# Date 2008-01-16 Time 06:43:29 PST -0800 (1200494609.24 s)
#phil __OFF__

Command line arguments: "../1261.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11568
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1261

-------------------------------------------------------------------------------
  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: (72.0062, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


================================== 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: (72.0062, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.99341
Completeness in resolution range: 0.94784
Completeness with d_max=infinity: 0.94505

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   1.9934

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: (72.0062, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.99341
Completeness in resolution range: 0.94784
Completeness with d_max=infinity: 0.94505

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.2666 [2174/2200]  1957   217  10.0%
  bin  2:  4.2666 -  3.3987 [2076/2096]  1870   206   9.9%
  bin  3:  3.3987 -  2.9727 [2067/2086]  1855   212  10.3%
  bin  4:  2.9727 -  2.7025 [2028/2058]  1826   202  10.0%
  bin  5:  2.7025 -  2.5097 [2036/2055]  1840   196   9.6%
  bin  6:  2.5097 -  2.3623 [2012/2037]  1801   211  10.5%
  bin  7:  2.3623 -  2.2444 [2015/2043]  1817   198   9.8%
  bin  8:  2.2444 -  2.1469 [1990/2026]  1794   196   9.8%
  bin  9:  2.1469 -  2.0645 [1990/2032]  1791   199  10.0%
  bin 10:  2.0645 -  1.9934 [1201/2034]  1079   122  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/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: 11
        2.42 -     3.04: 2167
        3.04 -     3.66: 4625
        3.66 -     4.28: 8924
        4.28 -     4.90: 12239
  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 341 " - " O   HOH Z 207 "  1.954 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.954 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.047 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27961 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_1261/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 72.00625 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3833   r_free= 0.3742   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.164743                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7593 0.99   1409  158 0.3108 0.2846      6.4195       6.335|
|  2:  4.7593 -  3.7966 0.99   1350  150 0.3157 0.3085      6.6407      6.5827|
|  3:  3.7966 -  3.3222 0.99   1332  142 0.3392 0.3302       6.485      6.5103|
|  4:  3.3222 -  3.0210 0.99   1326  154 0.3544 0.3626      6.3585      6.3208|
|  5:  3.0210 -  2.8059 0.99   1315  151 0.4046 0.3959      6.2413      6.2947|
|  6:  2.8059 -  2.6414 0.99   1315  139 0.3902 0.3961      6.1402      6.1326|
|  7:  2.6414 -  2.5097 0.99   1301  139 0.4324 0.4142      6.1519      6.1483|
|  8:  2.5097 -  2.4009 0.98   1282  144 0.4308 0.3783      6.0884      6.0455|
|  9:  2.4009 -  2.3088 0.98   1273  154 0.4355 0.4287      6.0433      6.0743|
| 10:  2.3088 -  2.2294 1.00   1318  145 0.4349 0.4239      6.0144      5.9755|
| 11:  2.2294 -  2.1598 0.98   1289  134 0.4400 0.4532      5.9735      5.9843|
| 12:  2.1598 -  2.0983 0.98   1266  142 0.4426 0.4599      5.8893      5.9676|
| 13:  2.0983 -  2.0432 0.99   1274  137 0.4584 0.4232      5.8176      5.7332|
| 14:  2.0432 -  1.9934 0.44    580   70 0.4068 0.4405       5.736      5.7664|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7593  1409   158  0.78  26.53   0.84     0.81      44274.55|
|  2:  4.7593 -  3.7966  1350   150  0.81  24.89   0.94     0.89      57860.37|
|  3:  3.7966 -  3.3222  1332   142  0.74  31.76   0.95     0.89      63229.62|
|  4:  3.3222 -  3.0210  1326   154  0.70  35.52   0.95     0.85      58084.71|
|  5:  3.0210 -  2.8059  1315   151  0.61  43.36   0.93     0.79      50889.65|
|  6:  2.8059 -  2.6414  1315   139  0.60  44.32   0.96     0.77      43924.65|
|  7:  2.6414 -  2.5097  1301   139  0.59  45.15   0.94     0.75      41130.34|
|  8:  2.5097 -  2.4009  1282   144  0.59  45.14   0.93     0.77      36902.45|
|  9:  2.4009 -  2.3088  1273   154  0.57  46.55   0.97     0.76      34891.01|
| 10:  2.3088 -  2.2294  1318   145  0.55  48.13   0.99     0.74      33034.55|
| 11:  2.2294 -  2.1598  1289   134  0.53  49.82   0.99     0.73      33089.16|
| 12:  2.1598 -  2.0983  1266   142  0.52  50.85   0.97     0.73      30119.77|
| 13:  2.0983 -  2.0432  1274   137  0.52  50.35   0.94     0.75      25488.41|
| 14:  2.0432 -  1.9934   580    70  0.59  45.20   1.02     0.78      18938.37|
|alpha:            min =        0.73 max =            0.89 mean =         0.79|
|beta:             min =    18938.37 max =        63229.62 mean =     41941.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.98 mean =        41.63|
|phase err.(test): min =        0.00 max =           89.83 mean =        41.11|
|-----------------------------------------------------------------------------|

============================== 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 = 4.826702              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.642   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098029              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.666   (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:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      191 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1976 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2802 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4591 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4333 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5586 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6653 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.149 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3833   r_free= 0.3742   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.164743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3719   r_free= 0.3657   ksol= 0.32   Bsol= 63.90   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,-2.89,-0.03,-0.00,-0.00,-0.00); trace/3= 0.04                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.147837                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.272658              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.788   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602297              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3719      final r-factor (work) = 0.2465          |
| start r-factor (free) = 0.3657      final r-factor (free) = 0.2752          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2980 = 4.27 * 0.50 * 6.1489 + 1.00 * 0.1620                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7694 = 4.27 * 0.50 * 5.9388 + 1.00 * 0.0821                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2465      final r-factor (work) = 0.2271          |
| start r-factor (free) = 0.2752      final r-factor (free) = 0.2819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5833 = 0.60 * 1.00 * 5.9388 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5058 = 0.60 * 1.00 * 5.7541 + 1.00 * 0.0401                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.36   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    70.36   17.04    None  None   None       |
|    Sol.    : 438    0      2.26    66.03   38.18    None  None   None       |
|    Mac.    : 2385   0      0.00    70.36   13.16    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 -   7.036:  483   |   5:    35.179 -  42.215:  117        |
|      1:     7.036 -  14.072: 1042   |   6:    42.215 -  49.250:   95        |
|      2:    14.072 -  21.107:  611   |   7:    49.250 -  56.286:   76        |
|      3:    21.107 -  28.143:  250   |   8:    56.286 -  63.322:   27        |
