# Date 2008-01-16 Time 04:01:44 PST -0800 (1200484904.39 s)
#phil __OFF__

Command line arguments: "../143.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32281
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 143

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 84.2302, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (68.845, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95106
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             d_min =   1.9511

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: (68.845, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95106
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1742 [2113/2140]  1902   211  10.0%
  bin  2:  4.1742 -  3.3259 [2029/2045]  1826   203  10.0%
  bin  3:  3.3259 -  2.9092 [2005/2024]  1802   203  10.1%
  bin  4:  2.9092 -  2.6449 [1991/2021]  1796   195   9.8%
  bin  5:  2.6449 -  2.4563 [1966/1985]  1767   199  10.1%
  bin  6:  2.4563 -  2.3120 [1958/1983]  1764   194   9.9%
  bin  7:  2.3120 -  2.1966 [1966/2000]  1769   197  10.0%
  bin  8:  2.1966 -  2.1013 [1937/1967]  1743   194  10.0%
  bin  9:  2.1013 -  2.0206 [1944/1986]  1748   196  10.1%
  bin 10:  2.0206 -  1.9511 [1680/1991]  1513   167   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.81 -     1.62: 7
        1.62 -     2.44: 84
        2.44 -     3.26: 3627
        3.26 -     4.08: 9727
        4.08 -     4.90: 15825
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.805 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.245 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.339 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.357 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.405 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29265 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_143/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.22605 84.23025 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: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4886   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.285159                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.3886 0.3871      6.5724      6.5664|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.4234 0.4091      6.8177      6.8085|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.4600 0.4851      6.7011      6.8047|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.4681 0.4787      6.5435      6.5278|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.5063 0.4942      6.3882      6.3555|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.5219 0.5469      6.3013      6.2853|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.5163 0.4814      6.2511      6.1911|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.5249 0.5265      6.2012      6.2154|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.5508 0.5178      6.1325      6.1334|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.5232 0.5639      6.1239      6.1268|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.5338 0.5693      6.0491       6.107|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.5389 0.5067      5.9897      6.0131|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.5243 0.5622      5.8954      5.8834|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.5287 0.4925      5.8609      5.7662|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.67  36.65   0.83     0.72      77878.81|
|  2:  4.6554 -  3.7149  1320   145  0.66  38.68   0.90     0.78     123967.51|
|  3:  3.7149 -  3.2511  1301   146  0.54  48.70   0.93     0.74     134909.07|
|  4:  3.2511 -  2.9565  1285   144  0.43  57.39   0.95     0.62     121601.56|
|  5:  2.9565 -  2.7461  1272   139  0.34  63.98   0.89     0.50      94211.54|
|  6:  2.7461 -  2.5851  1278   143  0.30  67.72   0.88     0.43      82160.99|
|  7:  2.5851 -  2.4563  1262   141  0.29  68.04   0.91     0.42      72896.66|
|  8:  2.4563 -  2.3498  1265   140  0.29  68.05   0.93     0.44      66028.30|
|  9:  2.3498 -  2.2597  1268   138  0.30  67.25   0.90     0.46      57971.60|
| 10:  2.2597 -  2.1819  1237   137  0.31  66.50   0.97     0.46      52335.56|
| 11:  2.1819 -  2.1139  1267   147  0.25  71.48   0.95     0.39      51109.89|
| 12:  2.1139 -  2.0537  1249   130  0.24  72.51   0.97     0.38      47944.67|
| 13:  2.0537 -  1.9997  1238   141  0.26  70.40   0.95     0.42      40593.36|
| 14:  1.9997 -  1.9511  1013   115  0.39  60.56   0.96     0.57      28231.39|
|alpha:            min =        0.38 max =            0.78 mean =         0.53|
|beta:             min =    28231.39 max =       134909.07 mean =     76267.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.01|
|phase err.(test): min =        0.00 max =           89.94 mean =        61.33|
|-----------------------------------------------------------------------------|

============================== 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 = 12.950641             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.821   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.348051              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.108   (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 |  0.805 -  1.215:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.215 -  1.624:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.624 -  2.034:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.034 -  2.443:       65 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.443 -  2.853:     1152 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.853 -  3.262:     2475 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.262 -  3.671:     3656 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.671 -  4.081:     6071 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.081 -  4.490:     6889 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.490 -  4.900:     8936 |
|-----------------------------------------------------------------------------|
|-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 |        0.239 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  0.805 |       1.389 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    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: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4886   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.285159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4777   ksol= 0.34   Bsol= 2.64   scale= 0.937    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.41,2.08,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.281356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.170488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.752   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.660875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.845   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4766      final r-factor (work) = 0.3778          |
| start r-factor (free) = 0.4777      final r-factor (free) = 0.4038          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0264 = 9.17 * 0.50 * 6.2783 + 1.00 * 0.2387                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.5058 = 9.17 * 0.50 * 6.1873 + 1.00 * 0.1356                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3778      final r-factor (work) = 0.3406          |
| start r-factor (free) = 0.4038      final r-factor (free) = 0.4080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2822 = 1.66 * 1.00 * 6.1873 + 1.00 * 0.0059                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1137 = 1.66 * 1.00 * 6.0750 + 1.00 * 0.0240                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.52  20.03    None  None   None       |
|    all(noH): 2823   0      0.00    102.52  20.03    None  None   None       |
|    Sol.    : 438    0      0.00    102.52  39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    94.47   16.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.252:  900   |   5:    51.259 -  61.510:   79        |
|      1:    10.252 -  20.503:  816   |   6:    61.510 -  71.762:   44        |
|      2:    20.503 -  30.755:  527   |   7:    71.762 -  82.014:   22        |
|      3:    30.755 -  41.007:  268   |   8:    82.014 -  92.265:    5        |
