# Date 2008-01-16 Time 04:10:06 PST -0800 (1200485406.56 s)
#phil __OFF__

Command line arguments: "../208.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26132
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 208

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.3993, 88.5498, 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: 3.26, 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: (68.845, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9447 1.96097
Completeness in resolution range: 0.917432
Completeness with d_max=infinity: 0.91469

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9447
                             d_min =   1.9610

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9447 1.96097
Completeness in resolution range: 0.917432
Completeness with d_max=infinity: 0.91469

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9451 -  4.1965 [2238/2266]  2008   230  10.3%
  bin  2:  4.1965 -  3.3432 [2153/2176]  1939   214   9.9%
  bin  3:  3.3432 -  2.9242 [2130/2155]  1926   204   9.6%
  bin  4:  2.9242 -  2.6584 [2108/2124]  1889   219  10.4%
  bin  5:  2.6584 -  2.4688 [2072/2111]  1860   212  10.2%
  bin  6:  2.4688 -  2.3238 [2098/2130]  1896   202   9.6%
  bin  7:  2.3238 -  2.2078 [2060/2097]  1855   205  10.0%
  bin  8:  2.2078 -  2.1120 [2085/2127]  1880   205   9.8%
  bin  9:  2.1120 -  2.0309 [1982/2077]  1787   195   9.8%
  bin 10:  2.0309 -  1.9610 [ 663/2089]   590    73  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/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:
        1.16 -     1.91: 13
        1.91 -     2.66: 97
        2.66 -     3.41: 4359
        3.41 -     4.15: 9353
        4.15 -     4.90: 14376
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.164 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.364 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.425 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.434 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.514 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28193 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_208/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.3993 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4532   r_free= 0.4546   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259484                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9451 -  4.6808 0.99   1452  161 0.3475 0.3616      6.5183      6.5129|
|  2:  4.6808 -  3.7344 0.99   1412  154 0.3815 0.3997      6.7469      6.8155|
|  3:  3.7344 -  3.2680 0.99   1369  156 0.4324 0.4038      6.6417      6.6227|
|  4:  3.2680 -  2.9717 0.99   1365  146 0.4453 0.4521      6.4631      6.4749|
|  5:  2.9717 -  2.7602 0.98   1356  151 0.4763 0.4691      6.3303      6.3754|
|  6:  2.7602 -  2.5983 0.99   1350  155 0.4860 0.5095      6.2558      6.1611|
|  7:  2.5983 -  2.4688 0.99   1318  156 0.4829 0.4391      6.1982      6.1326|
|  8:  2.4688 -  2.3618 0.99   1367  140 0.5076 0.5001      6.1572      6.1285|
|  9:  2.3618 -  2.2712 0.99   1339  147 0.5114 0.4920      6.1021      6.1676|
| 10:  2.2712 -  2.1931 0.98   1335  147 0.5181 0.5437      6.0776      6.0796|
| 11:  2.1931 -  2.1247 0.98   1294  156 0.5180 0.5251      6.0023       6.009|
| 12:  2.1247 -  2.0641 1.00   1345  144 0.5131 0.5076      5.9351      5.9278|
| 13:  2.0641 -  2.0099 0.78   1077  113 0.5100 0.5266      5.8664      5.8395|
| 14:  2.0099 -  1.9610 0.19    251   33 0.4738 0.4739      5.9031      5.7078|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9451 -  4.6808  1452   161  0.73  31.52   0.83     0.74      61265.37|
|  2:  4.6808 -  3.7344  1412   154  0.73  32.99   0.93     0.82      95005.08|
|  3:  3.7344 -  3.2680  1369   156  0.62  41.80   0.90     0.80     101882.53|
|  4:  3.2680 -  2.9717  1365   146  0.52  49.89   0.91     0.71      91648.64|
|  5:  2.9717 -  2.7602  1356   151  0.46  55.16   0.89     0.63      73540.45|
|  6:  2.7602 -  2.5983  1350   155  0.43  57.44   0.90     0.60      64811.19|
|  7:  2.5983 -  2.4688  1318   156  0.45  55.81   0.91     0.61      56460.18|
|  8:  2.4688 -  2.3618  1367   140  0.44  56.84   0.92     0.63      50520.00|
|  9:  2.3618 -  2.2712  1339   147  0.45  56.46   0.91     0.65      46646.07|
| 10:  2.2712 -  2.1931  1335   147  0.42  58.52   0.91     0.60      43086.03|
| 11:  2.1931 -  2.1247  1294   156  0.36  63.25   0.92     0.55      44995.60|
| 12:  2.1247 -  2.0641  1345   144  0.29  68.35   0.94     0.48      44046.56|
| 13:  2.0641 -  2.0099  1077   113  0.27  70.00   0.92     0.44      40043.82|
| 14:  2.0099 -  1.9610   251    33  0.35  63.82   1.03     0.43      29658.29|
|alpha:            min =        0.43 max =            0.82 mean =         0.64|
|beta:             min =    29658.29 max =       101882.53 mean =     62756.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.94 mean =        53.33|
|phase err.(test): min =        0.00 max =           89.97 mean =        53.47|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.548846             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.915285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.439   (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 |  1.164 -  1.538:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.538 -  1.911:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.911 -  2.285:       16 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.285 -  2.659:       81 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.659 -  3.032:     2062 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.032 -  3.406:     2297 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.406 -  3.779:     3957 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.779 -  4.153:     5396 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.153 -  4.526:     6400 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.526 -  4.900:     7976 |
|-----------------------------------------------------------------------------|
|-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 |        0.205 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.164 |       0.797 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4532   r_free= 0.4546   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4449   r_free= 0.4424   ksol= 0.31   Bsol= 38.87   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-0.75,4.63,-0.00,0.00,0.00); trace/3= 0.91                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.251101                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.474756             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.004   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.067944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.069   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4449      final r-factor (work) = 0.3047          |
| start r-factor (free) = 0.4424      final r-factor (free) = 0.3317          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9395 = 10.47 * 0.50 * 6.2501 + 1.00 * 0.2054                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0317 = 10.47 * 0.50 * 6.0901 + 1.00 * 0.1355                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3047      final r-factor (work) = 0.2747          |
| start r-factor (free) = 0.3317      final r-factor (free) = 0.3390          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5100 = 1.07 * 1.00 * 6.0901 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3257 = 1.07 * 1.00 * 5.9072 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.18   18.73    None  None   None       |
|    all(noH): 2823   0      0.00    98.18   18.73    None  None   None       |
|    Sol.    : 438    0      3.20    98.18   41.55    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   14.54    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 -   9.818:  946   |   5:    49.089 -  58.907:   90        |
|      1:     9.818 -  19.636:  940   |   6:    58.907 -  68.724:   54        |
|      2:    19.636 -  29.453:  407   |   7:    68.724 -  78.542:   24        |
|      3:    29.453 -  39.271:  218   |   8:    78.542 -  88.360:   15        |