|      4:    28.143 -  35.179:  117   |   9:    63.322 -  70.358:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2271 r_free = 0.2819             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2267 r_free = 0.2814             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2267   r_free= 0.2814   ksol= 0.32   Bsol= 63.90   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,-2.89,-0.03,-0.00,-0.00,-0.00); trace/3= 0.04                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.761866                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2256   r_free= 0.2810   ksol= 0.34   Bsol= 71.90   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-2.91,-0.88,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.761238                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.603688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.939   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.983   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2256      final r-factor (work) = 0.1581          |
| start r-factor (free) = 0.2810      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3374 = 4.60 * 0.50 * 5.7586 + 1.00 * 0.0821                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0055 = 4.60 * 0.50 * 5.6197 + 1.00 * 0.0699                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1581      final r-factor (work) = 0.1418          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2832 = 0.40 * 1.00 * 5.6197 + 1.00 * 0.0414                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1593 = 0.40 * 1.00 * 5.3884 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.53   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    82.53   17.60    None  None   None       |
|    Sol.    : 438    0      4.63    82.53   41.54    None  None   None       |
|    Mac.    : 2385   0      0.00    73.36   13.20    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 -   8.253:  619   |   5:    41.266 -  49.520:  107        |
|      1:     8.253 -  16.507: 1300   |   6:    49.520 -  57.773:   82        |
|      2:    16.507 -  24.760:  376   |   7:    57.773 -  66.026:   57        |
|      3:    24.760 -  33.013:  155   |   8:    66.026 -  74.279:   30        |
|      4:    33.013 -  41.266:   90   |   9:    74.279 -  82.533:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1418 r_free = 0.1896             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1417 r_free = 0.1894             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1894   ksol= 0.34   Bsol= 71.90   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-2.91,-0.88,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.348296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1414   r_free= 0.1891   ksol= 0.34   Bsol= 71.90   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-2.70,-1.00,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.346534                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.816559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.350  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.278950              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.089  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1414      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6578 = 2.82 * 0.50 * 5.3881 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5162 = 2.82 * 0.50 * 5.2901 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4855 = 0.28 * 1.00 * 5.2901 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4658 = 0.28 * 1.00 * 5.2227 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    86.00   17.25    None  None   None       |
|    all(noH): 2823   0      0.37    86.00   17.25    None  None   None       |
|    Sol.    : 438    0      2.56    86.00   40.43    None  None   None       |
|    Mac.    : 2385   0      0.37    77.75   13.00    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:     0.371 -   8.934:  738   |   5:    43.185 -  51.748:   94        |
|      1:     8.934 -  17.496: 1290   |   6:    51.748 -  60.310:   81        |
|      2:    17.496 -  26.059:  313   |   7:    60.310 -  68.873:   39        |
|      3:    26.059 -  34.622:  136   |   8:    68.873 -  77.436:   14        |
|      4:    34.622 -  43.185:  113   |   9:    77.436 -  85.999:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1661             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1203 r_free = 0.1659             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1659   ksol= 0.34   Bsol= 71.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-2.70,-1.00,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206905                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1658   ksol= 0.34   Bsol= 71.90   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.68,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206313                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.392028              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.733  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.139297              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.235  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9237 = 3.39 * 0.50 * 5.2225 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8676 = 3.39 * 0.50 * 5.1805 + 1.00 * 0.0813                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7304 = 0.14 * 1.00 * 5.1805 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7278 = 0.14 * 1.00 * 5.1742 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    83.55   16.63    None  None   None       |
|    all(noH): 2823   0      1.49    83.55   16.63    None  None   None       |
|    Sol.    : 438    0      1.95    83.55   37.52    None  None   None       |
|    Mac.    : 2385   0      1.49    73.63   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.487 -   9.693:  928   |   5:    42.517 -  50.723:  102        |
|      1:     9.693 -  17.899: 1152   |   6:    50.723 -  58.929:   64        |
|      2:    17.899 -  26.105:  282   |   7:    58.929 -  67.134:   20        |
|      3:    26.105 -  34.311:  136   |   8:    67.134 -  75.340:    7        |
|      4:    34.311 -  42.517:  129   |   9:    75.340 -  83.546:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1626             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1624             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1624   ksol= 0.34   Bsol= 71.90   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.68,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170591                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1613   ksol= 0.31   Bsol= 60.51   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.71,-1.16,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.879323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.323  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.132496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 165.311  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5295 = 2.88 * 0.50 * 5.1736 + 1.00 * 0.0813                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5122 = 2.88 * 0.50 * 5.1663 + 1.00 * 0.0745                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6915 = 0.13 * 1.00 * 5.1663 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6915 = 0.13 * 1.00 * 5.1693 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    81.46   16.39    None  None   None       |
|    all(noH): 2823   0      1.65    81.46   16.39    None  None   None       |
|    Sol.    : 438    0      3.79    81.46   36.68    None  None   None       |
|    Mac.    : 2385   0      1.65    72.79   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.651 -   9.632:  926   |   5:    41.558 -  49.539:  102        |
|      1:     9.632 -  17.614: 1153   |   6:    49.539 -  57.521:   63        |
|      2:    17.614 -  25.595:  284   |   7:    57.521 -  65.502:   18        |
|      3:    25.595 -  33.577:  137   |   8:    65.502 -  73.483:    7        |