|      4:    41.007 -  51.259:  157   |   9:    92.265 - 102.517:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3406 r_free = 0.4080             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3403 r_free = 0.4088             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3403   r_free= 0.4088   ksol= 0.34   Bsol= 2.64   scale= 1.027    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.41,2.08,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.078864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3366   r_free= 0.4083   ksol= 0.33   Bsol= 34.23   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.03,0.95,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.074102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.263078              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.811   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376895              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.194  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3366      final r-factor (work) = 0.2575          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.3211          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.2588 = 9.26 * 0.50 * 6.0722 + 1.00 * 0.1354                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7652 = 9.26 * 0.50 * 5.9746 + 1.00 * 0.0935                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2575      final r-factor (work) = 0.2334          |
| start r-factor (free) = 0.3211      final r-factor (free) = 0.2942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2758 = 0.38 * 1.00 * 5.9746 + 1.00 * 0.0240                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2003 = 0.38 * 1.00 * 5.8115 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.90   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    92.90   17.94    None  None   None       |
|    Sol.    : 438    0      3.18    92.90   38.99    None  None   None       |
|    Mac.    : 2385   0      0.00    92.71   14.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.290:  842   |   5:    46.450 -  55.740:   86        |
|      1:     9.290 -  18.580: 1066   |   6:    55.740 -  65.030:   50        |
|      2:    18.580 -  27.870:  388   |   7:    65.030 -  74.320:   18        |
|      3:    27.870 -  37.160:  209   |   8:    74.320 -  83.610:    3        |
|      4:    37.160 -  46.450:  154   |   9:    83.610 -  92.900:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2334 r_free = 0.2942             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2330 r_free = 0.2937             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2330   r_free= 0.2937   ksol= 0.33   Bsol= 34.23   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.03,0.95,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.770059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2325   r_free= 0.2921   ksol= 0.33   Bsol= 34.23   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.09,-0.49,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.767706                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.909235              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.978   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303747              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.178  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2325      final r-factor (work) = 0.1740          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.2275          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4557 = 3.91 * 0.50 * 5.8130 + 1.00 * 0.0935                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1048 = 3.91 * 0.50 * 5.6500 + 1.00 * 0.0612                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1740      final r-factor (work) = 0.1597          |
| start r-factor (free) = 0.2275      final r-factor (free) = 0.2152          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7267 = 0.30 * 1.00 * 5.6500 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6794 = 0.30 * 1.00 * 5.4800 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.52   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    92.52   17.74    None  None   None       |
|    Sol.    : 438    0      5.73    89.05   41.65    None  None   None       |
|    Mac.    : 2385   0      0.00    92.52   13.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.252:  864   |   5:    46.261 -  55.514:  118        |
|      1:     9.252 -  18.505: 1183   |   6:    55.514 -  64.766:   58        |
|      2:    18.505 -  27.757:  290   |   7:    64.766 -  74.018:   30        |
|      3:    27.757 -  37.009:  145   |   8:    74.018 -  83.271:    5        |
|      4:    37.009 -  46.261:  124   |   9:    83.271 -  92.523:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1597 r_free = 0.2152             target_work(ml) = 5.447         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1594 r_free = 0.2147             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1594   r_free= 0.2147   ksol= 0.33   Bsol= 34.23   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.09,-0.49,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.445296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1590   r_free= 0.2134   ksol= 0.32   Bsol= 34.23   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.16,-1.49,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.442126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.714166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.054  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.370789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.312   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1590      final r-factor (work) = 0.1313          |
| start r-factor (free) = 0.2134      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5059 = 2.71 * 0.50 * 5.4858 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3358 = 2.71 * 0.50 * 5.3623 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9985 = 0.37 * 1.00 * 5.3623 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9516 = 0.37 * 1.00 * 5.2400 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    93.81   17.64    None  None   None       |
|    all(noH): 2823   0      0.98    93.81   17.64    None  None   None       |
|    Sol.    : 438    0      5.13    92.32   42.46    None  None   None       |
|    Mac.    : 2385   0      0.98    93.81   13.08    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:     0.978 -  10.261: 1072   |   5:    47.393 -  56.676:  106        |
|      1:    10.261 -  19.544: 1079   |   6:    56.676 -  65.959:   68        |
|      2:    19.544 -  28.827:  224   |   7:    65.959 -  75.242:   32        |
|      3:    28.827 -  38.110:  121   |   8:    75.242 -  84.525:    8        |
|      4:    38.110 -  47.393:  107   |   9:    84.525 -  93.808:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1250 r_free = 0.1701             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1249 r_free = 0.1700             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1700   ksol= 0.32   Bsol= 34.23   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.16,-1.49,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.220486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1698   ksol= 0.32   Bsol= 34.23   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.35,-1.72,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.219729                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.561746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.212  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267863              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.467  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3901 = 3.56 * 0.50 * 5.2398 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2883 = 3.56 * 0.50 * 5.1750 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3950 = 0.27 * 1.00 * 5.1750 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7181 = 0.27 * 1.00 * 5.1413 + 1.00 * 0.3409                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.02   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.02   17.48    None  None   None       |
|    Sol.    : 438    0      6.28    92.37   42.03    None  None   None       |
|    Mac.    : 2385   0      0.00    94.02   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.402:  888   |   5:    47.011 -  56.413:  104        |
|      1:     9.402 -  18.804: 1234   |   6:    56.413 -  65.815:   70        |