|      4:    39.271 -  49.089:  126   |   9:    88.360 -  98.178:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2747 r_free = 0.3390             target_work(ml) = 5.913         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2745 r_free = 0.3401             target_work(ml) = 5.913         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2745   r_free= 0.3401   ksol= 0.31   Bsol= 38.87   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-0.75,4.63,-0.00,0.00,0.00); trace/3= 0.91                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.913062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2714   r_free= 0.3386   ksol= 0.33   Bsol= 60.35   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.13,1.57,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.908615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.092550              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.135   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.657  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2714      final r-factor (work) = 0.2069          |
| start r-factor (free) = 0.3386      final r-factor (free) = 0.2647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2245 = 4.09 * 0.50 * 5.9079 + 1.00 * 0.1354                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9580 = 4.09 * 0.50 * 5.8123 + 1.00 * 0.0645                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2069      final r-factor (work) = 0.1951          |
| start r-factor (free) = 0.2647      final r-factor (free) = 0.2461          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9499 = 0.33 * 1.00 * 5.8123 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8889 = 0.33 * 1.00 * 5.6494 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    94.65   18.03    None  None   None       |
|    all(noH): 2823   0      0.75    94.65   18.03    None  None   None       |
|    Sol.    : 438    0      5.80    94.65   41.40    None  None   None       |
|    Mac.    : 2385   0      0.75    78.61   13.74    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:     0.748 -  10.138: 1017   |   5:    47.699 -  57.090:  117        |
|      1:    10.138 -  19.529: 1005   |   6:    57.090 -  66.480:   35        |
|      2:    19.529 -  28.919:  309   |   7:    66.480 -  75.870:   24        |
|      3:    28.919 -  38.309:  161   |   8:    75.870 -  85.261:   12        |
|      4:    38.309 -  47.699:  141   |   9:    85.261 -  94.651:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1951 r_free = 0.2461             target_work(ml) = 5.619         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1950 r_free = 0.2458             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1950   r_free= 0.2458   ksol= 0.33   Bsol= 60.35   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.13,1.57,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.618433                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1951   r_free= 0.2448   ksol= 0.33   Bsol= 62.95   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.62,0.39,-0.00,0.00,0.00); trace/3= -1.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.618673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.830879              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.146737              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.528  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1951      final r-factor (work) = 0.1519          |
| start r-factor (free) = 0.2448      final r-factor (free) = 0.1976          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0644 = 2.83 * 0.50 * 5.6519 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8677 = 2.83 * 0.50 * 5.5154 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1519      final r-factor (work) = 0.1418          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1933          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3349 = 1.15 * 1.00 * 5.5154 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1677 = 1.15 * 1.00 * 5.3682 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.31    94.00   18.20    None  None   None       |
|    all(noH): 2823   0      0.31    94.00   18.20    None  None   None       |
|    Sol.    : 438    0      6.02    94.00   43.96    None  None   None       |
|    Mac.    : 2385   0      0.31    82.08   13.47    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:     0.309 -   9.678:  912   |   5:    47.154 -  56.523:  121        |
|      1:     9.678 -  19.047: 1158   |   6:    56.523 -  65.892:   73        |
|      2:    19.047 -  28.416:  264   |   7:    65.892 -  75.260:   31        |
|      3:    28.416 -  37.785:  117   |   8:    75.260 -  84.629:   11        |
|      4:    37.785 -  47.154:  130   |   9:    84.629 -  93.998:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1418 r_free = 0.1933             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1417 r_free = 0.1932             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1932   ksol= 0.33   Bsol= 62.95   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.62,0.39,-0.00,0.00,0.00); trace/3= -1.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.355384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1934   ksol= 0.33   Bsol= 68.70   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-1.97,-0.28,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.356067                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.408927              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.192838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.825  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1420      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1934      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5304 = 2.41 * 0.50 * 5.3712 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4601 = 2.41 * 0.50 * 5.3132 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1761      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6628 = 2.19 * 1.00 * 5.3132 + 1.00 * 0.0117                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5397 = 2.19 * 1.00 * 5.2566 + 1.00 * 0.0127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.36  18.27    None  None   None       |
|    all(noH): 2823   0      0.00    102.36  18.27    None  None   None       |
|    Sol.    : 438    0      5.34    102.36  45.25    None  None   None       |
|    Mac.    : 2385   0      0.00    93.05   13.31    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 -  10.236: 1076   |   5:    51.179 -  61.415:   99        |
|      1:    10.236 -  20.472: 1086   |   6:    61.415 -  71.651:   66        |
|      2:    20.472 -  30.707:  214   |   7:    71.651 -  81.886:   22        |
|      3:    30.707 -  40.943:  132   |   8:    81.886 -  92.122:   18        |
|      4:    40.943 -  51.179:  102   |   9:    92.122 - 102.358:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1749             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1748             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1748   ksol= 0.33   Bsol= 68.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-1.97,-0.28,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1747   ksol= 0.33   Bsol= 68.70   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-1.85,-0.30,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.432600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.652  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.126393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.549  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4542 = 2.43 * 0.50 * 5.2567 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4274 = 2.43 * 0.50 * 5.2326 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9066 = 1.13 * 1.00 * 5.2326 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8839 = 1.13 * 1.00 * 5.2131 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.29  17.86    None  None   None       |
|    all(noH): 2823   0      0.00    107.29  17.86    None  None   None       |
|    Sol.    : 438    0      0.00    107.29  43.86    None  None   None       |
|    Mac.    : 2385   0      0.54    96.06   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.729: 1220   |   5:    53.647 -  64.376:   85        |
|      1:    10.729 -  21.459:  997   |   6:    64.376 -  75.106:   46        |
