# Date 2008-01-16 Time 06:03:53 PST -0800 (1200492233.32 s)
#phil __OFF__

Command line arguments: "../989.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7545
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 989

-------------------------------------------------------------------------------
  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: (71.3037, 45.9914, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.96413
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913964

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   1.9641

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: (71.3037, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.96413
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913964

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2596 -  4.2049 [2240/2266]  2017   223  10.0%
  bin  2:  4.2049 -  3.3491 [2167/2187]  1953   214   9.9%
  bin  3:  3.3491 -  2.9292 [2116/2135]  1902   214  10.1%
  bin  4:  2.9292 -  2.6629 [2116/2146]  1895   221  10.4%
  bin  5:  2.6629 -  2.4729 [2107/2126]  1901   206   9.8%
  bin  6:  2.4729 -  2.3276 [2072/2097]  1865   207  10.0%
  bin  7:  2.3276 -  2.2114 [2091/2119]  1883   208   9.9%
  bin  8:  2.2114 -  2.1154 [2066/2102]  1856   210  10.2%
  bin  9:  2.1154 -  2.0342 [2012/2094]  1819   193   9.6%
  bin 10:  2.0342 -  1.9641 [ 602/2100]   539    63  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 36
        2.42 -     3.04: 2203
        3.04 -     3.66: 4662
        3.66 -     4.28: 8957
        4.28 -     4.90: 12209
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.972 3.040 -x,y-1/2,-z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28062 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_989/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/model_refine_001.geo

CPU time processing inputs: 9.04


============================ 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 = 71.30375 45.9914 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 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4869   r_free= 0.4897   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.297547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6909 0.99   1455  163 0.3953 0.3698      6.6168      6.5565|
|  2:  4.6909 -  3.7414 0.99   1399  154 0.4277 0.4301      6.8526      6.8379|
|  3:  3.7414 -  3.2737 0.99   1376  154 0.4503 0.4232      6.6744      6.6661|
|  4:  3.2737 -  2.9768 0.99   1380  153 0.4888 0.5184      6.5367      6.5374|
|  5:  2.9768 -  2.7648 0.99   1346  150 0.5224 0.5238       6.371       6.395|
|  6:  2.7648 -  2.6027 0.99   1369  150 0.5168 0.5459      6.2789      6.2303|
|  7:  2.6027 -  2.4729 0.99   1343  154 0.5257 0.5261      6.2367      6.1803|
|  8:  2.4729 -  2.3657 0.98   1327  148 0.5382 0.5541      6.1775      6.1582|
|  9:  2.3657 -  2.2749 0.98   1338  145 0.5326 0.5484      6.1327      6.2086|
| 10:  2.2749 -  2.1966 1.00   1349  156 0.5431 0.5501       6.064      6.0716|
| 11:  2.1966 -  2.1281 0.98   1314  143 0.5193 0.5027      6.0245      6.0403|
| 12:  2.1281 -  2.0674 0.98   1334  143 0.5360 0.5444      5.9313      5.9347|
| 13:  2.0674 -  2.0131 0.79   1058  118 0.5289 0.5194      5.8903      5.7948|
| 14:  2.0131 -  1.9641 0.18    242   28 0.5313 0.5315      5.8509      5.9256|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2596 -  4.6909  1455   163  0.72  32.45   0.80     0.77      67622.01|
|  2:  4.6909 -  3.7414  1399   154  0.69  36.34   0.88     0.79     117320.62|
|  3:  3.7414 -  3.2737  1376   154  0.52  49.91   0.90     0.71     132943.51|
|  4:  3.2737 -  2.9768  1380   153  0.38  60.86   0.87     0.55     128145.22|
|  5:  2.9768 -  2.7648  1346   150  0.31  66.85   0.85     0.46      97913.42|
|  6:  2.7648 -  2.6027  1369   150  0.27  69.63   0.88     0.40      83082.71|
|  7:  2.6027 -  2.4729  1343   154  0.28  69.33   0.88     0.39      72186.80|
|  8:  2.4729 -  2.3657  1327   148  0.25  71.59   0.87     0.37      66169.43|
|  9:  2.3657 -  2.2749  1338   145  0.25  71.68   0.90     0.37      62683.83|
| 10:  2.2749 -  2.1966  1349   156  0.24  72.32   0.89     0.37      55292.65|
| 11:  2.1966 -  2.1281  1314   143  0.22  73.57   0.93     0.34      53333.13|
| 12:  2.1281 -  2.0674  1334   143  0.22  73.48   0.88     0.36      47038.82|
| 13:  2.0674 -  2.0131  1058   118  0.25  71.70   0.92     0.41      40944.95|
| 14:  2.0131 -  1.9641   242    28  0.38  61.89   0.95     0.54      29614.47|
|alpha:            min =        0.34 max =            0.79 mean =         0.49|
|beta:             min =    29614.47 max =       132943.51 mean =     79089.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.57|
|phase err.(test): min =        0.00 max =           89.71 mean =        62.86|
|-----------------------------------------------------------------------------|

