " =    1.686
peak=    3.294 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.292 closest distance to " O   HOH Z 409 " =    2.545
peak=    3.289 closest distance to " CA  ILE A 234 " =    1.023
peak=    3.283 closest distance to " CB  LYS A 290 " =    1.373
peak=    3.277 closest distance to " O   MET A 105 " =    1.859
peak=    3.277 closest distance to " O   HOH Z 266 " =    3.343
peak=    3.276 closest distance to " OE2 GLU A  53 " =    1.998
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.471
peak=    3.263 closest distance to " CA  ARG A 195 " =    1.173
peak=    3.262 closest distance to " CG2 VAL A 197 " =    1.083
peak=    3.256 closest distance to " O   HOH Z 146 " =    1.644
peak=    3.253 closest distance to " CG  MET A 185 " =    1.300
peak=    3.245 closest distance to " OG BSER A  99 " =    2.268
peak=    3.245 closest distance to " CB  ALA A 291 " =    1.378
peak=    3.244 closest distance to " CA  MET A  40 " =    1.088
peak=    3.239 closest distance to " O   ASN A  74 " =    1.576
peak=    3.235 closest distance to " O   HOH Z  66 " =    2.072
peak=    3.232 closest distance to " CB  ASN A 215 " =    1.071
peak=    3.231 closest distance to " O   HOH Z 248 " =    1.562
peak=    3.227 closest distance to " CA  ALA A 299 " =    0.889
peak=    3.227 closest distance to " O   HOH Z 403 " =    1.348
peak=    3.226 closest distance to " O   HOH Z 336 " =    1.912
peak=    3.225 closest distance to " O   HOH Z 285 " =    2.625
peak=    3.224 closest distance to " O   HOH Z 152 " =    1.757
peak=    3.223 closest distance to " O   HOH Z  30 " =    1.585
peak=    3.222 closest distance to " O   HOH Z  64 " =    2.144
peak=    3.218 closest distance to " CB  ASN A  39 " =    0.887
peak=    3.218 closest distance to " O   HOH Z 153 " =    1.590
peak=    3.218 closest distance to " CA  ALA A  51 " =    0.932
peak=    3.216 closest distance to " ND2 ASN A 249 " =    0.811
peak=    3.216 closest distance to " O   HOH Z 227 " =    1.774
peak=    3.210 closest distance to " CB  ASN A 110 " =    1.103
peak=    3.209 closest distance to " NE2 HIS A 207 " =    1.405
peak=    3.205 closest distance to " O   HOH Z 148 " =    3.437
peak=    3.205 closest distance to " OG BSER A 134 " =    2.853
peak=    3.203 closest distance to " CA  TYR A 116 " =    1.266
peak=    3.201 closest distance to " CB  THR A 235 " =    1.156
peak=    3.196 closest distance to " CG BARG A 102 " =    1.755
peak=    3.187 closest distance to " O   HOH Z 329 " =    3.864
peak=    3.186 closest distance to " O   HOH Z 185 " =    1.769
peak=    3.186 closest distance to " O   HOH Z 417 " =    1.054
peak=    3.177 closest distance to " O   HOH Z  88 " =    3.974
peak=    3.175 closest distance to " CA  MET A 105 " =    0.944
peak=    3.174 closest distance to " CA  LEU A 101 " =    1.706
peak=    3.172 closest distance to " CA  ALA A 233 " =    1.652
peak=    3.172 closest distance to " CE AMET A  47 " =    1.425
peak=    3.172 closest distance to " O   HOH Z 271 " =    2.535
peak=    3.169 closest distance to " CG1 VAL A 189 " =    1.922
peak=    3.166 closest distance to " O   HOH Z 432 " =    1.733
peak=    3.165 closest distance to " O   HOH Z  88 " =    3.156
peak=    3.163 closest distance to " O   HOH Z 421 " =    2.004
peak=    3.159 closest distance to " N   CYS A 260 " =    0.884
peak=    3.157 closest distance to " N   GLN A 278 " =    1.223
peak=    3.153 closest distance to " O   HOH Z 109 " =    2.563
peak=    3.148 closest distance to " CG  GLN A  89 " =    1.487
peak=    3.147 closest distance to " O   HOH Z 433 " =    1.782