|      2:    21.459 -  32.188:  207   |   7:    75.106 -  85.835:   19        |
|      3:    32.188 -  42.918:  127   |   8:    85.835 -  96.564:   13        |
|      4:    42.918 -  53.647:  105   |   9:    96.564 - 107.294:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1678             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1678             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1678   ksol= 0.33   Bsol= 68.70   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-1.85,-0.30,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206997                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9451 -  4.6808 0.99   1452  161 0.0983 0.1342      5.4013      5.6029|
|  2:  4.6808 -  3.7344 0.99   1412  154 0.0823 0.1103      5.4337      5.6563|
|  3:  3.7344 -  3.2680 0.99   1369  156 0.1113 0.1567      5.5111      5.8459|
|  4:  3.2680 -  2.9717 0.99   1365  146 0.1336 0.1719      5.4959      5.6695|
|  5:  2.9717 -  2.7602 0.98   1356  151 0.1405 0.1718      5.3882      5.5665|
|  6:  2.7602 -  2.5983 0.99   1350  155 0.1338 0.2191      5.2736      5.5706|
|  7:  2.5983 -  2.4688 0.99   1318  156 0.1341 0.1776      5.2322      5.4027|
|  8:  2.4688 -  2.3618 0.99   1367  140 0.1260 0.1845      5.1503      5.3642|
|  9:  2.3618 -  2.2712 0.99   1339  147 0.1221 0.1873      5.0621      5.3511|
| 10:  2.2712 -  2.1931 0.98   1335  147 0.1221 0.1922      5.0073      5.2519|
| 11:  2.1931 -  2.1247 0.98   1294  156 0.1233 0.1926      4.9625      5.3119|
| 12:  2.1247 -  2.0641 1.00   1345  144 0.1206 0.1686      4.9209      5.1581|
| 13:  2.0641 -  2.0099 0.78   1077  113 0.1134 0.1854      4.8078      5.0347|
| 14:  2.0099 -  1.9610 0.19    251   33 0.1030 0.1830      4.7591      4.9869|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9451 -  4.6808  1452   161  0.94   9.73   0.97     0.94       7870.22|
|  2:  4.6808 -  3.7344  1412   154  0.95   8.49   1.01     0.99       9668.99|
|  3:  3.7344 -  3.2680  1369   156  0.93  12.23   1.03     1.02      11375.17|
|  4:  3.2680 -  2.9717  1365   146  0.90  15.40   1.01     1.00      11305.06|
|  5:  2.9717 -  2.7602  1356   151  0.89  17.59   1.00     0.98       9905.42|
|  6:  2.7602 -  2.5983  1350   155  0.88  17.91   0.98     0.94       8100.90|
|  7:  2.5983 -  2.4688  1318   156  0.89  17.57   0.99     0.96       7434.82|
|  8:  2.4688 -  2.3618  1367   140  0.89  17.21   1.00     0.96       6473.40|
|  9:  2.3618 -  2.2712  1339   147  0.89  17.19   0.99     0.94       5522.72|
| 10:  2.2712 -  2.1931  1335   147  0.89  17.01   0.98     0.95       4948.00|
| 11:  2.1931 -  2.1247  1294   156  0.89  17.36   0.98     0.94       4645.53|
| 12:  2.1247 -  2.0641  1345   144  0.89  17.48   1.00     1.00       4440.07|
| 13:  2.0641 -  2.0099  1077   113  0.89  17.56   0.97     0.94       3627.33|
| 14:  2.0099 -  1.9610   251    33  0.92  13.96   0.96     0.92       3006.22|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3006.22 max =        11375.17 mean =      7359.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.82 mean =        15.47|
|phase err.(test): min =        0.00 max =           89.15 mean =        14.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1676   ksol= 0.32   Bsol= 63.95   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.78,-0.25,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206942                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1676   ksol= 0.32   Bsol= 63.95   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.78,-0.25,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206942                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9451 -  4.6808 0.99   1452  161 0.0983 0.1317      5.3963      5.5835|
|  2:  4.6808 -  3.7344 0.99   1412  154 0.0831 0.1091      5.4343       5.655|
|  3:  3.7344 -  3.2680 0.99   1369  156 0.1119 0.1570      5.5128      5.8462|
|  4:  3.2680 -  2.9717 0.99   1365  146 0.1338 0.1731      5.4962      5.6732|
|  5:  2.9717 -  2.7602 0.98   1356  151 0.1404 0.1720      5.3886      5.5647|
|  6:  2.7602 -  2.5983 0.99   1350  155 0.1337 0.2190      5.2737      5.5709|
|  7:  2.5983 -  2.4688 0.99   1318  156 0.1341 0.1781       5.233      5.4043|
|  8:  2.4688 -  2.3618 0.99   1367  140 0.1259 0.1846      5.1506      5.3644|
|  9:  2.3618 -  2.2712 0.99   1339  147 0.1219 0.1870      5.0617      5.3511|
| 10:  2.2712 -  2.1931 0.98   1335  147 0.1221 0.1922      5.0075      5.2523|
| 11:  2.1931 -  2.1247 0.98   1294  156 0.1232 0.1924      4.9625      5.3113|
| 12:  2.1247 -  2.0641 1.00   1345  144 0.1206 0.1690      4.9213      5.1589|
| 13:  2.0641 -  2.0099 0.78   1077  113 0.1135 0.1853      4.8079      5.0336|
| 14:  2.0099 -  1.9610 0.19    251   33 0.1030 0.1830      4.7597      4.9879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9451 -  4.6808  1452   161  0.94   9.55   0.97     0.94       7648.11|
|  2:  4.6808 -  3.7344  1412   154  0.95   8.41   1.01     1.00       9520.41|
|  3:  3.7344 -  3.2680  1369   156  0.93  12.22   1.03     1.03      11345.58|
|  4:  3.2680 -  2.9717  1365   146  0.90  15.42   1.01     1.00      11315.98|
|  5:  2.9717 -  2.7602  1356   151  0.89  17.61   1.00     0.98       9926.44|
|  6:  2.7602 -  2.5983  1350   155  0.88  17.91   0.98     0.94       8097.55|
|  7:  2.5983 -  2.4688  1318   156  0.89  17.58   0.99     0.96       7448.71|
|  8:  2.4688 -  2.3618  1367   140  0.89  17.23   1.00     0.96       6481.66|
|  9:  2.3618 -  2.2712  1339   147  0.89  17.19   0.99     0.95       5525.46|
| 10:  2.2712 -  2.1931  1335   147  0.89  17.01   0.99     0.95       4949.00|
| 11:  2.1931 -  2.1247  1294   156  0.89  17.35   0.99     0.94       4644.04|
| 12:  2.1247 -  2.0641  1345   144  0.89  17.49   1.00     1.01       4444.89|
| 13:  2.0641 -  2.0099  1077   113  0.89  17.57   0.97     0.95       3627.16|
| 14:  2.0099 -  1.9610   251    33  0.92  13.97   0.97     0.93       3004.28|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3004.28 max =        11345.58 mean =      7331.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.45|
|phase err.(test): min =        0.00 max =           88.94 mean =        14.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.902)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.30  17.86    None  None   None       |
|    all(noH): 2823   0      0.00    107.30  17.86    None  None   None       |
|    Sol.    : 438    0      0.00    107.30  43.86    None  None   None       |
|    Mac.    : 2385   0      0.54    96.06   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.732: 1220   |   5:    53.650 -  64.379:   85        |
|      1:    10.732 -  21.462:  997   |   6:    64.379 -  75.109:   46        |
|      2:    21.462 -  32.191:  207   |   7:    75.109 -  85.838:   19        |
|      3:    32.191 -  42.921:  127   |   8:    85.838 -  96.567:   13        |
|      4:    42.921 -  53.650:  105   |   9:    96.567 - 107.297:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.571 - 4.716
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.716 - 4.716

peak=    7.078 closest distance to " O  BHOH Z  74 " =    1.102
peak=    5.242 closest distance to " O   HOH Z 403 " =    1.904
peak=    5.131 closest distance to " O   HOH Z  49 " =    1.218
peak=    5.104 closest distance to " CG  PRO A  54 " =    1.370
peak=    5.017 closest distance to " CB  ARG A 275 " =    0.993
peak=    4.700 closest distance to " O   HOH Z 113 " =    1.926
peak=    4.639 closest distance to " CB  GLN A 223 " =    1.486
peak=    4.600 closest distance to " CZ  PHE A 218 " =    1.177
peak=    4.596 closest distance to " O   HOH Z 248 " =    1.394
peak=    4.587 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.559 closest distance to " CD2 TRP A 179 " =    1.278
peak=    4.546 closest distance to " CG  GLN A  58 " =    0.959
peak=    4.534 closest distance to " CB  ARG A 190 " =    1.633
peak=    4.528 closest distance to " O   HOH Z 369 " =    2.383
peak=    4.527 closest distance to " O   HOH Z 287 " =    1.721
peak=    4.521 closest distance to " O   HOH Z 193 " =    1.235
peak=    4.461 closest distance to " O   HOH Z 188 " =    1.542
peak=    4.451 closest distance to " CB  SER A  63 " =    1.085
peak=    4.435 closest distance to " CG  PRO A  90 " =    1.185