============================== 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 = 13.218168             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.858   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.950874              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.849   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      197 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2006 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1855 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2807 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4611 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4346 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5555 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6654 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.313 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    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 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4869   r_free= 0.4897   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.297547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4864   ksol= 0.35   Bsol= 80.00   scale= 0.912   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.50,3.44,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.294890                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.667504             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.668   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.705653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.395   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4789      final r-factor (work) = 0.4038          |
| start r-factor (free) = 0.4864      final r-factor (free) = 0.4379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.7142 = 10.67 * 0.50 * 6.2885 + 1.00 * 0.1728                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.2949 = 10.67 * 0.50 * 6.2191 + 1.00 * 0.1236                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4038      final r-factor (work) = 0.3679          |
| start r-factor (free) = 0.4379      final r-factor (free) = 0.4537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6138 = 1.71 * 1.00 * 6.2191 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5042 = 1.71 * 1.00 * 6.1447 + 1.00 * 0.0235                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.55  20.95    None  None   None       |
|    all(noH): 2823   0      0.00    100.55  20.95    None  None   None       |
|    Sol.    : 438    0      0.00    100.55  38.99    None  None   None       |
|    Mac.    : 2385   0      0.00    91.53   17.63    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 -  10.055:  782   |   5:    50.273 -  60.328:   98        |
|      1:    10.055 -  20.109:  834   |   6:    60.328 -  70.383:   64        |
|      2:    20.109 -  30.164:  586   |   7:    70.383 -  80.437:   29        |
|      3:    30.164 -  40.219:  278   |   8:    80.437 -  90.492:    6        |
|      4:    40.219 -  50.273:  144   |   9:    90.492 - 100.547:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3679 r_free = 0.4537             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3673 r_free = 0.4552             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3673   r_free= 0.4552   ksol= 0.35   Bsol= 80.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.50,3.44,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.152274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3679   r_free= 0.4543   ksol= 0.37   Bsol= 96.87   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.36,2.25,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.154825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.354647             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.727592              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.424  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3679      final r-factor (work) = 0.2980          |
| start r-factor (free) = 0.4543      final r-factor (free) = 0.3704          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1631 = 13.35 * 0.50 * 6.1461 + 1.00 * 0.1233                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.7847 = 13.35 * 0.50 * 6.0904 + 1.00 * 0.1168                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2980      final r-factor (work) = 0.2735          |
| start r-factor (free) = 0.3704      final r-factor (free) = 0.3515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4548 = 0.73 * 1.00 * 6.0904 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3452 = 0.73 * 1.00 * 5.9516 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.23   20.11    None  None   None       |
|    all(noH): 2823   0      0.00    94.23   20.11    None  None   None       |
|    Sol.    : 438    0      0.00    94.23   41.81    None  None   None       |
|    Mac.    : 2385   0      0.00    79.90   16.13    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 -   9.423:  756   |   5:    47.115 -  56.538:   99        |
|      1:     9.423 -  18.846:  929   |   6:    56.538 -  65.961:   67        |
|      2:    18.846 -  28.269:  526   |   7:    65.961 -  75.384:   29        |
|      3:    28.269 -  37.692:  224   |   8:    75.384 -  84.808:   20        |
|      4:    37.692 -  47.115:  171   |   9:    84.808 -  94.231:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2735 r_free = 0.3515             target_work(ml) = 5.928         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2734 r_free = 0.3513             target_work(ml) = 5.928         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2734   r_free= 0.3513   ksol= 0.37   Bsol= 96.87   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.36,2.25,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.928041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2734   r_free= 0.3510   ksol= 0.36   Bsol= 90.86   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-1.39,0.83,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.927978                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.415985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.502  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.703850              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2734      final r-factor (work) = 0.2309          |
| start r-factor (free) = 0.3510      final r-factor (free) = 0.3028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2589 = 4.42 * 0.50 * 5.9520 + 1.00 * 0.1168                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0135 = 4.42 * 0.50 * 5.8662 + 1.00 * 0.0610                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2309      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.3028      final r-factor (free) = 0.2906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1438 = 0.70 * 1.00 * 5.8662 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0701 = 0.70 * 1.00 * 5.7623 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.33   19.77    None  None   None       |
|    all(noH): 2823   0      0.00    98.33   19.77    None  None   None       |
|    Sol.    : 438    0      1.81    98.33   45.39    None  None   None       |
|    Mac.    : 2385   0      0.00    88.02   15.07    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 -   9.833:  859   |   5:    49.167 -  59.000:  111        |
|      1:     9.833 -  19.667: 1029   |   6:    59.000 -  68.833:   70        |
|      2:    19.667 -  29.500:  386   |   7:    68.833 -  78.666:   36        |
|      3:    29.500 -  39.333:  180   |   8:    78.666 -  88.500:   19        |
|      4:    39.333 -  49.167:  132   |   9:    88.500 -  98.333:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2157 r_free = 0.2906             target_work(ml) = 5.744         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2157 r_free = 0.2903             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2157   r_free= 0.2903   ksol= 0.36   Bsol= 90.86   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-1.39,0.83,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.742949                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2157   r_free= 0.2902   ksol= 0.35   Bsol= 94.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.20,-0.00,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.742671                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.184021              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.056  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561686              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.525  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2157      final r-factor (work) = 0.1750          |
| start r-factor (free) = 0.2902      final r-factor (free) = 0.2345          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2370 = 3.18 * 0.50 * 5.7638 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0709 = 3.18 * 0.50 * 5.6588 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1628          |
| start r-factor (free) = 0.2345      final r-factor (free) = 0.2200          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1927 = 0.56 * 1.00 * 5.6588 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1084 = 0.56 * 1.00 * 5.5113 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.09  19.14    None  None   None       |
|    all(noH): 2823   0      0.00    100.09  19.14    None  None   None       |
|    Sol.    : 438    0      4.90    100.09  46.89    None  None   None       |
|    Mac.    : 2385   0      0.00    90.28   14.04    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 -  10.009:  950   |   5:    50.047 -  60.056:  104        |
|      1:    10.009 -  20.019: 1098   |   6:    60.056 -  70.065:   77        |
|      2:    20.019 -  30.028:  287   |   7:    70.065 -  80.075:   39        |
|      3:    30.028 -  40.037:  120   |   8:    80.075 -  90.084:   15        |
|      4:    40.037 -  50.047:  131   |   9:    90.084 - 100.093:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1628 r_free = 0.2200             target_work(ml) = 5.481         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1627 r_free = 0.2200             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2200   ksol= 0.35   Bsol= 94.22   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.20,-0.00,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.480239                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1631   r_free= 0.2203   ksol= 0.33   Bsol= 80.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.66,-0.46,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.479162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.057864              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.659  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.984359              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.077  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1631      final r-factor (work) = 0.1415          |
| start r-factor (free) = 0.2203      final r-factor (free) = 0.1953          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4896 = 3.06 * 0.50 * 5.5121 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3511 = 3.06 * 0.50 * 5.4219 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.1953      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7715 = 1.98 * 1.00 * 5.4219 + 1.00 * 0.0126                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5956 = 1.98 * 1.00 * 5.3325 + 1.00 * 0.0140                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.61  19.33    None  None   None       |
|    all(noH): 2823   0      0.00    109.61  19.33    None  None   None       |
|    Sol.    : 438    0      6.31    109.61  50.01    None  None   None       |
|    Mac.    : 2385   0      0.00    97.96   13.70    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 -  10.961: 1173   |   5:    54.807 -  65.769:   86        |
|      1:    10.961 -  21.923: 1007   |   6:    65.769 -  76.730:   80        |
|      2:    21.923 -  32.884:  212   |   7:    76.730 -  87.691:   39        |
|      3:    32.884 -  43.846:  110   |   8:    87.691 -  98.653:   19        |
|      4:    43.846 -  54.807:   93   |   9:    98.653 - 109.614:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1348 r_free = 0.1902             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1348 r_free = 0.1903             target_work(ml) = 5.316         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1348   r_free= 0.1903   ksol= 0.33   Bsol= 80.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.66,-0.46,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.315503                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6909 0.99   1455  163 0.0940 0.1426      5.3764      5.6392|
|  2:  4.6909 -  3.7414 0.99   1399  154 0.0884 0.1283      5.4969      5.7486|
|  3:  3.7414 -  3.2737 0.99   1376  154 0.1261 0.1845      5.6084      5.9411|
|  4:  3.2737 -  2.9768 0.99   1380  153 0.1598 0.2091      5.6462      5.8194|
|  5:  2.9768 -  2.7648 0.99   1346  150 0.1641 0.2156       5.519      5.7381|
|  6:  2.7648 -  2.6027 0.99   1369  150 0.1600 0.2381      5.4095      5.6398|
|  7:  2.6027 -  2.4729 0.99   1343  154 0.1523 0.2030      5.3308      5.4957|
|  8:  2.4729 -  2.3657 0.98   1327  148 0.1550 0.2135      5.2877      5.5329|
|  9:  2.3657 -  2.2749 0.98   1338  145 0.1553 0.2126      5.2427      5.4555|
| 10:  2.2749 -  2.1966 1.00   1349  156 0.1406 0.1930      5.1214      5.3089|
| 11:  2.1966 -  2.1281 0.98   1314  143 0.1368 0.2160      5.0907      5.4489|
| 12:  2.1281 -  2.0674 0.98   1334  143 0.1392 0.2216      5.0219      5.2822|
| 13:  2.0674 -  2.0131 0.79   1058  118 0.1302 0.1901      4.9218      5.0942|
| 14:  2.0131 -  1.9641 0.18    242   28 0.1185 0.1771      4.7983      5.0969|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2596 -  4.6909  1455   163  0.94   9.62   0.96     0.93       7870.10|
|  2:  4.6909 -  3.7414  1399   154  0.95   9.12   1.02     1.01      10775.39|
|  3:  3.7414 -  3.2737  1376   154  0.91  14.19   1.04     1.04      13665.17|
|  4:  3.2737 -  2.9768  1380   153  0.88  18.64   1.03     1.00      15611.35|
|  5:  2.9768 -  2.7648  1346   150  0.86  20.04   1.01     0.98      12694.33|
|  6:  2.7648 -  2.6027  1369   150  0.85  21.20   0.99     0.95      10605.72|
|  7:  2.6027 -  2.4729  1343   154  0.87  19.64   1.00     0.96       9042.85|
|  8:  2.4729 -  2.3657  1327   148  0.86  20.31   1.00     0.97       8305.93|
|  9:  2.3657 -  2.2749  1338   145  0.86  20.63   1.00     0.95       7583.19|
| 10:  2.2749 -  2.1966  1349   156  0.87  19.77   1.01     0.97       6340.11|
| 11:  2.1966 -  2.1281  1314   143  0.87  19.92   0.99     0.93       6066.68|
| 12:  2.1281 -  2.0674  1334   143  0.87  19.97   1.00     0.99       5485.15|
| 13:  2.0674 -  2.0131  1058   118  0.87  20.12   0.99     0.98       4636.29|
| 14:  2.0131 -  1.9641   242    28  0.91  15.32   0.98     0.96       3298.29|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3298.29 max =        15611.35 mean =      9151.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.78|
|phase err.(test): min =        0.00 max =           89.64 mean =        17.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1903   ksol= 0.33   Bsol= 80.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.82,-0.54,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.315194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1903   ksol= 0.33   Bsol= 80.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.82,-0.54,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.315194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6909 0.99   1455  163 0.0955 0.1408      5.3739      5.6165|
|  2:  4.6909 -  3.7414 0.99   1399  154 0.0891 0.1281      5.4969      5.7501|
|  3:  3.7414 -  3.2737 0.99   1376  154 0.1264 0.1839      5.6082      5.9398|
|  4:  3.2737 -  2.9768 0.99   1380  153 0.1598 0.2094      5.6466      5.8201|
|  5:  2.9768 -  2.7648 0.99   1346  150 0.1640 0.2156      5.5189      5.7381|
|  6:  2.7648 -  2.6027 0.99   1369  150 0.1600 0.2383      5.4092      5.6397|
|  7:  2.6027 -  2.4729 0.99   1343  154 0.1524 0.2027      5.3308      5.4953|
|  8:  2.4729 -  2.3657 0.98   1327  148 0.1550 0.2135      5.2875      5.5334|
|  9:  2.3657 -  2.2749 0.98   1338  145 0.1552 0.2125      5.2426      5.4552|
| 10:  2.2749 -  2.1966 1.00   1349  156 0.1405 0.1931      5.1212      5.3094|
| 11:  2.1966 -  2.1281 0.98   1314  143 0.1367 0.2161      5.0905      5.4488|
| 12:  2.1281 -  2.0674 0.98   1334  143 0.1392 0.2216      5.0219       5.282|
| 13:  2.0674 -  2.0131 0.79   1058  118 0.1302 0.1897      4.9213      5.0933|
| 14:  2.0131 -  1.9641 0.18    242   28 0.1186 0.1769      4.7975       5.095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2596 -  4.6909  1455   163  0.94   9.35   0.96     0.93       7611.30|
|  2:  4.6909 -  3.7414  1399   154  0.95   9.02   1.02     1.01      10585.81|
|  3:  3.7414 -  3.2737  1376   154  0.91  14.15   1.04     1.04      13586.82|
|  4:  3.2737 -  2.9768  1380   153  0.88  18.64   1.02     1.00      15615.68|
|  5:  2.9768 -  2.7648  1346   150  0.86  20.05   1.00     0.98      12703.51|
|  6:  2.7648 -  2.6027  1369   150  0.85  21.19   0.99     0.94      10602.53|
|  7:  2.6027 -  2.4729  1343   154  0.87  19.64   1.00     0.96       9039.97|
|  8:  2.4729 -  2.3657  1327   148  0.86  20.31   1.00     0.96       8300.12|
|  9:  2.3657 -  2.2749  1338   145  0.86  20.64   1.00     0.94       7588.21|
| 10:  2.2749 -  2.1966  1349   156  0.87  19.77   1.00     0.96       6342.65|
| 11:  2.1966 -  2.1281  1314   143  0.87  19.92   0.99     0.93       6069.64|
| 12:  2.1281 -  2.0674  1334   143  0.87  19.97   0.99     0.98       5483.75|
| 13:  2.0674 -  2.0131  1058   118  0.87  20.10   0.99     0.97       4629.48|
| 14:  2.0131 -  1.9641   242    28  0.91  15.27   0.97     0.95       3286.16|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3286.16 max =        15615.68 mean =      9108.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.74|
|phase err.(test): min =        0.00 max =           89.58 mean =        17.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.62  19.34    None  None   None       |
|    all(noH): 2823   0      0.00    109.62  19.34    None  None   None       |
|    Sol.    : 438    0      6.31    109.62  50.02    None  None   None       |
|    Mac.    : 2385   0      0.00    97.96   13.70    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 -  10.964: 1173   |   5:    54.810 -  65.772:   86        |
|      1:    10.964 -  21.926: 1007   |   6:    65.772 -  76.733:   80        |
|      2:    21.926 -  32.887:  212   |   7:    76.733 -  87.694:   39        |
|      3:    32.887 -  43.849:  110   |   8:    87.694 -  98.656:   19        |
|      4:    43.849 -  54.810:   93   |   9:    98.656 - 109.617:    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)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.638 - 5.751
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 347 from: 351
   mapped sites are within: 0.743 - 5.751

