# Date 2008-01-16 Time 05:48:50 PST -0800 (1200491330.18 s)
#phil __OFF__

Command line arguments: "../890.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15873
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 890

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 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: 3.37, per 1000 atoms: 1.19


================================== 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: (70.9525, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.98318
Completeness in resolution range: 0.93835
Completeness with d_max=infinity: 0.935572

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   1.9832

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: (70.9525, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.98318
Completeness in resolution range: 0.93835
Completeness with d_max=infinity: 0.935572

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.2446 [2192/2217]  1972   220  10.0%
  bin  2:  4.2446 -  3.3812 [2107/2127]  1898   209   9.9%
  bin  3:  3.3812 -  2.9574 [2082/2101]  1875   207   9.9%
  bin  4:  2.9574 -  2.6886 [2058/2088]  1847   211  10.3%
  bin  5:  2.6886 -  2.4968 [2050/2069]  1853   197   9.6%
  bin  6:  2.4968 -  2.3502 [2048/2073]  1839   209  10.2%
  bin  7:  2.3502 -  2.2328 [2004/2032]  1801   203  10.1%
  bin  8:  2.2328 -  2.1359 [2037/2073]  1829   208  10.2%
  bin  9:  2.1359 -  2.0539 [2019/2061]  1826   193   9.6%
  bin 10:  2.0539 -  1.9832 [ 992/2035]   890   102  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/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:
        1.79 -     2.41: 22
        2.41 -     3.03: 2095
        3.03 -     3.65: 4619
        3.65 -     4.28: 8930
        4.28 -     4.90: 12303
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.787 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.871 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.871 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.913 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27964 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_890/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 = 70.9525 46.4607 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: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4172   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.232499                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7346 0.99   1423  157 0.3446 0.3139      6.5209      6.3979|
|  2:  4.7346 -  3.7770 0.99   1373  154 0.3476 0.3673      6.7142      6.7281|
|  3:  3.7770 -  3.3052 0.99   1339  149 0.3847 0.3320      6.5811      6.5246|
|  4:  3.3052 -  3.0055 0.99   1345  150 0.4135 0.4273      6.4526      6.4606|
|  5:  3.0055 -  2.7915 0.99   1315  149 0.4619 0.4187      6.3092      6.3108|
|  6:  2.7915 -  2.6278 0.99   1329  143 0.4378 0.4810      6.1969      6.1802|
|  7:  2.6278 -  2.4968 0.99   1321  142 0.4587 0.4309      6.1927      6.1383|
|  8:  2.4968 -  2.3885 0.98   1302  151 0.4875 0.4809      6.1503      6.1387|
|  9:  2.3885 -  2.2969 0.98   1296  143 0.4757 0.4607      6.0923      6.1212|
| 10:  2.2969 -  2.2179 1.00   1315  150 0.4923 0.4947      6.0633      6.0606|
| 11:  2.2179 -  2.1488 0.98   1296  143 0.4894 0.4804      6.0204       5.978|
| 12:  2.1488 -  2.0875 0.98   1286  139 0.4933 0.4483      5.9244      5.9372|
| 13:  2.0875 -  2.0327 0.96   1267  140 0.4793 0.5098      5.8475      5.7965|
| 14:  2.0327 -  1.9832 0.32    423   49 0.4884 0.4492      5.8415      5.8376|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7346  1423   157  0.78  27.40   0.83     0.80      48706.70|
|  2:  4.7346 -  3.7770  1373   154  0.79  27.43   0.92     0.88      73520.48|
|  3:  3.7770 -  3.3052  1339   149  0.69  36.38   0.93     0.85      80480.08|
|  4:  3.3052 -  3.0055  1345   150  0.61  42.80   0.92     0.78      75805.09|
|  5:  3.0055 -  2.7915  1315   149  0.52  50.25   0.91     0.69      62690.39|
|  6:  2.7915 -  2.6278  1329   143  0.50  52.17   0.91     0.66      57051.85|
|  7:  2.6278 -  2.4968  1321   142  0.49  52.76   0.93     0.65      51715.30|
|  8:  2.4968 -  2.3885  1302   151  0.48  53.98   0.91     0.65      46784.34|
|  9:  2.3885 -  2.2969  1296   143  0.48  53.70   0.94     0.66      43303.30|
| 10:  2.2969 -  2.2179  1315   150  0.47  54.70   0.94     0.66      39358.19|
| 11:  2.2179 -  2.1488  1296   143  0.45  56.08   0.94     0.66      39740.60|
