# Date 2008-01-16 Time 04:15:31 PST -0800 (1200485731.54 s)
#phil __OFF__

Command line arguments: "../246.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29388
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 246

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.7567, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.95236
Completeness in resolution range: 0.959822
Completeness with d_max=infinity: 0.956868

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8093
                             d_min =   1.9524

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.95236
Completeness in resolution range: 0.959822
Completeness with d_max=infinity: 0.956868

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8097 -  4.1777 [2147/2171]  1929   218  10.2%
  bin  2:  4.1777 -  3.3284 [2051/2071]  1849   202   9.8%
  bin  3:  3.3284 -  2.9113 [2039/2058]  1833   206  10.1%
  bin  4:  2.9113 -  2.6467 [2008/2038]  1809   199   9.9%
  bin  5:  2.6467 -  2.4579 [2009/2028]  1810   199   9.9%
  bin  6:  2.4579 -  2.3136 [1976/2001]  1774   202  10.2%
  bin  7:  2.3136 -  2.1981 [1993/2021]  1793   200  10.0%
  bin  8:  2.1981 -  2.1027 [1972/2008]  1779   193   9.8%
  bin  9:  2.1027 -  2.0220 [1967/2009]  1773   194   9.9%
  bin 10:  2.0220 -  1.9524 [1427/2004]  1281   146  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 29
        2.15 -     2.84: 1079
        2.84 -     3.53: 4550
        3.53 -     4.21: 9532
        4.21 -     4.90: 13825
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.463 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.463 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.523 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.647 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.664 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29010 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_246/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.75675 85.95805 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 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4501   r_free= 0.4447   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.265390                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6597 0.99   1394  154 0.3781 0.3778      6.5687      6.5792|
|  2:  4.6597 -  3.7178 0.99   1336  151 0.3922 0.3604      6.7887      6.7377|
|  3:  3.7178 -  3.2535 0.99   1312  143 0.4324 0.4064      6.6957      6.7215|
|  4:  3.2535 -  2.9586 0.99   1303  149 0.4368 0.4179      6.5205      6.5128|
|  5:  2.9586 -  2.7480 0.99   1304  145 0.4820 0.4569      6.3603       6.362|
|  6:  2.7480 -  2.5869 0.99   1295  141 0.4752 0.5078      6.2671      6.1957|
|  7:  2.5869 -  2.4579 0.99   1286  141 0.4747 0.4774      6.2109       6.178|
|  8:  2.4579 -  2.3514 0.98   1270  144 0.4925 0.4970      6.1815      6.1723|
|  9:  2.3514 -  2.2612 0.98   1271  140 0.4792 0.4814      6.1008      6.1656|
| 10:  2.2612 -  2.1834 1.00   1294  145 0.4845 0.5163      6.0905       6.095|
| 11:  2.1834 -  2.1153 0.97   1255  136 0.4814 0.4885       6.003      6.0407|
| 12:  2.1153 -  2.0550 0.98   1254  144 0.4724 0.4480      5.9567      5.9449|
| 13:  2.0550 -  2.0011 0.99   1299  135 0.4849 0.4669      5.8558      5.8278|
| 14:  2.0011 -  1.9524 0.60    757   91 0.5164 0.4826        5.89      5.7556|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.6597  1394   154  0.68  36.14   0.82     0.74      79116.94|
|  2:  4.6597 -  3.7178  1336   151  0.70  35.12   0.92     0.83     106359.24|
|  3:  3.7178 -  3.2535  1312   143  0.61  42.71   0.94     0.81     110287.14|
|  4:  3.2535 -  2.9586  1303   149  0.53  49.21   0.95     0.73      99642.76|
|  5:  2.9586 -  2.7480  1304   145  0.45  55.68   0.91     0.65      77004.29|
|  6:  2.7480 -  2.5869  1295   141  0.44  56.74   0.90     0.61      66795.53|
|  7:  2.5869 -  2.4579  1286   141  0.41  58.70   0.95     0.59      61442.15|
|  8:  2.4579 -  2.3514  1270   144  0.40  60.15   0.95     0.57      57502.17|
|  9:  2.3514 -  2.2612  1271   140  0.39  60.67   0.94     0.57      53284.01|
| 10:  2.2612 -  2.1834  1294   145  0.41  59.57   0.98     0.59      45465.11|
| 11:  2.1834 -  2.1153  1255   136  0.41  58.96   0.99     0.64      41982.65|
| 12:  2.1153 -  2.0550  1254   144  0.45  55.95   1.02     0.68      35310.72|
| 13:  2.0550 -  2.0011  1299   135  0.45  56.28   0.98     0.70      29758.33|
| 14:  2.0011 -  1.9524   757    91  0.51  51.37   1.00     0.72      23229.12|
|alpha:            min =        0.57 max =            0.83 mean =         0.67|
|beta:             min =    23229.12 max =       110287.14 mean =     64982.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.51|
|phase err.(test): min =        0.00 max =           89.96 mean =        52.31|
|-----------------------------------------------------------------------------|

============================== 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 = 17.680369             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.722   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.933263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.641   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.463 -  1.807:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.807 -  2.151:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.151 -  2.494:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.494 -  2.838:     1035 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.838 -  3.182:     2054 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.182 -  3.525:     2496 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.525 -  3.869:     4729 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.869 -  4.213:     4803 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.213 -  4.556:     6239 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.556 -  4.900:     7586 |
|-----------------------------------------------------------------------------|
|-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 |        0.198 |
| 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  1.463 |       0.758 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    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 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4501   r_free= 0.4447   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.265390                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4397   r_free= 0.4342   ksol= 0.35   Bsol= 20.00   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,2.63,-1.77,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.257602                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.684629             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.489   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.033195              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.581   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4397      final r-factor (work) = 0.3350          |
| start r-factor (free) = 0.4342      final r-factor (free) = 0.3757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.1356 = 14.68 * 0.50 * 6.2565 + 1.00 * 0.1981                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.1755 = 14.68 * 0.50 * 6.1273 + 1.00 * 0.1868                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3350      final r-factor (work) = 0.3046          |
| start r-factor (free) = 0.3757      final r-factor (free) = 0.3939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3375 = 1.03 * 1.00 * 6.1273 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2607 = 1.03 * 1.00 * 6.0194 + 1.00 * 0.0416                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.80   17.98    None  None   None       |
|    all(noH): 2823   0      0.00    92.80   17.98    None  None   None       |
|    Sol.    : 438    0      0.98    86.44   35.29    None  None   None       |
|    Mac.    : 2385   0      0.00    92.80   14.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.280:  821   |   5:    46.399 -  55.679:   85        |
|      1:     9.280 -  18.560:  933   |   6:    55.679 -  64.958:   35        |
|      2:    18.560 -  27.839:  528   |   7:    64.958 -  74.238:   14        |
|      3:    27.839 -  37.119:  268   |   8:    74.238 -  83.518:    6        |