peak=    8.017 closest distance to " O   HOH Z 103 " =    1.200
peak=    5.709 closest distance to " O   HOH Z 222 " =    1.555
peak=    5.243 closest distance to " NE2 GLN A  11 " =    1.198
peak=    5.112 closest distance to " O   HOH Z 287 " =    2.173
peak=    5.098 closest distance to " O   HOH Z 245 " =    1.146
peak=    5.096 closest distance to " OE1 GLN A  73 " =    2.105
peak=    5.067 closest distance to " O   HOH Z  65 " =    1.469
peak=    5.062 closest distance to " CG  PRO A  90 " =    1.421
peak=    5.056 closest distance to " O   HOH Z  63 " =    1.739
peak=    5.005 closest distance to " O   HOH Z 131 " =    1.450
peak=    4.955 closest distance to " O   HOH Z 182 " =    1.264
peak=    4.948 closest distance to " O   HOH Z 207 " =    1.167
peak=    4.930 closest distance to " O   HOH Z 417 " =    2.390
peak=    4.881 closest distance to " CB  SER A  63 " =    1.430
peak=    4.827 closest distance to " O   HOH Z   7 " =    1.754
peak=    4.778 closest distance to " CG  PRO A  54 " =    1.465
peak=    4.760 closest distance to " O   HOH Z 295 " =    1.339
peak=    4.692 closest distance to " O   HOH Z  66 " =    1.056
peak=    4.661 closest distance to " O   HOH Z 427 " =    2.396
peak=    4.608 closest distance to " O   HOH Z 126 " =    2.029
peak=    4.554 closest distance to " O   HOH Z 403 " =    1.429
peak=    4.532 closest distance to " CB  PRO A  54 " =    1.181
peak=    4.521 closest distance to " O   HOH Z 105 " =    1.152
peak=    4.480 closest distance to " O   HOH Z 296 " =    1.235
peak=    4.471 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.457 closest distance to " NH1AARG A 145 " =    1.278
peak=    4.456 closest distance to " O   HOH Z  70 " =    1.065
peak=    4.450 closest distance to " CB  GLN A 223 " =    1.572
peak=    4.439 closest distance to " O   HOH Z  46 " =    1.104
peak=    4.439 closest distance to " O   PRO A 198 " =    1.298
peak=    4.384 closest distance to " CB  SER A 216 " =    1.148
peak=    4.358 closest distance to " O   HOH Z  11 " =    1.065
peak=    4.334 closest distance to " O   HOH Z 374 " =    1.197
peak=    4.317 closest distance to " O   HOH Z  67 " =    1.483
peak=    4.304 closest distance to " CB  PRO A  90 " =    1.148
peak=    4.291 closest distance to " O   HOH Z  69 " =    1.526
peak=    4.283 closest distance to " O   HOH Z 130 " =    1.074
peak=    4.247 closest distance to " NZ  LYS A 117 " =    3.023
peak=    4.239 closest distance to " CZ3 TRP A 266 " =    1.186
peak=    4.225 closest distance to " O   HOH Z 414 " =    2.247
peak=    4.208 closest distance to " O   HOH Z 414 " =    1.365
peak=    4.160 closest distance to " O   HOH Z 369 " =    2.147
peak=    4.159 closest distance to " O   HOH Z 117 " =    0.994
peak=    4.156 closest distance to " O   HOH Z 380 " =    1.987
peak=    4.144 closest distance to " CG2 THR A 221 " =    1.202
peak=    4.140 closest distance to " CG  PRO A 198 " =    1.232
peak=    4.139 closest distance to " CD  ARG A 159 " =    0.825
peak=    4.123 closest distance to " O   HOH Z 273 " =    1.419
peak=    4.120 closest distance to " O   HOH Z 375 " =    1.042
peak=    4.097 closest distance to " O   HOH Z 425 " =    1.598
peak=    4.096 closest distance to " O   HOH Z 132 " =    1.253
peak=    4.088 closest distance to " O   HOH Z  61 " =    1.766
peak=    4.087 closest distance to " O   HOH Z 411 " =    3.256
peak=    4.073 closest distance to " O   HOH Z 147 " =    1.120
peak=    4.039 closest distance to " O   HOH Z 385 " =    0.992
peak=    4.031 closest distance to " O   HOH Z 419 " =    2.025
peak=    4.028 closest distance to " CG  LEU A 167 " =    1.324
peak=    4.016 closest distance to " NH2 ARG A  56 " =    1.049
peak=    4.012 closest distance to " O   HOH Z 232 " =    2.149
peak=    3.999 closest distance to " ND2BASN A 224 " =    0.898
peak=    3.984 closest distance to " CB  ALA A 114 " =    0.852
peak=    3.982 closest distance to " O   HOH Z  39 " =    1.103
peak=    3.980 closest distance to " OE1 GLN A 240 " =    1.600
peak=    3.976 closest distance to " O   HOH Z  77 " =    1.300
peak=    3.975 closest distance to " CE3 TRP A 274 " =    1.423
peak=    3.972 closest distance to " O   HOH Z 145 " =    1.866
peak=    3.969 closest distance to " O   HOH Z 298 " =    2.234
peak=    3.933 closest distance to " O   HOH Z   9 " =    1.971
peak=    3.927 closest distance to " CA  ASN A 127 " =    1.242
peak=    3.921 closest distance to " O   GLN A  55 " =    1.585
peak=    3.907 closest distance to " CB  SER A 141 " =    1.039
peak=    3.904 closest distance to " NE2 HIS A 207 " =    1.024
peak=    3.892 closest distance to " CA  VAL A 125 " =    1.169
peak=    3.882 closest distance to " OE1 GLN A  77 " =    1.215
peak=    3.877 closest distance to " N   TYR A  15 " =    1.108
peak=    3.874 closest distance to " O   HOH Z 193 " =    1.691
peak=    3.867 closest distance to " CB  ALA A  43 " =    0.903
peak=    3.859 closest distance to " CA  ALA A  51 " =    1.026
peak=    3.853 closest distance to " O   HOH Z 359 " =    1.446
peak=    3.850 closest distance to " O   HOH Z  91 " =    2.429
peak=    3.847 closest distance to " O   HOH Z 139 " =    1.180
peak=    3.832 closest distance to " O   HOH Z  88 " =    4.024
peak=    3.830 closest distance to " O   HOH Z 316 " =    3.015
peak=    3.827 closest distance to " O   TYR A 116 " =    1.310
peak=    3.823 closest distance to " CA  TYR A  30 " =    1.190
peak=    3.821 closest distance to " O   HOH Z 211 " =    1.560
peak=    3.810 closest distance to " O   HOH Z  28 " =    1.129
peak=    3.808 closest distance to " CB  MET A  40 " =    0.860
peak=    3.806 closest distance to " O   HOH Z 255 " =    1.003
peak=    3.805 closest distance to " CZ  PHE A 218 " =    1.215
peak=    3.791 closest distance to " O   HOH Z 135 " =    1.448
peak=    3.764 closest distance to " CA  ARG A 195 " =    1.435
peak=    3.763 closest distance to " O   HOH Z 327 " =    1.820
peak=    3.760 closest distance to " CE  LYS A 119 " =    1.187
peak=    3.759 closest distance to " CB  TRP A 266 " =    1.076
peak=    3.752 closest distance to " NZ  LYS A 166 " =    0.943
peak=    3.750 closest distance to " CB  LYS A 290 " =    1.027
peak=    3.748 closest distance to " O   HOH Z 127 " =    1.112
peak=    3.739 closest distance to " CE  MET A  93 " =    1.399
peak=    3.734 closest distance to " O   HOH Z 278 " =    1.121
peak=    3.730 closest distance to " CB  ALA A 233 " =    1.091
peak=    3.729 closest distance to " O   HOH Z  97 " =    1.469
peak=    3.729 closest distance to " CD  LYS A  76 " =    1.718
peak=    3.722 closest distance to " N   VAL A 296 " =    1.881
peak=    3.715 closest distance to " N   GLN A 278 " =    1.196
peak=    3.708 closest distance to " O   HOH Z 158 " =    1.229
peak=    3.701 closest distance to " O   HOH Z 183 " =    1.538
peak=    3.698 closest distance to " CB  ASN A  39 " =    0.924
peak=    3.682 closest distance to " CB  PHE A  61 " =    1.108
peak=    3.681 closest distance to " O   HOH Z 218 " =    1.758
peak=    3.673 closest distance to " O   HOH Z 368 " =    3.814
peak=    3.672 closest distance to " C   GLN A  73 " =    1.123
peak=    3.672 closest distance to " O   HOH Z 126 " =    1.563
peak=    3.666 closest distance to " O   HOH Z 181 " =    2.268
peak=    3.661 closest distance to " O   HOH Z 427 " =    1.121
peak=    3.658 closest distance to " CD  ARG A 195 " =    3.531