|      2:    18.804 -  28.206:  247   |   7:    65.815 -  75.217:   32        |
|      3:    28.206 -  37.608:  125   |   8:    75.217 -  84.619:    8        |
|      4:    37.608 -  47.011:  109   |   9:    84.619 -  94.021:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1605             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1603             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1603   ksol= 0.32   Bsol= 34.23   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.35,-1.72,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132732                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.1006 0.1257      5.3809      5.5201|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.0847 0.1222      5.4429      5.6842|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.1073 0.1525      5.5016      5.8824|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.1239 0.1645      5.4751      5.6529|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.1221 0.1607      5.2765      5.4477|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.1143 0.1663      5.1667      5.3619|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.1184 0.1712      5.1228      5.3923|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.1163 0.1751      5.0699      5.3823|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.1162 0.1805       5.024      5.2963|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.1083 0.1877      4.9561      5.2088|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.1138 0.1751      4.9408      5.2574|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.1103 0.1738      4.8714      5.1983|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.1104 0.1813      4.7958      5.0743|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.1069 0.1759      4.6772      4.9138|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.94   8.91   0.99     0.97       6935.24|
|  2:  4.6554 -  3.7149  1320   145  0.95   8.24   1.04     1.03       9493.51|
|  3:  3.7149 -  3.2511  1301   146  0.93  11.91   1.05     1.04      11084.72|
|  4:  3.2511 -  2.9565  1285   144  0.92  13.80   1.03     1.02      10600.04|
|  5:  2.9565 -  2.7461  1272   139  0.91  14.76   1.01     0.98       7520.68|
|  6:  2.7461 -  2.5851  1278   143  0.91  14.92   1.00     0.97       6436.01|
|  7:  2.5851 -  2.4563  1262   141  0.90  15.42   1.00     0.98       5916.46|
|  8:  2.4563 -  2.3498  1265   140  0.91  14.85   1.01     1.00       5321.83|
|  9:  2.3498 -  2.2597  1268   138  0.91  15.41   1.03     1.00       4984.40|
| 10:  2.2597 -  2.1819  1237   137  0.91  15.18   1.01     0.98       4386.40|
| 11:  2.1819 -  2.1139  1267   147  0.90  16.50   1.02     0.98       4456.19|
| 12:  2.1139 -  2.0537  1249   130  0.91  15.58   1.03     1.00       3975.79|
| 13:  2.0537 -  1.9997  1238   141  0.91  15.71   1.02     1.02       3382.66|
| 14:  1.9997 -  1.9511  1013   115  0.91  14.71   1.01     0.98       2584.19|
|alpha:            min =        0.97 max =            1.04 mean =         1.00|
|beta:             min =     2584.19 max =        11084.72 mean =      6311.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.57 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1603   ksol= 0.32   Bsol= 34.23   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.35,-1.72,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132727                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1603   ksol= 0.32   Bsol= 34.23   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.35,-1.72,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132727                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.1006 0.1257      5.3809      5.5201|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.0847 0.1222      5.4429      5.6842|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.1073 0.1525      5.5017      5.8825|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.1239 0.1645      5.4751       5.653|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.1221 0.1607      5.2765      5.4476|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.1143 0.1663      5.1666       5.362|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.1184 0.1713      5.1228      5.3923|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.1163 0.1751      5.0699      5.3823|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.1162 0.1805       5.024      5.2963|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.1083 0.1878      4.9561      5.2088|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.1138 0.1751      4.9408      5.2574|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.1103 0.1738      4.8713      5.1981|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.1104 0.1813      4.7957      5.0742|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.1069 0.1759      4.6772      4.9137|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.94   8.91   0.99     0.97       6936.16|
|  2:  4.6554 -  3.7149  1320   145  0.95   8.24   1.04     1.03       9494.70|
|  3:  3.7149 -  3.2511  1301   146  0.93  11.91   1.05     1.04      11086.48|
|  4:  3.2511 -  2.9565  1285   144  0.92  13.80   1.03     1.02      10599.76|
|  5:  2.9565 -  2.7461  1272   139  0.91  14.76   1.01     0.98       7521.13|
|  6:  2.7461 -  2.5851  1278   143  0.91  14.92   1.00     0.97       6435.90|
|  7:  2.5851 -  2.4563  1262   141  0.90  15.43   1.00     0.98       5917.10|
|  8:  2.4563 -  2.3498  1265   140  0.91  14.85   1.01     1.00       5321.73|
|  9:  2.3498 -  2.2597  1268   138  0.91  15.42   1.03     1.01       4985.06|
| 10:  2.2597 -  2.1819  1237   137  0.91  15.18   1.01     0.98       4386.36|
| 11:  2.1819 -  2.1139  1267   147  0.90  16.50   1.02     0.98       4456.12|
| 12:  2.1139 -  2.0537  1249   130  0.91  15.58   1.03     1.01       3975.01|
| 13:  2.0537 -  1.9997  1238   141  0.91  15.71   1.02     1.02       3381.77|
| 14:  1.9997 -  1.9511  1013   115  0.91  14.71   1.01     0.98       2583.51|
|alpha:            min =        0.97 max =            1.04 mean =         1.00|
|beta:             min =     2583.51 max =        11086.48 mean =      6311.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.57 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.02   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.02   17.48    None  None   None       |
|    Sol.    : 438    0      6.29    92.37   42.04    None  None   None       |
|    Mac.    : 2385   0      0.00    94.02   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.405:  888   |   5:    47.013 -  56.416:  104        |
|      1:     9.405 -  18.807: 1234   |   6:    56.416 -  65.818:   70        |
|      2:    18.807 -  28.209:  247   |   7:    65.818 -  75.220:   32        |
|      3:    28.209 -  37.611:  125   |   8:    75.220 -  84.622:    8        |
|      4:    37.611 -  47.013:  109   |   9:    84.622 -  94.024:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.375 - 5.771
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 314
   mapped sites are within: 0.728 - 5.771

peak=    6.721 closest distance to " O   HOH Z 142 " =    2.066
peak=    6.612 closest distance to " O   HOH Z 126 " =    2.064
peak=    6.253 closest distance to " O   HOH Z 236 " =    1.670
peak=    6.240 closest distance to " O   HOH Z 278 " =    1.551
peak=    6.091 closest distance to " NE2 GLN A  11 " =    1.214
peak=    6.089 closest distance to " O   HOH Z 112 " =    1.577
peak=    5.715 closest distance to " O   HOH Z 202 " =    1.725
peak=    5.601 closest distance to " O   HOH Z 199 " =    1.030
peak=    5.478 closest distance to " NH2 ARG A  56 " =    1.940
peak=    5.448 closest distance to " O   HOH Z  37 " =    1.279
peak=    5.300 closest distance to " O   HOH Z 124 " =    1.625
peak=    5.229 closest distance to " O   HOH Z 213 " =    2.006
peak=    5.174 closest distance to " O   HOH Z 427 " =    2.601
peak=    5.087 closest distance to " O   HOH Z 193 " =    1.631
peak=    5.042 closest distance to " O   HOH Z 272 " =    1.867
peak=    4.961 closest distance to " O   HOH Z 260 " =    1.387
peak=    4.956 closest distance to " O   HOH Z 108 " =    1.662
peak=    4.924 closest distance to " C   PRO A 198 " =    1.479
peak=    4.914 closest distance to " O   HOH Z 214 " =    1.054
peak=    4.873 closest distance to " O   HOH Z 369 " =    2.125