peak=    3.147 closest distance to " NH2 ARG A 219 " =    1.883
peak=    3.140 closest distance to " O   HOH Z 435 " =    1.938
peak=    3.140 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.140 closest distance to " O   HOH Z 303 " =    3.207
peak=    3.134 closest distance to " O   HOH Z 325 " =    2.527
peak=    3.129 closest distance to " N   ASN A 127 " =    1.320
peak=    3.117 closest distance to " CG2 THR A 294 " =    1.630
peak=    3.116 closest distance to " CB  ALA A 114 " =    1.097
peak=    3.107 closest distance to " O   THR A 220 " =    1.339
peak=    3.106 closest distance to " O   HOH Z 261 " =    1.406
peak=    3.104 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.091 closest distance to " ND1 HIS A  81 " =    1.551
peak=    3.090 closest distance to " CZ2 TRP A 179 " =    1.600
peak=    3.080 closest distance to " O   HOH Z 423 " =    1.724
peak=    3.078 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.077 closest distance to " NE2 GLN A  58 " =    3.823
peak=    3.067 closest distance to " O   HOH Z  53 " =    2.505
peak=    3.052 closest distance to " O   HOH Z 132 " =    3.366
peak=    3.040 closest distance to " CB  ARG A 138 " =    0.895
peak=    3.034 closest distance to " O   HOH Z 181 " =    2.077
peak=    3.017 closest distance to " O   HOH Z 238 " =    3.727

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.643 - 5.978
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.756 - 5.978

peak=   -4.869 closest distance to " CB  PRO A 243 " =    2.608
peak=   -4.721 closest distance to " O   HOH Z 377 " =    2.147
peak=   -4.624 closest distance to " O   HOH Z 266 " =    4.951
peak=   -4.471 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.338 closest distance to " OG BSER A 134 " =    1.275
peak=   -4.323 closest distance to " CG  GLN A 223 " =    1.928
peak=   -4.319 closest distance to " O   VAL A  67 " =    2.653
peak=   -4.317 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -4.309 closest distance to " SG  CYS A 254 " =    3.359
peak=   -4.251 closest distance to " C   HIS A 108 " =    1.138
peak=   -4.118 closest distance to " CD1 LEU A 255 " =    2.849
peak=   -4.111 closest distance to " O   HOH Z 231 " =    2.238
peak=   -4.098 closest distance to " CE  MET A 105 " =    2.333
peak=   -4.085 closest distance to " O   VAL A  67 " =    2.923
peak=   -4.040 closest distance to " O   HOH Z 389 " =    1.901
peak=   -4.014 closest distance to " O   HOH Z 372 " =    2.436
peak=   -4.014 closest distance to " CG  GLN A  58 " =    1.065
peak=   -3.999 closest distance to " CB  PHE A 192 " =    1.959
peak=   -3.977 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.977 closest distance to " ND2 ASN A  45 " =    1.784
peak=   -3.926 closest distance to " O   HOH Z 313 " =    1.801
peak=   -3.915 closest distance to " CE2 PHE A 218 " =    2.417
peak=   -3.882 closest distance to " CB  ALA A  43 " =    2.472
peak=   -3.877 closest distance to " O   HOH Z 198 " =    1.920
peak=   -3.864 closest distance to " CB  ALA A 291 " =    2.190
peak=   -3.858 closest distance to " O   HOH Z 351 " =    1.615
peak=   -3.849 closest distance to " O   HOH Z 185 " =    2.112
peak=   -3.818 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.814 closest distance to " O   HOH Z 317 " =    1.510
peak=   -3.808 closest distance to " O   ARG A 145 " =    1.592
peak=   -3.790 closest distance to " OD1 ASP A 171 " =    1.607
peak=   -3.787 closest distance to " O   HOH Z 395 " =    5.146
peak=   -3.783 closest distance to " CB  ASN A  39 " =    2.283