peak=    3.649 closest distance to " O   HOH Z 180 " =    2.200
peak=    3.649 closest distance to " O   HOH Z 431 " =    1.145
peak=    3.649 closest distance to " OG ASER A 212 " =    1.465
peak=    3.648 closest distance to " O   HOH Z 422 " =    1.061
peak=    3.646 closest distance to " O   HOH Z  26 " =    1.401
peak=    3.640 closest distance to " C   ASN A 209 " =    1.528
peak=    3.640 closest distance to " O   HOH Z 410 " =    1.544
peak=    3.634 closest distance to " O   HOH Z 240 " =    1.992
peak=    3.624 closest distance to " CG  GLN A  58 " =    1.292
peak=    3.622 closest distance to " CA  TRP A  92 " =    1.168
peak=    3.613 closest distance to " O   HOH Z  92 " =    1.282
peak=    3.607 closest distance to " CA  ALA A 160 " =    1.082
peak=    3.605 closest distance to " CG  PRO A 243 " =    1.133
peak=    3.602 closest distance to " O   HOH Z 201 " =    1.779
peak=    3.601 closest distance to " O   HOH Z 216 " =    3.788
peak=    3.589 closest distance to " CB  GLU A 128 " =    1.053
peak=    3.588 closest distance to " OH  TYR A 116 " =    1.948
peak=    3.586 closest distance to " ND2 ASN A  60 " =    2.820
peak=    3.577 closest distance to " CB  SER A  99 " =    0.896
peak=    3.574 closest distance to " CB  VAL A 265 " =    1.348
peak=    3.566 closest distance to " N   GLU A 152 " =    1.440
peak=    3.566 closest distance to " O   HOH Z 361 " =    1.442
peak=    3.555 closest distance to " CG2 VAL A 257 " =    0.886
peak=    3.549 closest distance to " O   HOH Z 213 " =    2.161
peak=    3.547 closest distance to " O   MET A 105 " =    1.706
peak=    3.543 closest distance to " CA  TYR A 116 " =    1.419
peak=    3.541 closest distance to " O   HOH Z 357 " =    2.021
peak=    3.541 closest distance to " CB  VAL A 202 " =    1.489
peak=    3.541 closest distance to " OE2 GLU A  53 " =    1.155
peak=    3.540 closest distance to " CZ  PHE A  38 " =    1.258
peak=    3.532 closest distance to " CG1 VAL A 296 " =    1.202
peak=    3.529 closest distance to " O   HOH Z 119 " =    1.687
peak=    3.525 closest distance to " CG  TRP A 179 " =    2.234
peak=    3.522 closest distance to " CB  PHE A 130 " =    1.081
peak=    3.520 closest distance to " O   HOH Z 393 " =    1.479
peak=    3.513 closest distance to " CB  ASN A  60 " =    0.939
peak=    3.513 closest distance to " CB  SER A   3 " =    1.608
peak=    3.511 closest distance to " CB  ASP A 124 " =    0.898
peak=    3.510 closest distance to " O   HOH Z 102 " =    1.090
peak=    3.508 closest distance to " O   HOH Z  53 " =    2.303
peak=    3.508 closest distance to " CG  GLN A  89 " =    1.512
peak=    3.504 closest distance to " NH2AARG A 190 " =    1.866
peak=    3.496 closest distance to " O   HOH Z  58 " =    1.834
peak=    3.493 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.492 closest distance to " CB  ARG A 275 " =    1.053
peak=    3.491 closest distance to " CG  GLN A  11 " =    2.191
peak=    3.486 closest distance to " O   HOH Z 112 " =    1.232
peak=    3.484 closest distance to " O   HOH Z 124 " =    1.905
peak=    3.482 closest distance to " CA  GLU A 152 " =    1.213
peak=    3.477 closest distance to " O   HOH Z 437 " =    1.696
peak=    3.477 closest distance to " O   HOH Z 394 " =    1.758
peak=    3.473 closest distance to " CB  SER A 276 " =    1.088
peak=    3.471 closest distance to " O   HOH Z 220 " =    1.548
peak=    3.465 closest distance to " CB  SER A  62 " =    1.074
peak=    3.464 closest distance to " CE3 TRP A 150 " =    1.133
peak=    3.463 closest distance to " O   HOH Z 362 " =    2.147
peak=    3.462 closest distance to " O   HOH Z  76 " =    1.270
peak=    3.460 closest distance to " NZ  LYS A 119 " =    2.482
peak=    3.455 closest distance to " CB  GLU A 152 " =    1.109
peak=    3.454 closest distance to " CG  PRO A 213 " =    1.341
peak=    3.454 closest distance to " O   HOH Z 140 " =    2.034
peak=    3.453 closest distance to " NE2 GLN A  73 " =    1.758
peak=    3.453 closest distance to " CB  ALA A 160 " =    1.509
peak=    3.448 closest distance to " N   CYS A 260 " =    0.856
peak=    3.446 closest distance to " N   SER A 271 " =    0.980
peak=    3.443 closest distance to " O   HOH Z 185 " =    2.300
peak=    3.437 closest distance to " CB  LEU A 300 " =    0.996
peak=    3.434 closest distance to " CB  SER A 210 " =    1.029
peak=    3.434 closest distance to " CB  MET A  47 " =    1.075
peak=    3.431 closest distance to " N   PHE A 130 " =    1.309
peak=    3.429 closest distance to " CA  ILE A 106 " =    0.842
peak=    3.426 closest distance to " O   HOH Z 396 " =    1.226
peak=    3.423 closest distance to " CD2 TYR A  15 " =    1.283
peak=    3.423 closest distance to " O   HIS A 115 " =    0.984
peak=    3.421 closest distance to " O   HOH Z 207 " =    2.755
peak=    3.419 closest distance to " O   HOH Z 251 " =    1.634
peak=    3.417 closest distance to " CB  GLU A 175 " =    1.158
peak=    3.415 closest distance to " O   HOH Z   7 " =    3.100
peak=    3.405 closest distance to " CB  ARG A 102 " =    0.976
peak=    3.397 closest distance to " O   HOH Z 189 " =    3.511
peak=    3.395 closest distance to " CB  ARG A  79 " =    0.909
peak=    3.394 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.394 closest distance to " CB  TYR A  30 " =    1.310
peak=    3.390 closest distance to " O   HOH Z 171 " =    2.201
peak=    3.389 closest distance to " CB  TRP A 150 " =    1.115
peak=    3.388 closest distance to " O   HOH Z  78 " =    1.737
peak=    3.380 closest distance to " N   ARG A 156 " =    1.267
peak=    3.379 closest distance to " CB  GLU A 277 " =    3.660
peak=    3.378 closest distance to " CG2BVAL A  41 " =    1.102
peak=    3.374 closest distance to " O   HOH Z 172 " =    5.163
peak=    3.372 closest distance to " CB  PHE A 225 " =    1.515
peak=    3.370 closest distance to " C   PRO A  54 " =    0.780
peak=    3.366 closest distance to " O   HOH Z 112 " =    0.781
peak=    3.363 closest distance to " CB  ASP A 200 " =    0.984
peak=    3.357 closest distance to " O   HOH Z  40 " =    2.108
peak=    3.354 closest distance to " O   HOH Z 293 " =    1.477
peak=    3.353 closest distance to " CA  ALA A   7 " =    0.941
peak=    3.353 closest distance to " CD  LYS A 119 " =    1.732
peak=    3.352 closest distance to " O   HOH Z 153 " =    3.805
peak=    3.352 closest distance to " O   HOH Z 152 " =    1.648
peak=    3.350 closest distance to " CA  ASN A  74 " =    1.413
peak=    3.346 closest distance to " O   HOH Z 258 " =    2.055
peak=    3.346 closest distance to " CA  ARG A  36 " =    1.244
peak=    3.345 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.345 closest distance to " O   ASN A  60 " =    1.410
peak=    3.345 closest distance to " O   HOH Z 298 " =    4.186
peak=    3.343 closest distance to " CG  MET A 188 " =    0.796
peak=    3.340 closest distance to " O   HOH Z  68 " =    1.933
peak=    3.338 closest distance to " OE2 GLU A  53 " =    2.018
peak=    3.333 closest distance to " O   HOH Z  43 " =    1.254
peak=    3.331 closest distance to " CB  ASN A 285 " =    1.079
peak=    3.330 closest distance to " CD1 ILE A  33 " =    1.886
peak=    3.329 closest distance to " O   HOH Z 244 " =    1.634
peak=    3.326 closest distance to " CB  ARG A 156 " =    1.108
peak=    3.325 closest distance to " O   HOH Z 155 " =    1.855