|      4:    33.577 -  41.558:  130   |   9:    73.483 -  81.465:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1613             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1613             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1613   ksol= 0.31   Bsol= 60.51   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.71,-1.16,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.169031                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7593 0.99   1409  158 0.1003 0.1325      5.3974      5.5829|
|  2:  4.7593 -  3.7966 0.99   1350  150 0.0888 0.1125      5.4751      5.6423|
|  3:  3.7966 -  3.3222 0.99   1332  142 0.1081 0.1555      5.4925      5.8741|
|  4:  3.3222 -  3.0210 0.99   1326  154 0.1228 0.1700      5.4793      5.6311|
|  5:  3.0210 -  2.8059 0.99   1315  151 0.1374 0.1746      5.3448      5.5883|
|  6:  2.8059 -  2.6414 0.99   1315  139 0.1238 0.1928      5.2327      5.4709|
|  7:  2.6414 -  2.5097 0.99   1301  139 0.1305 0.1702      5.2017      5.3869|
|  8:  2.5097 -  2.4009 0.98   1282  144 0.1170 0.1784      5.0731      5.3649|
|  9:  2.4009 -  2.3088 0.98   1273  154 0.1210 0.1840      5.0578      5.3393|
| 10:  2.3088 -  2.2294 1.00   1318  145 0.1160 0.1775      4.9683      5.2029|
| 11:  2.2294 -  2.1598 0.98   1289  134 0.1146 0.1881      4.9654      5.3063|
| 12:  2.1598 -  2.0983 0.98   1266  142 0.1137 0.1648      4.8828      5.1352|
| 13:  2.0983 -  2.0432 0.99   1274  137 0.1149 0.1724      4.7912      5.0441|
| 14:  2.0432 -  1.9934 0.44    580   70 0.1022 0.1556       4.653      4.8753|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7593  1409   158  0.94   9.21   0.97     0.94       7299.56|
|  2:  4.7593 -  3.7966  1350   150  0.95   8.27   0.99     0.98       9624.44|
|  3:  3.7966 -  3.3222  1332   142  0.93  11.74   1.00     1.00      10828.40|
|  4:  3.3222 -  3.0210  1326   154  0.91  14.31   0.99     0.96      10960.09|
|  5:  3.0210 -  2.8059  1315   151  0.90  16.42   0.98     0.96       8633.81|
|  6:  2.8059 -  2.6414  1315   139  0.90  16.63   0.97     0.95       7506.41|
|  7:  2.6414 -  2.5097  1301   139  0.90  16.06   0.98     0.96       6688.39|
|  8:  2.5097 -  2.4009  1282   144  0.90  15.71   0.97     0.95       5381.77|
|  9:  2.4009 -  2.3088  1273   154  0.90  15.76   0.99     0.94       5106.15|
| 10:  2.3088 -  2.2294  1318   145  0.90  15.93   0.99     0.96       4480.14|
| 11:  2.2294 -  2.1598  1289   134  0.90  16.14   0.97     0.93       4489.02|
| 12:  2.1598 -  2.0983  1266   142  0.90  16.21   1.00     0.99       4128.43|
| 13:  2.0983 -  2.0432  1274   137  0.90  16.30   0.98     0.96       3371.98|
| 14:  2.0432 -  1.9934   580    70  0.92  13.99   0.95     0.92       2478.89|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2478.89 max =        10960.09 mean =      6705.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.44|
|phase err.(test): min =        0.00 max =           88.17 mean =        13.87|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1613   ksol= 0.31   Bsol= 55.23   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.54,-1.00,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.169289                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1613   ksol= 0.31   Bsol= 55.23   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.54,-1.00,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.169289                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7593 0.99   1409  158 0.1001 0.1319       5.395      5.5783|
|  2:  4.7593 -  3.7966 0.99   1350  150 0.0883 0.1122      5.4711      5.6398|
|  3:  3.7966 -  3.3222 0.99   1332  142 0.1080 0.1554      5.4909      5.8721|
|  4:  3.3222 -  3.0210 0.99   1326  154 0.1228 0.1702        5.48      5.6321|
|  5:  3.0210 -  2.8059 0.99   1315  151 0.1378 0.1750      5.3468      5.5904|
|  6:  2.8059 -  2.6414 0.99   1315  139 0.1240 0.1930      5.2345      5.4719|
|  7:  2.6414 -  2.5097 0.99   1301  139 0.1306 0.1703      5.2031       5.388|
|  8:  2.5097 -  2.4009 0.98   1282  144 0.1171 0.1787      5.0742      5.3663|
|  9:  2.4009 -  2.3088 0.98   1273  154 0.1211 0.1842      5.0589      5.3398|
| 10:  2.3088 -  2.2294 1.00   1318  145 0.1160 0.1778      4.9693       5.204|
| 11:  2.2294 -  2.1598 0.98   1289  134 0.1147 0.1882      4.9664      5.3069|
| 12:  2.1598 -  2.0983 0.98   1266  142 0.1138 0.1650      4.8836      5.1359|
| 13:  2.0983 -  2.0432 0.99   1274  137 0.1149 0.1725       4.792      5.0447|
| 14:  2.0432 -  1.9934 0.44    580   70 0.1022 0.1560      4.6539      4.8771|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7593  1409   158  0.94   9.18   0.97     0.94       7239.37|
|  2:  4.7593 -  3.7966  1350   150  0.95   8.23   1.00     0.99       9557.95|
|  3:  3.7966 -  3.3222  1332   142  0.93  11.71   1.01     1.00      10789.95|
|  4:  3.3222 -  3.0210  1326   154  0.91  14.31   0.99     0.96      10967.48|
|  5:  3.0210 -  2.8059  1315   151  0.90  16.45   0.98     0.96       8662.13|
|  6:  2.8059 -  2.6414  1315   139  0.89  16.66   0.98     0.95       7532.13|
|  7:  2.6414 -  2.5097  1301   139  0.90  16.08   0.99     0.96       6709.57|
|  8:  2.5097 -  2.4009  1282   144  0.90  15.72   0.98     0.95       5393.10|
|  9:  2.4009 -  2.3088  1273   154  0.90  15.77   0.99     0.95       5115.13|
| 10:  2.3088 -  2.2294  1318   145  0.90  15.94   0.99     0.96       4489.27|
| 11:  2.2294 -  2.1598  1289   134  0.90  16.16   0.98     0.93       4497.46|
| 12:  2.1598 -  2.0983  1266   142  0.90  16.23   1.00     0.99       4137.01|
| 13:  2.0983 -  2.0432  1274   137  0.90  16.31   0.98     0.97       3378.03|
| 14:  2.0432 -  1.9934   580    70  0.92  14.03   0.96     0.93       2484.83|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     2484.83 max =        10967.48 mean =      6702.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.44|
|phase err.(test): min =        0.00 max =           88.32 mean =        13.87|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    81.41   16.33    None  None   None       |
|    all(noH): 2823   0      1.59    81.41   16.33    None  None   None       |
|    Sol.    : 438    0      3.73    81.41   36.62    None  None   None       |
|    Mac.    : 2385   0      1.59    72.74   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.592 -   9.573:  926   |   5:    41.499 -  49.480:  102        |
|      1:     9.573 -  17.555: 1153   |   6:    49.480 -  57.462:   63        |
|      2:    17.555 -  25.536:  284   |   7:    57.462 -  65.443:   18        |
|      3:    25.536 -  33.518:  137   |   8:    65.443 -  73.424:    7        |
|      4:    33.518 -  41.499:  130   |   9:    73.424 -  81.406:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.473 - 4.804
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 301
   mapped sites are within: 0.710 - 4.804

peak=    5.618 closest distance to " O   HOH Z 111 " =    1.959
peak=    5.429 closest distance to " CB  GLN A 223 " =    1.455
peak=    4.976 closest distance to " CG  PRO A  54 " =    1.353
peak=    4.856 closest distance to " NE2 GLN A  11 " =    1.194
peak=    4.803 closest distance to " CB  SER A  63 " =    1.259
peak=    4.763 closest distance to " O   HOH Z 298 " =    2.069
peak=    4.762 closest distance to " O   HOH Z 232 " =    2.287
peak=    4.759 closest distance to " O   HOH Z 126 " =    1.842
peak=    4.725 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.706 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.629 closest distance to " CB  GLN A 183 " =    1.168
peak=    4.542 closest distance to " CB  ASN A 148 " =    1.421
peak=    4.476 closest distance to " CD  ARG A 159 " =    0.791
peak=    4.470 closest distance to " CB  ARG A  79 " =    1.487
peak=    4.449 closest distance to " O   HOH Z 369 " =    2.075
peak=    4.430 closest distance to " CB  ARG A 275 " =    0.955
peak=    4.404 closest distance to " C   PRO A 198 " =    1.514
peak=    4.391 closest distance to " CB  PRO A  54 " =    0.965
peak=    4.370 closest distance to " CZ  PHE A 218 " =    1.039
peak=    4.351 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.308 closest distance to " CB  TRP A 266 " =    0.942
peak=    4.297 closest distance to " CB  ARG A 190 " =    1.446
peak=    4.280 closest distance to " O   HOH Z  21 " =    1.762
peak=    4.263 closest distance to " CG  PRO A 198 " =    1.314