| 12:  2.1488 -  2.0875  1286   139  0.44  57.06   0.93     0.65      35931.62|
| 13:  2.0875 -  2.0327  1267   140  0.40  59.71   0.95     0.63      32693.09|
| 14:  2.0327 -  1.9832   423    49  0.44  56.81   0.94     0.61      26812.20|
|alpha:            min =        0.61 max =            0.88 mean =         0.71|
|beta:             min =    26812.20 max =        80480.08 mean =     52513.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.96|
|phase err.(test): min =        0.00 max =           90.00 mean =        47.70|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.301841             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.608046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.644   (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 |  1.787 -  2.098:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.098 -  2.410:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.410 -  2.721:      160 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.721 -  3.032:     1935 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.032 -  3.344:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.344 -  3.655:     2778 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.655 -  3.966:     4615 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.966 -  4.277:     4315 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.277 -  4.589:     5610 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.589 -  4.900:     6693 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.787 |       0.206 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    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: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4172   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.232499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4150   r_free= 0.4106   ksol= 0.31   Bsol= 54.73   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.15,5.23,-0.00,0.00,0.00); trace/3= 0.63                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.220769                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.271816             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.843   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.758243              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.321   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4150      final r-factor (work) = 0.2552          |
| start r-factor (free) = 0.4106      final r-factor (free) = 0.2885          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0849 = 10.27 * 0.50 * 6.2149 + 1.00 * 0.1659                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9633 = 10.27 * 0.50 * 6.0061 + 1.00 * 0.1164                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2552      final r-factor (work) = 0.2335          |
| start r-factor (free) = 0.2885      final r-factor (free) = 0.2943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5608 = 0.76 * 1.00 * 6.0061 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4660 = 0.76 * 1.00 * 5.7706 + 1.00 * 0.0904                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.04  17.28    None  None   None       |
|    all(noH): 2823   0      0.00    108.04  17.28    None  None   None       |
|    Sol.    : 438    0      1.46    65.78   39.10    None  None   None       |
|    Mac.    : 2385   0      0.00    108.04  13.27    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 -  10.804: 1057   |   5:    54.019 -  64.823:   47        |
|      1:    10.804 -  21.608: 1071   |   6:    64.823 -  75.626:    1        |
|      2:    21.608 -  32.411:  318   |   7:    75.626 -  86.430:    0        |
|      3:    32.411 -  43.215:  177   |   8:    86.430 -  97.234:    0        |