peak=    4.427 closest distance to " CA  ARG A  36 " =    1.077
peak=    4.367 closest distance to " O   HOH Z 188 " =    2.602
peak=    4.334 closest distance to " O   HOH Z 406 " =    1.585
peak=    4.325 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.280 closest distance to " NE2 GLN A  11 " =    1.123
peak=    4.267 closest distance to " CZ3 TRP A 266 " =    1.074
peak=    4.264 closest distance to " CB  GLU A 152 " =    1.145
peak=    4.257 closest distance to " CB  PRO A  54 " =    1.024
peak=    4.255 closest distance to " CD  ARG A 269 " =    0.996
peak=    4.232 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.202 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.195 closest distance to " O   HOH Z 234 " =    3.503
peak=    4.186 closest distance to " CB  GLU A 277 " =    3.642
peak=    4.181 closest distance to " O   HOH Z 214 " =    1.232
peak=    4.178 closest distance to " O   HOH Z  63 " =    1.799
peak=    4.165 closest distance to " ND2 ASN A 187 " =    1.653
peak=    4.153 closest distance to " O   HOH Z 132 " =    1.052
peak=    4.141 closest distance to " ND2 ASN A 249 " =    0.927
peak=    4.125 closest distance to " O   HOH Z 251 " =    1.677
peak=    4.096 closest distance to " CG  PRO A 243 " =    1.082
peak=    4.091 closest distance to " O   SER A  87 " =    2.245
peak=    4.070 closest distance to " O   HOH Z  76 " =    1.101
peak=    4.058 closest distance to " CA  ARG A 195 " =    1.279
peak=    4.043 closest distance to " CZ  PHE A  38 " =    1.122
peak=    4.043 closest distance to " NZ  LYS A 117 " =    2.894
peak=    4.042 closest distance to " O   HOH Z 142 " =    1.521
peak=    4.033 closest distance to " CE  LYS A  76 " =    0.894
peak=    4.031 closest distance to " O   HOH Z  43 " =    2.201
peak=    4.013 closest distance to " O   HOH Z 193 " =    1.535
peak=    4.011 closest distance to " CB  ARG A  79 " =    1.473
peak=    4.003 closest distance to " O   HOH Z 203 " =    1.457
peak=    3.994 closest distance to " O   HOH Z  97 " =    1.369
peak=    3.967 closest distance to " NH1AARG A 145 " =    1.445
peak=    3.960 closest distance to " O   HOH Z 368 " =    2.164
peak=    3.959 closest distance to " O   HOH Z  40 " =    1.785
peak=    3.942 closest distance to " CG  ARG A  66 " =    2.394
peak=    3.937 closest distance to " O   HOH Z 126 " =    1.572
peak=    3.924 closest distance to " CG2 ILE A 120 " =    1.362
peak=    3.891 closest distance to " O   HOH Z 380 " =    2.215
peak=    3.888 closest distance to " O   HOH Z 126 " =    1.828
peak=    3.888 closest distance to " O   HOH Z 132 " =    2.476
peak=    3.873 closest distance to " O   HOH Z 412 " =    3.857
peak=    3.867 closest distance to " CG  PRO A 198 " =    1.208
peak=    3.865 closest distance to " O   HOH Z 361 " =    3.538
peak=    3.860 closest distance to " CD  LYS A  76 " =    1.895
peak=    3.859 closest distance to " O   HOH Z 427 " =    2.963
peak=    3.855 closest distance to " CB  VAL A 265 " =    1.214
peak=    3.846 closest distance to " O   ASN A  74 " =    1.414
peak=    3.830 closest distance to " O   HOH Z  59 " =    2.104
peak=    3.825 closest distance to " O   HOH Z 227 " =    1.528
peak=    3.818 closest distance to " O   HOH Z 298 " =    1.772
peak=    3.804 closest distance to " CG2AVAL A 121 " =    2.235
peak=    3.803 closest distance to " O   HOH Z  15 " =    2.256
peak=    3.801 closest distance to " O   HOH Z 402 " =    1.389
peak=    3.800 closest distance to " CG  GLU A  37 " =    0.999
peak=    3.798 closest distance to " O   ALA A 165 " =    1.356
peak=    3.796 closest distance to " O   HOH Z  85 " =    1.371
peak=    3.779 closest distance to " O   HOH Z 365 " =    2.585
peak=    3.774 closest distance to " CB  PHE A 204 " =    0.807
peak=    3.773 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.770 closest distance to " O   HOH Z 265 " =    2.026
peak=    3.770 closest distance to " O   HOH Z 346 " =    1.548
peak=    3.769 closest distance to " O   PRO A 198 " =    1.587
peak=    3.766 closest distance to " O   HOH Z 261 " =    2.392
peak=    3.765 closest distance to " O   HOH Z 353 " =    2.703
peak=    3.763 closest distance to " O   HOH Z  19 " =    1.664
peak=    3.755 closest distance to " OG BSER A 164 " =    2.225
peak=    3.754 closest distance to " O   HOH Z 117 " =    1.066
peak=    3.746 closest distance to " O   THR A 182 " =    1.472
peak=    3.743 closest distance to " CB  ARG A  79 " =    0.871
peak=    3.735 closest distance to " CD1 LEU A  96 " =    0.815
peak=    3.715 closest distance to " O   HOH Z 359 " =    1.702
peak=    3.708 closest distance to " CB  TRP A 179 " =    1.410
peak=    3.706 closest distance to " O   HOH Z 280 " =    2.900
peak=    3.700 closest distance to " CE  LYS A 119 " =    1.184
peak=    3.696 closest distance to " CA  VAL A 125 " =    1.195
peak=    3.694 closest distance to " CB  PRO A  90 " =    1.078
peak=    3.691 closest distance to " O   HOH Z 290 " =    1.078
peak=    3.687 closest distance to " O   HOH Z 250 " =    1.331
peak=    3.680 closest distance to " O   HOH Z  44 " =    2.166
peak=    3.678 closest distance to " O   HOH Z 313 " =    2.130
peak=    3.672 closest distance to " O   HOH Z 325 " =    2.308
peak=    3.668 closest distance to " CG  PRO A 213 " =    1.245
peak=    3.655 closest distance to " O   HOH Z  62 " =    2.273
peak=    3.654 closest distance to " CA  ALA A 100 " =    1.012
peak=    3.649 closest distance to " CB  VAL A 202 " =    1.506
peak=    3.648 closest distance to " O   HOH Z  78 " =    1.676
peak=    3.640 closest distance to " CB  SER A  26 " =    1.943
peak=    3.636 closest distance to " O   HOH Z 327 " =    1.680
peak=    3.633 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.632 closest distance to " CB  GLU A 128 " =    1.058
peak=    3.630 closest distance to " O   HOH Z 199 " =    1.589
peak=    3.630 closest distance to " O   HOH Z 303 " =    2.201
peak=    3.630 closest distance to " O   HOH Z 357 " =    2.048
peak=    3.625 closest distance to " O   HOH Z 209 " =    2.244
peak=    3.625 closest distance to " CB  SER A  62 " =    0.909
peak=    3.620 closest distance to " O   HOH Z 299 " =    4.375
peak=    3.618 closest distance to " O   HOH Z 298 " =    2.264
peak=    3.618 closest distance to " CB  TRP A 266 " =    1.090
peak=    3.611 closest distance to " CG  GLN A  11 " =    1.723
peak=    3.599 closest distance to " O   THR A 220 " =    1.160
peak=    3.582 closest distance to " O   HOH Z 255 " =    1.129
peak=    3.581 closest distance to " O   HOH Z 361 " =    2.571
peak=    3.575 closest distance to " CB  PRO A 198 " =    1.214
peak=    3.564 closest distance to " O   HOH Z 112 " =    0.966
peak=    3.562 closest distance to " CB  GLU A  46 " =    1.064
peak=    3.556 closest distance to " CD1 ILE A 199 " =    1.193
peak=    3.556 closest distance to " O   HOH Z 423 " =    1.963
peak=    3.551 closest distance to " CG AARG A 275 " =    1.281
peak=    3.545 closest distance to " CA  ALA A 160 " =    0.958
peak=    3.544 closest distance to " CG1 ILE A  20 " =    1.319
peak=    3.540 closest distance to " O   HOH Z 345 " =    1.688
peak=    3.539 closest distance to " OG BSER A 212 " =    2.692
peak=    3.529 closest distance to " O   HOH Z 305 " =    3.575
peak=    3.526 closest distance to " N   ASN A  39 " =    1.260
peak=    3.525 closest distance to " O   HOH Z 117 " =    1.954
peak=    3.525 closest distance to " CD  LYS A 166 " =    1.345
peak=    3.506 closest distance to " O   HOH Z 393 " =    3.065
peak=    3.506 closest distance to " O   HOH Z 148 " =    3.487
peak=    3.501 closest distance to " OG ASER A 258 " =    3.090
peak=    3.499 closest distance to " O   HOH Z 180 " =    2.216
peak=    3.491 closest distance to " O   HOH Z 128 " =    2.409
peak=    3.487 closest distance to " CB  THR A  52 " =    0.785
peak=    3.485 closest distance to " CG1 ILE A  33 " =    1.202
peak=    3.483 closest distance to " CB  THR A  31 " =    1.697
peak=    3.482 closest distance to " O   HOH Z 422 " =    2.630
peak=    3.481 closest distance to " O   HOH Z 214 " =    2.973
peak=    3.475 closest distance to " CG1AVAL A 121 " =    0.864
peak=    3.473 closest distance to " O  BHOH Z 338 " =    2.146
peak=    3.470 closest distance to " NE2 GLN A  77 " =    3.167
peak=    3.459 closest distance to " O   HOH Z  80 " =    1.966