peak=    4.865 closest distance to " CB  ARG A 275 " =    0.882
peak=    4.746 closest distance to " O   HOH Z  78 " =    1.635
peak=    4.727 closest distance to " CG  PRO A  54 " =    1.124
peak=    4.683 closest distance to " O   HOH Z 192 " =    1.489
peak=    4.670 closest distance to " CG  PRO A 213 " =    1.176
peak=    4.608 closest distance to " O   HOH Z 373 " =    2.076
peak=    4.602 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.597 closest distance to " O   HOH Z 375 " =    1.021
peak=    4.591 closest distance to " CB  GLN A 223 " =    1.567
peak=    4.580 closest distance to " O   SER A  87 " =    2.333
peak=    4.576 closest distance to " O   HOH Z 207 " =    1.724
peak=    4.516 closest distance to " O   HOH Z 134 " =    1.336
peak=    4.469 closest distance to " O   HOH Z 234 " =    3.348
peak=    4.467 closest distance to " CB  GLN A 183 " =    1.180
peak=    4.459 closest distance to " O   HOH Z  63 " =    2.094
peak=    4.421 closest distance to " O   HOH Z 380 " =    1.620
peak=    4.414 closest distance to " O   HOH Z 371 " =    1.947
peak=    4.338 closest distance to " NZ  LYS A 117 " =    3.104
peak=    4.283 closest distance to " O   HOH Z  61 " =    1.577
peak=    4.249 closest distance to " O   HOH Z 232 " =    2.333
peak=    4.224 closest distance to " O   HOH Z  92 " =    1.246
peak=    4.221 closest distance to " O   HOH Z  11 " =    1.385
peak=    4.216 closest distance to " CG  GLN A  77 " =    0.823
peak=    4.215 closest distance to " CB  SER A  63 " =    1.167
peak=    4.171 closest distance to " CB  SER A   3 " =    1.314
peak=    4.127 closest distance to " O   HOH Z  93 " =    1.889
peak=    4.115 closest distance to " CA  TYR A  30 " =    0.997
peak=    4.115 closest distance to " OD1 ASN A  60 " =    1.184
peak=    4.112 closest distance to " CB  GLU A 152 " =    1.241
peak=    4.095 closest distance to " O   HOH Z 183 " =    2.180
peak=    4.088 closest distance to " O   HOH Z 128 " =    1.962
peak=    4.051 closest distance to " O   HOH Z 173 " =    2.018
peak=    4.045 closest distance to " O   HOH Z  44 " =    1.783
peak=    4.032 closest distance to " O   HOH Z 313 " =    1.776
peak=    4.022 closest distance to " O   HOH Z  54 " =    1.585
peak=    4.013 closest distance to " O   HOH Z  24 " =    1.369
peak=    4.003 closest distance to " O   HOH Z 166 " =    1.364
peak=    3.989 closest distance to " O   HOH Z 106 " =    2.277
peak=    3.986 closest distance to " O   HOH Z 250 " =    1.460
peak=    3.971 closest distance to " O   HOH Z 132 " =    0.993
peak=    3.961 closest distance to " O   HOH Z 316 " =    2.832
peak=    3.953 closest distance to " CB  SER A  26 " =    1.553
peak=    3.949 closest distance to " CG  ARG A  66 " =    2.874
peak=    3.949 closest distance to " CG1 ILE A  33 " =    1.209
peak=    3.920 closest distance to " OG BSER A 164 " =    2.366
peak=    3.916 closest distance to " O   HOH Z 203 " =    1.838
peak=    3.910 closest distance to " O   HOH Z  97 " =    1.880
peak=    3.892 closest distance to " O   HOH Z 276 " =    1.362
peak=    3.891 closest distance to " O   HOH Z 411 " =    3.588
peak=    3.875 closest distance to " O   HOH Z 327 " =    1.785
peak=    3.868 closest distance to " O   HOH Z 343 " =    1.584
peak=    3.863 closest distance to " O   HOH Z 303 " =    2.352
peak=    3.862 closest distance to " CG2 VAL A 257 " =    0.880
peak=    3.849 closest distance to " OD2 ASP A 286 " =    2.435
peak=    3.849 closest distance to " O   HOH Z 357 " =    1.842
peak=    3.847 closest distance to " OD1 ASN A  69 " =    2.760
peak=    3.846 closest distance to " ND2 ASN A 187 " =    1.578
peak=    3.832 closest distance to " NH2BARG A 145 " =    2.089
peak=    3.824 closest distance to " CB  ARG A  79 " =    1.459
peak=    3.818 closest distance to " O   HOH Z   6 " =    2.075
peak=    3.804 closest distance to " O   HOH Z 128 " =    1.902
peak=    3.798 closest distance to " O   HOH Z 426 " =    1.461
peak=    3.790 closest distance to " O   HOH Z 227 " =    1.918
peak=    3.783 closest distance to " NE2 GLN A  55 " =    1.076
peak=    3.782 closest distance to " O   HOH Z  10 " =    1.734
peak=    3.769 closest distance to " O   HOH Z 282 " =    1.435
peak=    3.767 closest distance to " O   HOH Z 368 " =    1.977
peak=    3.764 closest distance to " O   HOH Z 423 " =    1.308
peak=    3.760 closest distance to " O   HOH Z 209 " =    2.276
peak=    3.757 closest distance to " O   HOH Z 287 " =    1.596
peak=    3.750 closest distance to " O   HOH Z 403 " =    1.766
peak=    3.747 closest distance to " N   PHE A 130 " =    1.306
peak=    3.716 closest distance to " O   HOH Z 345 " =    3.147
peak=    3.716 closest distance to " NH2 ARG A 219 " =    1.832
peak=    3.690 closest distance to " O   HOH Z 328 " =    1.927
peak=    3.688 closest distance to " O   HOH Z  59 " =    1.606
peak=    3.688 closest distance to " CB  ARG A 102 " =    0.864
peak=    3.686 closest distance to " O   HOH Z 366 " =    2.414
peak=    3.677 closest distance to " NE AARG A 275 " =    1.259
peak=    3.676 closest distance to " O   HOH Z 289 " =    1.556
peak=    3.676 closest distance to " O   HOH Z 271 " =    1.374
peak=    3.675 closest distance to " CG  PRO A 198 " =    1.278
peak=    3.675 closest distance to " O   HOH Z 286 " =    2.166
peak=    3.674 closest distance to " O   HOH Z   9 " =    2.319
peak=    3.665 closest distance to " O   HOH Z 156 " =    2.718
peak=    3.664 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.658 closest distance to " O   HOH Z 419 " =    1.984
peak=    3.655 closest distance to " CB  PRO A  54 " =    0.949
peak=    3.654 closest distance to " O   HOH Z 407 " =    2.079
peak=    3.653 closest distance to " O   HOH Z 425 " =    1.970
peak=    3.649 closest distance to " O   HOH Z   1 " =    1.698
peak=    3.642 closest distance to " O   HOH Z  66 " =    1.996
peak=    3.642 closest distance to " O   HOH Z 298 " =    1.730
peak=    3.641 closest distance to " CB  ARG A 139 " =    1.165
peak=    3.631 closest distance to " O   HOH Z   1 " =    1.603
peak=    3.630 closest distance to " O   HOH Z 222 " =    2.307
peak=    3.627 closest distance to " CB  LEU A 228 " =    1.124
peak=    3.620 closest distance to " CG  MET A 185 " =    1.296
peak=    3.620 closest distance to " O   HOH Z 153 " =    1.751
peak=    3.618 closest distance to " CB  TYR A 169 " =    0.982
peak=    3.616 closest distance to " CB  TRP A 179 " =    1.206
peak=    3.613 closest distance to " O   HOH Z 189 " =    1.818
peak=    3.604 closest distance to " CG2 THR A 221 " =    1.217
peak=    3.601 closest distance to " CB  THR A  31 " =    1.720
peak=    3.600 closest distance to " O   HOH Z 234 " =    2.032
peak=    3.596 closest distance to " NH1BARG A 145 " =    1.354
peak=    3.592 closest distance to " CA  PHE A 283 " =    1.318
peak=    3.586 closest distance to " CD2 TRP A 179 " =    1.336
peak=    3.582 closest distance to " O   HOH Z 132 " =    2.032
peak=    3.581 closest distance to " O   HOH Z 394 " =    1.471
peak=    3.576 closest distance to " O   HOH Z  88 " =    2.879
peak=    3.576 closest distance to " CE  LYS A 119 " =    1.144
peak=    3.572 closest distance to " O   HOH Z 261 " =    1.746
peak=    3.571 closest distance to " NZ  LYS A  48 " =    2.167
peak=    3.568 closest distance to " O   HOH Z 425 " =    1.431
peak=    3.560 closest distance to " CG AARG A 275 " =    0.945
peak=    3.560 closest distance to " O   HOH Z 244 " =    1.664
peak=    3.556 closest distance to " O   HOH Z 402 " =    1.320
peak=    3.550 closest distance to " CA  ALA A 299 " =    0.936
peak=    3.529 closest distance to " O   HOH Z 344 " =    3.016
peak=    3.524 closest distance to " CA  ALA A  21 " =    1.074
peak=    3.520 closest distance to " O   HOH Z 269 " =    3.404
peak=    3.520 closest distance to " CH2 TRP A  92 " =    2.110
peak=    3.519 closest distance to " O   HOH Z 181 " =    1.688
peak=    3.516 closest distance to " O   HOH Z  63 " =    2.382
peak=    3.513 closest distance to " O   HOH Z 108 " =    1.453
peak=    3.507 closest distance to " OG  SER A  22 " =    2.607
peak=    3.505 closest distance to " O   HOH Z 278 " =    1.479
peak=    3.499 closest distance to " O   HOH Z  40 " =    1.732
peak=    3.498 closest distance to " O   HOH Z 365 " =    1.685
peak=    3.489 closest distance to " O   HOH Z 112 " =    1.524
peak=    3.488 closest distance to " N   TRP A 177 " =    1.543