peak=    4.245 closest distance to " O   HOH Z 234 " =    3.909
peak=    4.240 closest distance to " O   HOH Z  78 " =    1.741
peak=    4.219 closest distance to " CB  ASN A 187 " =    1.093
peak=    4.211 closest distance to " CA  TYR A  30 " =    1.006
peak=    4.208 closest distance to " NH1AARG A 145 " =    1.287
peak=    4.193 closest distance to " O   HOH Z 236 " =    2.144
peak=    4.182 closest distance to " O   HOH Z  15 " =    2.135
peak=    4.159 closest distance to " CD  ARG A  66 " =    2.118
peak=    4.127 closest distance to " ND2 ASN A 187 " =    1.452
peak=    4.114 closest distance to " O   HOH Z 272 " =    1.907
peak=    4.093 closest distance to " O   HOH Z 303 " =    2.126
peak=    4.088 closest distance to " CB  ALA A 104 " =    0.724
peak=    4.086 closest distance to " CE  LYS A  76 " =    0.851
peak=    4.078 closest distance to " O   HOH Z 144 " =    1.669
peak=    4.042 closest distance to " CG  PRO A 243 " =    1.081
peak=    4.037 closest distance to " CB  ASP A 124 " =    0.710
peak=    4.006 closest distance to " CB  GLU A 128 " =    1.010
peak=    4.004 closest distance to " CG2 VAL A 257 " =    0.960
peak=    3.992 closest distance to " O   HOH Z 193 " =    1.786
peak=    3.975 closest distance to " O   HOH Z  10 " =    1.926
peak=    3.968 closest distance to " O   HOH Z 368 " =    2.021
peak=    3.947 closest distance to " CB  GLU A  46 " =    1.017
peak=    3.945 closest distance to " CD1 LEU A 300 " =    1.245
peak=    3.917 closest distance to " O   HOH Z 261 " =    2.249
peak=    3.908 closest distance to " NH2 ARG A 156 " =    1.250
peak=    3.900 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.894 closest distance to " O   HOH Z 250 " =    1.498
peak=    3.865 closest distance to " CG  PRO A  90 " =    1.142
peak=    3.862 closest distance to " CG2 THR A 221 " =    0.893
peak=    3.847 closest distance to " O   HOH Z 158 " =    3.043
peak=    3.831 closest distance to " O   HOH Z  78 " =    2.224
peak=    3.823 closest distance to " CB  ILE A 120 " =    1.241
peak=    3.814 closest distance to " CA  SER A  87 " =    0.967
peak=    3.811 closest distance to " O   HOH Z 189 " =    2.840
peak=    3.810 closest distance to " O   HOH Z 180 " =    2.105
peak=    3.810 closest distance to " O   HOH Z 214 " =    2.048
peak=    3.806 closest distance to " O   HOH Z 213 " =    1.943
peak=    3.803 closest distance to " CG  LEU A 167 " =    1.303
peak=    3.798 closest distance to " CZ  PHE A 192 " =    0.948
peak=    3.797 closest distance to " O   HOH Z 265 " =    2.403
peak=    3.795 closest distance to " O   HOH Z 193 " =    1.965
peak=    3.794 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.794 closest distance to " CA  ASN A 215 " =    1.190
peak=    3.788 closest distance to " CD ALYS A 290 " =    1.028
peak=    3.788 closest distance to " ND1 HIS A  86 " =    1.655
peak=    3.776 closest distance to " CA  PRO A  54 " =    1.377
peak=    3.766 closest distance to " CB  VAL A 265 " =    1.308
peak=    3.765 closest distance to " CB  MET A  40 " =    0.786
peak=    3.763 closest distance to " O   HOH Z 427 " =    3.049
peak=    3.762 closest distance to " O   HOH Z 126 " =    1.782
peak=    3.754 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.749 closest distance to " CB  ASP A 140 " =    0.894
peak=    3.749 closest distance to " CA  THR A 264 " =    0.876
peak=    3.747 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.740 closest distance to " O   HOH Z 171 " =    3.932
peak=    3.739 closest distance to " O   HOH Z 133 " =    2.308
peak=    3.736 closest distance to " CB  TYR A 169 " =    0.722
peak=    3.735 closest distance to " O   HOH Z 188 " =    2.170
peak=    3.732 closest distance to " CB  SER A 216 " =    0.875
peak=    3.717 closest distance to " CB  SER A 212 " =    1.182
peak=    3.716 closest distance to " N   PHE A 130 " =    1.210
peak=    3.708 closest distance to " CB  ALA A  34 " =    1.045
peak=    3.703 closest distance to " OD2 ASP A 286 " =    2.947
peak=    3.664 closest distance to " CB  SER A   3 " =    1.484
peak=    3.653 closest distance to " O   TYR A 116 " =    1.303
peak=    3.652 closest distance to " CA  MET A  40 " =    1.202
peak=    3.645 closest distance to " CB  ASN A 110 " =    1.055
peak=    3.643 closest distance to " O   HOH Z  88 " =    3.508
peak=    3.635 closest distance to " CB  ASN A 142 " =    0.923
peak=    3.630 closest distance to " CG BARG A 275 " =    1.522
peak=    3.628 closest distance to " O   HOH Z 148 " =    3.329
peak=    3.612 closest distance to " CD  ARG A 219 " =    1.090
peak=    3.611 closest distance to " O   HOH Z 193 " =    2.097
peak=    3.611 closest distance to " CD  ARG A 269 " =    0.904
peak=    3.611 closest distance to " O   HOH Z 132 " =    2.748
peak=    3.608 closest distance to " N   ARG A 156 " =    1.402
peak=    3.607 closest distance to " NE2 HIS A 207 " =    1.304
peak=    3.603 closest distance to " CB  GLU A 277 " =    3.673
peak=    3.601 closest distance to " CB  LEU A 143 " =    1.112
peak=    3.593 closest distance to " O   HOH Z 217 " =    3.181
peak=    3.592 closest distance to " O   HOH Z 316 " =    3.136
peak=    3.589 closest distance to " O   HOH Z  44 " =    2.296
peak=    3.584 closest distance to " NH2AARG A 190 " =    1.982
peak=    3.581 closest distance to " O   ASN A 209 " =    1.320
peak=    3.578 closest distance to " CA  ARG A 195 " =    1.277
peak=    3.572 closest distance to " O   HOH Z 411 " =    3.730
peak=    3.570 closest distance to " CD2 TRP A 179 " =    1.287
peak=    3.570 closest distance to " OD1 ASN A  69 " =    2.612
peak=    3.562 closest distance to " CG  LYS A  76 " =    1.009
peak=    3.559 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.553 closest distance to " O   HOH Z 183 " =    1.477
peak=    3.553 closest distance to " CB  SER A 210 " =    0.738
peak=    3.544 closest distance to " CZ  PHE A 208 " =    1.102
peak=    3.537 closest distance to " CB  VAL A 202 " =    1.625
peak=    3.531 closest distance to " O   HOH Z 285 " =    2.554
peak=    3.529 closest distance to " CZ  PHE A  38 " =    1.237
peak=    3.524 closest distance to " CG2AVAL A  72 " =    1.686
peak=    3.513 closest distance to " O   HOH Z  58 " =    1.654
peak=    3.507 closest distance to " CA  TYR A 116 " =    1.358
peak=    3.496 closest distance to " N   ALA A   1 " =    2.243
peak=    3.493 closest distance to " O   HOH Z 368 " =    3.641
peak=    3.491 closest distance to " CD1 ILE A 106 " =    0.845
peak=    3.483 closest distance to " O   HOH Z 371 " =    2.906
peak=    3.480 closest distance to " CB  LEU A  83 " =    0.796
peak=    3.479 closest distance to " CB  ALA A 248 " =    0.995
peak=    3.471 closest distance to " O   HOH Z 386 " =    3.008
peak=    3.470 closest distance to " O   HOH Z 344 " =    3.241
peak=    3.469 closest distance to " CB  ALA A   1 " =    4.804
peak=    3.466 closest distance to " CB  GLN A 103 " =    0.944
peak=    3.460 closest distance to " O   HOH Z   1 " =    2.002
peak=    3.457 closest distance to " O   HOH Z   9 " =    2.015
peak=    3.456 closest distance to " CB  TYR A 116 " =    0.840
peak=    3.454 closest distance to " ND2 ASN A 110 " =    1.768
peak=    3.452 closest distance to " O   HOH Z 166 " =    3.640
peak=    3.446 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.444 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.431 closest distance to " O   HOH Z 135 " =    1.693
peak=    3.428 closest distance to " CA  ASP A 124 " =    0.714
peak=    3.427 closest distance to " O   HOH Z 133 " =    1.780
peak=    3.423 closest distance to " O   HOH Z 273 " =    2.720
peak=    3.423 closest distance to " CA  ALA A 154 " =    1.000
peak=    3.421 closest distance to " CB  ALA A 233 " =    1.350
peak=    3.416 closest distance to " O   HOH Z 218 " =    4.675
peak=    3.410 closest distance to " O   HOH Z 329 " =    3.982
peak=    3.410 closest distance to " CA  ALA A  51 " =    0.904
peak=    3.406 closest distance to " CG  GLN A  88 " =    1.070
peak=    3.403 closest distance to " CB  GLN A  88 " =    1.284
peak=    3.400 closest distance to " CB  ALA A 114 " =    1.045