|      4:    43.215 -  54.019:  151   |   9:    97.234 - 108.038:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2335 r_free = 0.2943             target_work(ml) = 5.782         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2332 r_free = 0.2940             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2332   r_free= 0.2940   ksol= 0.31   Bsol= 54.73   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.15,5.23,-0.00,0.00,0.00); trace/3= 0.63                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.781074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2311   r_free= 0.2921   ksol= 0.34   Bsol= 73.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.24,1.56,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.779586                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.649049              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.924   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.690164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.035   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2311      final r-factor (work) = 0.1806          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.2321          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7687 = 2.65 * 0.50 * 5.7774 + 1.00 * 0.1164                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5795 = 2.65 * 0.50 * 5.6785 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1806      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2321      final r-factor (free) = 0.2203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1172 = 0.69 * 1.00 * 5.6785 + 1.00 * 0.1981                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8219 = 0.69 * 1.00 * 5.5194 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.17   18.23    None  None   None       |
|    all(noH): 2823   0      0.00    87.17   18.23    None  None   None       |
|    Sol.    : 438    0      3.46    81.27   44.22    None  None   None       |
|    Mac.    : 2385   0      0.00    87.17   13.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.717:  773   |   5:    43.584 -  52.301:   99        |
|      1:     8.717 -  17.434: 1171   |   6:    52.301 -  61.018:   90        |
|      2:    17.434 -  26.151:  354   |   7:    61.018 -  69.735:   63        |
|      3:    26.151 -  34.867:  128   |   8:    69.735 -  78.452:   28        |
|      4:    34.867 -  43.584:  109   |   9:    78.452 -  87.169:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1669 r_free = 0.2203             target_work(ml) = 5.496         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1668 r_free = 0.2205             target_work(ml) = 5.496         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1668   r_free= 0.2205   ksol= 0.34   Bsol= 73.38   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.24,1.56,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.495618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2203   ksol= 0.34   Bsol= 78.92   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.21,0.58,-0.00,0.00,0.00); trace/3= -1.29                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.494825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.739118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.989  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.014376              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.833  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1667      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2203      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6166 = 2.74 * 0.50 * 5.5189 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4678 = 2.74 * 0.50 * 5.4082 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4985 = 1.01 * 1.00 * 5.4082 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3876 = 1.01 * 1.00 * 5.2988 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.95  18.15    None  None   None       |
|    all(noH): 2823   0      0.00    102.95  18.15    None  None   None       |
|    Sol.    : 438    0      0.00    102.95  45.74    None  None   None       |
|    Mac.    : 2385   0      0.00    85.48   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.295: 1130   |   5:    51.474 -  61.768:   89        |
|      1:    10.295 -  20.590: 1039   |   6:    61.768 -  72.063:   63        |
|      2:    20.590 -  30.884:  221   |   7:    72.063 -  82.358:   43        |
|      3:    30.884 -  41.179:  123   |   8:    82.358 -  92.653:   13        |