peak=    3.485 closest distance to " O   HOH Z 155 " =    1.731
peak=    3.483 closest distance to " O   HOH Z 158 " =    3.073
peak=    3.476 closest distance to " N   GLY A 196 " =    1.021
peak=    3.469 closest distance to " O   HOH Z 344 " =    1.310
peak=    3.469 closest distance to " CD BLYS A 290 " =    1.164
peak=    3.468 closest distance to " O   HOH Z 257 " =    2.150
peak=    3.464 closest distance to " CG  GLU A 277 " =    2.036
peak=    3.463 closest distance to " NH1 ARG A  14 " =    1.123
peak=    3.462 closest distance to " NE2 GLN A  73 " =    3.526
peak=    3.452 closest distance to " O   HOH Z 387 " =    1.925
peak=    3.451 closest distance to " O   HOH Z 218 " =    2.066
peak=    3.451 closest distance to " CA  LEU A 282 " =    1.286
peak=    3.449 closest distance to " O   HOH Z  61 " =    1.771
peak=    3.448 closest distance to " CA  ASN A 215 " =    1.158
peak=    3.447 closest distance to " O   HOH Z  40 " =    2.377
peak=    3.432 closest distance to " O   HOH Z 409 " =    2.259
peak=    3.432 closest distance to " O   HOH Z 388 " =    1.724
peak=    3.428 closest distance to " CA  THR A 264 " =    0.839
peak=    3.426 closest distance to " CD  GLN A  58 " =    5.771
peak=    3.423 closest distance to " CB  ALA A 114 " =    1.408
peak=    3.417 closest distance to " O   HOH Z 423 " =    2.269
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.475
peak=    3.411 closest distance to " O   HOH Z  68 " =    1.590
peak=    3.410 closest distance to " CB  VAL A 265 " =    1.396
peak=    3.408 closest distance to " O   HOH Z  43 " =    1.853
peak=    3.401 closest distance to " O   HOH Z 430 " =    1.786
peak=    3.389 closest distance to " O   HOH Z 135 " =    1.852
peak=    3.383 closest distance to " CE AMET A  47 " =    1.136
peak=    3.383 closest distance to " O   HOH Z  73 " =    1.849
peak=    3.380 closest distance to " O   HOH Z 389 " =    1.389
peak=    3.380 closest distance to " CB  GLU A 277 " =    3.376
peak=    3.374 closest distance to " CD  LYS A 166 " =    1.281
peak=    3.365 closest distance to " CB  ALA A   1 " =    4.523
peak=    3.364 closest distance to " O   HOH Z 132 " =    2.425
peak=    3.363 closest distance to " CG  GLN A  77 " =    2.193
peak=    3.362 closest distance to " O  BHOH Z  74 " =    1.432
peak=    3.360 closest distance to " O   HOH Z 125 " =    2.127
peak=    3.358 closest distance to " CD  GLN A 194 " =    1.489
peak=    3.352 closest distance to " O   HOH Z 356 " =    1.217
peak=    3.352 closest distance to " CB  TYR A  30 " =    1.421
peak=    3.352 closest distance to " O   HOH Z 227 " =    2.032
peak=    3.346 closest distance to " O   HOH Z 116 " =    2.223
peak=    3.337 closest distance to " O   HOH Z  43 " =    2.625
peak=    3.337 closest distance to " O   HOH Z 258 " =    1.393
peak=    3.337 closest distance to " O   HOH Z  88 " =    2.368
peak=    3.335 closest distance to " CA  VAL A  41 " =    1.085
peak=    3.335 closest distance to " O   SER A  26 " =    1.558
peak=    3.332 closest distance to " O   HOH Z 383 " =    2.017
peak=    3.325 closest distance to " O  BHOH Z 338 " =    2.298
peak=    3.321 closest distance to " O   HOH Z 435 " =    1.581
peak=    3.320 closest distance to " O   HOH Z   1 " =    1.596
peak=    3.320 closest distance to " O   HOH Z 118 " =    1.321
peak=    3.318 closest distance to " O   HOH Z   5 " =    1.133
peak=    3.318 closest distance to " O   HOH Z 299 " =    2.379
peak=    3.306 closest distance to " O   HOH Z 140 " =    1.880
peak=    3.304 closest distance to " O   HOH Z 336 " =    1.943
peak=    3.298 closest distance to " O   HOH Z 423 " =    1.931
peak=    3.288 closest distance to " O   HOH Z 346 " =    1.429
peak=    3.287 closest distance to " O   HOH Z 140 " =    1.371
peak=    3.285 closest distance to " O   HOH Z  19 " =    1.934
peak=    3.281 closest distance to " O   HOH Z 421 " =    1.689
peak=    3.278 closest distance to " O   HOH Z  20 " =    1.856
peak=    3.277 closest distance to " O   HOH Z 381 " =    1.815
peak=    3.275 closest distance to " O   HOH Z 303 " =    1.839
peak=    3.274 closest distance to " O   HOH Z  94 " =    1.900
peak=    3.272 closest distance to " O   HOH Z 365 " =    5.158
peak=    3.272 closest distance to " OG  SER A  62 " =    2.834
peak=    3.256 closest distance to " CA  ALA A 233 " =    1.201
peak=    3.254 closest distance to " O   HOH Z  48 " =    1.545
peak=    3.251 closest distance to " O   HOH Z 389 " =    2.932
peak=    3.249 closest distance to " O   HOH Z 100 " =    0.770
peak=    3.249 closest distance to " CB  ALA A  34 " =    1.000
peak=    3.248 closest distance to " CA  MET A  40 " =    1.060
peak=    3.248 closest distance to " O   HOH Z  64 " =    2.030
peak=    3.244 closest distance to " O   HOH Z  15 " =    1.439
peak=    3.244 closest distance to " O   HOH Z 353 " =    2.298
peak=    3.239 closest distance to " CB  GLU A 128 " =    1.015
peak=    3.238 closest distance to " CB  THR A 157 " =    0.974
peak=    3.235 closest distance to " O   HOH Z 118 " =    1.371
peak=    3.235 closest distance to " O   HOH Z 291 " =    1.430
peak=    3.235 closest distance to " O   HOH Z 291 " =    1.764
peak=    3.234 closest distance to " O   HOH Z 136 " =    0.728
peak=    3.231 closest distance to " CG2 THR A 220 " =    0.978
peak=    3.228 closest distance to " O   HOH Z 146 " =    1.662
peak=    3.217 closest distance to " O   HOH Z 260 " =    2.011
peak=    3.214 closest distance to " O   HOH Z 334 " =    1.524
peak=    3.212 closest distance to " O   HOH Z 193 " =    1.978
peak=    3.212 closest distance to " CG  ARG A  66 " =    0.938
peak=    3.212 closest distance to " CB  ARG A 190 " =    1.854
peak=    3.208 closest distance to " N   TYR A  15 " =    1.088
peak=    3.207 closest distance to " CG1BVAL A  72 " =    1.177
peak=    3.204 closest distance to " N   ASP A 162 " =    1.272
peak=    3.204 closest distance to " O   HOH Z 385 " =    0.731
peak=    3.203 closest distance to " CB  PRO A 163 " =    3.884
peak=    3.201 closest distance to " CA  VAL A 126 " =    1.082
peak=    3.196 closest distance to " CB  ASP A 200 " =    0.914
peak=    3.189 closest distance to " CB  MET A 188 " =    1.696
peak=    3.189 closest distance to " O   HOH Z 216 " =    1.746
peak=    3.188 closest distance to " O   HOH Z  80 " =    2.076
peak=    3.187 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.186 closest distance to " CB  ALA A  10 " =    1.172
peak=    3.185 closest distance to " O   HOH Z  80 " =    2.108
peak=    3.183 closest distance to " O   HOH Z 245 " =    1.267
peak=    3.182 closest distance to " OD1BASN A 224 " =    2.102
peak=    3.180 closest distance to " O   HOH Z 119 " =    1.577
peak=    3.177 closest distance to " OG BSER A 258 " =    2.836
peak=    3.175 closest distance to " CD  PRO A 243 " =    1.571
peak=    3.171 closest distance to " O   HOH Z  35 " =    2.437
peak=    3.171 closest distance to " N   ARG A 156 " =    1.228
peak=    3.170 closest distance to " O   HOH Z  59 " =    1.830
peak=    3.168 closest distance to " O   HOH Z 158 " =    2.571
peak=    3.163 closest distance to " CE1 TYR A 186 " =    1.257
peak=    3.159 closest distance to " N   ASN A  39 " =    1.072
peak=    3.159 closest distance to " CD2 LEU A 255 " =    1.119
peak=    3.158 closest distance to " CE  LYS A 166 " =    1.797
peak=    3.157 closest distance to " N   SER A 210 " =    1.401
peak=    3.156 closest distance to " NE2 GLN A 278 " =    3.357
peak=    3.155 closest distance to " CB  SER A  62 " =    1.295
peak=    3.155 closest distance to " CB  ALA A 291 " =    1.431
peak=    3.152 closest distance to " O   HOH Z 145 " =    1.017
peak=    3.151 closest distance to " CB  ALA A   1 " =    0.975
peak=    3.143 closest distance to " CG  MET A  40 " =    2.356
peak=    3.136 closest distance to " CA  LEU A 300 " =    0.986
peak=    3.129 closest distance to " CD1 LEU A 228 " =    1.658
peak=    3.128 closest distance to " OE1 GLU A   2 " =    2.070
peak=    3.127 closest distance to " O   HOH Z 284 " =    2.737
peak=    3.127 closest distance to " NH2AARG A 190 " =    1.384
peak=    3.126 closest distance to " O   HOH Z 337 " =    3.469
peak=    3.125 closest distance to " CB  LYS A 193 " =    0.922
peak=    3.121 closest distance to " O   HOH Z 148 " =    1.405
peak=    3.119 closest distance to " O   HOH Z 196 " =    1.513