|      4:    37.119 -  46.399:  131   |   9:    83.518 -  92.797:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3046 r_free = 0.3939             target_work(ml) = 6.031         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3041 r_free = 0.3943             target_work(ml) = 6.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3041   r_free= 0.3943   ksol= 0.35   Bsol= 20.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,2.63,-1.77,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.031049                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3036   r_free= 0.3908   ksol= 0.34   Bsol= 46.86   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,0.70,-0.34,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.026489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.816114              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.228   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.161564              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.098   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3036      final r-factor (work) = 0.2515          |
| start r-factor (free) = 0.3908      final r-factor (free) = 0.3233          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7147 = 7.82 * 0.50 * 6.0204 + 1.00 * 0.1868                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3893 = 7.82 * 0.50 * 5.9607 + 1.00 * 0.0944                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.2338          |
| start r-factor (free) = 0.3233      final r-factor (free) = 0.3161          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9428 = 1.16 * 1.00 * 5.9607 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7937 = 1.16 * 1.00 * 5.8344 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.04   18.55    None  None   None       |
|    all(noH): 2823   0      0.00    95.04   18.55    None  None   None       |
|    Sol.    : 438    0      1.75    91.28   39.90    None  None   None       |
|    Mac.    : 2385   0      0.00    95.04   14.62    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 -   9.504:  927   |   5:    47.522 -  57.026:   81        |
|      1:     9.504 -  19.009:  918   |   6:    57.026 -  66.531:   70        |
|      2:    19.009 -  28.513:  434   |   7:    66.531 -  76.035:   26        |
|      3:    28.513 -  38.018:  211   |   8:    76.035 -  85.539:    9        |
|      4:    38.018 -  47.522:  142   |   9:    85.539 -  95.044:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2338 r_free = 0.3161             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2336 r_free = 0.3162             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2336   r_free= 0.3162   ksol= 0.34   Bsol= 46.86   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,0.70,-0.34,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.824469                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.3153   ksol= 0.34   Bsol= 53.16   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.21,-0.03,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.822585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.628392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.879   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247827              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2339      final r-factor (work) = 0.1993          |
| start r-factor (free) = 0.3153      final r-factor (free) = 0.2729          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6790 = 3.63 * 0.50 * 5.8343 + 1.00 * 0.0944                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5006 = 3.63 * 0.50 * 5.7561 + 1.00 * 0.0578                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1993      final r-factor (work) = 0.1921          |
| start r-factor (free) = 0.2729      final r-factor (free) = 0.2566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4433 = 0.25 * 1.00 * 5.7561 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6838 = 0.25 * 1.00 * 5.6600 + 1.00 * 0.2811                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.95   17.81    None  None   None       |
|    all(noH): 2823   0      0.00    97.95   17.81    None  None   None       |
|    Sol.    : 438    0      4.69    89.73   39.66    None  None   None       |
|    Mac.    : 2385   0      0.00    97.95   13.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.795: 1004   |   5:    48.976 -  58.771:   95        |
|      1:     9.795 -  19.590: 1024   |   6:    58.771 -  68.566:   42        |
|      2:    19.590 -  29.386:  310   |   7:    68.566 -  78.362:   18        |
|      3:    29.386 -  39.181:  196   |   8:    78.362 -  88.157:    5        |
|      4:    39.181 -  48.976:  125   |   9:    88.157 -  97.952:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1921 r_free = 0.2566             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1917 r_free = 0.2558             target_work(ml) = 5.629         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1917   r_free= 0.2558   ksol= 0.34   Bsol= 53.16   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.21,-0.03,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.628951                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1915   r_free= 0.2545   ksol= 0.34   Bsol= 53.16   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.30,-0.50,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.627889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.279661              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.348  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.946148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.295   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1915      final r-factor (work) = 0.1540          |
| start r-factor (free) = 0.2545      final r-factor (free) = 0.2040          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3399 = 3.28 * 0.50 * 5.6604 + 1.00 * 0.0578                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1295 = 3.28 * 0.50 * 5.5329 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2040      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.9015 = 3.95 * 1.00 * 5.5329 + 1.00 * 0.0677                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.1855 = 3.95 * 1.00 * 5.3654 + 1.00 * 0.0130                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.16  18.19    None  None   None       |
|    all(noH): 2823   0      0.00    103.16  18.19    None  None   None       |
|    Sol.    : 438    0      6.09    94.50   46.00    None  None   None       |
|    Mac.    : 2385   0      0.00    103.16  13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.316: 1186   |   5:    51.582 -  61.898:  101        |
|      1:    10.316 -  20.633:  974   |   6:    61.898 -  72.214:   71        |
|      2:    20.633 -  30.949:  217   |   7:    72.214 -  82.530:   39        |
|      3:    30.949 -  41.265:  118   |   8:    82.530 -  92.847:   10        |
|      4:    41.265 -  51.582:  102   |   9:    92.847 - 103.163:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1399 r_free = 0.1919             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1399 r_free = 0.1917             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1917   ksol= 0.34   Bsol= 53.16   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.30,-0.50,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.334238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1401   r_free= 0.1915   ksol= 0.31   Bsol= 46.77   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-1.82,-0.63,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.332279                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.820733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.613  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.617485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.630  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9416 = 1.82 * 0.50 * 5.3661 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8712 = 1.82 * 0.50 * 5.2975 + 1.00 * 0.0486                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2843 = 0.62 * 1.00 * 5.2975 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2557 = 0.62 * 1.00 * 5.2548 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.09  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    103.09  17.56    None  None   None       |
|    Sol.    : 438    0      5.24    96.34   44.56    None  None   None       |