|      4:    41.179 -  51.474:   98   |   9:    92.653 - 102.947:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1793             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1299 r_free = 0.1792             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1792   ksol= 0.34   Bsol= 78.92   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.21,0.58,-0.00,0.00,0.00); trace/3= -1.29                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.275294                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1791   ksol= 0.34   Bsol= 80.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.32,0.01,-0.00,0.00,0.00); trace/3= -1.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.275192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.720836              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.257  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.109400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1302      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1791      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6208 = 1.72 * 0.50 * 5.2995 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5767 = 1.72 * 0.50 * 5.2573 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5877 = 0.11 * 1.00 * 5.2573 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5818 = 0.11 * 1.00 * 5.2498 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.52   16.64    None  None   None       |
|    all(noH): 2823   0      0.00    84.52   16.64    None  None   None       |
|    Sol.    : 438    0      2.42    84.52   38.71    None  None   None       |
|    Mac.    : 2385   0      0.00    77.16   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.452:  682   |   5:    42.261 -  50.713:   84        |
|      1:     8.452 -  16.904: 1349   |   6:    50.713 -  59.165:   63        |
|      2:    16.904 -  25.357:  322   |   7:    59.165 -  67.617:   35        |
|      3:    25.357 -  33.809:  139   |   8:    67.617 -  76.070:   10        |
|      4:    33.809 -  42.261:  128   |   9:    76.070 -  84.522:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1265 r_free = 0.1678             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1264 r_free = 0.1676             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1676   ksol= 0.34   Bsol= 80.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.32,0.01,-0.00,0.00,0.00); trace/3= -1.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.238538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1674   ksol= 0.32   Bsol= 61.90   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.43,-0.23,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.449339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.060  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.414890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.121  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8564 = 1.45 * 0.50 * 5.2482 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8388 = 1.45 * 0.50 * 5.2229 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1743 = 0.41 * 1.00 * 5.2229 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1700 = 0.41 * 1.00 * 5.2087 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    87.66   16.79    None  None   None       |
|    all(noH): 2823   0      0.22    87.66   16.79    None  None   None       |
|    Sol.    : 438    0      3.78    87.66   39.87    None  None   None       |
|    Mac.    : 2385   0      0.22    78.32   12.55    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:     0.222 -   8.965:  868   |   5:    43.939 -  52.682:   97        |
|      1:     8.965 -  17.709: 1222   |   6:    52.682 -  61.426:   73        |
|      2:    17.709 -  26.452:  266   |   7:    61.426 -  70.169:   27        |
|      3:    26.452 -  35.195:  136   |   8:    70.169 -  78.913:   13        |
|      4:    35.195 -  43.939:  114   |   9:    78.913 -  87.656:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1661             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1661             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1661   ksol= 0.32   Bsol= 61.90   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.43,-0.23,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.210811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7346 0.99   1423  157 0.1008 0.1319      5.4081       5.583|
|  2:  4.7346 -  3.7770 0.99   1373  154 0.0903 0.1174      5.4796      5.6706|
|  3:  3.7770 -  3.3052 0.99   1339  149 0.1144 0.1572      5.5284      5.8341|
|  4:  3.3052 -  3.0055 0.99   1345  150 0.1313 0.1768      5.5072      5.6596|
|  5:  3.0055 -  2.7915 0.99   1315  149 0.1452 0.1750      5.3839      5.6016|
|  6:  2.7915 -  2.6278 0.99   1329  143 0.1341 0.2101      5.2688      5.5476|
|  7:  2.6278 -  2.4968 0.99   1321  142 0.1384 0.1601      5.2417      5.3469|