peak=    3.318 closest distance to " CD2 PHE A  59 " =    1.980
peak=    3.317 closest distance to " O   HOH Z  30 " =    1.810
peak=    3.313 closest distance to " CG2 ILE A  20 " =    1.543
peak=    3.311 closest distance to " ND1 HIS A  86 " =    1.809
peak=    3.311 closest distance to " CB  HIS A  86 " =    0.986
peak=    3.310 closest distance to " N   ALA A 165 " =    1.247
peak=    3.310 closest distance to " O   HOH Z 357 " =    2.281
peak=    3.309 closest distance to " CG AARG A 275 " =    1.344
peak=    3.306 closest distance to " O   HOH Z  90 " =    2.220
peak=    3.306 closest distance to " O   HOH Z 100 " =    1.118
peak=    3.304 closest distance to " O   HOH Z  51 " =    1.850
peak=    3.304 closest distance to " O   HOH Z 272 " =    1.883
peak=    3.302 closest distance to " CA  SER A  95 " =    0.982
peak=    3.298 closest distance to " O   THR A 251 " =    1.200
peak=    3.295 closest distance to " CE3 TRP A  85 " =    1.030
peak=    3.294 closest distance to " CA  ARG A 156 " =    1.031
peak=    3.294 closest distance to " CB  ASN A 142 " =    0.971
peak=    3.293 closest distance to " NZ ALYS A 290 " =    0.967
peak=    3.293 closest distance to " CA  ILE A 234 " =    1.144
peak=    3.291 closest distance to " OG  SER A  26 " =    1.597
peak=    3.287 closest distance to " O   HOH Z 422 " =    2.423
peak=    3.286 closest distance to " O   HOH Z 299 " =    2.503
peak=    3.284 closest distance to " O   HOH Z 393 " =    3.196
peak=    3.281 closest distance to " O   HOH Z 280 " =    1.385
peak=    3.279 closest distance to " O   HOH Z 120 " =    0.975
peak=    3.277 closest distance to " CB  ALA A 299 " =    1.135
peak=    3.273 closest distance to " CB  GLN A 183 " =    1.199
peak=    3.273 closest distance to " O   HOH Z 236 " =    1.653
peak=    3.268 closest distance to " CB  ARG A 190 " =    1.469
peak=    3.266 closest distance to " CD1 LEU A 228 " =    1.716
peak=    3.264 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.257 closest distance to " NE1 TRP A 274 " =    0.938
peak=    3.256 closest distance to " O   HOH Z 332 " =    1.622
peak=    3.250 closest distance to " O   HOH Z  17 " =    1.989
peak=    3.249 closest distance to " O   HOH Z 434 " =    1.846
peak=    3.243 closest distance to " O   HOH Z   1 " =    1.639
peak=    3.240 closest distance to " CG  GLU A 277 " =    2.036
peak=    3.240 closest distance to " N   GLU A   2 " =    1.544
peak=    3.239 closest distance to " O   HOH Z 328 " =    1.561
peak=    3.236 closest distance to " O   HOH Z 390 " =    1.556
peak=    3.235 closest distance to " CB  GLU A 236 " =    1.499
peak=    3.233 closest distance to " CB  LEU A 237 " =    0.932
peak=    3.231 closest distance to " ND1 HIS A  81 " =    1.871
peak=    3.231 closest distance to " CA  SER A  87 " =    1.055
peak=    3.229 closest distance to " CG  ARG A 159 " =    0.917
peak=    3.228 closest distance to " CA  PHE A 283 " =    1.263
peak=    3.225 closest distance to " O   ASN A  69 " =    1.671
peak=    3.225 closest distance to " CB  ALA A  10 " =    1.008
peak=    3.225 closest distance to " NH2 ARG A  66 " =    5.751
peak=    3.219 closest distance to " CD1 LEU A 300 " =    0.984
peak=    3.218 closest distance to " N   PHE A  59 " =    0.773
peak=    3.216 closest distance to " O   HOH Z 248 " =    1.665
peak=    3.216 closest distance to " CG1 VAL A 202 " =    1.817
peak=    3.211 closest distance to " O   HOH Z 385 " =    2.593
peak=    3.211 closest distance to " O   HOH Z 215 " =    1.770
peak=    3.210 closest distance to " CA  ILE A 263 " =    1.057
peak=    3.209 closest distance to " CA  GLY A 196 " =    0.905
peak=    3.209 closest distance to " O   HOH Z 186 " =    3.177
peak=    3.207 closest distance to " O   HOH Z   2 " =    1.563
peak=    3.201 closest distance to " O   HOH Z 394 " =    3.857
peak=    3.201 closest distance to " O   HOH Z 225 " =    1.823
peak=    3.197 closest distance to " O   HOH Z 329 " =    4.216
peak=    3.196 closest distance to " CD BLYS A 290 " =    1.059
peak=    3.195 closest distance to " O   HOH Z 350 " =    1.654
peak=    3.192 closest distance to " CE1 PHE A 218 " =    1.172
peak=    3.189 closest distance to " CA  ASP A 124 " =    0.852
peak=    3.184 closest distance to " O   HOH Z 365 " =    2.679
peak=    3.184 closest distance to " O   HOH Z 352 " =    1.824
peak=    3.178 closest distance to " NE2 GLN A 205 " =    1.219
peak=    3.177 closest distance to " CB  LYS A 117 " =    1.234
peak=    3.175 closest distance to " CE2 PHE A  16 " =    0.878
peak=    3.172 closest distance to " CG2 ILE A 120 " =    1.137
peak=    3.172 closest distance to " O   ALA A 291 " =    1.531
peak=    3.172 closest distance to " O   HOH Z 325 " =    2.204
peak=    3.170 closest distance to " CG2 ILE A 239 " =    0.852
peak=    3.169 closest distance to " CG  GLN A  55 " =    0.756
peak=    3.166 closest distance to " O   THR A 220 " =    1.533
peak=    3.163 closest distance to " O   HOH Z 199 " =    1.588
peak=    3.163 closest distance to " CB  ASN A 187 " =    0.930
peak=    3.162 closest distance to " O   ASN A 142 " =    1.038
peak=    3.160 closest distance to " O   HOH Z 438 " =    2.441
peak=    3.158 closest distance to " O   HOH Z 373 " =    1.970
peak=    3.158 closest distance to " O   HOH Z 222 " =    2.201
peak=    3.152 closest distance to " O   HOH Z 217 " =    1.213
peak=    3.152 closest distance to " CD  ARG A  66 " =    1.908
peak=    3.143 closest distance to " N   ASN A 127 " =    1.434
peak=    3.140 closest distance to " O   HOH Z 353 " =    1.693
peak=    3.135 closest distance to " CG2 VAL A 232 " =    0.996
peak=    3.133 closest distance to " O   HOH Z 104 " =    2.101
peak=    3.126 closest distance to " O   HOH Z 234 " =    3.815
peak=    3.126 closest distance to " CA  ARG A 102 " =    1.145
peak=    3.119 closest distance to " O   HOH Z  10 " =    2.533
peak=    3.114 closest distance to " CB  LEU A  83 " =    0.743
peak=    3.113 closest distance to " O   HOH Z 368 " =    2.003
peak=    3.113 closest distance to " CD  ARG A 269 " =    0.961
peak=    3.102 closest distance to " CD  GLU A 152 " =    0.760
peak=    3.102 closest distance to " OD1 ASP A 238 " =    1.048
peak=    3.101 closest distance to " NH2BARG A 190 " =    1.266
peak=    3.099 closest distance to " O   HOH Z 184 " =    1.605
peak=    3.097 closest distance to " CB  ALA A 161 " =    1.025
peak=    3.096 closest distance to " CA  GLU A  46 " =    0.784
peak=    3.087 closest distance to " O   HOH Z 219 " =    1.989
peak=    3.074 closest distance to " O   HOH Z 356 " =    1.388
peak=    3.065 closest distance to " O   HOH Z 130 " =    2.015
peak=    3.064 closest distance to " O   HOH Z 130 " =    3.352
peak=    3.064 closest distance to " CG1 ILE A  20 " =    1.358
peak=    3.064 closest distance to " O   HOH Z 288 " =    1.827
peak=    3.060 closest distance to " O   HOH Z 116 " =    3.281
peak=    3.059 closest distance to " O   HOH Z 359 " =    4.206
peak=    3.058 closest distance to " CD1 ILE A 199 " =    1.194
peak=    3.055 closest distance to " O   HOH Z 389 " =    1.779
peak=    3.049 closest distance to " CA  ALA A 129 " =    1.230
peak=    3.042 closest distance to " O   HOH Z 189 " =    2.953
peak=    3.037 closest distance to " CB  ALA A 184 " =    1.112
peak=    3.029 closest distance to " OG ASER A 212 " =    1.954
peak=    3.001 closest distance to " CD  ARG A  66 " =    2.153