peak=   -3.759 closest distance to " CZ3 TRP A 179 " =    1.209
peak=   -3.750 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.748 closest distance to " ND2 ASN A  45 " =    1.148
peak=   -3.741 closest distance to " O   HOH Z  13 " =    1.673
peak=   -3.723 closest distance to " O   HOH Z 407 " =    3.032
peak=   -3.709 closest distance to " OD1 ASN A 187 " =    1.613
peak=   -3.709 closest distance to " CD2 PHE A 225 " =    1.153
peak=   -3.703 closest distance to " CG  PHE A 283 " =    2.612
peak=   -3.703 closest distance to " CB  ALA A 291 " =    2.165
peak=   -3.702 closest distance to " CE2 TYR A  30 " =    2.710
peak=   -3.688 closest distance to " CD1 PHE A  59 " =    1.917
peak=   -3.679 closest distance to " O   HOH Z 385 " =    2.006
peak=   -3.669 closest distance to " CA  GLY A  98 " =    1.821
peak=   -3.668 closest distance to " O   PRO A 243 " =    2.562
peak=   -3.661 closest distance to " N   ALA A  43 " =    2.591
peak=   -3.645 closest distance to " CA  GLY A 203 " =    2.270
peak=   -3.643 closest distance to " CB  ALA A 248 " =    2.305
peak=   -3.641 closest distance to " OD1 ASP A 191 " =    1.918
peak=   -3.632 closest distance to " NH2BARG A 275 " =    1.718
peak=   -3.631 closest distance to " CB  TYR A  15 " =    2.195
peak=   -3.626 closest distance to " O   PHE A 218 " =    1.552
peak=   -3.623 closest distance to " O   SER A 135 " =    1.450
peak=   -3.619 closest distance to " O   HOH Z 198 " =    1.537
peak=   -3.616 closest distance to " CB  ALA A 161 " =    2.507
peak=   -3.610 closest distance to " O   VAL A 189 " =    2.564
peak=   -3.605 closest distance to " O   HOH Z 140 " =    1.669
peak=   -3.594 closest distance to " CB  ALA A 248 " =    2.023
peak=   -3.593 closest distance to " CD  ARG A 139 " =    1.537
peak=   -3.592 closest distance to " O   ALA A 161 " =    1.666
peak=   -3.588 closest distance to " CB  PHE A 208 " =    2.228
peak=   -3.571 closest distance to " O   HOH Z  38 " =    1.674
peak=   -3.569 closest distance to " CZ  TYR A 169 " =    1.602
peak=   -3.567 closest distance to " O   HOH Z  43 " =    1.812
peak=   -3.564 closest distance to " N   THR A 157 " =    1.485
peak=   -3.564 closest distance to " N   GLN A  58 " =    1.679
peak=   -3.555 closest distance to " ND2 ASN A 249 " =    2.092
peak=   -3.550 closest distance to " CD2 LEU A 237 " =    2.713
peak=   -3.547 closest distance to " OD2 ASP A 171 " =    2.107
peak=   -3.540 closest distance to " OD1 ASN A 148 " =    1.544
peak=   -3.538 closest distance to " O   HOH Z 290 " =    1.310
peak=   -3.527 closest distance to " O   HOH Z 263 " =    3.014
peak=   -3.517 closest distance to " O   HOH Z  63 " =    1.826
peak=   -3.512 closest distance to " OD2 ASP A 191 " =    1.423
peak=   -3.503 closest distance to " CG2 THR A 178 " =    2.230
peak=   -3.503 closest distance to " CG2 ILE A 263 " =    2.261
peak=   -3.502 closest distance to " OG  SER A  97 " =    2.136
peak=   -3.499 closest distance to " O   HOH Z  60 " =    2.273
peak=   -3.498 closest distance to " N   ALA A 248 " =    1.594
peak=   -3.493 closest distance to " CB  TRP A  85 " =    2.442
peak=   -3.491 closest distance to " O   HOH Z 253 " =    3.818
peak=   -3.490 closest distance to " CB  ASP A 132 " =    2.357
peak=   -3.485 closest distance to " OXT GLY A 302 " =    2.931
peak=   -3.483 closest distance to " N   MET A 188 " =    1.903
peak=   -3.480 closest distance to " O   HOH Z 131 " =    4.112
peak=   -3.476 closest distance to " O   HOH Z 111 " =    2.080
peak=   -3.475 closest distance to " O   HOH Z 114 " =    2.938