|    Mac.    : 2385   0      0.00    103.09  12.59    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 -  10.309: 1237   |   5:    51.547 -  61.856:   94        |
|      1:    10.309 -  20.619:  963   |   6:    61.856 -  72.165:   67        |
|      2:    20.619 -  30.928:  209   |   7:    72.165 -  82.474:   30        |
|      3:    30.928 -  41.237:  115   |   8:    82.474 -  92.784:    9        |
|      4:    41.237 -  51.547:   93   |   9:    92.784 - 103.093:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1754             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1752             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1752   ksol= 0.31   Bsol= 46.77   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-1.82,-0.63,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236617                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6597 0.99   1394  154 0.1029 0.1338      5.4112      5.6042|
|  2:  4.6597 -  3.7178 0.99   1336  151 0.0921 0.1271      5.5184      5.7731|
|  3:  3.7178 -  3.2535 0.99   1312  143 0.1204 0.1591      5.5929      5.8948|
|  4:  3.2535 -  2.9586 0.99   1303  149 0.1415 0.1970      5.5776      5.7614|
|  5:  2.9586 -  2.7480 0.99   1304  145 0.1490 0.1946      5.4278      5.6674|
|  6:  2.7480 -  2.5869 0.99   1295  141 0.1329 0.2063      5.2894      5.5121|
|  7:  2.5869 -  2.4579 0.99   1286  141 0.1393 0.1782      5.2403      5.4349|
|  8:  2.4579 -  2.3514 0.98   1270  144 0.1361 0.1902      5.1944      5.4293|
|  9:  2.3514 -  2.2612 0.98   1271  140 0.1342 0.1843      5.1298      5.3496|
| 10:  2.2612 -  2.1834 1.00   1294  145 0.1266 0.1928      5.0553      5.2749|
| 11:  2.1834 -  2.1153 0.97   1255  136 0.1280 0.2009      5.0293      5.3922|
| 12:  2.1153 -  2.0550 0.98   1254  144 0.1265 0.1930      4.9729      5.2658|
| 13:  2.0550 -  2.0011 0.99   1299  135 0.1276 0.2018      4.8675      5.1597|
| 14:  2.0011 -  1.9524 0.60    757   91 0.1150 0.1615      4.7617      4.9263|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.6597  1394   154  0.93  10.06   0.98     0.96       7841.49|
|  2:  4.6597 -  3.7178  1336   151  0.95   8.91   1.04     1.02      10752.21|
|  3:  3.7178 -  3.2535  1312   143  0.92  13.59   1.05     1.04      13503.44|
|  4:  3.2535 -  2.9586  1303   149  0.90  16.08   1.03     1.00      13280.40|
|  5:  2.9586 -  2.7480  1304   145  0.89  17.45   1.02     1.00      10038.44|
|  6:  2.7480 -  2.5869  1295   141  0.88  17.77   0.99     0.96       8268.01|
|  7:  2.5869 -  2.4579  1286   141  0.89  17.64   1.01     0.97       7280.49|
|  8:  2.4579 -  2.3514  1270   144  0.89  17.51   1.01     0.99       6719.89|
|  9:  2.3514 -  2.2612  1271   140  0.90  16.95   1.02     0.98       5981.34|
| 10:  2.2612 -  2.1834  1294   145  0.88  17.86   1.01     0.97       5391.15|
| 11:  2.1834 -  2.1153  1255   136  0.88  18.12   1.01     0.96       5181.66|
| 12:  2.1153 -  2.0550  1254   144  0.89  17.41   1.02     1.01       4800.78|
| 13:  2.0550 -  2.0011  1299   135  0.89  18.00   1.02     1.00       3902.32|
| 14:  2.0011 -  1.9524   757    91  0.91  15.04   1.00     0.97       3007.11|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     3007.11 max =        13503.44 mean =      7740.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.85|
|phase err.(test): min =        0.00 max =           89.81 mean =        15.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1753   ksol= 0.31   Bsol= 43.12   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.90,-0.54,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.236510                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1753   ksol= 0.31   Bsol= 43.12   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.90,-0.54,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.236510                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6597 0.99   1394  154 0.1029 0.1340      5.4122      5.6042|
|  2:  4.6597 -  3.7178 0.99   1336  151 0.0919 0.1270       5.517      5.7705|
|  3:  3.7178 -  3.2535 0.99   1312  143 0.1201 0.1586      5.5914      5.8921|
|  4:  3.2535 -  2.9586 0.99   1303  149 0.1414 0.1971      5.5772      5.7624|
|  5:  2.9586 -  2.7480 0.99   1304  145 0.1490 0.1948      5.4278      5.6677|
|  6:  2.7480 -  2.5869 0.99   1295  141 0.1330 0.2063      5.2894      5.5119|
|  7:  2.5869 -  2.4579 0.99   1286  141 0.1394 0.1781      5.2408      5.4354|
|  8:  2.4579 -  2.3514 0.98   1270  144 0.1363 0.1906      5.1949      5.4306|
|  9:  2.3514 -  2.2612 0.98   1271  140 0.1343 0.1839      5.1303      5.3481|
| 10:  2.2612 -  2.1834 1.00   1294  145 0.1266 0.1928      5.0553      5.2759|
| 11:  2.1834 -  2.1153 0.97   1255  136 0.1279 0.2013      5.0296      5.3934|
| 12:  2.1153 -  2.0550 0.98   1254  144 0.1264 0.1930       4.973      5.2667|
| 13:  2.0550 -  2.0011 0.99   1299  135 0.1276 0.2015      4.8673      5.1581|
| 14:  2.0011 -  1.9524 0.60    757   91 0.1150 0.1612      4.7607       4.925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.6597  1394   154  0.93  10.07   0.98     0.96       7856.49|
|  2:  4.6597 -  3.7178  1336   151  0.95   8.90   1.04     1.02      10734.47|
|  3:  3.7178 -  3.2535  1312   143  0.92  13.56   1.05     1.04      13453.73|
|  4:  3.2535 -  2.9586  1303   149  0.90  16.07   1.03     1.00      13266.14|
|  5:  2.9586 -  2.7480  1304   145  0.89  17.45   1.02     1.00      10033.71|
|  6:  2.7480 -  2.5869  1295   141  0.88  17.78   0.99     0.96       8272.17|
|  7:  2.5869 -  2.4579  1286   141  0.89  17.64   1.01     0.97       7289.34|
|  8:  2.4579 -  2.3514  1270   144  0.89  17.52   1.01     0.99       6727.86|
|  9:  2.3514 -  2.2612  1271   140  0.90  16.96   1.02     0.98       5985.14|
| 10:  2.2612 -  2.1834  1294   145  0.88  17.87   1.01     0.97       5395.48|
| 11:  2.1834 -  2.1153  1255   136  0.88  18.14   1.01     0.96       5190.37|
| 12:  2.1153 -  2.0550  1254   144  0.89  17.42   1.02     1.01       4803.91|
| 13:  2.0550 -  2.0011  1299   135  0.89  17.99   1.02     1.00       3898.11|
| 14:  2.0011 -  1.9524   757    91  0.91  15.01   1.00     0.97       2995.98|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2995.98 max =        13453.73 mean =      7737.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.85|
|phase err.(test): min =        0.00 max =           89.96 mean =        15.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.326)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.10  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    103.10  17.56    None  None   None       |
|    Sol.    : 438    0      5.24    96.34   44.57    None  None   None       |
|    Mac.    : 2385   0      0.00    103.10  12.60    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 -  10.312: 1237   |   5:    51.550 -  61.859:   94        |
|      1:    10.312 -  20.622:  963   |   6:    61.859 -  72.168:   67        |
|      2:    20.622 -  30.931:  209   |   7:    72.168 -  82.477:   30        |
|      3:    30.931 -  41.240:  115   |   8:    82.477 -  92.787:    9        |
|      4:    41.240 -  51.550:   93   |   9:    92.787 - 103.096:    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: 0.531 - 5.794
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 314
   mapped sites are within: 0.722 - 5.794

peak=    7.018 closest distance to " O   HOH Z 385 " =    2.123
peak=    6.550 closest distance to " O   HOH Z 390 " =    1.132
peak=    6.451 closest distance to " O   HOH Z 245 " =    1.321
peak=    6.418 closest distance to " O   HOH Z 130 " =    1.177
peak=    6.288 closest distance to " O   HOH Z 431 " =    1.924
peak=    6.258 closest distance to " O   HOH Z 289 " =    1.402
peak=    6.202 closest distance to " O   HOH Z  65 " =    1.780
peak=    5.949 closest distance to " O   HOH Z 142 " =    1.880
peak=    5.825 closest distance to " O   HOH Z 422 " =    1.010
peak=    5.594 closest distance to " NE2 GLN A  11 " =    1.324
peak=    5.585 closest distance to " O   HOH Z 287 " =    2.047
peak=    5.531 closest distance to " O   HOH Z 117 " =    1.450
peak=    5.508 closest distance to " O   HOH Z 427 " =    1.593
peak=    5.387 closest distance to " O   HOH Z 375 " =    1.357
peak=    5.354 closest distance to " O   HOH Z 363 " =    1.216
peak=    5.253 closest distance to " O   HOH Z 222 " =    1.348
peak=    5.251 closest distance to " O   HOH Z  29 " =    1.386
peak=    5.200 closest distance to " O   PRO A 198 " =    1.316
peak=    5.178 closest distance to " O   HOH Z 417 " =    2.203