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.696 - 5.646
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.772 - 5.646

peak=   -4.603 closest distance to " OE1 GLN A  88 " =    0.929
peak=   -4.543 closest distance to " O   PRO A 198 " =    1.304
peak=   -4.379 closest distance to " CG  GLN A  88 " =    0.830
peak=   -4.343 closest distance to " O   HOH Z 216 " =    1.237
peak=   -4.292 closest distance to " CG2 ILE A  49 " =    2.871
peak=   -4.284 closest distance to " O   HOH Z 100 " =    0.947
peak=   -4.218 closest distance to " CB  PRO A 243 " =    2.540
peak=   -4.150 closest distance to " CB  ASP A  27 " =    2.531
peak=   -4.142 closest distance to " O   HOH Z  32 " =    1.803
peak=   -4.125 closest distance to " CD  ARG A  14 " =    3.209
peak=   -4.124 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -4.113 closest distance to " CB  GLN A  55 " =    1.272
peak=   -4.111 closest distance to " CG  MET A 105 " =    0.982
peak=   -4.102 closest distance to " C   ILE A 239 " =    2.071
peak=   -4.093 closest distance to " CD  ARG A 156 " =    1.955
peak=   -4.056 closest distance to " O   ALA A  10 " =    1.728
peak=   -4.035 closest distance to " NZ  LYS A 166 " =    1.428
peak=   -4.030 closest distance to " OG  SER A  97 " =    2.067
peak=   -4.029 closest distance to " CB  ALA A 291 " =    2.208
peak=   -3.994 closest distance to " O   PRO A 163 " =    1.833
peak=   -3.981 closest distance to " O   SER A 135 " =    1.398
peak=   -3.979 closest distance to " CA  HIS A 207 " =    1.126
peak=   -3.978 closest distance to " O   HOH Z 111 " =    1.448
peak=   -3.975 closest distance to " CD2 TYR A 116 " =    2.135
peak=   -3.975 closest distance to " O   HOH Z 275 " =    1.862
peak=   -3.968 closest distance to " CB  ALA A   9 " =    2.469
peak=   -3.959 closest distance to " CG  ARG A 219 " =    2.424
peak=   -3.901 closest distance to " CD1 TRP A 179 " =    1.227
peak=   -3.879 closest distance to " CB  ALA A  43 " =    2.637
peak=   -3.837 closest distance to " N   ALA A  43 " =    2.549
peak=   -3.791 closest distance to " O   HOH Z 231 " =    0.772
peak=   -3.786 closest distance to " O   HOH Z  60 " =    1.401
peak=   -3.777 closest distance to " O   HOH Z 143 " =    1.395
peak=   -3.758 closest distance to " CB  ALA A 131 " =    1.873
peak=   -3.757 closest distance to " O   HOH Z  39 " =    0.941
peak=   -3.749 closest distance to " O   HOH Z  68 " =    1.380
peak=   -3.742 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.739 closest distance to " O   HOH Z 316 " =    1.845
peak=   -3.735 closest distance to " CZ3 TRP A 179 " =    1.326
peak=   -3.718 closest distance to " NE2 GLN A 194 " =    1.992
peak=   -3.714 closest distance to " O   GLN A 240 " =    3.172
peak=   -3.710 closest distance to " O   HOH Z  28 " =    1.211
peak=   -3.709 closest distance to " O   SER A  22 " =    2.860
peak=   -3.704 closest distance to " O   ASP A 253 " =    1.845
peak=   -3.683 closest distance to " O   HOH Z 298 " =    2.347
peak=   -3.652 closest distance to " O   HOH Z 276 " =    1.045
peak=   -3.651 closest distance to " O   HOH Z 389 " =    2.498
peak=   -3.636 closest distance to " CG1BVAL A  41 " =    2.781
peak=   -3.633 closest distance to " O   HOH Z 313 " =    1.499
peak=   -3.621 closest distance to " O   HOH Z 103 " =    1.030
peak=   -3.620 closest distance to " N   ASP A 270 " =    1.390
peak=   -3.616 closest distance to " OG BSER A 134 " =    1.691
peak=   -3.614 closest distance to " CD1 TYR A 247 " =    2.843
peak=   -3.603 closest distance to " CA  ASN A 110 " =    0.942
peak=   -3.600 closest distance to " CD1 LEU A 101 " =    2.359
peak=   -3.594 closest distance to " C   LEU A 101 " =    1.381
peak=   -3.592 closest distance to " CG1 VAL A 125 " =    2.364
peak=   -3.580 closest distance to " OD1 ASN A  60 " =    0.890
peak=   -3.551 closest distance to " OG  SER A  87 " =    1.629
peak=   -3.551 closest distance to " CG  GLN A  88 " =    1.237
peak=   -3.547 closest distance to " NE2 GLN A 223 " =    1.466
peak=   -3.546 closest distance to " NE2 GLN A 240 " =    1.154
peak=   -3.543 closest distance to " O   HOH Z 404 " =    1.185
peak=   -3.539 closest distance to " O   HOH Z 198 " =    1.829
peak=   -3.532 closest distance to " O   HOH Z 131 " =    3.927
peak=   -3.522 closest distance to " O   HOH Z 385 " =    1.323
peak=   -3.522 closest distance to " CA  GLY A  98 " =    1.824
peak=   -3.514 closest distance to " O   HOH Z 438 " =    1.637
peak=   -3.511 closest distance to " O   LEU A 300 " =    2.173
peak=   -3.487 closest distance to " CB  HIS A  86 " =    1.144
peak=   -3.484 closest distance to " CG  ARG A 259 " =    2.462
peak=   -3.482 closest distance to " N   ASP A 171 " =    2.535
peak=   -3.480 closest distance to " O   HOH Z  77 " =    1.772
peak=   -3.479 closest distance to " O   ILE A  49 " =    1.557
peak=   -3.473 closest distance to " NE2 GLN A  55 " =    1.051
peak=   -3.469 closest distance to " N   GLN A  58 " =    1.400
peak=   -3.466 closest distance to " CZ  PHE A 225 " =    1.230
peak=   -3.462 closest distance to " CB  ALA A 227 " =    2.364
peak=   -3.458 closest distance to " O   HOH Z 181 " =    1.155
peak=   -3.454 closest distance to " O   ASP A 162 " =    2.247
peak=   -3.445 closest distance to " O   GLU A 152 " =    1.510
peak=   -3.439 closest distance to " NH2AARG A 275 " =    5.646
peak=   -3.434 closest distance to " O   GLY A  80 " =    2.554
peak=   -3.432 closest distance to " CB  PRO A  54 " =    2.379
peak=   -3.428 closest distance to " O   HOH Z 348 " =    1.930
peak=   -3.421 closest distance to " CA  HIS A  86 " =    2.100
peak=   -3.420 closest distance to " O   ASP A  27 " =    1.859
peak=   -3.415 closest distance to " O   HOH Z 165 " =    1.756
peak=   -3.412 closest distance to " CB  TYR A  68 " =    1.079
peak=   -3.403 closest distance to " CG1 VAL A 265 " =    2.588
peak=   -3.400 closest distance to " O   HOH Z 277 " =    1.684
peak=   -3.399 closest distance to " CD  GLN A  55 " =    1.185
peak=   -3.394 closest distance to " O   HOH Z 185 " =    2.256
peak=   -3.392 closest distance to " O   HOH Z 257 " =    1.115
peak=   -3.390 closest distance to " C   PHE A  59 " =    1.116
peak=   -3.383 closest distance to " CB  ALA A 160 " =    2.109
peak=   -3.381 closest distance to " CA  GLY A 133 " =    2.197
peak=   -3.376 closest distance to " OE1 GLU A 277 " =    2.260
peak=   -3.375 closest distance to " CG  LEU A  83 " =    2.263
peak=   -3.375 closest distance to " O   HOH Z 163 " =    1.688
peak=   -3.373 closest distance to " CG2 VAL A 189 " =    2.671
peak=   -3.362 closest distance to " O   HOH Z 380 " =    4.803
peak=   -3.361 closest distance to " O   HOH Z  24 " =    1.107
peak=   -3.359 closest distance to " O   HOH Z 181 " =    1.811
peak=   -3.357 closest distance to " OG ASER A 134 " =    1.322
peak=   -3.351 closest distance to " N   LEU A 282 " =    2.151
peak=   -3.346 closest distance to " NH2 ARG A  79 " =    2.249