|  8:  2.4968 -  2.3885 0.98   1302  151 0.1279 0.1743      5.1461      5.3916|
|  9:  2.3885 -  2.2969 0.98   1296  143 0.1265 0.2008      5.0968      5.3818|
| 10:  2.2969 -  2.2179 1.00   1315  150 0.1237 0.1770      5.0027      5.2464|
| 11:  2.2179 -  2.1488 0.98   1296  143 0.1211 0.1903      4.9963      5.3562|
| 12:  2.1488 -  2.0875 0.98   1286  139 0.1263 0.1873      4.9395      5.2096|
| 13:  2.0875 -  2.0327 0.96   1267  140 0.1152 0.1699      4.8322      5.0435|
| 14:  2.0327 -  1.9832 0.32    423   49 0.1043 0.1658      4.7213      4.9663|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7346  1423   157  0.94   9.14   0.97     0.94       7287.60|
|  2:  4.7346 -  3.7770  1373   154  0.95   8.35   1.00     0.99       9616.17|
|  3:  3.7770 -  3.3052  1339   149  0.93  12.04   1.01     1.01      11229.38|
|  4:  3.3052 -  3.0055  1345   150  0.91  14.82   1.00     0.97      11249.16|
|  5:  3.0055 -  2.7915  1315   149  0.90  16.61   0.99     0.97       9074.36|
|  6:  2.7915 -  2.6278  1329   143  0.89  17.59   0.97     0.94       7849.93|
|  7:  2.6278 -  2.4968  1321   142  0.89  16.88   0.98     0.95       7149.93|
|  8:  2.4968 -  2.3885  1302   151  0.90  16.74   0.98     0.95       6147.17|
|  9:  2.3885 -  2.2969  1296   143  0.90  16.83   0.99     0.95       5681.10|
| 10:  2.2969 -  2.2179  1315   150  0.90  16.37   0.99     0.95       4708.93|
| 11:  2.2179 -  2.1488  1296   143  0.89  16.98   0.97     0.91       4683.13|
| 12:  2.1488 -  2.0875  1286   139  0.90  16.87   0.99     0.99       4410.62|
| 13:  2.0875 -  2.0327  1267   140  0.89  17.97   0.98     0.95       3839.54|
| 14:  2.0327 -  1.9832   423    49  0.92  14.76   0.96     0.92       2951.21|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2951.21 max =        11249.16 mean =      7088.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1660   ksol= 0.32   Bsol= 61.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.28,-0.12,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.210883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1660   ksol= 0.32   Bsol= 61.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.28,-0.12,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.210883                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7346 0.99   1423  157 0.1008 0.1320      5.4086       5.584|
|  2:  4.7346 -  3.7770 0.99   1373  154 0.0903 0.1174      5.4799      5.6706|
|  3:  3.7770 -  3.3052 0.99   1339  149 0.1144 0.1572      5.5284      5.8344|
|  4:  3.3052 -  3.0055 0.99   1345  150 0.1313 0.1768      5.5074      5.6597|
|  5:  3.0055 -  2.7915 0.99   1315  149 0.1451 0.1749      5.3838      5.6013|
|  6:  2.7915 -  2.6278 0.99   1329  143 0.1341 0.2101      5.2689      5.5479|
|  7:  2.6278 -  2.4968 0.99   1321  142 0.1384 0.1601      5.2418       5.347|
|  8:  2.4968 -  2.3885 0.98   1302  151 0.1278 0.1743      5.1462      5.3915|
|  9:  2.3885 -  2.2969 0.98   1296  143 0.1264 0.2008      5.0968      5.3819|
| 10:  2.2969 -  2.2179 1.00   1315  150 0.1237 0.1769      5.0027      5.2456|
| 11:  2.2179 -  2.1488 0.98   1296  143 0.1211 0.1902      4.9963       5.356|
| 12:  2.1488 -  2.0875 0.98   1286  139 0.1263 0.1873      4.9393      5.2098|
| 13:  2.0875 -  2.0327 0.96   1267  140 0.1152 0.1699      4.8323      5.0432|
| 14:  2.0327 -  1.9832 0.32    423   49 0.1044 0.1658      4.7217      4.9666|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.7346  1423   157  0.94   9.15   0.97     0.94       7297.53|
|  2:  4.7346 -  3.7770  1373   154  0.95   8.37   1.00     0.99       9624.82|
|  3:  3.7770 -  3.3052  1339   149  0.93  12.04   1.01     1.01      11232.91|
|  4:  3.3052 -  3.0055  1345   150  0.91  14.82   1.00     0.97      11251.18|
|  5:  3.0055 -  2.7915  1315   149  0.90  16.61   0.99     0.98       9074.79|
|  6:  2.7915 -  2.6278  1329   143  0.89  17.59   0.98     0.95       7849.12|
|  7:  2.6278 -  2.4968  1321   142  0.89  16.89   0.99     0.96       7150.29|
|  8:  2.4968 -  2.3885  1302   151  0.90  16.75   0.99     0.95       6147.94|
|  9:  2.3885 -  2.2969  1296   143  0.90  16.83   1.00     0.95       5682.88|
| 10:  2.2969 -  2.2179  1315   150  0.90  16.37   1.00     0.96       4706.61|
| 11:  2.2179 -  2.1488  1296   143  0.89  16.97   0.98     0.92       4680.33|
| 12:  2.1488 -  2.0875  1286   139  0.90  16.86   1.00     1.00       4407.99|