peak=   -3.469 closest distance to " O   HOH Z  52 " =    1.318
peak=   -3.462 closest distance to " O   HOH Z 266 " =    4.731
peak=   -3.449 closest distance to " O   HOH Z 211 " =    1.629
peak=   -3.449 closest distance to " O   HOH Z 298 " =    1.286
peak=   -3.447 closest distance to " NH2AARG A 275 " =    5.211
peak=   -3.439 closest distance to " O   HOH Z 351 " =    1.695
peak=   -3.437 closest distance to " O   HOH Z 362 " =    5.978
peak=   -3.437 closest distance to " O   HOH Z 353 " =    2.121
peak=   -3.433 closest distance to " O   SER A  95 " =    1.465
peak=   -3.429 closest distance to " O   PRO A 163 " =    1.979
peak=   -3.425 closest distance to " CB  PRO A 163 " =    2.419
peak=   -3.424 closest distance to " O   HOH Z 191 " =    5.649
peak=   -3.420 closest distance to " O   SER A  22 " =    2.455
peak=   -3.420 closest distance to " O   HOH Z  90 " =    2.470
peak=   -3.401 closest distance to " CG  ASP A 231 " =    0.756
peak=   -3.400 closest distance to " O   HOH Z 102 " =    1.603
peak=   -3.395 closest distance to " O   HOH Z  15 " =    1.545
peak=   -3.386 closest distance to " CB  ILE A  33 " =    2.844
peak=   -3.376 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.372 closest distance to " CD1 LEU A 228 " =    2.087
peak=   -3.370 closest distance to " CA  GLY A 133 " =    1.972
peak=   -3.369 closest distance to " NE  ARG A  36 " =    1.900
peak=   -3.362 closest distance to " O   HOH Z 339 " =    1.868
peak=   -3.359 closest distance to " OG  SER A 245 " =    1.304
peak=   -3.357 closest distance to " N   ASP A 286 " =    2.410
peak=   -3.354 closest distance to " O   HOH Z 359 " =    3.370
peak=   -3.350 closest distance to " OG  SER A  87 " =    1.355
peak=   -3.341 closest distance to " O   HOH Z 165 " =    2.197
peak=   -3.322 closest distance to " O   HOH Z 166 " =    2.136
peak=   -3.321 closest distance to " C   ALA A 158 " =    1.395
peak=   -3.320 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.319 closest distance to " NH1 ARG A 195 " =    2.665
peak=   -3.312 closest distance to " O   MET A  40 " =    2.726
peak=   -3.311 closest distance to " CB  CYS A 254 " =    2.318
peak=   -3.306 closest distance to " O   HOH Z  73 " =    2.350
peak=   -3.301 closest distance to " O   ALA A  10 " =    1.649
peak=   -3.300 closest distance to " O   VAL A 189 " =    1.641
peak=   -3.290 closest distance to " O   HOH Z  24 " =    1.287
peak=   -3.289 closest distance to " O   HOH Z 137 " =    1.399
peak=   -3.289 closest distance to " CA  GLY A  57 " =    2.225
peak=   -3.289 closest distance to " OE2 GLU A 152 " =    1.118
peak=   -3.287 closest distance to " CB  ASP A 132 " =    2.254
peak=   -3.281 closest distance to " O   SER A 146 " =    1.055
peak=   -3.279 closest distance to " CB  ASP A 286 " =    2.261
peak=   -3.277 closest distance to " O   HOH Z 394 " =    1.407
peak=   -3.276 closest distance to " CG1 VAL A 230 " =    1.993
peak=   -3.275 closest distance to " O   VAL A 174 " =    2.247
peak=   -3.272 closest distance to " CG  TRP A 266 " =    1.856
peak=   -3.272 closest distance to " C   GLY A  17 " =    1.075
peak=   -3.271 closest distance to " CA  GLY A 241 " =    2.219
peak=   -3.268 closest distance to " N   SER A 212 " =    2.001
peak=   -3.265 closest distance to " OE1 GLN A 223 " =    1.963
peak=   -3.261 closest distance to " OG BSER A 134 " =    1.610
peak=   -3.260 closest distance to " NH2 ARG A  79 " =    1.999
peak=   -3.257 closest distance to " CE3 TRP A 274 " =    2.284