peak=    5.091 closest distance to " CB  PRO A  54 " =    1.159
peak=    5.044 closest distance to " CB  ARG A 275 " =    1.135
peak=    5.029 closest distance to " O   HOH Z  49 " =    1.354
peak=    5.014 closest distance to " CG  PRO A  54 " =    1.364
peak=    4.994 closest distance to " O   HOH Z  63 " =    2.214
peak=    4.987 closest distance to " O   HOH Z 236 " =    1.515
peak=    4.986 closest distance to " O   HOH Z 416 " =    1.316
peak=    4.977 closest distance to " O   HOH Z 112 " =    1.666
peak=    4.903 closest distance to " O   HOH Z 414 " =    1.530
peak=    4.901 closest distance to " O   HOH Z  92 " =    1.360
peak=    4.901 closest distance to " O   HOH Z 145 " =    1.580
peak=    4.894 closest distance to " O   HOH Z  78 " =    1.750
peak=    4.892 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.890 closest distance to " CG  PRO A 213 " =    1.341
peak=    4.866 closest distance to " O   HOH Z 124 " =    1.526
peak=    4.861 closest distance to " O   HOH Z   9 " =    1.356
peak=    4.830 closest distance to " O   HOH Z   7 " =    1.680
peak=    4.800 closest distance to " O   HOH Z 427 " =    1.500
peak=    4.796 closest distance to " O   HOH Z 403 " =    1.426
peak=    4.775 closest distance to " O   HOH Z 415 " =    1.094
peak=    4.737 closest distance to " O   HOH Z 424 " =    1.229
peak=    4.660 closest distance to " O   HOH Z 211 " =    1.234
peak=    4.571 closest distance to " O   HOH Z 293 " =    1.471
peak=    4.545 closest distance to " O   HOH Z 214 " =    1.344
peak=    4.531 closest distance to " O   HOH Z  61 " =    1.552
peak=    4.526 closest distance to " O   HOH Z 139 " =    1.368
peak=    4.517 closest distance to " O   HOH Z  63 " =    1.843
peak=    4.419 closest distance to " O   HOH Z 423 " =    1.942
peak=    4.352 closest distance to " NH2 ARG A  56 " =    2.057
peak=    4.342 closest distance to " O   ASP A 286 " =    2.393
peak=    4.314 closest distance to " OG ASER A 258 " =    2.984
peak=    4.310 closest distance to " CG  PRO A  90 " =    1.199
peak=    4.295 closest distance to " CG  ARG A  66 " =    2.387
peak=    4.248 closest distance to " OD1 ASP A 286 " =    1.143
peak=    4.244 closest distance to " O   HOH Z 369 " =    1.890
peak=    4.234 closest distance to " NZ  LYS A 117 " =    3.113
peak=    4.216 closest distance to " O   HOH Z 392 " =    1.354
peak=    4.212 closest distance to " O   HOH Z 213 " =    1.689
peak=    4.203 closest distance to " O   HOH Z 298 " =    1.946
peak=    4.183 closest distance to " O   HOH Z  24 " =    1.782
peak=    4.182 closest distance to " O   HOH Z 425 " =    1.462
peak=    4.172 closest distance to " O   SER A  87 " =    2.442
peak=    4.165 closest distance to " NE1 TRP A 274 " =    1.092
peak=    4.163 closest distance to " O   HOH Z 158 " =    1.367
peak=    4.156 closest distance to " CB  ASN A 148 " =    1.335
peak=    4.148 closest distance to " NZ  LYS A 117 " =    1.114
peak=    4.133 closest distance to " CA  TYR A  30 " =    1.002
peak=    4.123 closest distance to " O   HOH Z 378 " =    1.010
peak=    4.103 closest distance to " O   HOH Z  59 " =    1.409
peak=    4.101 closest distance to " CG2 ILE A 120 " =    1.094
peak=    4.095 closest distance to " O   HOH Z 223 " =    1.054
peak=    4.091 closest distance to " O   HOH Z 193 " =    1.752
peak=    4.084 closest distance to " O   HOH Z 156 " =    3.265
peak=    4.067 closest distance to " CB  SER A 216 " =    1.023
peak=    4.066 closest distance to " CB  SER A   3 " =    1.211
peak=    4.048 closest distance to " O   HOH Z  11 " =    1.513
peak=    4.045 closest distance to " O   HOH Z 402 " =    1.449
peak=    4.025 closest distance to " NH1AARG A 145 " =    1.220
peak=    4.022 closest distance to " O   HOH Z 380 " =    1.986
peak=    4.018 closest distance to " O   HOH Z  69 " =    2.317
peak=    4.014 closest distance to " O  BHOH Z  74 " =    1.126
peak=    4.012 closest distance to " CB  GLN A 223 " =    1.482
peak=    4.006 closest distance to " CB  LEU A 300 " =    0.969
peak=    3.979 closest distance to " O   HOH Z 212 " =    1.801
peak=    3.978 closest distance to " O   HOH Z 371 " =    2.313
peak=    3.946 closest distance to " O   HOH Z 368 " =    3.627
peak=    3.938 closest distance to " O   HOH Z 272 " =    1.818
peak=    3.917 closest distance to " CG  PRO A 198 " =    1.244
peak=    3.917 closest distance to " O   HOH Z 365 " =    2.429
peak=    3.915 closest distance to " O   HOH Z 166 " =    1.641
peak=    3.902 closest distance to " CB  SER A 276 " =    1.241
peak=    3.899 closest distance to " CB  GLU A 128 " =    1.019
peak=    3.883 closest distance to " O   HOH Z 434 " =    1.331
peak=    3.868 closest distance to " CD  LYS A 166 " =    1.561
peak=    3.858 closest distance to " O   HOH Z 358 " =    1.254
peak=    3.845 closest distance to " O   HOH Z  65 " =    1.351
peak=    3.823 closest distance to " OG  SER A  62 " =    2.961
peak=    3.822 closest distance to " O   HOH Z 412 " =    1.941
peak=    3.817 closest distance to " O   HOH Z 151 " =    1.702
peak=    3.815 closest distance to " O   HOH Z 352 " =    1.591
peak=    3.811 closest distance to " OG BSER A 212 " =    2.793
peak=    3.811 closest distance to " N   GLN A 278 " =    0.997
peak=    3.809 closest distance to " O   HOH Z 234 " =    3.593
peak=    3.794 closest distance to " CB  THR A  31 " =    1.606
peak=    3.790 closest distance to " O   HOH Z 227 " =    1.844
peak=    3.785 closest distance to " O   HOH Z 419 " =    2.120
peak=    3.771 closest distance to " N   GLU A   2 " =    1.334
peak=    3.766 closest distance to " O   HOH Z  77 " =    1.084
peak=    3.765 closest distance to " NZ  LYS A 119 " =    2.442
peak=    3.753 closest distance to " O   HOH Z 426 " =    1.083
peak=    3.751 closest distance to " CB  GLU A 277 " =    1.074
peak=    3.730 closest distance to " O   HOH Z   7 " =    3.298
peak=    3.725 closest distance to " CB  TRP A 179 " =    1.296
peak=    3.720 closest distance to " O   HOH Z 106 " =    2.499
peak=    3.716 closest distance to " CB  GLN A 183 " =    1.014
peak=    3.699 closest distance to " N   ALA A   1 " =    2.641
peak=    3.697 closest distance to " O   HOH Z 302 " =    1.490
peak=    3.696 closest distance to " O   HOH Z 130 " =    2.233
peak=    3.696 closest distance to " O   HOH Z 425 " =    1.980
peak=    3.694 closest distance to " OE1 GLU A   2 " =    2.193
peak=    3.693 closest distance to " CB  VAL A 265 " =    1.283
peak=    3.693 closest distance to " O   HOH Z 327 " =    1.721
peak=    3.686 closest distance to " OG BSER A 164 " =    2.341
peak=    3.684 closest distance to " O   HOH Z  32 " =    2.193
peak=    3.684 closest distance to " CA  PHE A 283 " =    1.313
peak=    3.679 closest distance to " CG1BVAL A 121 " =    2.160
peak=    3.673 closest distance to " CB  GLU A 152 " =    1.271
peak=    3.660 closest distance to " O   HOH Z  39 " =    1.159
peak=    3.654 closest distance to " OD1 ASN A  45 " =    1.210
peak=    3.646 closest distance to " O   HOH Z 244 " =    1.506
peak=    3.614 closest distance to " CB  ASN A 215 " =    1.135
peak=    3.602 closest distance to " NZ BLYS A 290 " =    0.886
peak=    3.600 closest distance to " O   HOH Z 365 " =    1.527
peak=    3.596 closest distance to " O   HOH Z  93 " =    1.916
peak=    3.590 closest distance to " O   HOH Z 394 " =    1.862
peak=    3.572 closest distance to " CB  PHE A 130 " =    1.006
peak=    3.572 closest distance to " CE  LYS A 119 " =    1.249
peak=    3.562 closest distance to " OD2 ASP A 286 " =    2.312
peak=    3.562 closest distance to " O   HOH Z 128 " =    2.028
peak=    3.560 closest distance to " O   HOH Z 158 " =    3.007
peak=    3.543 closest distance to " O   HOH Z 258 " =    2.037
peak=    3.541 closest distance to " N   ALA A   1 " =    1.371
peak=    3.537 closest distance to " O   HOH Z 431 " =    1.235
peak=    3.534 closest distance to " NE2 GLN A  58 " =    4.012
peak=    3.534 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.532 closest distance to " CA  ASN A 127 " =    1.027
peak=    3.530 closest distance to " O   HOH Z 384 " =    1.268
peak=    3.530 closest distance to " CB  SER A  63 " =    1.339
peak=    3.529 closest distance to " O   HOH Z 290 " =    1.091
peak=    3.529 closest distance to " O   ASN A 285 " =    0.885
peak=    3.525 closest distance to " O   HOH Z 422 " =    2.332
peak=    3.522 closest distance to " CA  MET A  40 " =    1.196