peak=    3.398 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.397 closest distance to " O   HOH Z 419 " =    3.177
peak=    3.397 closest distance to " O   HOH Z 294 " =    1.554
peak=    3.395 closest distance to " CB  ARG A 138 " =    1.044
peak=    3.395 closest distance to " O   HOH Z 185 " =    1.919
peak=    3.390 closest distance to " O   LEU A 300 " =    1.305
peak=    3.384 closest distance to " O   HOH Z 406 " =    1.710
peak=    3.383 closest distance to " CA  ALA A 233 " =    1.212
peak=    3.381 closest distance to " O   HOH Z 147 " =    1.840
peak=    3.381 closest distance to " O   HOH Z 426 " =    1.687
peak=    3.376 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.376 closest distance to " O   HOH Z 291 " =    1.564
peak=    3.373 closest distance to " CG1 VAL A 189 " =    2.003
peak=    3.368 closest distance to " CA  THR A 221 " =    0.953
peak=    3.362 closest distance to " O   HOH Z 248 " =    1.809
peak=    3.362 closest distance to " O  BHOH Z 338 " =    2.386
peak=    3.359 closest distance to " O   HOH Z 425 " =    2.154
peak=    3.356 closest distance to " O   HOH Z 403 " =    1.570
peak=    3.351 closest distance to " O   HOH Z 345 " =    1.759
peak=    3.351 closest distance to " CG  ARG A 159 " =    0.907
peak=    3.350 closest distance to " CG1 ILE A 151 " =    1.060
peak=    3.349 closest distance to " CB  HIS A 108 " =    0.774
peak=    3.348 closest distance to " N   ASN A  39 " =    1.254
peak=    3.346 closest distance to " OG  SER A  28 " =    1.635
peak=    3.344 closest distance to " CA  ASP A 191 " =    0.762
peak=    3.341 closest distance to " O   HOH Z  98 " =    1.868
peak=    3.334 closest distance to " O   HOH Z 402 " =    1.468
peak=    3.332 closest distance to " CA  ILE A 234 " =    0.945
peak=    3.330 closest distance to " O   THR A 220 " =    1.285
peak=    3.329 closest distance to " O   HOH Z 353 " =    2.678
peak=    3.326 closest distance to " NE  ARG A  79 " =    1.134
peak=    3.322 closest distance to " O   HOH Z 319 " =    2.155
peak=    3.319 closest distance to " NH2AARG A 275 " =    3.628
peak=    3.318 closest distance to " OD1 ASN A 217 " =    1.594
peak=    3.315 closest distance to " O   HOH Z 128 " =    2.241
peak=    3.313 closest distance to " O   SER A  87 " =    2.293
peak=    3.312 closest distance to " O   HOH Z 423 " =    1.586
peak=    3.309 closest distance to " CA  TYR A 186 " =    1.604
peak=    3.306 closest distance to " OG  SER A  22 " =    2.809
peak=    3.298 closest distance to " CG AARG A 275 " =    1.278
peak=    3.293 closest distance to " CA  GLU A  46 " =    1.158
peak=    3.293 closest distance to " CA  GLN A 223 " =    0.964
peak=    3.291 closest distance to " O   HOH Z 281 " =    4.006
peak=    3.291 closest distance to " O   HOH Z 409 " =    2.674
peak=    3.288 closest distance to " O   HOH Z 280 " =    3.107
peak=    3.285 closest distance to " O   HOH Z 419 " =    1.889
peak=    3.283 closest distance to " O   HOH Z  44 " =    2.985
peak=    3.283 closest distance to " CB  GLU A 236 " =    0.864
peak=    3.282 closest distance to " O   HOH Z 109 " =    2.762
peak=    3.282 closest distance to " O   HOH Z 108 " =    2.692
peak=    3.281 closest distance to " ND1 HIS A  81 " =    1.708
peak=    3.278 closest distance to " O   HOH Z 332 " =    1.562
peak=    3.276 closest distance to " CA  ASN A 217 " =    1.225
peak=    3.276 closest distance to " CA  ILE A  33 " =    1.581
peak=    3.274 closest distance to " CD2 TYR A 186 " =    1.043
peak=    3.272 closest distance to " CD  ARG A  14 " =    1.209
peak=    3.271 closest distance to " O   HOH Z 313 " =    1.707
peak=    3.270 closest distance to " CG  MET A 113 " =    1.508
peak=    3.269 closest distance to " N   VAL A 126 " =    1.272
peak=    3.264 closest distance to " CA  ALA A  21 " =    1.195
peak=    3.262 closest distance to " CA  ARG A  36 " =    1.167
peak=    3.261 closest distance to " O   HOH Z 305 " =    3.676
peak=    3.261 closest distance to " O   ALA A 165 " =    1.513
peak=    3.259 closest distance to " O   HOH Z 287 " =    2.207
peak=    3.257 closest distance to " CB  ALA A 291 " =    1.137
peak=    3.255 closest distance to " CB  ALA A 100 " =    1.285
peak=    3.254 closest distance to " O   HOH Z 302 " =    1.953
peak=    3.252 closest distance to " CA  GLY A 241 " =    0.740
peak=    3.249 closest distance to " O   HOH Z 327 " =    2.109
peak=    3.248 closest distance to " CA  ALA A 295 " =    1.058
peak=    3.246 closest distance to " N   ASN A 127 " =    1.254
peak=    3.243 closest distance to " O   HOH Z 380 " =    4.745
peak=    3.243 closest distance to " O   HOH Z  29 " =    2.569
peak=    3.242 closest distance to " O   MET A 105 " =    1.750
peak=    3.240 closest distance to " O   HOH Z  57 " =    1.298
peak=    3.240 closest distance to " CB  ALA A 137 " =    0.927
peak=    3.240 closest distance to " CB  SER A 245 " =    3.102
peak=    3.236 closest distance to " CA  LYS A 117 " =    1.121
peak=    3.236 closest distance to " O   HOH Z   1 " =    1.736
peak=    3.231 closest distance to " ND2 ASN A 249 " =    1.953
peak=    3.229 closest distance to " CB  PRO A 163 " =    4.219
peak=    3.227 closest distance to " CB  LEU A 237 " =    0.760
peak=    3.225 closest distance to " O   HOH Z 365 " =    2.860
peak=    3.223 closest distance to " CG  GLN A 278 " =    1.442
peak=    3.222 closest distance to " N   ARG A 190 " =    1.066
peak=    3.220 closest distance to " O   THR A 251 " =    1.227
peak=    3.216 closest distance to " O   HOH Z 128 " =    2.170
peak=    3.214 closest distance to " O   HOH Z  66 " =    2.178
peak=    3.213 closest distance to " O   HOH Z 126 " =    1.578
peak=    3.213 closest distance to " CG1 ILE A 120 " =    1.100
peak=    3.212 closest distance to " O   HOH Z  53 " =    2.567
peak=    3.210 closest distance to " CZ3 TRP A 123 " =    1.268
peak=    3.207 closest distance to " OG BSER A 134 " =    3.053
peak=    3.203 closest distance to " CB  TRP A 150 " =    1.372
peak=    3.202 closest distance to " O   HOH Z 258 " =    1.755
peak=    3.198 closest distance to " CB  LYS A 193 " =    1.011
peak=    3.197 closest distance to " O  BHOH Z  74 " =    1.265
peak=    3.196 closest distance to " CD2 LEU A 255 " =    1.587
peak=    3.195 closest distance to " CB  ALA A 291 " =    0.791
peak=    3.191 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.184 closest distance to " O   HOH Z 213 " =    2.639
peak=    3.180 closest distance to " O   HOH Z 285 " =    1.872
peak=    3.179 closest distance to " O   HOH Z 216 " =    2.845
peak=    3.178 closest distance to " OD1 ASP A 171 " =    1.259
peak=    3.178 closest distance to " CB  THR A  82 " =    1.499
peak=    3.178 closest distance to " CA  GLY A 136 " =    0.860
peak=    3.175 closest distance to " O   HOH Z 299 " =    2.568
peak=    3.175 closest distance to " O   HOH Z 172 " =    3.338
peak=    3.174 closest distance to " NH2 ARG A 219 " =    1.781
peak=    3.173 closest distance to " O   HOH Z 187 " =    2.287
peak=    3.171 closest distance to " CA  GLY A 267 " =    1.110
peak=    3.169 closest distance to " O   HOH Z 417 " =    3.420
peak=    3.168 closest distance to " CB  ASN A 224 " =    0.980
peak=    3.168 closest distance to " O   HOH Z 359 " =    1.506
peak=    3.168 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.163 closest distance to " OH  TYR A 186 " =    0.995
peak=    3.162 closest distance to " O   HOH Z  68 " =    2.036
peak=    3.155 closest distance to " O   THR A  18 " =    1.990
peak=    3.153 closest distance to " O   HOH Z 325 " =    4.110
peak=    3.146 closest distance to " O   PHE A 192 " =    1.307
peak=    3.143 closest distance to " O   HOH Z 154 " =    1.951
peak=    3.139 closest distance to " OD1BASN A 224 " =    2.380
peak=    3.135 closest distance to " CA  LEU A 282 " =    1.064
peak=    3.127 closest distance to " CB  ILE A 199 " =    1.016
peak=    3.125 closest distance to " O   HOH Z  49 " =    3.023
peak=    3.124 closest distance to " O   HOH Z 214 " =    3.721
peak=    3.110 closest distance to " O   HOH Z 299 " =    4.405