peak=   -3.256 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.256 closest distance to " O   HOH Z 298 " =    2.447
peak=   -3.255 closest distance to " CE  LYS A  76 " =    2.809
peak=   -3.252 closest distance to " CD1 LEU A 101 " =    2.221
peak=   -3.242 closest distance to " O   TRP A  70 " =    1.473
peak=   -3.241 closest distance to " O   VAL A 197 " =    1.554
peak=   -3.235 closest distance to " CZ2 TRP A 274 " =    0.944
peak=   -3.232 closest distance to " CB  ALA A 131 " =    1.978
peak=   -3.229 closest distance to " NE2 GLN A 278 " =    1.686
peak=   -3.225 closest distance to " O   HOH Z  60 " =    2.053
peak=   -3.224 closest distance to " N   PHE A  59 " =    1.883
peak=   -3.221 closest distance to " C   PRO A  90 " =    1.500
peak=   -3.219 closest distance to " CG  GLU A 277 " =    1.303
peak=   -3.216 closest distance to " C   TRP A 274 " =    1.447
peak=   -3.216 closest distance to " O   HOH Z 393 " =    3.462
peak=   -3.214 closest distance to " ND2 ASN A  69 " =    1.644
peak=   -3.213 closest distance to " O   HOH Z 166 " =    1.292
peak=   -3.212 closest distance to " O   ALA A 292 " =    2.004
peak=   -3.210 closest distance to " CG  GLU A 152 " =    1.316
peak=   -3.208 closest distance to " CG  GLU A   2 " =    2.040
peak=   -3.207 closest distance to " O   ALA A  34 " =    2.441
peak=   -3.202 closest distance to " SD  MET A 188 " =    2.210
peak=   -3.200 closest distance to " CG1 VAL A 197 " =    2.088
peak=   -3.193 closest distance to " CD1 TYR A 247 " =    2.766
peak=   -3.192 closest distance to " CD2 PHE A  61 " =    2.197
peak=   -3.192 closest distance to " O   HOH Z   6 " =    1.509
peak=   -3.191 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.184 closest distance to " OD1 ASN A 176 " =    1.295
peak=   -3.177 closest distance to " CB  CYS A 201 " =    2.374
peak=   -3.173 closest distance to " O   GLY A  80 " =    2.445
peak=   -3.171 closest distance to " O   HOH Z 357 " =    2.081
peak=   -3.167 closest distance to " ND2BASN A 224 " =    1.828
peak=   -3.166 closest distance to " SG ACYS A 201 " =    1.718
peak=   -3.165 closest distance to " CB  GLN A  11 " =    1.835
peak=   -3.158 closest distance to " O   ILE A  49 " =    1.737
peak=   -3.154 closest distance to " OD2 ASP A  50 " =    1.552
peak=   -3.153 closest distance to " O   HOH Z 244 " =    1.987
peak=   -3.146 closest distance to " ND2 ASN A  60 " =    1.425
peak=   -3.144 closest distance to " CG2 VAL A 189 " =    1.938
peak=   -3.139 closest distance to " O   HOH Z 174 " =    2.532
peak=   -3.134 closest distance to " OG  SER A  62 " =    1.636
peak=   -3.131 closest distance to " O   HOH Z 281 " =    2.653
peak=   -3.129 closest distance to " C   MET A 188 " =    1.426
peak=   -3.125 closest distance to " O   HOH Z 369 " =    2.176
peak=   -3.124 closest distance to " O   HOH Z 256 " =    1.491
peak=   -3.122 closest distance to " O   HOH Z  51 " =    1.274
peak=   -3.122 closest distance to " OE1 GLN A 183 " =    1.509
peak=   -3.118 closest distance to " CG  ARG A 269 " =    2.554
peak=   -3.109 closest distance to " O   HOH Z 189 " =    1.825
peak=   -3.105 closest distance to " CE BMET A  47 " =    1.427
peak=   -3.103 closest distance to " O   ASP A 162 " =    2.169
peak=   -3.090 closest distance to " O   HOH Z  10 " =    1.421
peak=   -3.090 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.083 closest distance to " OH  TYR A 214 " =    1.260
peak=   -3.083 closest distance to " O   HOH Z  93 " =    2.312
peak=   -3.073 closest distance to " CD  GLN A  77 " =    1.557