peak=    3.521 closest distance to " CB  GLU A 277 " =    3.471
peak=    3.518 closest distance to " CA  LEU A 282 " =    1.076
peak=    3.512 closest distance to " CA  ILE A 234 " =    1.055
peak=    3.507 closest distance to " O   HOH Z 126 " =    1.404
peak=    3.503 closest distance to " O   HOH Z  68 " =    1.955
peak=    3.499 closest distance to " CB  VAL A 202 " =    1.687
peak=    3.489 closest distance to " O   HOH Z 214 " =    1.823
peak=    3.486 closest distance to " CB  ASN A 148 " =    1.885
peak=    3.485 closest distance to " O   HOH Z 400 " =    0.722
peak=    3.484 closest distance to " N   SER A 210 " =    1.121
peak=    3.483 closest distance to " OG BSER A  99 " =    2.277
peak=    3.482 closest distance to " O   HOH Z 386 " =    1.447
peak=    3.478 closest distance to " O   GLY A 302 " =    2.473
peak=    3.476 closest distance to " CB  ALA A 114 " =    1.115
peak=    3.476 closest distance to " CB  TRP A 266 " =    1.105
peak=    3.473 closest distance to " CG2 VAL A 202 " =    1.514
peak=    3.466 closest distance to " CE AMET A  47 " =    1.329
peak=    3.460 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.455 closest distance to " OG  SER A  22 " =    2.689
peak=    3.455 closest distance to " O   HOH Z 196 " =    1.550
peak=    3.453 closest distance to " CA  MET A 105 " =    0.806
peak=    3.452 closest distance to " O   HOH Z  47 " =    1.542
peak=    3.452 closest distance to " CG  PRO A 243 " =    1.155
peak=    3.450 closest distance to " O   HOH Z 259 " =    2.221
peak=    3.449 closest distance to " O   HOH Z 393 " =    1.352
peak=    3.447 closest distance to " O   HOH Z 248 " =    2.070
peak=    3.446 closest distance to " NH1 ARG A  14 " =    0.967
peak=    3.442 closest distance to " CG  TRP A 179 " =    2.184
peak=    3.441 closest distance to " CB  ARG A 190 " =    1.891
peak=    3.441 closest distance to " O   HOH Z 249 " =    1.305
peak=    3.440 closest distance to " C   ALA A 299 " =    0.986
peak=    3.440 closest distance to " O   HOH Z 418 " =    0.753
peak=    3.438 closest distance to " O   HOH Z 193 " =    1.643
peak=    3.437 closest distance to " O   HOH Z 222 " =    2.464
peak=    3.435 closest distance to " CG2 THR A 221 " =    1.298
peak=    3.433 closest distance to " CE3 TRP A 274 " =    1.402
peak=    3.432 closest distance to " O   HOH Z  88 " =    3.219
peak=    3.431 closest distance to " O   HOH Z 119 " =    4.232
peak=    3.428 closest distance to " O   HOH Z 272 " =    2.128
peak=    3.427 closest distance to " CG  LEU A 167 " =    1.258
peak=    3.423 closest distance to " O   HOH Z 288 " =    1.837
peak=    3.413 closest distance to " O   HOH Z 423 " =    1.590
peak=    3.413 closest distance to " O   HOH Z 153 " =    3.445
peak=    3.407 closest distance to " CB  PHE A 225 " =    1.240
peak=    3.407 closest distance to " O   HOH Z 112 " =    2.337
peak=    3.405 closest distance to " O   HOH Z  17 " =    1.744
peak=    3.397 closest distance to " O   HOH Z 207 " =    2.271
peak=    3.394 closest distance to " CG1 ILE A 120 " =    1.445
peak=    3.388 closest distance to " O   HOH Z  44 " =    2.912
peak=    3.387 closest distance to " O   HOH Z   1 " =    1.680
peak=    3.385 closest distance to " O   HOH Z  44 " =    1.752
peak=    3.382 closest distance to " O   HOH Z 413 " =    1.769
peak=    3.379 closest distance to " CG  LYS A 166 " =    1.398
peak=    3.367 closest distance to " O   HOH Z  80 " =    1.981
peak=    3.362 closest distance to " CB  ARG A 219 " =    0.800
peak=    3.348 closest distance to " CB  ARG A 138 " =    0.786
peak=    3.346 closest distance to " CB  THR A 235 " =    1.174
peak=    3.342 closest distance to " O   HOH Z 344 " =    3.177
peak=    3.338 closest distance to " O   HOH Z 172 " =    1.936
peak=    3.337 closest distance to " CB  ASP A 200 " =    0.844
peak=    3.334 closest distance to " N   ARG A 156 " =    1.298
peak=    3.325 closest distance to " O   HOH Z  26 " =    1.432
peak=    3.325 closest distance to " O   HOH Z 189 " =    2.735
peak=    3.325 closest distance to " O   HOH Z 389 " =    1.540
peak=    3.319 closest distance to " CB  THR A 157 " =    1.086
peak=    3.315 closest distance to " CH2 TRP A 150 " =    1.103
peak=    3.314 closest distance to " O   HOH Z 329 " =    3.630
peak=    3.314 closest distance to " CB  TYR A 116 " =    1.159
peak=    3.312 closest distance to " CG  GLN A  11 " =    2.051
peak=    3.311 closest distance to " O   HOH Z 411 " =    3.642
peak=    3.307 closest distance to " CA  ASN A 215 " =    1.007
peak=    3.306 closest distance to " CG2BVAL A  41 " =    0.722
peak=    3.305 closest distance to " CB  ARG A 156 " =    1.061
peak=    3.301 closest distance to " O   ASN A  74 " =    1.589
peak=    3.301 closest distance to " CB  ALA A 292 " =    0.954
peak=    3.299 closest distance to " CB  HIS A 108 " =    0.824
peak=    3.298 closest distance to " O   HOH Z 261 " =    2.000
peak=    3.297 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.285 closest distance to " O   HOH Z 147 " =    1.397
peak=    3.283 closest distance to " CG2 VAL A 232 " =    1.066
peak=    3.280 closest distance to " NE2 GLN A 278 " =    3.594
peak=    3.280 closest distance to " CE BMET A  47 " =    1.029
peak=    3.279 closest distance to " CB  ALA A 114 " =    1.356
peak=    3.279 closest distance to " OE2 GLU A  53 " =    2.046
peak=    3.278 closest distance to " OG1 THR A 246 " =    1.307
peak=    3.277 closest distance to " O   HOH Z 405 " =    1.661
peak=    3.276 closest distance to " O   HOH Z 167 " =    1.926
peak=    3.275 closest distance to " O   HOH Z 158 " =    2.431
peak=    3.274 closest distance to " O   HOH Z 222 " =    1.949
peak=    3.273 closest distance to " O   HOH Z 368 " =    1.742
peak=    3.268 closest distance to " CB  LEU A 228 " =    1.121
peak=    3.265 closest distance to " O   HOH Z 423 " =    1.804
peak=    3.264 closest distance to " CA  ALA A  21 " =    1.089
peak=    3.261 closest distance to " CA  LYS A 290 " =    1.441
peak=    3.260 closest distance to " O   HOH Z 152 " =    2.058
peak=    3.260 closest distance to " NE2 GLN A  73 " =    1.390
peak=    3.252 closest distance to " O   HOH Z 359 " =    1.363
peak=    3.252 closest distance to " O   HOH Z 424 " =    2.878
peak=    3.248 closest distance to " CZ  PHE A  38 " =    1.194
peak=    3.242 closest distance to " NE AARG A 275 " =    1.336
peak=    3.241 closest distance to " O   HOH Z 311 " =    1.504
peak=    3.240 closest distance to " O   HOH Z  58 " =    1.504
peak=    3.236 closest distance to " N   TYR A  15 " =    1.194
peak=    3.232 closest distance to " O   HOH Z  97 " =    1.834
peak=    3.230 closest distance to " O   HOH Z 410 " =    1.547
peak=    3.225 closest distance to " O   HOH Z 357 " =    1.808
peak=    3.224 closest distance to " O   HOH Z  50 " =    1.794
peak=    3.223 closest distance to " CA  GLY A 241 " =    3.481
peak=    3.223 closest distance to " O   HOH Z 334 " =    1.252
peak=    3.223 closest distance to " O   HOH Z 123 " =    1.312
peak=    3.219 closest distance to " CB  SER A 273 " =    0.924
peak=    3.218 closest distance to " CD  LYS A 119 " =    1.996
peak=    3.218 closest distance to " OG1 THR A 221 " =    1.357
peak=    3.217 closest distance to " CG2 ILE A 239 " =    1.172
peak=    3.212 closest distance to " CD  GLN A  58 " =    5.794
peak=    3.210 closest distance to " CB  MET A 105 " =    1.101
peak=    3.210 closest distance to " O   HOH Z 437 " =    2.077
peak=    3.209 closest distance to " CD  PRO A 243 " =    1.578
peak=    3.207 closest distance to " CG  LYS A  76 " =    1.485
peak=    3.207 closest distance to " CA  ASN A 284 " =    1.012
peak=    3.205 closest distance to " CB  LYS A 290 " =    1.014
peak=    3.199 closest distance to " O   HOH Z   9 " =    1.947
peak=    3.196 closest distance to " CB  ASP A 140 " =    0.876
peak=    3.194 closest distance to " CD  ARG A 138 " =    0.750
peak=    3.193 closest distance to " O   HOH Z 280 " =    2.428
peak=    3.191 closest distance to " O   HOH Z  17 " =    1.967
peak=    3.187 closest distance to " CG  GLN A  58 " =    1.027
peak=    3.183 closest distance to " O   HOH Z  46 " =    1.062
peak=    3.178 closest distance to " O   HOH Z 108 " =    2.049
peak=    3.176 closest distance to " O   HOH Z 389 " =    2.865
peak=    3.169 closest distance to " CA  ARG A 102 " =    1.132
peak=    3.161 closest distance to " O   ALA A 165 " =    1.231