peak=    3.109 closest distance to " CB  ALA A 242 " =    0.842
peak=    3.109 closest distance to " NZ  LYS A 181 " =    0.711
peak=    3.100 closest distance to " O   HOH Z 392 " =    2.018
peak=    3.080 closest distance to " O   HOH Z 358 " =    3.705
peak=    3.074 closest distance to " ND2 ASN A 249 " =    0.894
peak=    3.071 closest distance to " O   HOH Z 383 " =    2.039
peak=    3.060 closest distance to " O   HOH Z 391 " =    2.932
peak=    3.056 closest distance to " OG  SER A  62 " =    3.037
peak=    3.050 closest distance to " CG2 VAL A 189 " =    1.324
peak=    3.049 closest distance to " CB  ALA A  43 " =    0.840
peak=    3.048 closest distance to " O   HOH Z  43 " =    2.081
peak=    3.044 closest distance to " O   HOH Z 124 " =    1.814
peak=    3.044 closest distance to " O   HOH Z 163 " =    1.857
peak=    3.036 closest distance to " CG2 ILE A  20 " =    1.253
peak=    3.024 closest distance to " O   HOH Z 175 " =    2.166
peak=    3.018 closest distance to " O   HOH Z 213 " =    2.176

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.424 - 5.633
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 206
   mapped sites are within: 0.703 - 5.633

peak=   -4.405 closest distance to " CB  PRO A 243 " =    2.580
peak=   -4.271 closest distance to " CZ3 TRP A 179 " =    1.121
peak=   -4.269 closest distance to " O   VAL A  67 " =    2.692
peak=   -4.158 closest distance to " O   HOH Z 290 " =    1.129
peak=   -4.137 closest distance to " O   HOH Z 389 " =    2.091
peak=   -4.133 closest distance to " N   ALA A  43 " =    2.534
peak=   -4.109 closest distance to " O   HOH Z  38 " =    1.211
peak=   -4.105 closest distance to " O   PRO A 198 " =    1.260
peak=   -4.081 closest distance to " CD  ARG A  14 " =    3.345
peak=   -4.075 closest distance to " CD  GLN A  58 " =    0.865
peak=   -4.063 closest distance to " O   HOH Z 407 " =    3.416
peak=   -4.052 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -4.052 closest distance to " O   HOH Z 266 " =    5.305
peak=   -3.993 closest distance to " CG  GLN A 223 " =    2.010
peak=   -3.924 closest distance to " O   VAL A 189 " =    2.580
peak=   -3.897 closest distance to " O   HOH Z  73 " =    2.042
peak=   -3.879 closest distance to " CB  ALA A  43 " =    2.584
peak=   -3.848 closest distance to " O   TYR A 247 " =    2.921
peak=   -3.839 closest distance to " CD1 LEU A 101 " =    2.522
peak=   -3.836 closest distance to " O   GLY A 211 " =    1.472
peak=   -3.813 closest distance to " CA  GLY A 241 " =    3.074
peak=   -3.811 closest distance to " CD  ARG A 156 " =    2.133
peak=   -3.806 closest distance to " O   HOH Z  10 " =    1.487
peak=   -3.803 closest distance to " CD  GLN A 223 " =    0.773
peak=   -3.773 closest distance to " CG1 VAL A 197 " =    2.311
peak=   -3.760 closest distance to " O   GLY A 203 " =    2.366
peak=   -3.756 closest distance to " O   HOH Z 435 " =    2.854
peak=   -3.755 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.742 closest distance to " CA  GLY A 241 " =    2.329
peak=   -3.718 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -3.710 closest distance to " O   HOH Z 185 " =    2.402
peak=   -3.710 closest distance to " O   HOH Z 118 " =    3.476
peak=   -3.709 closest distance to " OG  SER A  97 " =    2.209
peak=   -3.708 closest distance to " O   HOH Z 231 " =    2.028
peak=   -3.707 closest distance to " O   HOH Z 241 " =    1.207
peak=   -3.706 closest distance to " O   HOH Z 377 " =    2.119
peak=   -3.706 closest distance to " O   HOH Z 426 " =    1.640
peak=   -3.695 closest distance to " OG BSER A 134 " =    1.757
peak=   -3.691 closest distance to " O   HOH Z  60 " =    2.478
peak=   -3.683 closest distance to " NH2AARG A 275 " =    5.633
peak=   -3.683 closest distance to " O   HOH Z 377 " =    0.708
peak=   -3.674 closest distance to " O   HOH Z 114 " =    1.317
peak=   -3.674 closest distance to " CD2 TYR A 293 " =    2.050
peak=   -3.668 closest distance to " O   HOH Z 372 " =    2.484
peak=   -3.642 closest distance to " CB  ALA A 291 " =    2.270
peak=   -3.636 closest distance to " O   HOH Z  52 " =    1.217
peak=   -3.631 closest distance to " OD1 ASN A 148 " =    1.534
peak=   -3.629 closest distance to " CD  GLN A  88 " =    0.798
peak=   -3.628 closest distance to " CE  MET A 105 " =    2.270
peak=   -3.609 closest distance to " CE BMET A  47 " =    1.761
peak=   -3.607 closest distance to " O   HOH Z 351 " =    1.501
peak=   -3.596 closest distance to " CB  TRP A  85 " =    2.465
peak=   -3.591 closest distance to " CG1 VAL A 250 " =    2.745
peak=   -3.588 closest distance to " C   LEU A 222 " =    0.797
peak=   -3.579 closest distance to " CG1 VAL A 112 " =    2.987
peak=   -3.577 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.577 closest distance to " CD1 LEU A 228 " =    2.439
peak=   -3.576 closest distance to " OG BSER A 134 " =    1.382
peak=   -3.575 closest distance to " NH2 ARG A  79 " =    1.626
peak=   -3.567 closest distance to " O   HOH Z 353 " =    2.122
peak=   -3.556 closest distance to " O   HOH Z 211 " =    1.510
peak=   -3.548 closest distance to " O   HOH Z 198 " =    1.289
peak=   -3.547 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.545 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.540 closest distance to " CB  PHE A 192 " =    1.942
peak=   -3.540 closest distance to " CA  GLY A 203 " =    2.375
peak=   -3.514 closest distance to " OXT GLY A 302 " =    3.057
peak=   -3.511 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.508 closest distance to " C   ASN A 285 " =    2.506
peak=   -3.498 closest distance to " O   ILE A 109 " =    2.703
peak=   -3.496 closest distance to " CA  SER A 135 " =    1.311
peak=   -3.487 closest distance to " CE  LYS A  76 " =    2.668
peak=   -3.473 closest distance to " O   HOH Z 394 " =    1.502
peak=   -3.470 closest distance to " C   ALA A 158 " =    1.485
peak=   -3.470 closest distance to " ND2BASN A 224 " =    1.712
peak=   -3.463 closest distance to " O   HOH Z 359 " =    3.238
peak=   -3.455 closest distance to " O   HOH Z 111 " =    1.900
peak=   -3.455 closest distance to " CG  ARG A 269 " =    2.630
peak=   -3.449 closest distance to " ND2 ASN A 249 " =    2.123
peak=   -3.447 closest distance to " CZ3 TRP A 274 " =    0.957
peak=   -3.439 closest distance to " O   ASP A 272 " =    2.439
peak=   -3.438 closest distance to " CA  GLY A 241 " =    2.866
peak=   -3.427 closest distance to " O   PRO A 163 " =    2.054
peak=   -3.427 closest distance to " C   MET A 188 " =    1.395
peak=   -3.425 closest distance to " CG2 ILE A 263 " =    2.425
peak=   -3.417 closest distance to " CE2 PHE A  61 " =    2.642
peak=   -3.417 closest distance to " CB  ASP A 286 " =    2.018
peak=   -3.416 closest distance to " N   THR A 157 " =    1.627
peak=   -3.410 closest distance to " OH  TYR A 247 " =    2.140
peak=   -3.409 closest distance to " O   HOH Z 219 " =    4.890
peak=   -3.406 closest distance to " CG2 ILE A  20 " =    2.821
peak=   -3.405 closest distance to " CD2 LEU A 300 " =    2.907
peak=   -3.403 closest distance to " CA  GLY A  98 " =    1.978
peak=   -3.402 closest distance to " O   VAL A  67 " =    2.948
peak=   -3.398 closest distance to " C   HIS A 108 " =    1.128
peak=   -3.398 closest distance to " OD1 ASP A 171 " =    1.629
peak=   -3.394 closest distance to " O   HOH Z 417 " =    2.798
peak=   -3.391 closest distance to " O   HOH Z  43 " =    1.597
peak=   -3.389 closest distance to " N   THR A  52 " =    1.775
peak=   -3.372 closest distance to " O   HOH Z  70 " =    2.227
peak=   -3.369 closest distance to " CD1 ILE A 263 " =    3.024
peak=   -3.366 closest distance to " CB  CYS A 254 " =    2.315
peak=   -3.361 closest distance to " CD  ARG A 195 " =    5.165
peak=   -3.361 closest distance to " O   HOH Z 231 " =    0.821
peak=   -3.358 closest distance to " O   HOH Z   6 " =    1.464
peak=   -3.353 closest distance to " CD  GLU A 152 " =    0.797
peak=   -3.351 closest distance to " O   HOH Z 313 " =    2.047
peak=   -3.326 closest distance to " ND2 ASN A  60 " =    1.461
peak=   -3.325 closest distance to " O   SER A 210 " =    1.917