peak=   -3.050 closest distance to " O   HOH Z 350 " =    1.833
peak=   -3.041 closest distance to " CG  PRO A 163 " =    2.612
peak=   -3.038 closest distance to " CA  GLY A  57 " =    2.073
peak=   -3.037 closest distance to " O   HOH Z 310 " =    1.420

================= 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    :  0.3368 0.3296   6.100661e+00   6.077964e+00
   1_bss:  0.3201 0.3144   6.078537e+00   6.050451e+00
   1_xyz:  0.2271 0.2544   5.748778e+00   5.827323e+00
   1_adp:  0.2076 0.2645   5.697318e+00   5.859071e+00
   1_occ:  0.2073 0.2641   5.696113e+00   5.857748e+00
   2_bss:  0.2055 0.2599   5.686846e+00   5.845269e+00
   2_xyz:  0.1530 0.1973   5.407877e+00   5.604278e+00
   2_adp:  0.1445 0.1866   5.355775e+00   5.551221e+00
   2_occ:  0.1444 0.1867   5.355124e+00   5.551026e+00
   3_bss:  0.1440 0.1856   5.349881e+00   5.544799e+00
   3_xyz:  0.1230 0.1645   5.209839e+00   5.424750e+00
   3_adp:  0.1187 0.1604   5.180041e+00   5.401765e+00
   3_occ:  0.1186 0.1606   5.179968e+00   5.401717e+00
   4_bss:  0.1186 0.1604   5.179083e+00   5.400854e+00
   4_xyz:  0.1110 0.1534   5.124166e+00   5.360424e+00
   4_adp:  0.1095 0.1527   5.117131e+00   5.358224e+00
   4_occ:  0.1094 0.1527   5.117057e+00   5.358215e+00
   5_bss:  0.1096 0.1533   5.118842e+00   5.358736e+00
   5_xyz:  0.1059 0.1530   5.103361e+00   5.359888e+00
   5_adp:  0.1051 0.1538   5.103107e+00   5.364886e+00
   5_occ:  0.1051 0.1538   5.103047e+00   5.364834e+00
   5_bss:  0.1050 0.1537   5.102790e+00   5.364619e+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:  0.341  42.019  -2.940   2.577  -1.695   0.000  -0.000  -0.000
   1_xyz:  0.341  42.019  -2.940   2.577  -1.695   0.000  -0.000  -0.000
   1_adp:  0.341  42.019  -2.940   2.577  -1.695   0.000  -0.000  -0.000
   1_occ:  0.341  42.019  -2.940   2.577  -1.695   0.000  -0.000  -0.000
   2_bss:  0.330  47.289  -2.844  -0.763  -1.403  -0.000  -0.000  -0.000
   2_xyz:  0.330  47.289  -2.844  -0.763  -1.403  -0.000  -0.000  -0.000
   2_adp:  0.330  47.289  -2.844  -0.763  -1.403  -0.000  -0.000  -0.000
   2_occ:  0.330  47.289  -2.844  -0.763  -1.403  -0.000  -0.000  -0.000
   3_bss:  0.330  47.289  -2.734  -2.072  -1.216  -0.000  -0.000  -0.000
   3_xyz:  0.330  47.289  -2.734  -2.072  -1.216  -0.000  -0.000  -0.000
   3_adp:  0.330  47.289  -2.734  -2.072  -1.216  -0.000  -0.000  -0.000
   3_occ:  0.330  47.289  -2.734  -2.072  -1.216  -0.000  -0.000  -0.000
   4_bss:  0.330  47.289  -2.747  -2.454  -1.235  -0.000  -0.000  -0.000
   4_xyz:  0.330  47.289  -2.747  -2.454  -1.235  -0.000  -0.000  -0.000
   4_adp:  0.330  47.289  -2.747  -2.454  -1.235  -0.000  -0.000  -0.000
   4_occ:  0.330  47.289  -2.747  -2.454  -1.235  -0.000  -0.000  -0.000
   5_bss:  0.330  47.289  -2.616  -2.453  -1.111  -0.000  -0.000  -0.000
   5_xyz:  0.330  47.289  -2.616  -2.453  -1.111  -0.000  -0.000  -0.000
   5_adp:  0.330  47.289  -2.616  -2.453  -1.111  -0.000  -0.000  -0.000
   5_occ:  0.330  47.289  -2.616  -2.453  -1.111  -0.000  -0.000  -0.000
   5_bss:  0.323  46.952  -2.369  -2.277  -0.880  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.443 0.6996  0.8908    33406.620
   1_bss:  34.379 0.7097  0.8791    30174.613
   1_xyz:  24.896 0.8141  0.9736    16779.164
   1_adp:  26.089 0.8008  0.9629    18125.501
   1_occ:  26.069 0.8010  0.9629    18068.925
   2_bss:  25.395 0.8080  0.9394    17352.487
   2_xyz:  18.739 0.8735  0.9869     9846.557
   2_adp:  17.271 0.8878  0.9925     8887.170
   2_occ:  17.266 0.8878  0.9923     8873.532
   3_bss:  17.071 0.8895  0.9818     8716.645