peak=    3.458 closest distance to " O   ASP A 124 " =    1.551
peak=    3.457 closest distance to " O   HOH Z 425 " =    1.263
peak=    3.457 closest distance to " O   HOH Z 246 " =    1.378
peak=    3.446 closest distance to " O   HOH Z 210 " =    0.966
peak=    3.445 closest distance to " CA  ALA A 154 " =    1.037
peak=    3.441 closest distance to " N   ARG A 156 " =    1.484
peak=    3.441 closest distance to " O   HOH Z 394 " =    3.696
peak=    3.439 closest distance to " O   HOH Z 116 " =    1.068
peak=    3.435 closest distance to " CA  ASN A 127 " =    1.222
peak=    3.430 closest distance to " O   HOH Z  54 " =    1.692
peak=    3.427 closest distance to " O   HOH Z 291 " =    1.427
peak=    3.424 closest distance to " O  BHOH Z 338 " =    1.118
peak=    3.411 closest distance to " O   HOH Z 214 " =    2.030
peak=    3.408 closest distance to " CB  ASP A 298 " =    1.100
peak=    3.407 closest distance to " CB  SER A 141 " =    1.201
peak=    3.407 closest distance to " CB  ALA A 291 " =    0.974
peak=    3.404 closest distance to " O   HOH Z 285 " =    2.037
peak=    3.401 closest distance to " OG  SER A  62 " =    2.766
peak=    3.400 closest distance to " CD  PRO A  54 " =    0.973
peak=    3.399 closest distance to " O   HOH Z 176 " =    1.517
peak=    3.396 closest distance to " O   HOH Z 299 " =    4.254
peak=    3.395 closest distance to " CB  ALA A 248 " =    1.391
peak=    3.394 closest distance to " CG1BVAL A  72 " =    1.845
peak=    3.393 closest distance to " CG  GLN A  55 " =    2.302
peak=    3.387 closest distance to " CA  TYR A 116 " =    1.355
peak=    3.382 closest distance to " O   HOH Z  63 " =    2.272
peak=    3.375 closest distance to " N   CYS A 260 " =    0.892
peak=    3.372 closest distance to " O   HOH Z 213 " =    2.237
peak=    3.372 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.369 closest distance to " CA  ALA A 158 " =    1.309
peak=    3.365 closest distance to " OG  SER A  22 " =    2.512
peak=    3.357 closest distance to " CA  ASN A 215 " =    1.014
peak=    3.355 closest distance to " O   HOH Z 350 " =    1.998
peak=    3.355 closest distance to " O   HOH Z  61 " =    1.729
peak=    3.354 closest distance to " O   HOH Z 258 " =    1.998
peak=    3.352 closest distance to " O   HOH Z 215 " =    1.270
peak=    3.349 closest distance to " CB  ASP A 107 " =    1.238
peak=    3.345 closest distance to " CB  LEU A  83 " =    0.716
peak=    3.342 closest distance to " O   HOH Z 371 " =    3.106
peak=    3.341 closest distance to " CB  SER A   3 " =    1.456
peak=    3.339 closest distance to " O   HOH Z 417 " =    2.918
peak=    3.338 closest distance to " CA  ALA A 291 " =    0.746
peak=    3.338 closest distance to " O   HOH Z  52 " =    1.293
peak=    3.337 closest distance to " CE3 TRP A 150 " =    1.135
peak=    3.335 closest distance to " NH2BARG A 145 " =    2.205
peak=    3.327 closest distance to " O   HOH Z  94 " =    2.685
peak=    3.323 closest distance to " CA  SER A  87 " =    1.045
peak=    3.320 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.320 closest distance to " CB  ASN A 285 " =    0.980
peak=    3.311 closest distance to " O   HOH Z 130 " =    2.796
peak=    3.310 closest distance to " OG BSER A 134 " =    2.804
peak=    3.303 closest distance to " O   HOH Z 170 " =    2.244
peak=    3.298 closest distance to " O   HOH Z 327 " =    2.184
peak=    3.298 closest distance to " O   HOH Z 132 " =    2.404
peak=    3.291 closest distance to " O   TYR A 116 " =    1.392
peak=    3.290 closest distance to " CA  ILE A 234 " =    0.989
peak=    3.285 closest distance to " O   HOH Z 213 " =    1.762
peak=    3.285 closest distance to " O   HOH Z 193 " =    1.732
peak=    3.285 closest distance to " CA  GLU A 152 " =    0.842
peak=    3.283 closest distance to " CB  GLU A 236 " =    1.336
peak=    3.283 closest distance to " O   HOH Z   1 " =    2.153
peak=    3.282 closest distance to " O   HOH Z 383 " =    1.991
peak=    3.281 closest distance to " CB  ASN A 110 " =    1.081
peak=    3.274 closest distance to " O   HOH Z 421 " =    1.667
peak=    3.261 closest distance to " CD  ARG A  66 " =    2.405
peak=    3.259 closest distance to " O   HOH Z 371 " =    1.564
peak=    3.253 closest distance to " O   HOH Z  21 " =    1.868
peak=    3.253 closest distance to " OE1 GLN A  11 " =    2.060
peak=    3.251 closest distance to " O   HOH Z 329 " =    4.262
peak=    3.250 closest distance to " CE1 HIS A  81 " =    1.564
peak=    3.248 closest distance to " CG  MET A 185 " =    1.153
peak=    3.248 closest distance to " O   HOH Z  80 " =    1.849
peak=    3.247 closest distance to " O   HOH Z 285 " =    2.263
peak=    3.245 closest distance to " OD1 ASN A  69 " =    2.421
peak=    3.242 closest distance to " O   HOH Z 119 " =    4.425
peak=    3.240 closest distance to " CG2 THR A 221 " =    1.199
peak=    3.240 closest distance to " CB  ALA A 114 " =    0.894
peak=    3.239 closest distance to " CB  SER A  99 " =    1.424
peak=    3.238 closest distance to " CD  ARG A 139 " =    1.234
peak=    3.237 closest distance to " O   HOH Z 198 " =    1.305
peak=    3.235 closest distance to " CA  ALA A  84 " =    1.053
peak=    3.234 closest distance to " N   VAL A 265 " =    1.392
peak=    3.232 closest distance to " O   HOH Z  89 " =    2.004
peak=    3.231 closest distance to " CA  ASP A 162 " =    1.010
peak=    3.229 closest distance to " CB  ASN A  39 " =    0.819
peak=    3.228 closest distance to " CB  SER A 210 " =    0.823
peak=    3.226 closest distance to " CA  MET A 188 " =    1.019
peak=    3.225 closest distance to " O   HOH Z 158 " =    3.009
peak=    3.221 closest distance to " CG2 VAL A 197 " =    1.090
peak=    3.219 closest distance to " O   HOH Z 162 " =    2.063
peak=    3.219 closest distance to " CB  ASP A 124 " =    0.862
peak=    3.215 closest distance to " CB  ALA A 227 " =    1.269
peak=    3.213 closest distance to " N   GLY A 111 " =    1.276
peak=    3.213 closest distance to " CB  SER A  62 " =    1.079
peak=    3.209 closest distance to " CA  LEU A  83 " =    1.304
peak=    3.208 closest distance to " CB  ASP A 191 " =    1.179
peak=    3.205 closest distance to " CA  MET A 105 " =    1.084
peak=    3.204 closest distance to " O   HOH Z 361 " =    3.028
peak=    3.202 closest distance to " CG2 ILE A 239 " =    0.816
peak=    3.199 closest distance to " OE2 GLU A  53 " =    1.301
peak=    3.197 closest distance to " O   HOH Z 102 " =    1.206
peak=    3.195 closest distance to " CA  ASP A 140 " =    1.617
peak=    3.193 closest distance to " N   PHE A 130 " =    1.389
peak=    3.190 closest distance to " CB  ARG A 138 " =    0.832
peak=    3.189 closest distance to " CG2 VAL A 257 " =    0.765
peak=    3.186 closest distance to " CD2 LEU A 297 " =    0.756
peak=    3.184 closest distance to " NH2AARG A 275 " =    3.439
peak=    3.183 closest distance to " O   HOH Z 111 " =    1.399
peak=    3.179 closest distance to " O   LEU A 228 " =    1.813
peak=    3.175 closest distance to " O   HOH Z 128 " =    1.633
peak=    3.174 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.172 closest distance to " CB  ARG A 156 " =    1.101
peak=    3.167 closest distance to " O   HOH Z 389 " =    1.828
peak=    3.167 closest distance to " O   HOH Z 395 " =    3.130
peak=    3.166 closest distance to " CB  ARG A 219 " =    1.079
peak=    3.164 closest distance to " OE2 GLU A  53 " =    1.936
peak=    3.158 closest distance to " O   HOH Z  28 " =    1.870
peak=    3.153 closest distance to " CB  SER A 271 " =    1.371
peak=    3.149 closest distance to " O   HOH Z  20 " =    0.935
peak=    3.146 closest distance to " O   HOH Z 345 " =    3.035
peak=    3.144 closest distance to " CB  ARG A 156 " =    1.097
peak=    3.137 closest distance to " CG2 ILE A 234 " =    1.066
peak=    3.131 closest distance to " CA  LEU A 101 " =    1.361
peak=    3.131 closest distance to " CA  ASN A 176 " =    1.280
peak=    3.130 closest distance to " CA  SER A  32 " =    1.692
peak=    3.127 closest distance to " CA  ALA A 295 " =    0.999
peak=    3.124 closest distance to " O   HOH Z  35 " =    2.469
peak=    3.122 closest distance to " O   HOH Z 293 " =    2.094
peak=    3.120 closest distance to " O   ASN A 284 " =    1.759