peak=   -3.341 closest distance to " OG  SER A 245 " =    1.548
peak=   -3.340 closest distance to " CB  ASP A 132 " =    2.700
peak=   -3.339 closest distance to " O   HOH Z 286 " =    1.577
peak=   -3.331 closest distance to " C   VAL A  72 " =    0.918
peak=   -3.330 closest distance to " O   HOH Z 285 " =    1.650
peak=   -3.330 closest distance to " CD  LYS A 166 " =    2.558
peak=   -3.320 closest distance to " O   HOH Z  52 " =    2.180
peak=   -3.320 closest distance to " CB  PHE A 130 " =    1.129
peak=   -3.316 closest distance to " ND2 ASN A  60 " =    3.991
peak=   -3.314 closest distance to " O   HOH Z 134 " =    1.678
peak=   -3.306 closest distance to " O   HOH Z 351 " =    1.547
peak=   -3.304 closest distance to " CG2 THR A 178 " =    2.188
peak=   -3.303 closest distance to " O   HOH Z 207 " =    1.392
peak=   -3.300 closest distance to " O   ASP A 171 " =    1.012
peak=   -3.299 closest distance to " N   THR A 157 " =    1.578
peak=   -3.289 closest distance to " CA  GLY A 241 " =    2.307
peak=   -3.286 closest distance to " CE2 TYR A  30 " =    2.475
peak=   -3.281 closest distance to " CD  PRO A 213 " =    2.183
peak=   -3.272 closest distance to " CE3 TRP A  70 " =    1.630
peak=   -3.271 closest distance to " O   HOH Z  10 " =    1.602
peak=   -3.270 closest distance to " O   HOH Z 426 " =    1.718
peak=   -3.269 closest distance to " O   HOH Z 300 " =    2.244
peak=   -3.267 closest distance to " O   HOH Z 201 " =    1.865
peak=   -3.266 closest distance to " C   HIS A 108 " =    1.318
peak=   -3.265 closest distance to " O   HOH Z 231 " =    2.146
peak=   -3.263 closest distance to " O   SER A 141 " =    1.807
peak=   -3.258 closest distance to " CB  ASP A 171 " =    2.320
peak=   -3.258 closest distance to " CD  GLN A  58 " =    1.144
peak=   -3.256 closest distance to " N   PRO A  54 " =    1.007
peak=   -3.249 closest distance to " O   HOH Z 181 " =    1.626
peak=   -3.246 closest distance to " O   HOH Z 165 " =    2.391
peak=   -3.243 closest distance to " CA  GLY A 203 " =    2.472
peak=   -3.240 closest distance to " O   HOH Z  11 " =    1.676
peak=   -3.233 closest distance to " O   HOH Z 434 " =    1.698
peak=   -3.231 closest distance to " CZ  PHE A 130 " =    1.099
peak=   -3.230 closest distance to " O   HOH Z  69 " =    1.466
peak=   -3.228 closest distance to " NH2 ARG A  56 " =    1.241
peak=   -3.228 closest distance to " O   HOH Z 193 " =    1.460
peak=   -3.226 closest distance to " CG  MET A 188 " =    1.146
peak=   -3.226 closest distance to " O   HOH Z 407 " =    3.214
peak=   -3.225 closest distance to " OD2 ASP A 171 " =    1.544
peak=   -3.222 closest distance to " CD1 LEU A 282 " =    2.785
peak=   -3.222 closest distance to " O   HOH Z 251 " =    0.941
peak=   -3.220 closest distance to " CD1 LEU A 167 " =    1.792
peak=   -3.220 closest distance to " O   HOH Z  73 " =    2.051
peak=   -3.219 closest distance to " ND2 ASN A 285 " =    2.137
peak=   -3.218 closest distance to " O   HOH Z 166 " =    1.651
peak=   -3.216 closest distance to " CD2 LEU A 143 " =    2.439
peak=   -3.216 closest distance to " O   HOH Z 133 " =    1.360
peak=   -3.215 closest distance to " O   HOH Z  71 " =    1.392
peak=   -3.211 closest distance to " O   HOH Z 238 " =    1.064
peak=   -3.209 closest distance to " O   HOH Z 364 " =    1.724
peak=   -3.208 closest distance to " O   ALA A   1 " =    1.817
peak=   -3.207 closest distance to " CG2 THR A 221 " =    2.386
peak=   -3.206 closest distance to " O   ARG A  56 " =    4.490
peak=   -3.203 closest distance to " C   LEU A 222 " =    1.129
peak=   -3.201 closest distance to " CD2 TYR A 169 " =    2.343
peak=   -3.199 closest distance to " O   HOH Z 128 " =    2.586
peak=   -3.198 closest distance to " CZ  PHE A  38 " =    2.417
peak=   -3.197 closest distance to " OG  SER A  63 " =    1.431
peak=   -3.196 closest distance to " NE2 GLN A  77 " =    1.873
peak=   -3.191 closest distance to " O   HOH Z 275 " =    1.630
peak=   -3.190 closest distance to " O   HOH Z 140 " =    1.077
peak=   -3.188 closest distance to " CG1 VAL A  78 " =    2.555
peak=   -3.186 closest distance to " CG2BVAL A  72 " =    1.987
peak=   -3.180 closest distance to " CB  ASP A 132 " =    2.589
peak=   -3.180 closest distance to " ND2 ASN A  39 " =    1.923
peak=   -3.177 closest distance to " O   HOH Z  64 " =    0.940
peak=   -3.175 closest distance to " O   HOH Z 102 " =    1.787
peak=   -3.170 closest distance to " O   HOH Z  32 " =    1.619
peak=   -3.164 closest distance to " O   HOH Z 268 " =    2.955
peak=   -3.161 closest distance to " OH  TYR A 247 " =    1.488
peak=   -3.161 closest distance to " C   ASN A 285 " =    2.359
peak=   -3.160 closest distance to " O   HOH Z 364 " =    2.332
peak=   -3.158 closest distance to " CG  LEU A 167 " =    1.055
peak=   -3.157 closest distance to " O   HOH Z 281 " =    2.683
peak=   -3.157 closest distance to " O   HOH Z 357 " =    1.792
peak=   -3.155 closest distance to " CD  GLU A 277 " =    1.175
peak=   -3.153 closest distance to " O   HOH Z 412 " =    4.526
peak=   -3.152 closest distance to " C   ALA A 158 " =    1.534
peak=   -3.152 closest distance to " O   HOH Z 188 " =    0.912
peak=   -3.150 closest distance to " CD2 PHE A  61 " =    2.024
peak=   -3.149 closest distance to " CB  TRP A  85 " =    2.049
peak=   -3.145 closest distance to " CZ2 TRP A 274 " =    1.012
peak=   -3.145 closest distance to " NH2 ARG A  66 " =    3.481
peak=   -3.144 closest distance to " O   HOH Z 179 " =    1.675
peak=   -3.142 closest distance to " CG2 THR A  52 " =    3.157
peak=   -3.139 closest distance to " CG1 VAL A 126 " =    2.569
peak=   -3.136 closest distance to " OD2 ASP A  50 " =    2.434
peak=   -3.134 closest distance to " SG BCYS A 201 " =    2.408
peak=   -3.129 closest distance to " O   HOH Z 200 " =    3.443
peak=   -3.127 closest distance to " CB  GLN A  11 " =    1.537
peak=   -3.126 closest distance to " CG2 ILE A  20 " =    2.741
peak=   -3.122 closest distance to " CD1 TYR A 214 " =    1.527
peak=   -3.117 closest distance to " CZ  PHE A  59 " =    1.792
peak=   -3.116 closest distance to " O   SER A  28 " =    1.202
peak=   -3.102 closest distance to " O   HOH Z 389 " =    1.224
peak=   -3.097 closest distance to " O   LYS A  76 " =    1.842
peak=   -3.096 closest distance to " CG1 VAL A 250 " =    2.556
peak=   -3.096 closest distance to " O   HOH Z 427 " =    1.705
peak=   -3.096 closest distance to " N   HIS A  81 " =    1.199
peak=   -3.092 closest distance to " OG  SER A  28 " =    2.056
peak=   -3.079 closest distance to " CG  ASN A  39 " =    1.684
peak=   -3.076 closest distance to " O   HOH Z 211 " =    0.809
peak=   -3.068 closest distance to " ND2 ASN A  45 " =    2.735
peak=   -3.057 closest distance to " O   HOH Z 103 " =    0.779
peak=   -3.041 closest distance to " O   HOH Z 126 " =    1.650
peak=   -3.034 closest distance to " N   TRP A 274 " =    1.152
peak=   -3.027 closest distance to " O   HOH Z 278 " =    1.227