peak=    3.161 closest distance to " O   HOH Z 194 " =    1.812
peak=    3.157 closest distance to " CE  MET A  40 " =    1.109
peak=    3.148 closest distance to " CG2 ILE A  20 " =    1.138
peak=    3.148 closest distance to " CA  GLY A 241 " =    3.916
peak=    3.146 closest distance to " O   HOH Z 250 " =    1.326
peak=    3.141 closest distance to " ND1 HIS A  81 " =    1.170
peak=    3.140 closest distance to " O   HOH Z 215 " =    1.018
peak=    3.131 closest distance to " N   ASN A 127 " =    1.340
peak=    3.129 closest distance to " CA  ARG A  36 " =    1.151
peak=    3.121 closest distance to " NH2BARG A 145 " =    1.870
peak=    3.120 closest distance to " O   HOH Z 173 " =    2.157
peak=    3.118 closest distance to " CA  PRO A  54 " =    0.734
peak=    3.107 closest distance to " CB  GLN A 278 " =    0.842
peak=    3.096 closest distance to " O   HOH Z  40 " =    1.587
peak=    3.095 closest distance to " O   HOH Z 326 " =    1.826
peak=    3.091 closest distance to " O   HOH Z 122 " =    1.746
peak=    3.090 closest distance to " O   HOH Z 189 " =    1.998
peak=    3.090 closest distance to " O   HOH Z 185 " =    1.640
peak=    3.089 closest distance to " N   ASN A 148 " =    1.099
peak=    3.085 closest distance to " CD2 LEU A 167 " =    1.233
peak=    3.078 closest distance to " O   HOH Z 128 " =    1.347
peak=    3.076 closest distance to " CB  SER A  62 " =    1.168
peak=    3.071 closest distance to " O   HOH Z 423 " =    1.352
peak=    3.065 closest distance to " O   HOH Z   3 " =    2.145
peak=    3.062 closest distance to " CB  ASN A  74 " =    1.073
peak=    3.054 closest distance to " CD1AILE A 234 " =    1.096
peak=    3.040 closest distance to " O   HOH Z  33 " =    1.397
peak=    3.036 closest distance to " CB  ALA A 291 " =    1.370
peak=    3.030 closest distance to " O   HOH Z 248 " =    1.813

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.797 - 4.932
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.797 - 4.932

peak=   -4.637 closest distance to " O   PRO A 198 " =    1.150
peak=   -4.262 closest distance to " O   HOH Z 385 " =    1.006
peak=   -4.224 closest distance to " O   HOH Z  24 " =    1.037
peak=   -4.150 closest distance to " O   HOH Z 425 " =    0.860
peak=   -4.120 closest distance to " O   PHE A 218 " =    1.384
peak=   -4.114 closest distance to " O   MET A  40 " =    2.849
peak=   -4.099 closest distance to " O   SER A 135 " =    1.493
peak=   -4.093 closest distance to " O   HOH Z  60 " =    1.893
peak=   -4.055 closest distance to " CD1 TRP A 179 " =    1.229
peak=   -4.013 closest distance to " N   GLN A  58 " =    1.201
peak=   -4.013 closest distance to " O   SER A  22 " =    2.603
peak=   -4.005 closest distance to " O   HOH Z 185 " =    1.880
peak=   -3.998 closest distance to " O   ILE A  49 " =    1.605
peak=   -3.985 closest distance to " OG  SER A  97 " =    2.127
peak=   -3.965 closest distance to " OE1 GLU A 277 " =    1.968
peak=   -3.936 closest distance to " O   HOH Z 416 " =    0.827
peak=   -3.933 closest distance to " CB  ALA A 248 " =    2.085
peak=   -3.911 closest distance to " O   HOH Z 415 " =    1.055
peak=   -3.881 closest distance to " N   THR A 157 " =    1.489
peak=   -3.869 closest distance to " O   HOH Z  22 " =    2.625
peak=   -3.836 closest distance to " CD  ARG A  14 " =    3.245
peak=   -3.833 closest distance to " O   HOH Z 313 " =    1.149
peak=   -3.830 closest distance to " OE1 GLN A 183 " =    1.387
peak=   -3.830 closest distance to " N   ALA A   1 " =    1.336
peak=   -3.817 closest distance to " O   HOH Z  88 " =    1.763
peak=   -3.816 closest distance to " CG  MET A 105 " =    0.919
peak=   -3.813 closest distance to " CD  ARG A 156 " =    1.952
peak=   -3.804 closest distance to " CA  GLY A  98 " =    1.758
peak=   -3.799 closest distance to " CZ2 TRP A 274 " =    0.950
peak=   -3.794 closest distance to " O   HOH Z  77 " =    1.844
peak=   -3.773 closest distance to " O   HOH Z 196 " =    1.830
peak=   -3.761 closest distance to " O   HOH Z  65 " =    0.935
peak=   -3.754 closest distance to " O   HOH Z 197 " =    3.328
peak=   -3.750 closest distance to " O   HOH Z  39 " =    1.240
peak=   -3.749 closest distance to " O   HOH Z 298 " =    0.957
peak=   -3.739 closest distance to " NE2 GLN A  55 " =    0.837
peak=   -3.738 closest distance to " N   ARG A 275 " =    0.797
peak=   -3.724 closest distance to " OD2 ASP A 171 " =    1.899
peak=   -3.707 closest distance to " CB  CYS A 201 " =    2.036
peak=   -3.703 closest distance to " OG  SER A  63 " =    1.501
peak=   -3.702 closest distance to " O   HOH Z  56 " =    1.692
peak=   -3.647 closest distance to " O   HOH Z 426 " =    1.553
peak=   -3.640 closest distance to " O   HOH Z 372 " =    2.619
peak=   -3.619 closest distance to " O   HOH Z 407 " =    2.960
peak=   -3.618 closest distance to " ND2 ASN A 209 " =    1.676
peak=   -3.616 closest distance to " O   ASP A 191 " =    1.913
peak=   -3.586 closest distance to " CZ  PHE A  59 " =    1.393
peak=   -3.586 closest distance to " OG BSER A 134 " =    1.386
peak=   -3.585 closest distance to " O   HOH Z 147 " =    0.981
peak=   -3.581 closest distance to " OG  SER A  63 " =    1.212
peak=   -3.578 closest distance to " CB  ALA A 291 " =    2.188
peak=   -3.578 closest distance to " NH2 ARG A  79 " =    2.070
peak=   -3.567 closest distance to " O   TYR A 186 " =    1.582
peak=   -3.566 closest distance to " O   VAL A 125 " =    2.050
peak=   -3.564 closest distance to " CB  PRO A 243 " =    2.478
peak=   -3.562 closest distance to " CG  LEU A  83 " =    2.139
peak=   -3.561 closest distance to " O   ALA A  10 " =    1.587
peak=   -3.552 closest distance to " O   HOH Z 198 " =    1.724
peak=   -3.550 closest distance to " OD2 ASP A 191 " =    1.434
peak=   -3.531 closest distance to " O   HOH Z 351 " =    1.555
peak=   -3.523 closest distance to " CG  PRO A 243 " =    1.496
peak=   -3.519 closest distance to " CD2 TYR A 293 " =    1.718
peak=   -3.517 closest distance to " CA  GLY A 133 " =    1.927
peak=   -3.512 closest distance to " CB  TYR A  15 " =    2.159
peak=   -3.508 closest distance to " O   HOH Z 244 " =    1.382
peak=   -3.493 closest distance to " CG2 ILE A  20 " =    2.683
peak=   -3.490 closest distance to " O   HOH Z 359 " =    1.654
peak=   -3.490 closest distance to " CE3 TRP A  70 " =    2.085
peak=   -3.472 closest distance to " O   GLU A 152 " =    1.399
peak=   -3.471 closest distance to " O   HOH Z 122 " =    2.478
peak=   -3.459 closest distance to " C   ILE A 239 " =    1.889
peak=   -3.458 closest distance to " CE  LYS A  76 " =    3.002
peak=   -3.456 closest distance to " O   PRO A 243 " =    2.516
peak=   -3.455 closest distance to " O   HOH Z  76 " =    1.235
peak=   -3.455 closest distance to " O   HOH Z 129 " =    4.092
peak=   -3.451 closest distance to " OG  SER A 245 " =    1.848
peak=   -3.448 closest distance to " O   HOH Z 290 " =    1.029
peak=   -3.447 closest distance to " O   HOH Z 102 " =    1.668
peak=   -3.447 closest distance to " CD2 LEU A 237 " =    2.567
peak=   -3.446 closest distance to " O   HOH Z 428 " =    1.958
peak=   -3.441 closest distance to " O   HOH Z 368 " =    2.646
peak=   -3.438 closest distance to " O   HOH Z 288 " =    1.383
peak=   -3.431 closest distance to " OG  SER A  32 " =    0.928
peak=   -3.419 closest distance to " C   GLN A 205 " =    1.894
peak=   -3.417 closest distance to " O   HOH Z 414 " =    1.604
peak=   -3.410 closest distance to " CG  GLN A  11 " =    2.013
peak=   -3.408 closest distance to " ND2 ASN A 285 " =    1.916
peak=   -3.405 closest distance to " ND2 ASN A 252 " =    1.883
peak=   -3.405 closest distance to " O   VAL A  67 " =    2.830
peak=   -3.404 closest distance to " O   HOH Z  90 " =    2.439
peak=   -3.401 closest distance to " OG  SER A  87 " =    1.327
peak=   -3.389 closest distance to " O   ALA A   1 " =    1.376
peak=   -3.386 closest distance to " OD2 ASP A  27 " =    1.636
peak=   -3.384 closest distance to " O   HOH Z 217 " =    1.736
peak=   -3.383 closest distance to " N   VAL A 232 " =    2.225
peak=   -3.383 closest distance to " O   SER A  95 " =    1.258
peak=   -3.374 closest distance to " O   HOH Z 250 " =    1.195
peak=   -3.370 closest distance to " CA  ASN A 127 " =    1.248
peak=   -3.365 closest distance to " NH2 ARG A 219 " =    1.742
peak=   -3.364 closest distance to " CA  GLY A 203 " =    2.345
peak=   -3.359 closest distance to " O   HOH Z 412 " =    4.932