peak=    3.112 closest distance to " OG  SER A  28 " =    1.543
peak=    3.111 closest distance to " O   HOH Z 162 " =    1.566
peak=    3.106 closest distance to " N   HIS A 108 " =    1.803
peak=    3.104 closest distance to " OE1 GLN A  55 " =    1.474
peak=    3.100 closest distance to " CA  ALA A 129 " =    1.434
peak=    3.094 closest distance to " O   HOH Z 375 " =    2.140
peak=    3.093 closest distance to " CB  MET A 105 " =    0.987
peak=    3.087 closest distance to " NE2 GLN A  58 " =    4.716
peak=    3.081 closest distance to " N   THR A  52 " =    1.176
peak=    3.073 closest distance to " O   HOH Z   3 " =    1.552
peak=    3.069 closest distance to " CD1 LEU A 167 " =    0.983
peak=    3.040 closest distance to " N   TYR A 247 " =    1.301
peak=    3.037 closest distance to " CD1 LEU A 300 " =    1.010
peak=    3.018 closest distance to " O   THR A 251 " =    1.343

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.864 - 5.954
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.864 - 5.954

peak=   -4.827 closest distance to " CD  ARG A  14 " =    3.397
peak=   -4.653 closest distance to " O   PRO A 198 " =    1.322
peak=   -4.400 closest distance to " CG1 VAL A 250 " =    2.687
peak=   -4.398 closest distance to " C   HIS A 108 " =    1.116
peak=   -4.394 closest distance to " CD2 TYR A 293 " =    1.847
peak=   -4.374 closest distance to " O   HOH Z 377 " =    2.009
peak=   -4.342 closest distance to " OG BSER A 134 " =    1.417
peak=   -4.260 closest distance to " CG  GLN A  58 " =    1.009
peak=   -4.257 closest distance to " CG2 ILE A  20 " =    2.981
peak=   -4.155 closest distance to " O   HOH Z 193 " =    0.875
peak=   -4.140 closest distance to " O   HOH Z 266 " =    5.669
peak=   -4.113 closest distance to " CG2 ILE A  49 " =    2.782
peak=   -4.050 closest distance to " O   HOH Z  52 " =    1.119
peak=   -4.020 closest distance to " O   VAL A  67 " =    2.758
peak=   -4.002 closest distance to " CB  PRO A 243 " =    2.748
peak=   -3.975 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.952 closest distance to " O   HOH Z 348 " =    2.177
peak=   -3.891 closest distance to " CE2 PHE A  61 " =    2.703
peak=   -3.877 closest distance to " CD  GLN A 223 " =    1.633
peak=   -3.874 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.850 closest distance to " CB  ALA A  43 " =    2.548
peak=   -3.822 closest distance to " CE  MET A 105 " =    2.573
peak=   -3.819 closest distance to " O   HOH Z 278 " =    1.062
peak=   -3.785 closest distance to " CA  GLY A 241 " =    2.384
peak=   -3.780 closest distance to " OXT GLY A 302 " =    3.109
peak=   -3.779 closest distance to " CD  ARG A 156 " =    2.173
peak=   -3.763 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.760 closest distance to " O   HOH Z  68 " =    1.418
peak=   -3.756 closest distance to " O   HOH Z 211 " =    1.242
peak=   -3.751 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.750 closest distance to " O   HOH Z 198 " =    1.408
peak=   -3.717 closest distance to " O   HOH Z 421 " =    3.946
peak=   -3.715 closest distance to " O   HOH Z 394 " =    1.614
peak=   -3.710 closest distance to " N   THR A  52 " =    1.736
peak=   -3.689 closest distance to " O   HOH Z 216 " =    1.089
peak=   -3.676 closest distance to " ND2 ASN A 249 " =    2.281
peak=   -3.675 closest distance to " O   SER A 210 " =    1.919
peak=   -3.667 closest distance to " O   HOH Z 150 " =    2.355
peak=   -3.666 closest distance to " O   HOH Z 165 " =    2.003
peak=   -3.663 closest distance to " O   HOH Z   6 " =    1.980
peak=   -3.654 closest distance to " O   VAL A 174 " =    2.263
peak=   -3.648 closest distance to " O   HOH Z 166 " =    1.792
peak=   -3.645 closest distance to " N   ALA A  43 " =    2.552
peak=   -3.641 closest distance to " NE2 GLN A  11 " =    1.674
peak=   -3.636 closest distance to " CD2 TYR A 247 " =    2.476
peak=   -3.625 closest distance to " O   TRP A  92 " =    2.029
peak=   -3.621 closest distance to " CE BMET A  47 " =    1.410
peak=   -3.621 closest distance to " CE3 TRP A 150 " =    2.304
peak=   -3.610 closest distance to " CB  HIS A  86 " =    1.156
peak=   -3.605 closest distance to " CD  ARG A  79 " =    1.238
peak=   -3.596 closest distance to " OE1 GLN A 223 " =    2.244
peak=   -3.588 closest distance to " CB  ALA A 184 " =    2.387
peak=   -3.587 closest distance to " NH2 ARG A  66 " =    0.964
peak=   -3.569 closest distance to " O   ALA A  34 " =    2.450
peak=   -3.557 closest distance to " O   HOH Z 102 " =    1.622
peak=   -3.557 closest distance to " CB  PHE A 192 " =    2.062
peak=   -3.556 closest distance to " CD2 HIS A 207 " =    2.185
peak=   -3.552 closest distance to " CD1 PHE A  59 " =    2.103
peak=   -3.541 closest distance to " CH2 TRP A 179 " =    1.284
peak=   -3.535 closest distance to " CZ  PHE A  38 " =    2.357
peak=   -3.531 closest distance to " O   HOH Z 106 " =    1.949
peak=   -3.530 closest distance to " O   HOH Z  13 " =    1.874
peak=   -3.530 closest distance to " O   HOH Z  64 " =    1.496
peak=   -3.529 closest distance to " CZ3 TRP A 274 " =    2.271
peak=   -3.526 closest distance to " O   HOH Z 196 " =    1.966
peak=   -3.524 closest distance to " CG1 VAL A 112 " =    2.748
peak=   -3.517 closest distance to " CD2 PHE A  61 " =    2.161
peak=   -3.513 closest distance to " O   HOH Z 131 " =    4.162
peak=   -3.511 closest distance to " O   HOH Z 191 " =    5.954
peak=   -3.502 closest distance to " O   HOH Z 203 " =    1.049
peak=   -3.495 closest distance to " O   HOH Z 113 " =    1.475
peak=   -3.487 closest distance to " CG2 VAL A 189 " =    2.160
peak=   -3.482 closest distance to " O   HOH Z 252 " =    3.887
peak=   -3.481 closest distance to " O   HOH Z 326 " =    5.073
peak=   -3.470 closest distance to " O   ALA A 227 " =    1.371
peak=   -3.462 closest distance to " CE1 TYR A 247 " =    2.740
peak=   -3.462 closest distance to " O   ILE A 106 " =    1.783
peak=   -3.458 closest distance to " O   HOH Z 174 " =    2.590
peak=   -3.457 closest distance to " O   PRO A 163 " =    2.022
peak=   -3.457 closest distance to " O   HOH Z 210 " =    1.053
peak=   -3.450 closest distance to " O   SER A   3 " =    1.010
peak=   -3.442 closest distance to " O   HOH Z 264 " =    1.763
peak=   -3.442 closest distance to " O   GLU A 152 " =    1.409
peak=   -3.441 closest distance to " CA  GLY A 203 " =    2.367
peak=   -3.436 closest distance to " CZ  TYR A 169 " =    1.870
peak=   -3.435 closest distance to " O   HOH Z 149 " =    1.893
peak=   -3.434 closest distance to " O   HOH Z 114 " =    3.397
peak=   -3.431 closest distance to " O   PHE A 218 " =    1.508
peak=   -3.430 closest distance to " O   VAL A 189 " =    1.853
peak=   -3.426 closest distance to " N   ALA A 226 " =    1.886
peak=   -3.424 closest distance to " O   HOH Z 265 " =    2.522
peak=   -3.421 closest distance to " CD2 LEU A 282 " =    2.197
peak=   -3.419 closest distance to " C   ASN A 285 " =    2.194
peak=   -3.409 closest distance to " O   HOH Z 285 " =    1.550
peak=   -3.407 closest distance to " CB  TRP A  85 " =    2.474
peak=   -3.393 closest distance to " SD  MET A 105 " =    1.026
peak=   -3.389 closest distance to " O   HOH Z 244 " =    1.430
peak=   -3.383 closest distance to " CG  GLN A  58 " =    1.260
peak=   -3.377 closest distance to " CG  TRP A 266 " =    1.955
peak=   -3.375 closest distance to " CA  ASP A  65 " =    1.420
peak=   -3.372 closest distance to " O   HOH Z 351 " =    1.727
peak=   -3.370 closest distance to " O   HOH Z 345 " =    2.993
peak=   -3.368 closest distance to " O   HOH Z 359 " =    3.038
peak=   -3.368 closest distance to " OD2 ASP A 191 " =    1.519
peak=   -3.366 closest distance to " O   HOH Z 171 " =    2.629
peak=   -3.365 closest distance to " O   HOH Z 366 " =    1.608
peak=   -3.362 closest distance to " O   HOH Z 287 " =    2.027
peak=   -3.361 closest distance to " CG  PRO A 243 " =    1.694
peak=   -3.354 closest distance to " CG  ARG A 269 " =    2.227
peak=   -3.347 closest distance to " ND2 ASN A  45 " =    2.070
peak=   -3.344 closest distance to " O   HOH Z 374 " =    2.023
peak=   -3.343 closest distance to " CB  ALA A 129 " =    2.497
peak=   -3.337 closest distance to " O   HOH Z 185 " =    2.338
peak=   -3.333 closest distance to " OG BSER A  99 " =    1.065