   3_xyz:  14.817 0.9080  0.9889     6837.186
   3_adp:  14.302 0.9125  0.9859     6555.925
   3_occ:  14.305 0.9125  0.9857     6553.857
   4_bss:  14.285 0.9126  0.9811     6543.128
   4_xyz:  13.422 0.9195  0.9844     5978.271
   4_adp:  13.339 0.9203  0.9793     5938.801
   4_occ:  13.340 0.9203  0.9792     5937.503
   5_bss:  13.369 0.9201  0.9824     5960.442
   5_xyz:  13.382 0.9200  0.9823     6010.561
   5_adp:  13.480 0.9192  0.9755     6041.054
   5_occ:  13.480 0.9192  0.9754     6041.270
   5_bss:  13.477 0.9192  0.9833     6035.821
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6444e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6444e-01
   1_xyz:   1.158  0.009  0.075 14.958  0.005  4.106   7.6690e-02
   1_adp:   1.158  0.009  0.075 14.958  0.005  4.106   7.6690e-02
   1_occ:   1.158  0.009  0.075 14.958  0.005  4.106   7.6690e-02
   2_bss:   1.158  0.009  0.075 14.958  0.005  4.106   7.6690e-02
   2_xyz:   0.960  0.006  0.069 14.307  0.004  4.112   5.3264e-02
   2_adp:   0.960  0.006  0.069 14.307  0.004  4.112   5.3264e-02
   2_occ:   0.960  0.006  0.069 14.307  0.004  4.112   5.3264e-02
   3_bss:   0.960  0.006  0.069 14.307  0.004  4.112   5.3264e-02
   3_xyz:   0.858  0.005  0.065 14.412  0.003  4.109   4.7179e-02
   3_adp:   0.858  0.005  0.065 14.412  0.003  4.109   4.7179e-02
   3_occ:   0.858  0.005  0.065 14.412  0.003  4.109   4.7179e-02
   4_bss:   0.858  0.005  0.065 14.412  0.003  4.109   4.7179e-02
   4_xyz:   0.944  0.006  0.072 14.592  0.004  4.111   5.4202e-02
   4_adp:   0.944  0.006  0.072 14.592  0.004  4.111   5.4202e-02
   4_occ:   0.944  0.006  0.072 14.592  0.004  4.111   5.4202e-02
   5_bss:   0.944  0.006  0.072 14.592  0.004  4.111   5.4202e-02
   5_xyz:   1.020  0.008  0.078 14.771  0.004  4.111   6.2821e-02
   5_adp:   1.020  0.008  0.078 14.771  0.004  4.111   6.2821e-02
   5_occ:   1.020  0.008  0.078 14.771  0.004  4.111   6.2821e-02
   5_bss:   1.020  0.008  0.078 14.771  0.004  4.111   6.2821e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3923e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3923e-01
   1_xyz:   7.629  0.041  0.282 83.933  0.041  2.082   7.4929e-02
   1_adp:   7.629  0.041  0.282 83.933  0.041  2.082   7.4929e-02
   1_occ:   7.629  0.041  0.282 83.933  0.041  2.082   7.4929e-02
   2_bss:   7.629  0.041  0.282 83.933  0.041  2.082   7.4929e-02
   2_xyz:   6.003  0.042  0.198 81.014  0.034  2.410   4.1397e-02
   2_adp:   6.003  0.042  0.198 81.014  0.034  2.410   4.1397e-02
   2_occ:   6.003  0.042  0.198 81.014  0.034  2.410   4.1397e-02
   3_bss:   6.003  0.042  0.198 81.014  0.034  2.410   4.1397e-02
   3_xyz:   6.384  0.045  0.199 83.699  0.030  2.367   3.3335e-02
   3_adp:   6.384  0.045  0.199 83.699  0.030  2.367   3.3335e-02
   3_occ:   6.384  0.045  0.199 83.699  0.030  2.367   3.3335e-02
   4_bss:   6.384  0.045  0.199 83.699  0.030  2.367   3.3335e-02
   4_xyz:   6.450  0.042  0.228 84.496  0.037  2.319   3.7841e-02
   4_adp:   6.450  0.042  0.228 84.496  0.037  2.319   3.7841e-02
   4_occ:   6.450  0.042  0.228 84.496  0.037  2.319   3.7841e-02
   5_bss:   6.450  0.042  0.228 84.496  0.037  2.319   3.7841e-02
   5_xyz:   6.465  0.047  0.254 84.294  0.035  2.266   5.1629e-02
   5_adp:   6.465  0.047  0.254 84.294  0.035  2.266   5.1629e-02
   5_occ:   6.465  0.047  0.254 84.294  0.035  2.266   5.1629e-02
   5_bss:   6.465  0.047  0.254 84.294  0.035  2.266   5.1629e-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:  82.18   0.00  17.22  74.19   0.00  13.32  82.18   6.06  38.50