peak=   -3.321 closest distance to " CZ  TYR A 169 " =    1.672
peak=   -3.318 closest distance to " OD1AASN A 224 " =    1.686
peak=   -3.316 closest distance to " O   HOH Z  51 " =    1.197
peak=   -3.314 closest distance to " CB  ASP A  27 " =    2.555
peak=   -3.310 closest distance to " O   HOH Z  22 " =    2.382
peak=   -3.310 closest distance to " O   HOH Z 198 " =    2.279
peak=   -3.307 closest distance to " CB  PHE A 283 " =    2.837
peak=   -3.305 closest distance to " CG2 THR A 221 " =    2.132
peak=   -3.305 closest distance to " O   HOH Z  15 " =    1.638
peak=   -3.304 closest distance to " N   MET A 188 " =    1.895
peak=   -3.303 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -3.298 closest distance to " O   GLY A  80 " =    2.523
peak=   -3.290 closest distance to " CB  ALA A 248 " =    2.533
peak=   -3.286 closest distance to " CG  PRO A 163 " =    2.513
peak=   -3.273 closest distance to " O   HOH Z 317 " =    1.553
peak=   -3.268 closest distance to " O   ALA A  10 " =    1.692
peak=   -3.268 closest distance to " C   GLY A  13 " =    0.926
peak=   -3.268 closest distance to " O   HOH Z 266 " =    5.041
peak=   -3.267 closest distance to " N   THR A  18 " =    1.352
peak=   -3.264 closest distance to " CB  PHE A 225 " =    2.156
peak=   -3.256 closest distance to " O   HOH Z 281 " =    2.663
peak=   -3.254 closest distance to " CH2 TRP A 177 " =    2.264
peak=   -3.254 closest distance to " O   HOH Z 275 " =    1.769
peak=   -3.251 closest distance to " CZ BARG A 275 " =    1.813
peak=   -3.246 closest distance to " CG  TRP A 266 " =    1.789
peak=   -3.245 closest distance to " ND2 ASN A  60 " =    4.171
peak=   -3.241 closest distance to " O   HOH Z 390 " =    2.281
peak=   -3.240 closest distance to " CA  ASP A 298 " =    1.107
peak=   -3.240 closest distance to " O   PRO A 198 " =    1.330
peak=   -3.240 closest distance to " O   LEU A 101 " =    2.987
peak=   -3.237 closest distance to " NH1AARG A 275 " =    1.866
peak=   -3.235 closest distance to " CG2 THR A 178 " =    2.291
peak=   -3.233 closest distance to " O   HOH Z  51 " =    1.645
peak=   -3.233 closest distance to " CB  ALA A   9 " =    2.547
peak=   -3.222 closest distance to " SD BMET A  47 " =    0.888
peak=   -3.221 closest distance to " CD1 LEU A   5 " =    2.698
peak=   -3.221 closest distance to " CB  ASN A  39 " =    2.231
peak=   -3.212 closest distance to " O   ALA A  34 " =    2.170
peak=   -3.212 closest distance to " O   HOH Z 275 " =    1.562
peak=   -3.209 closest distance to " O   VAL A 197 " =    1.510
peak=   -3.207 closest distance to " ND2 ASN A  45 " =    1.882
peak=   -3.206 closest distance to " O   HOH Z 396 " =    2.103
peak=   -3.205 closest distance to " O   MET A  40 " =    2.883
peak=   -3.200 closest distance to " O   ASN A 301 " =    1.524
peak=   -3.192 closest distance to " CG2 ILE A  49 " =    2.765
peak=   -3.190 closest distance to " ND2 ASN A 187 " =    1.320
peak=   -3.189 closest distance to " O   HOH Z  53 " =    1.707
peak=   -3.187 closest distance to " CD1 LEU A 297 " =    2.507
peak=   -3.186 closest distance to " CG  GLU A  53 " =    1.533
peak=   -3.186 closest distance to " NE2 GLN A 103 " =    1.723
peak=   -3.186 closest distance to " O   HOH Z 252 " =    4.106
peak=   -3.186 closest distance to " CD  ARG A 139 " =    1.597
peak=   -3.185 closest distance to " CG  ARG A  66 " =    2.117
peak=   -3.185 closest distance to " CB  PRO A  54 " =    2.518
peak=   -3.184 closest distance to " CE2 PHE A 218 " =    2.446
peak=   -3.180 closest distance to " CE3 TRP A 274 " =    2.527
peak=   -3.179 closest distance to " CD1 LEU A 228 " =    2.301
peak=   -3.178 closest distance to " NE2 GLN A 194 " =    1.875
peak=   -3.173 closest distance to " C   LEU A 143 " =    1.315
peak=   -3.172 closest distance to " OG  SER A 206 " =    1.816
peak=   -3.166 closest distance to " OD1 ASP A 191 " =    1.721
peak=   -3.157 closest distance to " O   HOH Z  90 " =    1.539
peak=   -3.152 closest distance to " CG1 VAL A 125 " =    1.900
peak=   -3.151 closest distance to " CD1 ILE A 239 " =    2.052
peak=   -3.150 closest distance to " CG  LEU A 282 " =    2.471
peak=   -3.149 closest distance to " CB  ASP A 132 " =    2.300
peak=   -3.148 closest distance to " N   GLN A  58 " =    1.802
peak=   -3.146 closest distance to " O   SER A  22 " =    2.398
peak=   -3.144 closest distance to " C   SER A 206 " =    1.495
peak=   -3.142 closest distance to " NH2 ARG A 159 " =    2.449
peak=   -3.140 closest distance to " CB  ASP A 132 " =    2.390
peak=   -3.136 closest distance to " O   TRP A  70 " =    1.499
peak=   -3.134 closest distance to " O   HOH Z  58 " =    0.703
peak=   -3.133 closest distance to " O   HOH Z 322 " =    1.188
peak=   -3.131 closest distance to " CZ  PHE A  38 " =    2.066
peak=   -3.124 closest distance to " O   HOH Z 103 " =    1.802
peak=   -3.123 closest distance to " SG ACYS A 201 " =    2.125
peak=   -3.117 closest distance to " O   HOH Z 111 " =    1.326
peak=   -3.117 closest distance to " O   SER A  62 " =    2.184
peak=   -3.109 closest distance to " O   ASP A 270 " =    2.024
peak=   -3.104 closest distance to " O   PRO A 243 " =    2.526
peak=   -3.099 closest distance to " O   PHE A 218 " =    1.527
peak=   -3.093 closest distance to " O   HOH Z 298 " =    1.225
peak=   -3.090 closest distance to " N   SER A   3 " =    2.000
peak=   -3.090 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.084 closest distance to " ND2 ASN A  60 " =    2.048
peak=   -3.084 closest distance to " CB  ALA A 114 " =    2.489
peak=   -3.071 closest distance to " CD  GLN A  11 " =    1.161
peak=   -3.057 closest distance to " CA  GLY A 287 " =    1.404
peak=   -2.961 closest distance to " O   ALA A 100 " =    2.198

================= 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    :  0.3833 0.3742   6.164743e+00   6.153440e+00
   1_bss:  0.3719 0.3657   6.147837e+00   6.136074e+00
   1_xyz:  0.2465 0.2752   5.811260e+00   5.887416e+00
   1_adp:  0.2271 0.2819   5.763002e+00   5.910212e+00
   1_occ:  0.2267 0.2814   5.761866e+00   5.909515e+00
   2_bss:  0.2256 0.2810   5.761238e+00   5.908177e+00
   2_xyz:  0.1581 0.2057   5.437054e+00   5.633536e+00
   2_adp:  0.1418 0.1896   5.349025e+00   5.560718e+00
   2_occ:  0.1417 0.1894   5.348296e+00   5.560298e+00
   3_bss:  0.1414 0.1891   5.346534e+00   5.557592e+00
   3_xyz:  0.1237 0.1710   5.233173e+00   5.464478e+00
   3_adp:  0.1204 0.1661   5.207393e+00   5.439695e+00
   3_occ:  0.1203 0.1659   5.206905e+00   5.439341e+00
   4_bss:  0.1202 0.1658   5.206313e+00   5.438629e+00
   4_xyz:  0.1131 0.1634   5.168910e+00   5.418604e+00
   4_adp:  0.1142 0.1626   5.171142e+00   5.414731e+00
   4_occ:  0.1141 0.1624   5.170591e+00   5.414423e+00
   5_bss:  0.1143 0.1613   5.168614e+00   5.410495e+00
   5_xyz:  0.1137 0.1615   5.168268e+00   5.413389e+00
   5_adp:  0.1140 0.1613   5.168982e+00   5.412979e+00
   5_occ:  0.1139 0.1613   5.169031e+00   5.413262e+00
   5_bss:  0.1139 0.1613   5.169289e+00   5.413363e+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:  0.323  63.900   3.031  -2.893  -0.025  -0.000  -0.000  -0.000
   1_xyz:  0.323  63.900   3.031  -2.893  -0.025  -0.000  -0.000  -0.000
   1_adp:  0.323  63.900   3.031  -2.893  -0.025  -0.000  -0.000  -0.000
   1_occ:  0.323  63.900   3.031  -2.893  -0.025  -0.000  -0.000  -0.000
   2_bss:  0.339  71.900  -0.099  -2.912  -0.876  -0.000  -0.000  -0.000
   2_xyz:  0.339  71.900  -0.099  -2.912  -0.876  -0.000  -0.000  -0.000
   2_adp:  0.339  71.900  -0.099  -2.912  -0.876  -0.000  -0.000  -0.000
   2_occ:  0.339  71.900  -0.099  -2.912  -0.876  -0.000  -0.000  -0.000
   3_bss:  0.338  71.900  -1.348  -2.703  -0.997  -0.000  -0.000  -0.000
   3_xyz:  0.338  71.900  -1.348  -2.703  -0.997  -0.000  -0.000  -0.000
   3_adp:  0.338  71.900  -1.348  -2.703  -0.997  -0.000  -0.000  -0.000
   3_occ:  0.338  71.900  -1.348  -2.703  -0.997  -0.000  -0.000  -0.000
   4_bss:  0.338  71.900  -1.850  -2.680  -1.100  -0.000  -0.000  -0.000
   4_xyz:  0.338  71.900  -1.850  -2.680  -1.100  -0.000  -0.000  -0.000