peak=   -3.331 closest distance to " CD  PRO A 243 " =    1.961
peak=   -3.313 closest distance to " O   HOH Z  19 " =    2.277
peak=   -3.310 closest distance to " ND2BASN A 224 " =    1.835
peak=   -3.308 closest distance to " O   SER A 276 " =    1.541
peak=   -3.305 closest distance to " CG1AVAL A  41 " =    2.575
peak=   -3.304 closest distance to " O   HOH Z 145 " =    3.176
peak=   -3.303 closest distance to " OD1 ASP A 171 " =    1.530
peak=   -3.302 closest distance to " OH  TYR A 172 " =    1.891
peak=   -3.302 closest distance to " ND2 ASN A  45 " =    1.334
peak=   -3.298 closest distance to " O   HOH Z 116 " =    1.729
peak=   -3.297 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -3.297 closest distance to " O   HOH Z 154 " =    1.800
peak=   -3.297 closest distance to " O   ALA A  10 " =    1.741
peak=   -3.280 closest distance to " OE1 GLN A 223 " =    2.140
peak=   -3.279 closest distance to " CG  GLU A  53 " =    1.639
peak=   -3.275 closest distance to " O   HOH Z 218 " =    4.009
peak=   -3.275 closest distance to " O   HOH Z 357 " =    2.324
peak=   -3.273 closest distance to " O   HOH Z 281 " =    2.608
peak=   -3.272 closest distance to " O   HOH Z 393 " =    1.349
peak=   -3.270 closest distance to " CB  ALA A  10 " =    2.377
peak=   -3.267 closest distance to " O   HOH Z 407 " =    2.708
peak=   -3.265 closest distance to " CA  GLY A  57 " =    2.150
peak=   -3.265 closest distance to " NE2 GLN A 278 " =    1.803
peak=   -3.264 closest distance to " CB  GLU A 277 " =    1.412
peak=   -3.260 closest distance to " CG  GLU A 236 " =    1.171
peak=   -3.254 closest distance to " O   ILE A 263 " =    2.180
peak=   -3.252 closest distance to " CB  PHE A  16 " =    2.453
peak=   -3.252 closest distance to " O   HOH Z 283 " =    2.519
peak=   -3.248 closest distance to " OG BSER A 134 " =    1.890
peak=   -3.247 closest distance to " O   TRP A  70 " =    1.774
peak=   -3.247 closest distance to " O   ILE A 109 " =    2.577
peak=   -3.239 closest distance to " CZ  ARG A 259 " =    0.938
peak=   -3.236 closest distance to " O   HOH Z 148 " =    3.879
peak=   -3.232 closest distance to " CD1 LEU A  25 " =    2.525
peak=   -3.232 closest distance to " OD2 ASP A 270 " =    1.085
peak=   -3.231 closest distance to " O   HOH Z 215 " =    1.311
peak=   -3.229 closest distance to " O   HOH Z 210 " =    1.975
peak=   -3.220 closest distance to " O   HOH Z 301 " =    2.541
peak=   -3.220 closest distance to " CG2 THR A  18 " =    2.878
peak=   -3.217 closest distance to " OE2 GLU A 152 " =    1.445
peak=   -3.213 closest distance to " CD  LYS A 289 " =    2.303
peak=   -3.213 closest distance to " CD1 ILE A 106 " =    2.288
peak=   -3.207 closest distance to " O   HOH Z 110 " =    1.353
peak=   -3.204 closest distance to " CG2BVAL A  41 " =    1.326
peak=   -3.202 closest distance to " O   HOH Z  60 " =    1.913
peak=   -3.200 closest distance to " O   HOH Z 314 " =    1.620
peak=   -3.200 closest distance to " O   HOH Z  88 " =    2.050
peak=   -3.198 closest distance to " CG  GLN A 103 " =    2.428
peak=   -3.195 closest distance to " O   HOH Z  38 " =    1.855
peak=   -3.194 closest distance to " CA  GLY A 133 " =    2.029
peak=   -3.193 closest distance to " O   HOH Z  63 " =    1.489
peak=   -3.192 closest distance to " CG  ASP A 286 " =    1.575
peak=   -3.192 closest distance to " CB  ALA A 248 " =    2.199
peak=   -3.192 closest distance to " CZ2 TRP A 150 " =    1.148
peak=   -3.191 closest distance to " CG  LEU A  83 " =    2.142
peak=   -3.180 closest distance to " O   HOH Z 423 " =    2.482
peak=   -3.178 closest distance to " O   HOH Z 100 " =    1.100
peak=   -3.177 closest distance to " O   HOH Z  10 " =    1.612
peak=   -3.169 closest distance to " CA  GLY A 241 " =    3.122
peak=   -3.168 closest distance to " OD1 ASN A 148 " =    1.391
peak=   -3.163 closest distance to " OD2 ASP A 171 " =    2.447
peak=   -3.159 closest distance to " CG  ASP A 132 " =    2.332
peak=   -3.158 closest distance to " OE1 GLN A 183 " =    1.473
peak=   -3.154 closest distance to " OD1 ASN A 301 " =    1.839
peak=   -3.152 closest distance to " CG  ASN A 148 " =    2.258
peak=   -3.152 closest distance to " OG BSER A 210 " =    1.622
peak=   -3.141 closest distance to " O   HOH Z 197 " =    1.995
peak=   -3.139 closest distance to " C   THR A 279 " =    1.178
peak=   -3.138 closest distance to " CG1 VAL A  78 " =    2.712
peak=   -3.135 closest distance to " O   HOH Z 166 " =    1.635
peak=   -3.135 closest distance to " O   HOH Z 150 " =    1.889
peak=   -3.134 closest distance to " CB  TYR A  15 " =    2.243
peak=   -3.131 closest distance to " CB  SER A 210 " =    1.150
peak=   -3.130 closest distance to " O   HOH Z 103 " =    1.883
peak=   -3.127 closest distance to " NE2 GLN A  88 " =    1.898
peak=   -3.126 closest distance to " O   HOH Z  91 " =    1.407
peak=   -3.121 closest distance to " O   HOH Z 250 " =    1.864
peak=   -3.120 closest distance to " O   HOH Z 246 " =    1.001
peak=   -3.120 closest distance to " O   ASN A 252 " =    1.350
peak=   -3.118 closest distance to " CG2BVAL A  41 " =    2.136
peak=   -3.113 closest distance to " OH  TYR A 172 " =    1.830
peak=   -3.108 closest distance to " O   TYR A 186 " =    1.661
peak=   -3.106 closest distance to " N   SER A 276 " =    1.398
peak=   -3.101 closest distance to " CZ  ARG A 156 " =    2.910
peak=   -3.100 closest distance to " CB  ALA A   9 " =    2.448
peak=   -3.098 closest distance to " O   HOH Z 111 " =    1.894
peak=   -3.095 closest distance to " CE  LYS A  76 " =    0.864
peak=   -3.093 closest distance to " OD2 ASP A 140 " =    1.406
peak=   -3.084 closest distance to " NH2 ARG A  79 " =    2.294
peak=   -3.080 closest distance to " O   HOH Z  43 " =    1.355
peak=   -3.079 closest distance to " O   HOH Z 252 " =    3.829
peak=   -3.075 closest distance to " CA  GLY A 241 " =    2.797
peak=   -3.074 closest distance to " O   HOH Z  71 " =    2.868
peak=   -3.067 closest distance to " O   SER A 146 " =    1.175
peak=   -3.056 closest distance to " O   HOH Z 221 " =    1.279

================= 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    :  0.4532 0.4546   6.259484e+00   6.252435e+00
   1_bss:  0.4449 0.4424   6.251101e+00   6.242273e+00
   1_xyz:  0.3047 0.3317   5.967812e+00   6.052590e+00
   1_adp:  0.2747 0.3390   5.912505e+00   6.066267e+00
   1_occ:  0.2745 0.3401   5.913062e+00   6.068418e+00
   2_bss:  0.2714 0.3386   5.908615e+00   6.065305e+00
   2_xyz:  0.2069 0.2647   5.672703e+00   5.864865e+00
   2_adp:  0.1951 0.2461   5.619212e+00   5.803909e+00
   2_occ:  0.1950 0.2458   5.618433e+00   5.803185e+00
   3_bss:  0.1951 0.2448   5.618673e+00   5.802741e+00
   3_xyz:  0.1519 0.1976   5.400407e+00   5.605513e+00
   3_adp:  0.1418 0.1933   5.356042e+00   5.580423e+00
   3_occ:  0.1417 0.1932   5.355384e+00   5.579676e+00
   4_bss:  0.1420 0.1934   5.356067e+00   5.578868e+00
   4_xyz:  0.1282 0.1761   5.268042e+00   5.496799e+00
   4_adp:  0.1246 0.1749   5.251058e+00   5.485616e+00
   4_occ:  0.1246 0.1748   5.250769e+00   5.485343e+00
   5_bss:  0.1245 0.1747   5.250913e+00   5.485507e+00
   5_xyz:  0.1191 0.1700   5.217479e+00   5.460035e+00
   5_adp:  0.1178 0.1678   5.207144e+00   5.448826e+00
   5_occ:  0.1177 0.1678   5.206997e+00   5.448805e+00
   5_bss:  0.1179 0.1676   5.206942e+00   5.447422e+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:  0.310  38.868  -1.151  -0.752   4.632  -0.000   0.000   0.000
   1_xyz:  0.310  38.868  -1.151  -0.752   4.632  -0.000   0.000   0.000
   1_adp:  0.310  38.868  -1.151  -0.752   4.632  -0.000   0.000   0.000
   1_occ:  0.310  38.868  -1.151  -0.752   4.632  -0.000   0.000   0.000
   2_bss:  0.332  60.355  -2.108  -1.134   1.568  -0.000   0.000   0.000
   2_xyz:  0.332  60.355  -2.108  -1.134   1.568  -0.000   0.000   0.000
   2_adp:  0.332  60.355  -2.108  -1.134   1.568  -0.000   0.000   0.000
   2_occ:  0.332  60.355  -2.108  -1.134   1.568  -0.000   0.000   0.000
   3_bss:  0.330  62.951  -2.923  -1.624   0.387  -0.000   0.000   0.000
   3_xyz:  0.330  62.951  -2.923  -1.624   0.387  -0.000   0.000   0.000
   3_adp:  0.330  62.951  -2.923  -1.624   0.387  -0.000   0.000   0.000
   3_occ:  0.330  62.951  -2.923  -1.624   0.387  -0.000   0.000   0.000
   4_bss:  0.333  68.704  -3.264  -1.966  -0.281  -0.000  -0.000  -0.000