   1_occ:  82.18   0.00  17.22  74.19   0.00  13.32  82.18   6.06  38.50
   2_bss:  82.18   0.00  17.22  74.19   0.00  13.32  82.18   6.06  38.50
   2_xyz:  82.18   0.00  17.22  74.19   0.00  13.32  82.18   6.06  38.50
   2_adp:  74.42   0.00  16.71  72.48   0.00  12.99  74.42   6.55  36.97
   2_occ:  74.42   0.00  16.71  72.48   0.00  12.99  74.42   6.55  36.97
   3_bss:  74.42   0.00  16.71  72.48   0.00  12.99  74.42   6.55  36.97
   3_xyz:  74.42   0.00  16.71  72.48   0.00  12.99  74.42   6.55  36.97
   3_adp:  77.45   0.93  16.80  77.45   0.93  12.85  75.09   3.02  38.27
   3_occ:  77.45   0.93  16.80  77.45   0.93  12.85  75.09   3.02  38.27
   4_bss:  77.45   0.93  16.80  77.45   0.93  12.85  75.09   3.02  38.27
   4_xyz:  77.45   0.93  16.80  77.45   0.93  12.85  75.09   3.02  38.27
   4_adp:  79.32   0.77  16.77  79.32   0.77  12.75  75.82   4.28  38.64
   4_occ:  79.32   0.77  16.77  79.32   0.77  12.75  75.82   4.28  38.64
   5_bss:  79.32   0.77  16.77  79.32   0.77  12.75  75.82   4.28  38.64
   5_xyz:  79.32   0.77  16.77  79.32   0.77  12.75  75.82   4.28  38.64
   5_adp:  89.82   0.00  16.98  89.82   0.00  12.75  82.75   6.02  40.02
   5_occ:  89.82   0.00  16.98  89.82   0.00  12.75  82.75   6.02  40.02
   5_bss:  89.82   0.00  16.98  89.82   0.00  12.75  82.76   6.03  40.02
------------------------------------------------------------------------
 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:    1.505    0.015    0.268
   1_adp:    1.505    0.015    0.268
   1_occ:    1.505    0.015    0.268
   2_bss:    1.505    0.015    0.268
   2_xyz:    1.041    0.035    0.370
   2_adp:    1.041    0.035    0.370
   2_occ:    1.041    0.035    0.370
   3_bss:    1.041    0.035    0.370
   3_xyz:    0.974    0.030    0.435
   3_adp:    0.974    0.030    0.435
   3_occ:    0.974    0.030    0.435
   4_bss:    0.974    0.030    0.435
   4_xyz:    1.120    0.032    0.461
   4_adp:    1.120    0.032    0.461
   4_occ:    1.120    0.032    0.461
   5_bss:    1.120    0.032    0.461
   5_xyz:    1.180    0.051    0.473
   5_adp:    1.180    0.051    0.473
   5_occ:    1.180    0.051    0.473
   5_bss:    1.180    0.051    0.473
------------------------------------------------------------------------

CPU time actual refinement: 321.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/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_511/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_511/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.21 
  Macro-tasks:
    bulk solvent and scale       = 37.42  
    individual site refinement   = 132.33 
    weights calculation          = 28.95  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 205.42 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 101.67 
    alpha_beta                      = 8.27   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.50 
    fmodel                         = 6.83   
    r_factors                      = 0.21   
    phase_errors                   = 11.15  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 241.80 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.564 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    642 calls, 101.39 s
gradients_fft:          587 calls,  97.12 s

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

# Date 2008-01-16 Time 05:00:45 PST -0800 (1200488445.43 s)
Start R-work = 0.3368, R-free = 0.3296 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1731 (no bulk solvent and anisotropic scale)

Start R-work = 0.3201, R-free = 0.3144
Final R-work = 0.1050, R-free = 0.1537