peak=    3.117 closest distance to " O   HOH Z  15 " =    1.921
peak=    3.110 closest distance to " O   HOH Z 417 " =    2.103
peak=    3.108 closest distance to " ND2 ASN A  60 " =    0.879
peak=    3.106 closest distance to " O   HOH Z 422 " =    2.626
peak=    3.104 closest distance to " CB  ASN A 215 " =    0.985
peak=    3.103 closest distance to " O   HOH Z 111 " =    2.530
peak=    3.095 closest distance to " NH2 ARG A 269 " =    1.036
peak=    3.093 closest distance to " O   HOH Z  85 " =    2.024
peak=    3.091 closest distance to " O   HOH Z 305 " =    3.191
peak=    3.089 closest distance to " O   HOH Z 144 " =    2.152
peak=    3.087 closest distance to " O   HOH Z 180 " =    2.176
peak=    3.085 closest distance to " O   HOH Z 418 " =    2.395
peak=    3.078 closest distance to " O   HOH Z  38 " =    2.391
peak=    3.077 closest distance to " CG1 ILE A 120 " =    1.385
peak=    3.076 closest distance to " O   HOH Z 215 " =    0.778
peak=    3.067 closest distance to " O   GLY A  57 " =    2.366
peak=    3.066 closest distance to " O   HOH Z 215 " =    1.044
peak=    3.055 closest distance to " O   HOH Z 115 " =    1.654
peak=    3.044 closest distance to " CB  VAL A 265 " =    2.268
peak=    3.032 closest distance to " CB  ASN A 110 " =    1.085
peak=    3.021 closest distance to " CB  PRO A  90 " =    1.832
peak=    3.013 closest distance to " O   HOH Z 365 " =    3.116
peak=    3.012 closest distance to " CA  CYS A 168 " =    0.949
peak=    3.003 closest distance to " O   HOH Z 365 " =    1.662
peak=    2.989 closest distance to " O   HOH Z 166 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.735 - 5.681
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.735 - 5.681

peak=   -4.537 closest distance to " C   HIS A 108 " =    1.191
peak=   -4.502 closest distance to " N   GLN A  58 " =    1.617
peak=   -4.451 closest distance to " OD1 ASN A  39 " =    2.163
peak=   -4.409 closest distance to " CZ  PHE A  59 " =    1.448
peak=   -4.376 closest distance to " SG  CYS A 254 " =    3.288
peak=   -4.346 closest distance to " CA  VAL A  67 " =    2.867
peak=   -4.328 closest distance to " O   PRO A 198 " =    1.334
peak=   -4.243 closest distance to " CD  ARG A 156 " =    1.964
peak=   -4.135 closest distance to " O   HOH Z 290 " =    1.168
peak=   -4.112 closest distance to " O   VAL A  67 " =    2.639
peak=   -4.070 closest distance to " ND2 ASN A  45 " =    1.079
peak=   -4.043 closest distance to " CB  PRO A 280 " =    2.187
peak=   -4.025 closest distance to " CB  PRO A 243 " =    2.469
peak=   -4.000 closest distance to " OXT GLY A 302 " =    2.626
peak=   -3.978 closest distance to " CB  CYS A 201 " =    2.272
peak=   -3.955 closest distance to " O   HOH Z 102 " =    1.611
peak=   -3.953 closest distance to " CB  ALA A 248 " =    1.917
peak=   -3.953 closest distance to " O   HOH Z 385 " =    1.881
peak=   -3.946 closest distance to " CG  PHE A 283 " =    2.523
peak=   -3.918 closest distance to " O   HOH Z  13 " =    1.278
peak=   -3.898 closest distance to " O   HOH Z  52 " =    1.678
peak=   -3.891 closest distance to " CD1 ILE A 263 " =    2.915
peak=   -3.890 closest distance to " OG  SER A   3 " =    1.225
peak=   -3.882 closest distance to " O   HOH Z 407 " =    2.786
peak=   -3.878 closest distance to " O   HOH Z 137 " =    1.393
peak=   -3.863 closest distance to " O   HOH Z 351 " =    1.427
peak=   -3.862 closest distance to " N   SER A 276 " =    1.200
peak=   -3.858 closest distance to " O   HOH Z 263 " =    3.126
peak=   -3.854 closest distance to " O   HOH Z  43 " =    1.840
peak=   -3.844 closest distance to " O   HOH Z  98 " =    1.878
peak=   -3.836 closest distance to " C   ASN A 285 " =    2.226
peak=   -3.817 closest distance to " O   ALA A 161 " =    1.700
peak=   -3.793 closest distance to " O   HOH Z 126 " =    1.806
peak=   -3.787 closest distance to " N   GLN A 122 " =    1.384
peak=   -3.777 closest distance to " CD1 LEU A 255 " =    2.765
peak=   -3.764 closest distance to " O   SER A 146 " =    0.735
peak=   -3.764 closest distance to " O   MET A  40 " =    2.685
peak=   -3.752 closest distance to " CA  TYR A  30 " =    2.894
peak=   -3.746 closest distance to " O   PRO A 198 " =    1.218
peak=   -3.743 closest distance to " O   ALA A  51 " =    1.296
peak=   -3.741 closest distance to " O   HOH Z 385 " =    2.024
peak=   -3.732 closest distance to " OD1 ASP A 191 " =    1.849
peak=   -3.716 closest distance to " OD2 ASP A 191 " =    1.419
peak=   -3.715 closest distance to " O   HOH Z 198 " =    1.838
peak=   -3.710 closest distance to " CG1BVAL A  41 " =    2.884
peak=   -3.704 closest distance to " OG  SER A 245 " =    1.285
peak=   -3.702 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.695 closest distance to " O   HOH Z 131 " =    3.991
peak=   -3.687 closest distance to " O   VAL A 153 " =    2.322
peak=   -3.684 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -3.657 closest distance to " O   TRP A  92 " =    1.671
peak=   -3.635 closest distance to " O   HOH Z 231 " =    2.168
peak=   -3.626 closest distance to " OG BSER A 134 " =    1.418
peak=   -3.620 closest distance to " CB  ALA A   7 " =    2.003
peak=   -3.618 closest distance to " O   HOH Z 427 " =    1.497
peak=   -3.606 closest distance to " O   ILE A  49 " =    1.392
peak=   -3.605 closest distance to " N   HIS A 115 " =    2.013
peak=   -3.595 closest distance to " O   HOH Z  88 " =    1.780
peak=   -3.592 closest distance to " CB  ALA A 291 " =    2.260
peak=   -3.587 closest distance to " OG  SER A  97 " =    2.005
peak=   -3.586 closest distance to " CG  GLN A 223 " =    1.562
peak=   -3.576 closest distance to " O   HOH Z   3 " =    1.374
peak=   -3.572 closest distance to " O   SER A 135 " =    1.485
peak=   -3.571 closest distance to " OG BSER A 134 " =    1.400
peak=   -3.564 closest distance to " O   HOH Z  47 " =    1.458
peak=   -3.550 closest distance to " C   GLN A 205 " =    1.940
peak=   -3.546 closest distance to " O   HOH Z 218 " =    3.128
peak=   -3.537 closest distance to " O   HOH Z  11 " =    1.856
peak=   -3.528 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.528 closest distance to " O   HOH Z   3 " =    1.956
peak=   -3.518 closest distance to " O   TRP A  70 " =    1.421
peak=   -3.517 closest distance to " C   ALA A 158 " =    1.241
peak=   -3.512 closest distance to " CE2 TYR A  30 " =    2.845
peak=   -3.508 closest distance to " CG  GLU A 152 " =    1.119
peak=   -3.508 closest distance to " O   HOH Z 266 " =    4.485
peak=   -3.497 closest distance to " O   HOH Z 103 " =    1.502
peak=   -3.490 closest distance to " CG  LYS A 193 " =    2.094
peak=   -3.472 closest distance to " O   HOH Z 211 " =    1.660
peak=   -3.468 closest distance to " N   THR A 157 " =    1.572
peak=   -3.467 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.467 closest distance to " O   HOH Z  24 " =    1.259
peak=   -3.464 closest distance to " O   HOH Z 147 " =    1.536
peak=   -3.464 closest distance to " O   HOH Z 143 " =    2.440
peak=   -3.463 closest distance to " CG  MET A 105 " =    0.930
peak=   -3.460 closest distance to " O   HOH Z 410 " =    2.240
peak=   -3.457 closest distance to " O   HOH Z 438 " =    0.951
peak=   -3.453 closest distance to " OD2 ASP A  50 " =    1.346
peak=   -3.451 closest distance to " OG  SER A  63 " =    1.323
peak=   -3.434 closest distance to " NH1AARG A 275 " =    1.797
peak=   -3.432 closest distance to " CE3 TRP A 274 " =    2.256
peak=   -3.423 closest distance to " CD  GLN A  88 " =    0.893
peak=   -3.420 closest distance to " N   GLN A  58 " =    1.240
peak=   -3.405 closest distance to " O   ARG A  66 " =    1.123
peak=   -3.404 closest distance to " CB  SER A 210 " =    1.405
peak=   -3.401 closest distance to " O   HOH Z 421 " =    3.022
peak=   -3.399 closest distance to " O   PHE A 218 " =    1.437
peak=   -3.396 closest distance to " SG ACYS A 201 " =    1.654
peak=   -3.394 closest distance to " CD2 LEU A 237 " =    2.506
peak=   -3.392 closest distance to " ND2 ASN A  39 " =    1.297
peak=   -3.389 closest distance to " O   HOH Z 423 " =    2.124
peak=   -3.388 closest distance to " N   PHE A  59 " =    2.020
peak=   -3.385 closest distance to " CB  ASP A 132 " =    2.312
peak=   -3.380 closest distance to " O   PRO A 163 " =    1.216
peak=   -3.373 closest distance to " CA  GLY A 133 " =    1.926
peak=   -3.363 closest distance to " OG  SER A  87 " =    1.822