peak=   -3.358 closest distance to " O   HOH Z 266 " =    4.559
peak=   -3.355 closest distance to " N   VAL A  72 " =    1.819
peak=   -3.354 closest distance to " O   HOH Z 131 " =    4.244
peak=   -3.352 closest distance to " O   ASP A 162 " =    2.126
peak=   -3.348 closest distance to " ND2 ASN A 187 " =    1.441
peak=   -3.338 closest distance to " O   HOH Z  49 " =    1.243
peak=   -3.338 closest distance to " CB  ALA A  43 " =    2.124
peak=   -3.336 closest distance to " O   HOH Z 265 " =    2.000
peak=   -3.335 closest distance to " CG  ARG A 219 " =    2.252
peak=   -3.332 closest distance to " OG BSER A  99 " =    1.276
peak=   -3.327 closest distance to " N   ALA A  43 " =    2.451
peak=   -3.326 closest distance to " CG  PHE A 225 " =    1.116
peak=   -3.325 closest distance to " CB  ASN A  39 " =    2.232
peak=   -3.325 closest distance to " O   HOH Z 348 " =    2.013
peak=   -3.318 closest distance to " O   HOH Z 218 " =    3.718
peak=   -3.317 closest distance to " CD1 LEU A   5 " =    2.299
peak=   -3.312 closest distance to " O   HOH Z  28 " =    1.841
peak=   -3.305 closest distance to " O   HOH Z 393 " =    2.722
peak=   -3.304 closest distance to " O   HOH Z 231 " =    2.038
peak=   -3.297 closest distance to " O   HOH Z  88 " =    2.521
peak=   -3.297 closest distance to " CZ3 TRP A 123 " =    1.666
peak=   -3.296 closest distance to " O   ALA A  34 " =    2.572
peak=   -3.296 closest distance to " OE1 GLN A 223 " =    2.093
peak=   -3.286 closest distance to " CD  GLN A 278 " =    1.302
peak=   -3.285 closest distance to " O   HOH Z  61 " =    1.118
peak=   -3.284 closest distance to " O   HOH Z 286 " =    1.723
peak=   -3.282 closest distance to " N   ARG A 159 " =    1.942
peak=   -3.281 closest distance to " O   HOH Z 166 " =    1.322
peak=   -3.275 closest distance to " O   THR A 235 " =    1.463
peak=   -3.274 closest distance to " CZ  TYR A 169 " =    1.962
peak=   -3.273 closest distance to " CB  GLN A  55 " =    1.340
peak=   -3.268 closest distance to " O   GLY A 111 " =    2.610
peak=   -3.266 closest distance to " OG  SER A 245 " =    1.380
peak=   -3.262 closest distance to " OE2 GLU A 152 " =    1.001
peak=   -3.260 closest distance to " O   HOH Z 236 " =    2.218
peak=   -3.250 closest distance to " O   HOH Z 438 " =    0.815
peak=   -3.249 closest distance to " O   HOH Z 404 " =    1.436
peak=   -3.247 closest distance to " O   HOH Z  69 " =    1.924
peak=   -3.243 closest distance to " O   HOH Z 388 " =    2.154
peak=   -3.243 closest distance to " NE2 GLN A 278 " =    1.708
peak=   -3.243 closest distance to " O   PRO A 163 " =    1.098
peak=   -3.242 closest distance to " CE2 TYR A  30 " =    2.679
peak=   -3.241 closest distance to " O   HOH Z  93 " =    1.882
peak=   -3.241 closest distance to " ND2 ASN A  39 " =    1.330
peak=   -3.240 closest distance to " O   HOH Z 211 " =    1.410
peak=   -3.233 closest distance to " CG1 VAL A 174 " =    2.897
peak=   -3.230 closest distance to " CA  ILE A 263 " =    0.945
peak=   -3.228 closest distance to " NE  ARG A  36 " =    1.920
peak=   -3.225 closest distance to " CE3 TRP A 274 " =    2.412
peak=   -3.221 closest distance to " CG  ASP A 231 " =    0.853
peak=   -3.220 closest distance to " O   VAL A 174 " =    2.191
peak=   -3.220 closest distance to " O   TRP A  70 " =    1.418
peak=   -3.218 closest distance to " CD2 PHE A  61 " =    2.431
peak=   -3.216 closest distance to " N   ALA A 226 " =    2.104
peak=   -3.215 closest distance to " O   HOH Z 298 " =    2.477
peak=   -3.214 closest distance to " CD  GLU A 236 " =    1.078
peak=   -3.212 closest distance to " O   HOH Z 165 " =    2.268
peak=   -3.212 closest distance to " O   HOH Z 125 " =    3.345
peak=   -3.208 closest distance to " CE2 PHE A 218 " =    2.409
peak=   -3.207 closest distance to " O   HOH Z 347 " =    0.987
peak=   -3.207 closest distance to " C   HIS A 108 " =    1.276
peak=   -3.203 closest distance to " CB  SER A 210 " =    1.232
peak=   -3.201 closest distance to " CA  GLY A 241 " =    2.042
peak=   -3.200 closest distance to " O   HOH Z 163 " =    2.015
peak=   -3.196 closest distance to " O   GLY A  80 " =    2.472
peak=   -3.194 closest distance to " O   HOH Z   1 " =    3.722
peak=   -3.192 closest distance to " O   HOH Z 126 " =    1.811
peak=   -3.189 closest distance to " O   HOH Z 139 " =    2.695
peak=   -3.184 closest distance to " OG  SER A 273 " =    1.931
peak=   -3.181 closest distance to " O   HOH Z 193 " =    1.584
peak=   -3.179 closest distance to " CG2BVAL A  72 " =    1.528
peak=   -3.179 closest distance to " O   HOH Z 283 " =    2.212
peak=   -3.176 closest distance to " OE1 GLN A  58 " =    2.733
peak=   -3.175 closest distance to " O   HOH Z 377 " =    1.352
peak=   -3.174 closest distance to " OG BSER A 134 " =    1.751
peak=   -3.174 closest distance to " O   VAL A 189 " =    2.316
peak=   -3.172 closest distance to " OE2 GLU A 152 " =    2.106
peak=   -3.170 closest distance to " O   ARG A 145 " =    1.502
peak=   -3.163 closest distance to " O   HOH Z 213 " =    1.159
peak=   -3.162 closest distance to " OD2 ASP A 171 " =    1.369
peak=   -3.160 closest distance to " NH1 ARG A  56 " =    2.376
peak=   -3.153 closest distance to " CG  ARG A 259 " =    2.794
peak=   -3.149 closest distance to " CB  ASP A  27 " =    2.309
peak=   -3.132 closest distance to " CG  ARG A 219 " =    2.301
peak=   -3.130 closest distance to " CD1 TYR A 214 " =    1.446
peak=   -3.128 closest distance to " O   HOH Z 137 " =    1.467
peak=   -3.126 closest distance to " O   HOH Z 234 " =    4.504
peak=   -3.126 closest distance to " O   HOH Z 130 " =    0.864
peak=   -3.125 closest distance to " O   HOH Z 292 " =    1.564
peak=   -3.125 closest distance to " CG  GLN A 240 " =    2.324
peak=   -3.121 closest distance to " OG BSER A 210 " =    2.195
peak=   -3.120 closest distance to " CE2 PHE A  61 " =    2.627
peak=   -3.092 closest distance to " O   HOH Z  52 " =    1.162
peak=   -3.091 closest distance to " O   ASN A 301 " =    1.248
peak=   -3.084 closest distance to " OD2 ASP A 171 " =    2.458
peak=   -3.072 closest distance to " O   HOH Z  37 " =    1.437
peak=   -3.067 closest distance to " O   PRO A  54 " =    1.479
peak=   -3.065 closest distance to " O   HOH Z 128 " =    2.396
peak=   -3.048 closest distance to " O   HOH Z 300 " =    1.289
peak=   -3.047 closest distance to " O   HOH Z 413 " =    4.426
peak=   -3.034 closest distance to " OD1 ASN A 148 " =    1.760

================= 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    :  0.4501 0.4447   6.265390e+00   6.254843e+00
   1_bss:  0.4397 0.4342   6.257602e+00   6.239092e+00
   1_xyz:  0.3350 0.3757   6.070986e+00   6.147798e+00
   1_adp:  0.3046 0.3939   6.031410e+00   6.165991e+00
   1_occ:  0.3041 0.3943   6.031049e+00   6.166107e+00
   2_bss:  0.3036 0.3908   6.026489e+00   6.163295e+00
   2_xyz:  0.2515 0.3233   5.863770e+00   6.029722e+00
   2_adp:  0.2338 0.3161   5.824446e+00   6.013784e+00
   2_occ:  0.2336 0.3162   5.824469e+00   6.014294e+00
   3_bss:  0.2339 0.3153   5.822585e+00   6.012502e+00
   3_xyz:  0.1993 0.2729   5.674318e+00   5.887668e+00
   3_adp:  0.1921 0.2566   5.631348e+00   5.834341e+00
   3_occ:  0.1917 0.2558   5.628951e+00   5.831681e+00
   4_bss:  0.1915 0.2545   5.627889e+00   5.830379e+00
   4_xyz:  0.1540 0.2040   5.412382e+00   5.632633e+00
   4_adp:  0.1399 0.1919   5.334702e+00   5.574614e+00
   4_occ:  0.1399 0.1917   5.334238e+00   5.573788e+00
   5_bss:  0.1401 0.1915   5.332279e+00   5.572038e+00
   5_xyz:  0.1280 0.1812   5.263020e+00   5.510683e+00
   5_adp:  0.1252 0.1754   5.237013e+00   5.479827e+00
   5_occ:  0.1251 0.1752   5.236617e+00   5.479108e+00
   5_bss:  0.1251 0.1753   5.236510e+00   5.478877e+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:  0.354  20.000  -2.005   2.630  -1.769   0.000  -0.000  -0.000
   1_xyz:  0.354  20.000  -2.005   2.630  -1.769   0.000  -0.000  -0.000
   1_adp:  0.354  20.000  -2.005   2.630  -1.769   0.000  -0.000  -0.000
   1_occ:  0.354  20.000  -2.005   2.630  -1.769   0.000  -0.000  -0.000
   2_bss:  0.343  46.857  -1.356   0.703  -0.342   0.000  -0.000  -0.000
   2_xyz:  0.343  46.857  -1.356   0.703  -0.342   0.000  -0.000  -0.000
   2_adp:  0.343  46.857  -1.356   0.703  -0.342   0.000  -0.000  -0.000
   2_occ:  0.343  46.857  -1.356   0.703  -0.342   0.000  -0.000  -0.000
   3_bss:  0.340  53.157  -1.237  -0.209  -0.028  -0.000  -0.000  -0.000
   3_xyz:  0.340  53.157  -1.237  -0.209  -0.028  -0.000  -0.000  -0.000