| 13:  2.0875 -  2.0327  1267   140  0.89  17.97   0.98     0.96       3839.64|
| 14:  2.0327 -  1.9832   423    49  0.92  14.76   0.97     0.93       2952.32|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2952.32 max =        11251.18 mean =      7089.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.133)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    87.65   16.78    None  None   None       |
|    all(noH): 2823   0      0.22    87.65   16.78    None  None   None       |
|    Sol.    : 438    0      3.77    87.65   39.87    None  None   None       |
|    Mac.    : 2385   0      0.22    78.32   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.216 -   8.960:  868   |   5:    43.934 -  52.677:   97        |
|      1:     8.960 -  17.703: 1222   |   6:    52.677 -  61.421:   73        |
|      2:    17.703 -  26.447:  266   |   7:    61.421 -  70.164:   27        |
|      3:    26.447 -  35.190:  136   |   8:    70.164 -  78.908:   13        |
|      4:    35.190 -  43.934:  114   |   9:    78.908 -  87.651:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.597 - 5.022
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 296
   mapped sites are within: 0.726 - 5.022

peak=    5.413 closest distance to " CG  PRO A  54 " =    1.407
peak=    5.322 closest distance to " CB  GLN A 223 " =    1.456
peak=    5.284 closest distance to " NE2 GLN A  11 " =    1.176
peak=    5.133 closest distance to " O   HOH Z 144 " =    2.035
peak=    5.082 closest distance to " CG  PRO A 280 " =    0.983
peak=    5.005 closest distance to " NH2 ARG A  56 " =    2.079
peak=    4.898 closest distance to " CZ  PHE A 218 " =    1.069
peak=    4.872 closest distance to " O   HOH Z 423 " =    1.684
peak=    4.773 closest distance to " CB  ASN A 148 " =    1.475
peak=    4.743 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.581 closest distance to " CB  PRO A  54 " =    1.074
peak=    4.555 closest distance to " CG2 VAL A 257 " =    0.932
peak=    4.553 closest distance to " CG  PRO A 198 " =    1.317
peak=    4.541 closest distance to " O   HOH Z 287 " =    2.060
peak=    4.536 closest distance to " CB  ARG A 190 " =    1.584
peak=    4.516 closest distance to " CG  PRO A 213 " =    1.262
peak=    4.503 closest distance to " CA  ARG A 195 " =    1.370
peak=    4.503 closest distance to " CB  ARG A 275 " =    0.949
peak=    4.487 closest distance to " CD  ARG A 159 " =    0.783
peak=    4.474 closest distance to " O   HOH Z 298 " =    2.152
peak=    4.413 closest distance to " O   HOH Z 126 " =    2.007
peak=    4.385 closest distance to " O   HOH Z 369 " =    2.058
peak=    4.324 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.281 closest distance to " O   HOH Z  78 " =    1.748
peak=    4.251 closest distance to " O   HOH Z 406 " =    1.794
peak=    4.244 closest distance to " CB  SER A  63 " =    1.279
peak=    4.227 closest distance to " CZ3 TRP A 266 " =    1.101
peak=    4.211 closest distance to " CB  VAL A 265 " =    1.290
peak=    4.206 closest distance to " ND2 ASN A 187 " =    1.584
peak=    4.174 closest distance to " CB  ASN A 142 " =    0.899
peak=    4.173 closest distance to " O   HOH Z 188 " =    2.753
peak=    4.163 closest distance to " CB  SER A 210 " =    0.814
peak=    4.153 closest distance to " CB  ARG A  79 " =    1.333
peak=    4.148 closest distance to " O   HOH Z 303 " =    2.256
peak=    4.130 closest distance to " CA  TYR A  30 " =    0.999
peak=    4.094 closest distance to " CE  LYS A  76 " =    0.927
peak=    4.069 closest distance to " CG  PRO A 243 " =    1.135
peak=    4.063 closest distance to " O   HOH Z  57 " =    2.131
peak=    4.057 closest distance to " CD2 TRP A 179 " =    1.265
peak=    4.055 closest distance to " CB  ASP A 124 " =    0.833
peak=    4.053 closest distance to " CB  ASN A  39 " =    0.914
peak=    4.048 closest distance to " CB  LEU A 228 " =    1.081
peak=    4.004 closest distance to " CA  SER A  87 " =    0.985
peak=    4.002 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.991 closest distance to " CB  ALA A 104 " =    0.729
peak=    3.988 closest distance to " NH1AARG A 145 " =    1.333
peak=    3.935 closest distance to " CB  GLU A 128 " =    0.872
peak=    3.933 closest distance to " NE2 HIS A 207 " =    1.098
peak=    3.911 closest distance to " CB  SER A 216 " =    0.947
peak=    3.907 closest distance to " CB  TRP A 266 " =    1.014
peak=    3.899 closest distance to " O   HOH Z 286 " =    2.511