peak=   -3.363 closest distance to " CB  ASN A  39 " =    2.194
peak=   -3.363 closest distance to " CB  ALA A  51 " =    1.787
peak=   -3.362 closest distance to " O   HOH Z 388 " =    1.857
peak=   -3.361 closest distance to " OD1 ASP A 200 " =    1.209
peak=   -3.359 closest distance to " O   HOH Z  93 " =    1.418
peak=   -3.358 closest distance to " O   HOH Z 250 " =    1.392
peak=   -3.353 closest distance to " CE3 TRP A 123 " =    1.288
peak=   -3.352 closest distance to " O   HOH Z 198 " =    1.461
peak=   -3.350 closest distance to " OH  TYR A 214 " =    1.302
peak=   -3.346 closest distance to " O   HOH Z 166 " =    1.536
peak=   -3.335 closest distance to " O   HOH Z 298 " =    1.386
peak=   -3.332 closest distance to " O   HOH Z  15 " =    1.554
peak=   -3.330 closest distance to " OE2 GLU A 152 " =    1.170
peak=   -3.323 closest distance to " O   SER A  26 " =    1.094
peak=   -3.321 closest distance to " CD1 ILE A 239 " =    2.476
peak=   -3.314 closest distance to " O   HOH Z  97 " =    1.531
peak=   -3.313 closest distance to " N   GLY A 302 " =    1.367
peak=   -3.309 closest distance to " CB  ALA A 161 " =    2.460
peak=   -3.308 closest distance to " NH2 ARG A 139 " =    1.453
peak=   -3.305 closest distance to " CG2 THR A  52 " =    2.916
peak=   -3.299 closest distance to " NE2 GLN A  58 " =    0.966
peak=   -3.298 closest distance to " O   HOH Z 337 " =    1.545
peak=   -3.298 closest distance to " OD1 ASP A 191 " =    1.350
peak=   -3.294 closest distance to " NH1 ARG A  56 " =    2.422
peak=   -3.291 closest distance to " OG  SER A  87 " =    1.431
peak=   -3.289 closest distance to " CB  PHE A 192 " =    1.748
peak=   -3.289 closest distance to " OG ASER A 216 " =    1.204
peak=   -3.288 closest distance to " O   HOH Z 281 " =    3.142
peak=   -3.287 closest distance to " O   HOH Z  56 " =    1.561
peak=   -3.283 closest distance to " O   SER A  95 " =    1.351
peak=   -3.282 closest distance to " CD  ARG A  36 " =    1.624
peak=   -3.280 closest distance to " CE  MET A 105 " =    2.321
peak=   -3.279 closest distance to " CB  ALA A 244 " =    2.044
peak=   -3.267 closest distance to " OE2 GLU A   2 " =    0.943
peak=   -3.265 closest distance to " CA  ALA A 227 " =    2.266
peak=   -3.261 closest distance to " O   HOH Z 148 " =    1.953
peak=   -3.259 closest distance to " CG2 VAL A 202 " =    2.019
peak=   -3.256 closest distance to " O   HOH Z 407 " =    3.064
peak=   -3.248 closest distance to " O   HOH Z 145 " =    2.749
peak=   -3.239 closest distance to " CD1 LEU A 101 " =    2.270
peak=   -3.233 closest distance to " CD1 ILE A 199 " =    2.286
peak=   -3.233 closest distance to " CG1 VAL A 197 " =    1.718
peak=   -3.232 closest distance to " O   HOH Z 174 " =    4.609
peak=   -3.232 closest distance to " O   HOH Z  63 " =    1.424
peak=   -3.231 closest distance to " CG  TRP A 266 " =    1.669
peak=   -3.230 closest distance to " O   HOH Z 109 " =    5.681
peak=   -3.228 closest distance to " O   HOH Z 234 " =    3.769
peak=   -3.227 closest distance to " ND2 ASN A 142 " =    1.901
peak=   -3.218 closest distance to " O   HOH Z 165 " =    2.296
peak=   -3.218 closest distance to " O   HOH Z 378 " =    2.096
peak=   -3.217 closest distance to " O   PRO A 163 " =    1.719
peak=   -3.216 closest distance to " CD1 LEU A 228 " =    2.000
peak=   -3.213 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.208 closest distance to " OD1 ASN A 148 " =    1.684
peak=   -3.206 closest distance to " OG BSER A  99 " =    1.723
peak=   -3.206 closest distance to " O   HOH Z 256 " =    1.395
peak=   -3.204 closest distance to " CE2 PHE A 218 " =    2.470
peak=   -3.203 closest distance to " O   HOH Z 139 " =    3.542
peak=   -3.203 closest distance to " O   HOH Z 360 " =    2.418
peak=   -3.200 closest distance to " O   HOH Z 185 " =    1.986
peak=   -3.198 closest distance to " N   ALA A 248 " =    1.648
peak=   -3.191 closest distance to " O   HOH Z   2 " =    1.733
peak=   -3.188 closest distance to " ND2 ASN A  69 " =    1.392
peak=   -3.185 closest distance to " CE2 PHE A 204 " =    2.087
peak=   -3.181 closest distance to " OG ASER A 134 " =    1.173
peak=   -3.175 closest distance to " O   HOH Z 137 " =    1.483
peak=   -3.171 closest distance to " O   HOH Z 417 " =    2.296
peak=   -3.166 closest distance to " O   ASP A 162 " =    2.189
peak=   -3.166 closest distance to " O   HOH Z 233 " =    2.373
peak=   -3.164 closest distance to " O   GLN A 240 " =    1.553
peak=   -3.161 closest distance to " OG1 THR A  82 " =    1.688
peak=   -3.160 closest distance to " O   HOH Z 310 " =    1.606
peak=   -3.156 closest distance to " CD  ARG A 139 " =    1.537
peak=   -3.155 closest distance to " CH2 TRP A 123 " =    1.962
peak=   -3.147 closest distance to " CE1 HIS A  81 " =    1.463
peak=   -3.146 closest distance to " CG1 VAL A 296 " =    2.363
peak=   -3.145 closest distance to " O   HOH Z 111 " =    4.487
peak=   -3.143 closest distance to " CG  ARG A 219 " =    2.038
peak=   -3.141 closest distance to " OG1 THR A 246 " =    1.086
peak=   -3.140 closest distance to " O   HOH Z 107 " =    1.688
peak=   -3.137 closest distance to " OD1 ASP A 171 " =    1.703
peak=   -3.129 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.129 closest distance to " O   HOH Z 429 " =    2.007
peak=   -3.128 closest distance to " C   LEU A 143 " =    1.157
peak=   -3.127 closest distance to " O   GLN A  89 " =    1.497
peak=   -3.122 closest distance to " O   HOH Z  60 " =    1.711
peak=   -3.106 closest distance to " CG  PRO A 163 " =    2.649
peak=   -3.103 closest distance to " O   HOH Z 105 " =    3.804
peak=   -3.098 closest distance to " CG2 THR A 178 " =    2.132
peak=   -3.092 closest distance to " OD1 ASN A 301 " =    1.921
peak=   -3.085 closest distance to " CB  LEU A  25 " =    2.360
peak=   -3.064 closest distance to " O   HOH Z 363 " =    1.737
peak=   -3.062 closest distance to " CD2 LEU A 300 " =    2.882
peak=   -3.053 closest distance to " O   ASN A 224 " =    0.961
peak=   -3.050 closest distance to " O   HOH Z 361 " =    3.384
peak=   -3.041 closest distance to " O   VAL A 125 " =    1.959
peak=   -3.028 closest distance to " O   SER A 216 " =    1.448
peak=   -3.006 closest distance to " OE1 GLN A  58 " =    2.932

================= 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    :  0.4852 0.4886   6.285159e+00   6.283099e+00
   1_bss:  0.4766 0.4777   6.281356e+00   6.266306e+00
   1_xyz:  0.3778 0.4038   6.134617e+00   6.175670e+00
   1_adp:  0.3406 0.4080   6.078898e+00   6.181282e+00
   1_occ:  0.3403 0.4088   6.078864e+00   6.182050e+00
   2_bss:  0.3366 0.4083   6.074102e+00   6.180472e+00
   2_xyz:  0.2575 0.3211   5.853195e+00   6.015134e+00
   2_adp:  0.2334 0.2942   5.771298e+00   5.946322e+00
   2_occ:  0.2330 0.2937   5.770059e+00   5.945818e+00
   3_bss:  0.2325 0.2921   5.767706e+00   5.941411e+00
   3_xyz:  0.1740 0.2275   5.518757e+00   5.727681e+00
   3_adp:  0.1597 0.2152   5.447003e+00   5.665510e+00
   3_occ:  0.1594 0.2147   5.445296e+00   5.663320e+00
   4_bss:  0.1590 0.2134   5.442126e+00   5.658939e+00
   4_xyz:  0.1313 0.1758   5.262451e+00   5.487990e+00
   4_adp:  0.1250 0.1701   5.221047e+00   5.450999e+00
   4_occ:  0.1249 0.1700   5.220486e+00   5.450332e+00
   5_bss:  0.1251 0.1698   5.219729e+00   5.449984e+00
   5_xyz:  0.1124 0.1625   5.146698e+00   5.400528e+00
   5_adp:  0.1109 0.1605   5.133319e+00   5.387409e+00
   5_occ:  0.1108 0.1603   5.132732e+00   5.386994e+00
   5_bss:  0.1108 0.1603   5.132727e+00   5.386995e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.340   2.638  -1.146   0.410   2.082   0.000   0.000   0.000
   1_xyz:  0.340   2.638  -1.146   0.410   2.082   0.000   0.000   0.000
   1_adp:  0.340   2.638  -1.146   0.410   2.082   0.000   0.000   0.000
   1_occ:  0.340   2.638  -1.146   0.410   2.082   0.000   0.000   0.000
   2_bss:  0.332  34.228  -1.090   0.030   0.950   0.000   0.000   0.000
   2_xyz:  0.332  34.228  -1.090   0.030   0.950   0.000   0.000   0.000
   2_adp:  0.332  34.228  -1.090   0.030   0.950   0.000   0.000   0.000
   2_occ:  0.332  34.228  -1.090   0.030   0.950   0.000   0.000   0.000
   3_bss:  0.332  34.228  -2.055  -1.090  -0.493  -0.000  -0.000  -0.000
   3_xyz:  0.332  34.228  -2.055  -1.090  -0.493  -0.000  -0.000  -0.000
   3_adp:  0.332  34.228  -2.055  -1.090  -0.493  -0.000  -0.000  -0.000