================= 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    :  0.4869 0.4897   6.297547e+00   6.286399e+00
   1_bss:  0.4789 0.4864   6.294890e+00   6.283406e+00
   1_xyz:  0.4038 0.4379   6.186996e+00   6.229682e+00
   1_adp:  0.3679 0.4537   6.152148e+00   6.244039e+00
   1_occ:  0.3673 0.4552   6.152274e+00   6.244576e+00
   2_bss:  0.3679 0.4543   6.154825e+00   6.244991e+00
   2_xyz:  0.2980 0.3704   5.979192e+00   6.119272e+00
   2_adp:  0.2735 0.3515   5.928363e+00   6.082749e+00
   2_occ:  0.2734 0.3513   5.928041e+00   6.082768e+00
   3_bss:  0.2734 0.3510   5.927978e+00   6.081934e+00
   3_xyz:  0.2309 0.3028   5.787292e+00   5.973235e+00
   3_adp:  0.2157 0.2906   5.743621e+00   5.939745e+00
   3_occ:  0.2157 0.2903   5.742949e+00   5.939206e+00
   4_bss:  0.2157 0.2902   5.742671e+00   5.938728e+00
   4_xyz:  0.1750 0.2345   5.538744e+00   5.760795e+00
   4_adp:  0.1628 0.2200   5.480548e+00   5.703041e+00
   4_occ:  0.1627 0.2200   5.480239e+00   5.702954e+00
   5_bss:  0.1631 0.2203   5.479162e+00   5.702186e+00
   5_xyz:  0.1415 0.1953   5.353388e+00   5.589252e+00
   5_adp:  0.1348 0.1902   5.315424e+00   5.553190e+00
   5_occ:  0.1348 0.1903   5.315503e+00   5.553491e+00
   5_bss:  0.1352 0.1903   5.315194e+00   5.551576e+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:  0.348  80.000  -1.527   0.500   3.443   0.000   0.000   0.000
   1_xyz:  0.348  80.000  -1.527   0.500   3.443   0.000   0.000   0.000
   1_adp:  0.348  80.000  -1.527   0.500   3.443   0.000   0.000   0.000
   1_occ:  0.348  80.000  -1.527   0.500   3.443   0.000   0.000   0.000
   2_bss:  0.370  96.872  -0.670  -0.356   2.254  -0.000   0.000   0.000
   2_xyz:  0.370  96.872  -0.670  -0.356   2.254  -0.000   0.000   0.000
   2_adp:  0.370  96.872  -0.670  -0.356   2.254  -0.000   0.000   0.000
   2_occ:  0.370  96.872  -0.670  -0.356   2.254  -0.000   0.000   0.000
   3_bss:  0.356  90.861  -1.266  -1.392   0.831  -0.000   0.000   0.000
   3_xyz:  0.356  90.861  -1.266  -1.392   0.831  -0.000   0.000   0.000
   3_adp:  0.356  90.861  -1.266  -1.392   0.831  -0.000   0.000   0.000
   3_occ:  0.356  90.861  -1.266  -1.392   0.831  -0.000   0.000   0.000
   4_bss:  0.349  94.215  -2.030  -2.201  -0.001  -0.000  -0.000  -0.000
   4_xyz:  0.349  94.215  -2.030  -2.201  -0.001  -0.000  -0.000  -0.000
   4_adp:  0.349  94.215  -2.030  -2.201  -0.001  -0.000  -0.000  -0.000
   4_occ:  0.349  94.215  -2.030  -2.201  -0.001  -0.000  -0.000  -0.000
   5_bss:  0.334  80.000  -2.198  -2.664  -0.462  -0.000  -0.000  -0.000
   5_xyz:  0.334  80.000  -2.198  -2.664  -0.462  -0.000  -0.000  -0.000
   5_adp:  0.334  80.000  -2.198  -2.664  -0.462  -0.000  -0.000  -0.000
   5_occ:  0.334  80.000  -2.198  -2.664  -0.462  -0.000  -0.000  -0.000
   5_bss:  0.332  80.003  -2.267  -2.816  -0.538  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.599 0.3589  0.4894    79090.900
   1_bss:  62.076 0.3649  0.5187    78172.128
   1_xyz:  51.865 0.4960  0.6908    59152.953
   1_adp:  53.805 0.4706  0.6784    62838.123
   1_occ:  53.981 0.4683  0.6744    63113.484
   2_bss:  53.928 0.4690  0.6674    63173.760
   2_xyz:  40.844 0.6310  0.8766    38971.232
   2_adp:  37.991 0.6655  0.8991    34810.233
   2_occ:  37.981 0.6657  0.8992    34819.856
   3_bss:  37.887 0.6667  0.8694    34681.573
   3_xyz:  31.553 0.7393  0.9435    24853.548
   3_adp:  29.789 0.7594  0.9437    22651.878
   3_occ:  29.769 0.7596  0.9435    22585.505
   4_bss:  29.721 0.7600  0.9184    22552.855
   4_xyz:  23.420 0.8263  0.9691    14344.627
   4_adp:  21.594 0.8454  0.9717    12737.860
   4_occ:  21.585 0.8455  0.9715    12721.108
   5_bss:  21.524 0.8460  0.9596    12656.407
   5_xyz:  18.571 0.8746  0.9764     9807.729
   5_adp:  17.712 0.8830  0.9729     9152.270
   5_occ:  17.715 0.8830  0.9728     9151.482
   5_bss:  17.681 0.8832  0.9696     9109.205
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7280e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7280e-01
   1_xyz:   1.516  0.011  0.101 15.797  0.006  4.105   1.2361e-01
   1_adp:   1.516  0.011  0.101 15.797  0.006  4.105   1.2361e-01
   1_occ:   1.516  0.011  0.101 15.797  0.006  4.105   1.2361e-01
   2_bss:   1.516  0.011  0.101 15.797  0.006  4.105   1.2361e-01
   2_xyz:   1.450  0.012  0.102 15.555  0.006  4.109   1.1685e-01
   2_adp:   1.450  0.012  0.102 15.555  0.006  4.109   1.1685e-01
   2_occ:   1.450  0.012  0.102 15.555  0.006  4.109   1.1685e-01
   3_bss:   1.450  0.012  0.102 15.555  0.006  4.109   1.1685e-01
   3_xyz:   1.010  0.007  0.072 14.774  0.004  4.119   6.0972e-02
   3_adp:   1.010  0.007  0.072 14.774  0.004  4.119   6.0972e-02
   3_occ:   1.010  0.007  0.072 14.774  0.004  4.119   6.0972e-02
   4_bss:   1.010  0.007  0.072 14.774  0.004  4.119   6.0972e-02
   4_xyz:   1.030  0.007  0.075 14.426  0.004  4.113   6.2012e-02
   4_adp:   1.030  0.007  0.075 14.426  0.004  4.113   6.2012e-02
   4_occ:   1.030  0.007  0.075 14.426  0.004  4.113   6.2012e-02
   5_bss:   1.030  0.007  0.075 14.426  0.004  4.113   6.2012e-02
   5_xyz:   1.016  0.008  0.074 14.497  0.004  4.123   6.1454e-02
   5_adp:   1.016  0.008  0.074 14.497  0.004  4.123   6.1454e-02
   5_occ:   1.016  0.008  0.074 14.497  0.004  4.123   6.1454e-02
   5_bss:   1.016  0.008  0.074 14.497  0.004  4.123   6.1454e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4272e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4272e-01
   1_xyz:   8.561  0.061  0.364 83.712  0.048  2.019   9.1796e-02
   1_adp:   8.561  0.061  0.364 83.712  0.048  2.019   9.1796e-02
   1_occ:   8.561  0.061  0.364 83.712  0.048  2.019   9.1796e-02
   2_bss:   8.561  0.061  0.364 83.712  0.048  2.019   9.1796e-02
   2_xyz:   8.821  0.081  0.326 80.959  0.053  2.104   1.0788e-01
   2_adp:   8.821  0.081  0.326 80.959  0.053  2.104   1.0788e-01
   2_occ:   8.821  0.081  0.326 80.959  0.053  2.104   1.0788e-01
   3_bss:   8.821  0.081  0.326 80.959  0.053  2.104   1.0788e-01
   3_xyz:   7.323  0.042  0.244 77.915  0.031  2.355   6.1908e-02
   3_adp:   7.323  0.042  0.244 77.915  0.031  2.355   6.1908e-02
   3_occ:   7.323  0.042  0.244 77.915  0.031  2.355   6.1908e-02
   4_bss:   7.323  0.042  0.244 77.915  0.031  2.355   6.1908e-02
   4_xyz:   6.381  0.038  0.208 81.125  0.042  2.297   5.4456e-02
   4_adp:   6.381  0.038  0.208 81.125  0.042  2.297   5.4456e-02
   4_occ:   6.381  0.038  0.208 81.125  0.042  2.297   5.4456e-02
   5_bss:   6.381  0.038  0.208 81.125  0.042  2.297   5.4456e-02
   5_xyz:   8.179  0.047  0.250 81.087  0.033  2.331   4.3225e-02
   5_adp:   8.179  0.047  0.250 81.087  0.033  2.331   4.3225e-02
   5_occ:   8.179  0.047  0.250 81.087  0.033  2.331   4.3225e-02
   5_bss:   8.179  0.047  0.250 81.087  0.033  2.331   4.3225e-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: 100.55   0.00  20.95  91.53   0.00  17.63 100.55   0.00  38.99
   1_occ: 100.55   0.00  20.95  91.53   0.00  17.63 100.55   0.00  38.99
   2_bss: 100.55   0.00  20.95  91.53   0.00  17.63 100.55   0.00  38.99
   2_xyz: 100.55   0.00  20.95  91.53   0.00  17.63 100.55   0.00  38.99
   2_adp:  94.23   0.00  20.11  79.90   0.00  16.13  94.23   0.00  41.81
   2_occ:  94.23   0.00  20.11  79.90   0.00  16.13  94.23   0.00  41.81
   3_bss:  94.23   0.00  20.11  79.90   0.00  16.13  94.23   0.00  41.81
   3_xyz:  94.23   0.00  20.11  79.90   0.00  16.13  94.23   0.00  41.81
   3_adp:  98.33   0.00  19.77  88.02   0.00  15.07  98.33   1.81  45.39
   3_occ:  98.33   0.00  19.77  88.02   0.00  15.07  98.33   1.81  45.39
   4_bss:  98.33   0.00  19.77  88.02   0.00  15.07  98.33   1.81  45.39
   4_xyz:  98.33   0.00  19.77  88.02   0.00  15.07  98.33   1.81  45.39
   4_adp: 100.09   0.00  19.14  90.28   0.00  14.04 100.09   4.90  46.89
   4_occ: 100.09   0.00  19.14  90.28   0.00  14.04 100.09   4.90  46.89
   5_bss: 100.09   0.00  19.14  90.28   0.00  14.04 100.09   4.90  46.89
   5_xyz: 100.09   0.00  19.14  90.28   0.00  14.04 100.09   4.90  46.89
   5_adp: 109.61   0.00  19.33  97.96   0.00  13.70 109.61   6.31  50.01
   5_occ: 109.61   0.00  19.33  97.96   0.00  13.70 109.61   6.31  50.01
   5_bss: 109.62   0.00  19.34  97.96   0.00  13.70 109.62   6.31  50.02
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.710    0.010    0.307
   1_adp:    1.710    0.010    0.307
   1_occ:    1.710    0.010    0.307
   2_bss:    1.710    0.010    0.307
   2_xyz:    1.418    0.050    0.572
   2_adp:    1.418    0.050    0.572
   2_occ:    1.418    0.050    0.572
   3_bss:    1.418    0.050    0.572
   3_xyz:    1.397    0.048    0.668
   3_adp:    1.397    0.048    0.668
   3_occ:    1.397    0.048    0.668
   4_bss:    1.397    0.048    0.668
   4_xyz:    1.412    0.058    0.773
   4_adp:    1.412    0.058    0.773
   4_occ:    1.412    0.058    0.773
   5_bss:    1.412    0.058    0.773
   5_xyz:    1.474    0.102    0.822
   5_adp:    1.474    0.102    0.822
   5_occ:    1.474    0.102    0.822
   5_bss:    1.474    0.102    0.822
------------------------------------------------------------------------

CPU time actual refinement: 371.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/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_989/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_989/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 371.28 
  Macro-tasks:
    bulk solvent and scale       = 65.85  
    individual site refinement   = 144.99 
    weights calculation          = 30.18  
    collect and process          = 6.39   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 247.50 
  Micro-tasks:
    mask                            = 3.15   
    f_calc                          = 112.61 
    alpha_beta                      = 8.30   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.90 
    fmodel                         = 10.26  
    r_factors                      = 0.35   
    phase_errors                   = 10.12  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 266.07 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.247 micro seconds
Total CPU time: 6.41 minutes
from_scatterers_fft:    614 calls, 112.32 s
gradients_fft:          559 calls, 107.03 s

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

# Date 2008-01-16 Time 06:10:16 PST -0800 (1200492616.60 s)
Start R-work = 0.4869, R-free = 0.4897 (no bulk solvent and anisotropic scale)
Final R-work = 0.1563, R-free = 0.2072 (no bulk solvent and anisotropic scale)

Start R-work = 0.4789, R-free = 0.4864
Final R-work = 0.1352, R-free = 0.1903