   3_adp:  0.340  53.157  -1.237  -0.209  -0.028  -0.000  -0.000  -0.000
   3_occ:  0.340  53.157  -1.237  -0.209  -0.028  -0.000  -0.000  -0.000
   4_bss:  0.337  53.157  -1.895  -1.299  -0.501  -0.000  -0.000  -0.000
   4_xyz:  0.337  53.157  -1.895  -1.299  -0.501  -0.000  -0.000  -0.000
   4_adp:  0.337  53.157  -1.895  -1.299  -0.501  -0.000  -0.000  -0.000
   4_occ:  0.337  53.157  -1.895  -1.299  -0.501  -0.000  -0.000  -0.000
   5_bss:  0.314  46.769  -2.066  -1.823  -0.633  -0.000  -0.000  -0.000
   5_xyz:  0.314  46.769  -2.066  -1.823  -0.633  -0.000  -0.000  -0.000
   5_adp:  0.314  46.769  -2.066  -1.823  -0.633  -0.000  -0.000  -0.000
   5_occ:  0.314  46.769  -2.066  -1.823  -0.633  -0.000  -0.000  -0.000
   5_bss:  0.311  43.121  -2.051  -1.895  -0.536  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.490 0.4912  0.6728    64985.650
   1_bss:  51.543 0.5018  0.6769    61313.225
   1_xyz:  41.909 0.6200  0.8183    42202.881
   1_adp:  43.465 0.6005  0.7946    45168.412
   1_occ:  43.520 0.5999  0.7925    45215.695
   2_bss:  42.880 0.6073  0.8076    44034.370
   2_xyz:  33.929 0.7131  0.9279    28771.840
   2_adp:  32.769 0.7267  0.9297    27452.603
   2_occ:  32.788 0.7264  0.9292    27491.143
   3_bss:  32.644 0.7279  0.9253    27238.740
   3_xyz:  27.365 0.7858  0.9762    19379.689
   3_adp:  25.250 0.8090  0.9886    17075.304
   3_occ:  25.162 0.8099  0.9889    16942.580
   4_bss:  25.079 0.8106  0.9632    16833.133
   4_xyz:  19.466 0.8665  0.9992    10696.452
   4_adp:  18.009 0.8806  0.9962     9458.671
   4_occ:  17.995 0.8807  0.9962     9439.307
   5_bss:  17.944 0.8810  0.9863     9370.954
   5_xyz:  16.556 0.8934  0.9924     8212.421
   5_adp:  15.800 0.9003  0.9882     7755.942
   5_occ:  15.790 0.9004  0.9882     7740.580
   5_bss:  15.789 0.9003  0.9887     7737.489
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   1.9808e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   1.9808e-01
   1_xyz:   1.827  0.016  0.124 16.140  0.008  4.103   1.8678e-01
   1_adp:   1.827  0.016  0.124 16.140  0.008  4.103   1.8678e-01
   1_occ:   1.827  0.016  0.124 16.140  0.008  4.103   1.8678e-01
   2_bss:   1.827  0.016  0.124 16.140  0.008  4.103   1.8678e-01
   2_xyz:   1.251  0.009  0.088 14.884  0.005  4.104   9.4421e-02
   2_adp:   1.251  0.009  0.088 14.884  0.005  4.104   9.4421e-02
   2_occ:   1.251  0.009  0.088 14.884  0.005  4.104   9.4421e-02
   3_bss:   1.251  0.009  0.088 14.884  0.005  4.104   9.4421e-02
   3_xyz:   0.948  0.007  0.067 14.304  0.003  4.107   5.7827e-02
   3_adp:   0.948  0.007  0.067 14.304  0.003  4.107   5.7827e-02
   3_occ:   0.948  0.007  0.067 14.304  0.003  4.107   5.7827e-02
   4_bss:   0.948  0.007  0.067 14.304  0.003  4.107   5.7827e-02
   4_xyz:   0.976  0.006  0.069 14.543  0.003  4.107   5.6391e-02
   4_adp:   0.976  0.006  0.069 14.543  0.003  4.107   5.6391e-02
   4_occ:   0.976  0.006  0.069 14.543  0.003  4.107   5.6391e-02
   5_bss:   0.976  0.006  0.069 14.543  0.003  4.107   5.6391e-02
   5_xyz:   0.874  0.005  0.063 14.264  0.003  4.109   4.8589e-02
   5_adp:   0.874  0.005  0.063 14.264  0.003  4.109   4.8589e-02
   5_occ:   0.874  0.005  0.063 14.264  0.003  4.109   4.8589e-02
   5_bss:   0.874  0.005  0.063 14.264  0.003  4.109   4.8589e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.463   2.3780e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.463   2.3780e-01
   1_xyz:  11.296  0.085  0.520 82.558  0.036  1.929   2.3208e-01
   1_adp:  11.296  0.085  0.520 82.558  0.036  1.929   2.3208e-01
   1_occ:  11.296  0.085  0.520 82.558  0.036  1.929   2.3208e-01
   2_bss:  11.296  0.085  0.520 82.558  0.036  1.929   2.3208e-01
   2_xyz:   7.809  0.081  0.322 78.830  0.029  2.053   2.0443e-01
   2_adp:   7.809  0.081  0.322 78.830  0.029  2.053   2.0443e-01
   2_occ:   7.809  0.081  0.322 78.830  0.029  2.053   2.0443e-01
   3_bss:   7.809  0.081  0.322 78.830  0.029  2.053   2.0443e-01
   3_xyz:   8.331  0.079  0.265 76.105  0.020  2.326   4.7922e-02
   3_adp:   8.331  0.079  0.265 76.105  0.020  2.326   4.7922e-02
   3_occ:   8.331  0.079  0.265 76.105  0.020  2.326   4.7922e-02
   4_bss:   8.331  0.079  0.265 76.105  0.020  2.326   4.7922e-02
   4_xyz:   7.827  0.043  0.242 80.203  0.032  2.303   4.3845e-02
   4_adp:   7.827  0.043  0.242 80.203  0.032  2.303   4.3845e-02
   4_occ:   7.827  0.043  0.242 80.203  0.032  2.303   4.3845e-02
   5_bss:   7.827  0.043  0.242 80.203  0.032  2.303   4.3845e-02
   5_xyz:   7.391  0.043  0.197 80.814  0.031  2.363   3.1453e-02
   5_adp:   7.391  0.043  0.197 80.814  0.031  2.363   3.1453e-02
   5_occ:   7.391  0.043  0.197 80.814  0.031  2.363   3.1453e-02
   5_bss:   7.391  0.043  0.197 80.814  0.031  2.363   3.1453e-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:  92.80   0.00  17.98  92.80   0.00  14.80  86.44   0.98  35.29
   1_occ:  92.80   0.00  17.98  92.80   0.00  14.80  86.44   0.98  35.29
   2_bss:  92.80   0.00  17.98  92.80   0.00  14.80  86.44   0.98  35.29
   2_xyz:  92.80   0.00  17.98  92.80   0.00  14.80  86.44   0.98  35.29
   2_adp:  95.04   0.00  18.55  95.04   0.00  14.62  91.28   1.75  39.90
   2_occ:  95.04   0.00  18.55  95.04   0.00  14.62  91.28   1.75  39.90
   3_bss:  95.04   0.00  18.55  95.04   0.00  14.62  91.28   1.75  39.90
   3_xyz:  95.04   0.00  18.55  95.04   0.00  14.62  91.28   1.75  39.90
   3_adp:  97.95   0.00  17.81  97.95   0.00  13.80  89.73   4.69  39.66
   3_occ:  97.95   0.00  17.81  97.95   0.00  13.80  89.73   4.69  39.66
   4_bss:  97.95   0.00  17.81  97.95   0.00  13.80  89.73   4.69  39.66
   4_xyz:  97.95   0.00  17.81  97.95   0.00  13.80  89.73   4.69  39.66
   4_adp: 103.16   0.00  18.19 103.16   0.00  13.09  94.50   6.09  46.00
   4_occ: 103.16   0.00  18.19 103.16   0.00  13.09  94.50   6.09  46.00
   5_bss: 103.16   0.00  18.19 103.16   0.00  13.09  94.50   6.09  46.00
   5_xyz: 103.16   0.00  18.19 103.16   0.00  13.09  94.50   6.09  46.00
   5_adp: 103.09   0.00  17.56 103.09   0.00  12.59  96.34   5.24  44.56
   5_occ: 103.09   0.00  17.56 103.09   0.00  12.59  96.34   5.24  44.56
   5_bss: 103.10   0.00  17.56 103.10   0.00  12.60  96.34   5.24  44.57
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.742    0.028    0.459
   1_adp:    1.742    0.028    0.459
   1_occ:    1.742    0.028    0.459
   2_bss:    1.742    0.028    0.459
   2_xyz:    1.617    0.059    0.560
   2_adp:    1.617    0.059    0.560
   2_occ:    1.617    0.059    0.560
   3_bss:    1.617    0.059    0.560
   3_xyz:    1.630    0.048    0.660
   3_adp:    1.630    0.048    0.660
   3_occ:    1.630    0.048    0.660
   4_bss:    1.630    0.048    0.660
   4_xyz:    1.543    0.087    0.765
   4_adp:    1.543    0.087    0.765
   4_occ:    1.543    0.087    0.765
   5_bss:    1.543    0.087    0.765
   5_xyz:    1.665    0.054    0.786
   5_adp:    1.665    0.054    0.786
   5_occ:    1.665    0.054    0.786
   5_bss:    1.665    0.054    0.786
------------------------------------------------------------------------

CPU time actual refinement: 346.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/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_246/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_246/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.40 
  Macro-tasks:
    bulk solvent and scale       = 43.53  
    individual site refinement   = 142.42 
    weights calculation          = 29.22  
    collect and process          = 6.57   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 221.84 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 110.73 
    alpha_beta                      = 8.51   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 119.34 
    fmodel                         = 7.35   
    r_factors                      = 0.25   
    phase_errors                   = 10.68  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 260.71 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.887 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    655 calls, 110.34 s
gradients_fft:          600 calls, 106.03 s

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

# Date 2008-01-16 Time 04:21:30 PST -0800 (1200486090.89 s)
Start R-work = 0.4501, R-free = 0.4447 (no bulk solvent and anisotropic scale)
Final R-work = 0.1452, R-free = 0.1905 (no bulk solvent and anisotropic scale)

Start R-work = 0.4397, R-free = 0.4342
Final R-work = 0.1251, R-free = 0.1753