   4_adp:  0.338  71.900  -1.850  -2.680  -1.100  -0.000  -0.000  -0.000
   4_occ:  0.338  71.900  -1.850  -2.680  -1.100  -0.000  -0.000  -0.000
   5_bss:  0.314  60.509  -2.060  -2.711  -1.164  -0.000  -0.000  -0.000
   5_xyz:  0.314  60.509  -2.060  -2.711  -1.164  -0.000  -0.000  -0.000
   5_adp:  0.314  60.509  -2.060  -2.711  -1.164  -0.000  -0.000  -0.000
   5_occ:  0.314  60.509  -2.060  -2.711  -1.164  -0.000  -0.000  -0.000
   5_bss:  0.312  55.228  -1.959  -2.542  -0.998  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.579 0.6257  0.7868    41939.020
   1_bss:  40.701 0.6352  0.8054    39850.023
   1_xyz:  27.620 0.7848  0.9557    20004.979
   1_adp:  28.640 0.7730  0.9425    21034.715
   1_occ:  28.645 0.7728  0.9418    20984.880
   2_bss:  28.517 0.7743  0.9015    20906.187
   2_xyz:  19.875 0.8621  0.9731    10728.728
   2_adp:  17.918 0.8811  0.9816     9212.559
   2_occ:  17.903 0.8812  0.9814     9200.193
   3_bss:  17.880 0.8814  0.9675     9142.020
   3_xyz:  15.659 0.9010  0.9758     7411.925
   3_adp:  14.996 0.9071  0.9739     7060.662
   3_occ:  14.988 0.9071  0.9737     7049.381
   4_bss:  14.973 0.9073  0.9671     7035.602
   4_xyz:  14.550 0.9107  0.9698     6764.436
   4_adp:  14.412 0.9121  0.9676     6766.380
   4_occ:  14.411 0.9121  0.9676     6753.619
   5_bss:  14.362 0.9123  0.9638     6639.317
   5_xyz:  14.400 0.9121  0.9617     6694.580
   5_adp:  14.373 0.9124  0.9578     6703.412
   5_occ:  14.379 0.9123  0.9577     6705.039
   5_bss:  14.386 0.9123  0.9605     6702.406
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6197e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6197e-01
   1_xyz:   1.197  0.009  0.081 15.481  0.005  4.114   8.2077e-02
   1_adp:   1.197  0.009  0.081 15.481  0.005  4.114   8.2077e-02
   1_occ:   1.197  0.009  0.081 15.481  0.005  4.114   8.2077e-02
   2_bss:   1.197  0.009  0.081 15.481  0.005  4.114   8.2077e-02
   2_xyz:   1.118  0.009  0.078 14.579  0.004  4.134   6.9874e-02
   2_adp:   1.118  0.009  0.078 14.579  0.004  4.134   6.9874e-02
   2_occ:   1.118  0.009  0.078 14.579  0.004  4.134   6.9874e-02
   3_bss:   1.118  0.009  0.078 14.579  0.004  4.134   6.9874e-02
   3_xyz:   1.040  0.009  0.079 14.570  0.004  4.114   6.6267e-02
   3_adp:   1.040  0.009  0.079 14.570  0.004  4.114   6.6267e-02
   3_occ:   1.040  0.009  0.079 14.570  0.004  4.114   6.6267e-02
   4_bss:   1.040  0.009  0.079 14.570  0.004  4.114   6.6267e-02
   4_xyz:   1.156  0.012  0.085 14.762  0.004  4.119   8.1328e-02
   4_adp:   1.156  0.012  0.085 14.762  0.004  4.119   8.1328e-02
   4_occ:   1.156  0.012  0.085 14.762  0.004  4.119   8.1328e-02
   5_bss:   1.156  0.012  0.085 14.762  0.004  4.119   8.1328e-02
   5_xyz:   1.099  0.011  0.082 14.633  0.004  4.122   7.4503e-02
   5_adp:   1.099  0.011  0.082 14.633  0.004  4.122   7.4503e-02
   5_occ:   1.099  0.011  0.082 14.633  0.004  4.122   7.4503e-02
   5_bss:   1.099  0.011  0.082 14.633  0.004  4.122   7.4503e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4315e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4315e-01
   1_xyz:   9.899  0.051  0.322 85.062  0.037  2.204   8.4068e-02
   1_adp:   9.899  0.051  0.322 85.062  0.037  2.204   8.4068e-02
   1_occ:   9.899  0.051  0.322 85.062  0.037  2.204   8.4068e-02
   2_bss:   9.899  0.051  0.322 85.062  0.037  2.204   8.4068e-02
   2_xyz:   8.078  0.047  0.255 81.564  0.032  2.329   6.7535e-02
   2_adp:   8.078  0.047  0.255 81.564  0.032  2.329   6.7535e-02
   2_occ:   8.078  0.047  0.255 81.564  0.032  2.329   6.7535e-02
   3_bss:   8.078  0.047  0.255 81.564  0.032  2.329   6.7535e-02
   3_xyz:   8.725  0.047  0.233 81.522  0.035  2.335   5.1773e-02
   3_adp:   8.725  0.047  0.233 81.522  0.035  2.335   5.1773e-02
   3_occ:   8.725  0.047  0.233 81.522  0.035  2.335   5.1773e-02
   4_bss:   8.725  0.047  0.233 81.522  0.035  2.335   5.1773e-02
   4_xyz:   8.282  0.051  0.284 84.414  0.041  2.303   6.0803e-02
   4_adp:   8.282  0.051  0.284 84.414  0.041  2.303   6.0803e-02
   4_occ:   8.282  0.051  0.284 84.414  0.041  2.303   6.0803e-02
   5_bss:   8.282  0.051  0.284 84.414  0.041  2.303   6.0803e-02
   5_xyz:   8.156  0.050  0.260 83.184  0.037  2.312   5.4073e-02
   5_adp:   8.156  0.050  0.260 83.184  0.037  2.312   5.4073e-02
   5_occ:   8.156  0.050  0.260 83.184  0.037  2.312   5.4073e-02
   5_bss:   8.156  0.050  0.260 83.184  0.037  2.312   5.4073e-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:  70.36   0.00  17.04  70.36   0.00  13.16  66.03   2.26  38.18
   1_occ:  70.36   0.00  17.04  70.36   0.00  13.16  66.03   2.26  38.18
   2_bss:  70.36   0.00  17.04  70.36   0.00  13.16  66.03   2.26  38.18
   2_xyz:  70.36   0.00  17.04  70.36   0.00  13.16  66.03   2.26  38.18
   2_adp:  82.53   0.00  17.60  73.36   0.00  13.20  82.53   4.63  41.54
   2_occ:  82.53   0.00  17.60  73.36   0.00  13.20  82.53   4.63  41.54
   3_bss:  82.53   0.00  17.60  73.36   0.00  13.20  82.53   4.63  41.54
   3_xyz:  82.53   0.00  17.60  73.36   0.00  13.20  82.53   4.63  41.54
   3_adp:  86.00   0.37  17.25  77.75   0.37  13.00  86.00   2.56  40.43
   3_occ:  86.00   0.37  17.25  77.75   0.37  13.00  86.00   2.56  40.43
   4_bss:  86.00   0.37  17.25  77.75   0.37  13.00  86.00   2.56  40.43
   4_xyz:  86.00   0.37  17.25  77.75   0.37  13.00  86.00   2.56  40.43
   4_adp:  83.55   1.49  16.63  73.63   1.49  12.80  83.55   1.95  37.52
   4_occ:  83.55   1.49  16.63  73.63   1.49  12.80  83.55   1.95  37.52
   5_bss:  83.55   1.49  16.63  73.63   1.49  12.80  83.55   1.95  37.52
   5_xyz:  83.55   1.49  16.63  73.63   1.49  12.80  83.55   1.95  37.52
   5_adp:  81.46   1.65  16.39  72.79   1.65  12.67  81.46   3.79  36.68
   5_occ:  81.46   1.65  16.39  72.79   1.65  12.67  81.46   3.79  36.68
   5_bss:  81.41   1.59  16.33  72.74   1.59  12.61  81.41   3.73  36.62
------------------------------------------------------------------------
 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:    1.470    0.016    0.309
   1_adp:    1.470    0.016    0.309
   1_occ:    1.470    0.016    0.309
   2_bss:    1.470    0.016    0.309
   2_xyz:    1.156    0.018    0.451
   2_adp:    1.156    0.018    0.451
   2_occ:    1.156    0.018    0.451
   3_bss:    1.156    0.018    0.451
   3_xyz:    1.146    0.040    0.495
   3_adp:    1.146    0.040    0.495
   3_occ:    1.146    0.040    0.495
   4_bss:    1.146    0.040    0.495
   4_xyz:    1.223    0.039    0.514
   4_adp:    1.223    0.039    0.514
   4_occ:    1.223    0.039    0.514
   5_bss:    1.223    0.039    0.514
   5_xyz:    1.293    0.032    0.525
   5_adp:    1.293    0.032    0.525
   5_occ:    1.293    0.032    0.525
   5_bss:    1.293    0.032    0.525
------------------------------------------------------------------------

CPU time actual refinement: 344.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/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_1261/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1261/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.77 
  Macro-tasks:
    bulk solvent and scale       = 36.63  
    individual site refinement   = 143.62 
    weights calculation          = 29.74  
    collect and process          = 6.55   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 216.67 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 113.89 
    alpha_beta                      = 8.10   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 121.99 
    fmodel                         = 6.77   
    r_factors                      = 0.19   
    phase_errors                   = 11.02  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 265.30 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.870 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    652 calls, 113.58 s
gradients_fft:          597 calls, 108.35 s

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

# Date 2008-01-16 Time 06:49:27 PST -0800 (1200494967.35 s)
Start R-work = 0.3833, R-free = 0.3742 (no bulk solvent and anisotropic scale)
Final R-work = 0.1374, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.3719, R-free = 0.3657
Final R-work = 0.1139, R-free = 0.1613