   3_occ:  0.332  34.228  -2.055  -1.090  -0.493  -0.000  -0.000  -0.000
   4_bss:  0.320  34.228  -2.740  -2.161  -1.489  -0.000  -0.000  -0.000
   4_xyz:  0.320  34.228  -2.740  -2.161  -1.489  -0.000  -0.000  -0.000
   4_adp:  0.320  34.228  -2.740  -2.161  -1.489  -0.000  -0.000  -0.000
   4_occ:  0.320  34.228  -2.740  -2.161  -1.489  -0.000  -0.000  -0.000
   5_bss:  0.318  34.228  -2.840  -2.350  -1.715  -0.000  -0.000  -0.000
   5_xyz:  0.318  34.228  -2.840  -2.350  -1.715  -0.000  -0.000  -0.000
   5_adp:  0.318  34.228  -2.840  -2.350  -1.715  -0.000  -0.000  -0.000
   5_occ:  0.318  34.228  -2.840  -2.350  -1.715  -0.000  -0.000  -0.000
   5_bss:  0.318  34.231  -2.829  -2.352  -1.719  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.042 0.3802  0.5253    76264.524
   1_bss:  59.585 0.3971  0.5548    71424.095
   1_xyz:  44.215 0.5922  0.8075    46510.043
   1_adp:  44.739 0.5853  0.8040    47027.542
   1_occ:  44.830 0.5842  0.8020    47123.687
   2_bss:  44.510 0.5879  0.8025    46687.326
   2_xyz:  33.337 0.7198  0.9628    27053.127
   2_adp:  29.383 0.7651  0.9948    22307.761
   2_occ:  29.332 0.7656  0.9949    22256.854
   3_bss:  29.181 0.7669  0.9531    21925.954
   3_xyz:  21.999 0.8422  1.0113    13116.980
   3_adp:  20.138 0.8612  1.0196    11622.848
   3_occ:  20.076 0.8617  1.0198    11549.403
   4_bss:  19.917 0.8630  0.9857    11342.337
   4_xyz:  16.051 0.8976  1.0020     7717.539
   4_adp:  15.207 0.9051  1.0022     7225.864
   4_occ:  15.192 0.9053  1.0022     7213.729
   5_bss:  15.169 0.9054  0.9959     7200.906
   5_xyz:  14.221 0.9130  0.9989     6447.512
   5_adp:  13.901 0.9158  0.9975     6314.934
   5_occ:  13.888 0.9159  0.9975     6310.970
   5_bss:  13.888 0.9159  0.9977     6311.187
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.3872e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.3872e-01
   1_xyz:   1.509  0.011  0.096 15.767  0.007  4.101   1.3561e-01
   1_adp:   1.509  0.011  0.096 15.767  0.007  4.101   1.3561e-01
   1_occ:   1.509  0.011  0.096 15.767  0.007  4.101   1.3561e-01
   2_bss:   1.509  0.011  0.096 15.767  0.007  4.101   1.3561e-01
   2_xyz:   1.316  0.010  0.089 15.040  0.005  4.103   9.3541e-02
   2_adp:   1.316  0.010  0.089 15.040  0.005  4.103   9.3541e-02
   2_occ:   1.316  0.010  0.089 15.040  0.005  4.103   9.3541e-02
   3_bss:   1.316  0.010  0.089 15.040  0.005  4.103   9.3541e-02
   3_xyz:   1.018  0.007  0.067 14.627  0.004  4.103   6.1224e-02
   3_adp:   1.018  0.007  0.067 14.627  0.004  4.103   6.1224e-02
   3_occ:   1.018  0.007  0.067 14.627  0.004  4.103   6.1224e-02
   4_bss:   1.018  0.007  0.067 14.627  0.004  4.103   6.1224e-02
   4_xyz:   1.005  0.006  0.069 14.604  0.004  4.104   5.8734e-02
   4_adp:   1.005  0.006  0.069 14.604  0.004  4.104   5.8734e-02
   4_occ:   1.005  0.006  0.069 14.604  0.004  4.104   5.8734e-02
   5_bss:   1.005  0.006  0.069 14.604  0.004  4.104   5.8734e-02
   5_xyz:   1.128  0.008  0.075 15.157  0.005  4.103   7.2330e-02
   5_adp:   1.128  0.008  0.075 15.157  0.005  4.103   7.2330e-02
   5_occ:   1.128  0.008  0.075 15.157  0.005  4.103   7.2330e-02
   5_bss:   1.128  0.008  0.075 15.157  0.005  4.103   7.2330e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.805   2.4042e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.805   2.4042e-01
   1_xyz:   9.973  0.068  0.465 87.276  0.085  1.489   1.1093e-01
   1_adp:   9.973  0.068  0.465 87.276  0.085  1.489   1.1093e-01
   1_occ:   9.973  0.068  0.465 87.276  0.085  1.489   1.1093e-01
   2_bss:   9.973  0.068  0.465 87.276  0.085  1.489   1.1093e-01
   2_xyz:   9.184  0.060  0.316 79.857  0.046  2.118   8.4332e-02
   2_adp:   9.184  0.060  0.316 79.857  0.046  2.118   8.4332e-02
   2_occ:   9.184  0.060  0.316 79.857  0.046  2.118   8.4332e-02
   3_bss:   9.184  0.060  0.316 79.857  0.046  2.118   8.4332e-02
   3_xyz:   7.145  0.042  0.229 80.208  0.039  2.247   4.3241e-02
   3_adp:   7.145  0.042  0.229 80.208  0.039  2.247   4.3241e-02
   3_occ:   7.145  0.042  0.229 80.208  0.039  2.247   4.3241e-02
   4_bss:   7.145  0.042  0.229 80.208  0.039  2.247   4.3241e-02
   4_xyz:   7.097  0.035  0.223 84.345  0.042  2.325   4.1599e-02
   4_adp:   7.097  0.035  0.223 84.345  0.042  2.325   4.1599e-02
   4_occ:   7.097  0.035  0.223 84.345  0.042  2.325   4.1599e-02
   5_bss:   7.097  0.035  0.223 84.345  0.042  2.325   4.1599e-02
   5_xyz:   7.124  0.054  0.247 84.671  0.044  2.218   6.3448e-02
   5_adp:   7.124  0.054  0.247 84.671  0.044  2.218   6.3448e-02
   5_occ:   7.124  0.054  0.247 84.671  0.044  2.218   6.3448e-02
   5_bss:   7.124  0.054  0.247 84.671  0.044  2.218   6.3448e-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: 102.52   0.00  20.03  94.47   0.00  16.46 102.52   0.00  39.50
   1_occ: 102.52   0.00  20.03  94.47   0.00  16.46 102.52   0.00  39.50
   2_bss: 102.52   0.00  20.03  94.47   0.00  16.46 102.52   0.00  39.50
   2_xyz: 102.52   0.00  20.03  94.47   0.00  16.46 102.52   0.00  39.50
   2_adp:  92.90   0.00  17.94  92.71   0.00  14.08  92.90   3.18  38.99
   2_occ:  92.90   0.00  17.94  92.71   0.00  14.08  92.90   3.18  38.99
   3_bss:  92.90   0.00  17.94  92.71   0.00  14.08  92.90   3.18  38.99
   3_xyz:  92.90   0.00  17.94  92.71   0.00  14.08  92.90   3.18  38.99
   3_adp:  92.52   0.00  17.74  92.52   0.00  13.35  89.05   5.73  41.65
   3_occ:  92.52   0.00  17.74  92.52   0.00  13.35  89.05   5.73  41.65
   4_bss:  92.52   0.00  17.74  92.52   0.00  13.35  89.05   5.73  41.65
   4_xyz:  92.52   0.00  17.74  92.52   0.00  13.35  89.05   5.73  41.65
   4_adp:  93.81   0.98  17.64  93.81   0.98  13.08  92.32   5.13  42.46
   4_occ:  93.81   0.98  17.64  93.81   0.98  13.08  92.32   5.13  42.46
   5_bss:  93.81   0.98  17.64  93.81   0.98  13.08  92.32   5.13  42.46
   5_xyz:  93.81   0.98  17.64  93.81   0.98  13.08  92.32   5.13  42.46
   5_adp:  94.02   0.00  17.48  94.02   0.00  12.97  92.37   6.28  42.03
   5_occ:  94.02   0.00  17.48  94.02   0.00  12.97  92.37   6.28  42.03
   5_bss:  94.02   0.00  17.48  94.02   0.00  12.97  92.37   6.29  42.04
------------------------------------------------------------------------
 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:    3.471    0.016    0.358
   1_adp:    3.471    0.016    0.358
   1_occ:    3.471    0.016    0.358
   2_bss:    3.471    0.016    0.358
   2_xyz:    2.362    0.026    0.586
   2_adp:    2.362    0.026    0.586
   2_occ:    2.362    0.026    0.586
   3_bss:    2.362    0.026    0.586
   3_xyz:    2.343    0.019    0.693
   3_adp:    2.343    0.019    0.693
   3_occ:    2.343    0.019    0.693
   4_bss:    2.343    0.019    0.693
   4_xyz:    2.318    0.077    0.761
   4_adp:    2.318    0.077    0.761
   4_occ:    2.318    0.077    0.761
   5_bss:    2.318    0.077    0.761
   5_xyz:    2.245    0.078    0.787
   5_adp:    2.245    0.078    0.787
   5_occ:    2.245    0.078    0.787
   5_bss:    2.245    0.078    0.787
------------------------------------------------------------------------

CPU time actual refinement: 343.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/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_143/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_143/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.82 
  Macro-tasks:
    bulk solvent and scale       = 44.81  
    individual site refinement   = 137.73 
    weights calculation          = 30.05  
    collect and process          = 6.61   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 219.29 
  Micro-tasks:
    mask                            = 2.24   
    f_calc                          = 110.95 
    alpha_beta                      = 8.52   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 112.51 
    fmodel                         = 7.39   
    r_factors                      = 0.20   
    phase_errors                   = 11.14  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 254.42 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.940 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    631 calls, 110.41 s
gradients_fft:          576 calls, 101.81 s

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

# Date 2008-01-16 Time 04:07:41 PST -0800 (1200485261.74 s)
Start R-work = 0.4852, R-free = 0.4886 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1822 (no bulk solvent and anisotropic scale)

Start R-work = 0.4766, R-free = 0.4777
Final R-work = 0.1108, R-free = 0.1603