   4_xyz:  0.333  68.704  -3.264  -1.966  -0.281  -0.000  -0.000  -0.000
   4_adp:  0.333  68.704  -3.264  -1.966  -0.281  -0.000  -0.000  -0.000
   4_occ:  0.333  68.704  -3.264  -1.966  -0.281  -0.000  -0.000  -0.000
   5_bss:  0.333  68.704  -3.080  -1.852  -0.304  -0.000  -0.000  -0.000
   5_xyz:  0.333  68.704  -3.080  -1.852  -0.304  -0.000  -0.000  -0.000
   5_adp:  0.333  68.704  -3.080  -1.852  -0.304  -0.000  -0.000  -0.000
   5_occ:  0.333  68.704  -3.080  -1.852  -0.304  -0.000  -0.000  -0.000
   5_bss:  0.324  63.951  -2.936  -1.775  -0.255  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.342 0.4789  0.6365    62751.891
   1_bss:  51.984 0.4948  0.6855    59836.381
   1_xyz:  35.584 0.6951  0.9184    31015.994
   1_adp:  36.398 0.6848  0.9101    32006.653
   1_occ:  36.515 0.6834  0.9081    32228.249
   2_bss:  36.190 0.6871  0.8693    31831.829
   2_xyz:  26.862 0.7910  0.9632    18334.551
   2_adp:  24.442 0.8175  0.9783    16028.027
   2_occ:  24.411 0.8178  0.9787    15993.735
   3_bss:  24.342 0.8185  0.9510    15940.682
   3_xyz:  19.002 0.8709  0.9846    10140.607
   3_adp:  18.313 0.8776  0.9818     9709.538
   3_occ:  18.296 0.8777  0.9819     9693.699
   4_bss:  18.257 0.8781  0.9667     9680.769
   4_xyz:  16.548 0.8934  0.9720     8110.422
   4_adp:  16.239 0.8963  0.9646     7941.609
   4_occ:  16.233 0.8964  0.9646     7935.856
   5_bss:  16.235 0.8963  0.9678     7939.664
   5_xyz:  15.658 0.9014  0.9721     7501.380
   5_adp:  15.417 0.9035  0.9660     7362.062
   5_occ:  15.418 0.9035  0.9658     7359.045
   5_bss:  15.403 0.9036  0.9687     7330.958
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   2.0535e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   2.0535e-01
   1_xyz:   1.588  0.013  0.098 15.607  0.007  4.106   1.3548e-01
   1_adp:   1.588  0.013  0.098 15.607  0.007  4.106   1.3548e-01
   1_occ:   1.588  0.013  0.098 15.607  0.007  4.106   1.3548e-01
   2_bss:   1.588  0.013  0.098 15.607  0.007  4.106   1.3548e-01
   2_xyz:   1.079  0.007  0.075 14.556  0.004  4.122   6.4500e-02
   2_adp:   1.079  0.007  0.075 14.556  0.004  4.122   6.4500e-02
   2_occ:   1.079  0.007  0.075 14.556  0.004  4.122   6.4500e-02
   3_bss:   1.079  0.007  0.075 14.556  0.004  4.122   6.4500e-02
   3_xyz:   1.038  0.007  0.072 14.680  0.004  4.114   6.1017e-02
   3_adp:   1.038  0.007  0.072 14.680  0.004  4.114   6.1017e-02
   3_occ:   1.038  0.007  0.072 14.680  0.004  4.114   6.1017e-02
   4_bss:   1.038  0.007  0.072 14.680  0.004  4.114   6.1017e-02
   4_xyz:   1.034  0.008  0.076 14.566  0.004  4.121   6.0495e-02
   4_adp:   1.034  0.008  0.076 14.566  0.004  4.121   6.0495e-02
   4_occ:   1.034  0.008  0.076 14.566  0.004  4.121   6.0495e-02
   5_bss:   1.034  0.008  0.076 14.566  0.004  4.121   6.0495e-02
   5_xyz:   1.049  0.008  0.078 14.520  0.004  4.114   6.2956e-02
   5_adp:   1.049  0.008  0.078 14.520  0.004  4.114   6.2956e-02
   5_occ:   1.049  0.008  0.078 14.520  0.004  4.114   6.2956e-02
   5_bss:   1.049  0.008  0.078 14.520  0.004  4.114   6.2956e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.164   2.4458e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.164   2.4458e-01
   1_xyz:   9.995  0.085  0.354 83.833  0.041  2.004   1.0053e-01
   1_adp:   9.995  0.085  0.354 83.833  0.041  2.004   1.0053e-01
   1_occ:   9.995  0.085  0.354 83.833  0.041  2.004   1.0053e-01
   2_bss:   9.995  0.085  0.354 83.833  0.041  2.004   1.0053e-01
   2_xyz:   6.765  0.044  0.247 79.351  0.046  2.311   6.2721e-02
   2_adp:   6.765  0.044  0.247 79.351  0.046  2.311   6.2721e-02
   2_occ:   6.765  0.044  0.247 79.351  0.046  2.311   6.2721e-02
   3_bss:   6.765  0.044  0.247 79.351  0.046  2.311   6.2721e-02
   3_xyz:   7.464  0.045  0.228 82.655  0.042  2.256   5.0259e-02
   3_adp:   7.464  0.045  0.228 82.655  0.042  2.256   5.0259e-02
   3_occ:   7.464  0.045  0.228 82.655  0.042  2.256   5.0259e-02
   4_bss:   7.464  0.045  0.228 82.655  0.042  2.256   5.0259e-02
   4_xyz:   7.233  0.044  0.238 83.876  0.039  2.272   4.3676e-02
   4_adp:   7.233  0.044  0.238 83.876  0.039  2.272   4.3676e-02
   4_occ:   7.233  0.044  0.238 83.876  0.039  2.272   4.3676e-02
   5_bss:   7.233  0.044  0.238 83.876  0.039  2.272   4.3676e-02
   5_xyz:   7.496  0.048  0.269 81.727  0.033  2.327   4.1920e-02
   5_adp:   7.496  0.048  0.269 81.727  0.033  2.327   4.1920e-02
   5_occ:   7.496  0.048  0.269 81.727  0.033  2.327   4.1920e-02
   5_bss:   7.496  0.048  0.269 81.727  0.033  2.327   4.1920e-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:  98.18   0.00  18.73  85.37   0.00  14.54  98.18   3.20  41.55
   1_occ:  98.18   0.00  18.73  85.37   0.00  14.54  98.18   3.20  41.55
   2_bss:  98.18   0.00  18.73  85.37   0.00  14.54  98.18   3.20  41.55
   2_xyz:  98.18   0.00  18.73  85.37   0.00  14.54  98.18   3.20  41.55
   2_adp:  94.65   0.75  18.03  78.61   0.75  13.74  94.65   5.80  41.40
   2_occ:  94.65   0.75  18.03  78.61   0.75  13.74  94.65   5.80  41.40
   3_bss:  94.65   0.75  18.03  78.61   0.75  13.74  94.65   5.80  41.40
   3_xyz:  94.65   0.75  18.03  78.61   0.75  13.74  94.65   5.80  41.40
   3_adp:  94.00   0.31  18.20  82.08   0.31  13.47  94.00   6.02  43.96
   3_occ:  94.00   0.31  18.20  82.08   0.31  13.47  94.00   6.02  43.96
   4_bss:  94.00   0.31  18.20  82.08   0.31  13.47  94.00   6.02  43.96
   4_xyz:  94.00   0.31  18.20  82.08   0.31  13.47  94.00   6.02  43.96
   4_adp: 102.36   0.00  18.27  93.05   0.00  13.31 102.36   5.34  45.25
   4_occ: 102.36   0.00  18.27  93.05   0.00  13.31 102.36   5.34  45.25
   5_bss: 102.36   0.00  18.27  93.05   0.00  13.31 102.36   5.34  45.25
   5_xyz: 102.36   0.00  18.27  93.05   0.00  13.31 102.36   5.34  45.25
   5_adp: 107.29   0.00  17.86  96.06   0.54  13.08 107.29   0.00  43.86
   5_occ: 107.29   0.00  17.86  96.06   0.54  13.08 107.29   0.00  43.86
   5_bss: 107.30   0.00  17.86  96.06   0.54  13.08 107.30   0.00  43.86
------------------------------------------------------------------------
 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:    2.444    0.011    0.449
   1_adp:    2.444    0.011    0.449
   1_occ:    2.444    0.011    0.449
   2_bss:    2.444    0.011    0.449
   2_xyz:    2.139    0.037    0.534
   2_adp:    2.139    0.037    0.534
   2_occ:    2.139    0.037    0.534
   3_bss:    2.139    0.037    0.534
   3_xyz:    1.915    0.063    0.641
   3_adp:    1.915    0.063    0.641
   3_occ:    1.915    0.063    0.641
   4_bss:    1.915    0.063    0.641
   4_xyz:    1.683    0.029    0.674
   4_adp:    1.683    0.029    0.674
   4_occ:    1.683    0.029    0.674
   5_bss:    1.683    0.029    0.674
   5_xyz:    1.497    0.109    0.696
   5_adp:    1.497    0.109    0.696
   5_occ:    1.497    0.109    0.696
   5_bss:    1.497    0.109    0.696
------------------------------------------------------------------------

CPU time actual refinement: 342.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/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_208/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_208/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.94 
  Macro-tasks:
    bulk solvent and scale       = 38.65  
    individual site refinement   = 140.02 
    weights calculation          = 30.49  
    collect and process          = 6.72   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 216.02 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 109.84 
    alpha_beta                      = 8.44   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 118.36 
    fmodel                         = 6.58   
    r_factors                      = 0.19   
    phase_errors                   = 10.81  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 258.12 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.842 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    655 calls, 109.48 s
gradients_fft:          600 calls, 104.87 s

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

# Date 2008-01-16 Time 04:16:01 PST -0800 (1200485761.05 s)
Start R-work = 0.4532, R-free = 0.4546 (no bulk solvent and anisotropic scale)
Final R-work = 0.1407, R-free = 0.1849 (no bulk solvent and anisotropic scale)

Start R-work = 0.4449, R-free = 0.4424
Final R-work = 0.1179, R-free = 0.1676