peak=    3.898 closest distance to " CZ  PHE A  38 " =    1.230
peak=    3.895 closest distance to " O   HOH Z 214 " =    2.339
peak=    3.893 closest distance to " CB  GLU A 277 " =    3.751
peak=    3.891 closest distance to " CD  ARG A 269 " =    0.921
peak=    3.877 closest distance to " CB  MET A  40 " =    0.757
peak=    3.864 closest distance to " CG  LEU A 167 " =    1.262
peak=    3.864 closest distance to " O   HOH Z  21 " =    1.781
peak=    3.851 closest distance to " O   HOH Z   9 " =    1.485
peak=    3.849 closest distance to " CB  SER A 212 " =    1.328
peak=    3.846 closest distance to " O   HOH Z 313 " =    2.078
peak=    3.839 closest distance to " CB  ASN A 187 " =    1.128
peak=    3.837 closest distance to " O   HOH Z  78 " =    2.029
peak=    3.831 closest distance to " O   HOH Z 427 " =    2.829
peak=    3.806 closest distance to " CD  ARG A  66 " =    2.132
peak=    3.803 closest distance to " O   HOH Z 272 " =    1.779
peak=    3.801 closest distance to " CB  ASN A 110 " =    1.137
peak=    3.799 closest distance to " O   HOH Z   7 " =    1.300
peak=    3.796 closest distance to " O   HOH Z 394 " =    3.973
peak=    3.791 closest distance to " CA  VAL A 125 " =    1.147
peak=    3.782 closest distance to " CB  ALA A 114 " =    0.804
peak=    3.774 closest distance to " CA  THR A 264 " =    0.907
peak=    3.766 closest distance to " N   PHE A 130 " =    1.195
peak=    3.729 closest distance to " O   HOH Z 353 " =    2.583
peak=    3.720 closest distance to " O   TYR A 116 " =    1.316
peak=    3.718 closest distance to " O   HOH Z   1 " =    1.956
peak=    3.714 closest distance to " O   ASN A  74 " =    1.493
peak=    3.713 closest distance to " O   HOH Z 285 " =    2.114
peak=    3.710 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.709 closest distance to " CD1 LEU A 300 " =    1.063
peak=    3.704 closest distance to " O   PRO A 198 " =    1.595
peak=    3.704 closest distance to " O   HOH Z  53 " =    2.442
peak=    3.702 closest distance to " CB  PRO A  90 " =    1.111
peak=    3.698 closest distance to " O   THR A 220 " =    1.368
peak=    3.696 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.685 closest distance to " CB  GLU A  46 " =    0.992
peak=    3.674 closest distance to " O   HOH Z 240 " =    2.362
peak=    3.673 closest distance to " O   HOH Z 380 " =    1.707
peak=    3.668 closest distance to " O   HOH Z 234 " =    3.923
peak=    3.663 closest distance to " O   HOH Z 148 " =    3.506
peak=    3.655 closest distance to " CA  ILE A 234 " =    0.988
peak=    3.650 closest distance to " O   PHE A 192 " =    1.349
peak=    3.639 closest distance to " NZ  LYS A 119 " =    2.740
peak=    3.639 closest distance to " ND2 ASN A 249 " =    0.794
peak=    3.634 closest distance to " CD  LYS A 166 " =    1.293
peak=    3.617 closest distance to " O   HOH Z  88 " =    3.973
peak=    3.614 closest distance to " O   HOH Z 403 " =    1.535
peak=    3.606 closest distance to " CA  TYR A 116 " =    1.369
peak=    3.603 closest distance to " O   HOH Z  10 " =    1.775
peak=    3.599 closest distance to " O   HOH Z 248 " =    1.558
peak=    3.596 closest distance to " O   HOH Z 167 " =    1.691
peak=    3.591 closest distance to " OG  SER A  62 " =    2.963
peak=    3.591 closest distance to " CA  ARG A  36 " =    1.088
peak=    3.588 closest distance to " CB  LEU A  83 " =    0.729
peak=    3.583 closest distance to " OG  SER A 135 " =    1.202
peak=    3.575 closest distance to " CG2 ILE A 239 " =    0.787
peak=    3.560 closest distance to " O   HOH Z 411 " =    3.811
peak=    3.559 closest distance to " O   HOH Z 116 " =    3.189
peak=    3.558 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.554 closest distance to " CB  GLU A  37 " =    1.001
peak=    3.547 closest distance to " CG2 ILE A 120 " =    1.266
peak=    3.545 closest distance to " O   HOH Z 265 " =    1.964
peak=    3.538 closest distance to " CA  ASN A 127 " =    1.108
peak=    3.536 closest distance to " CB  SER A   3 " =    1.357
peak=    3.534 closest distance to " O   HOH Z 368 " =    4.299
peak=    3.530 closest distance to " CD BLYS A 290 " =    1.010
peak=    3.529 closest distance to " CG  PHE A 204 " =    0.917
peak=    3.523 closest distance to " CB  ALA A 160 " =    1.350
peak=    3.523 closest distance to " CG AARG A 275 " =    1.270
peak=    3.515 closest distance to " CG2 THR A 221 " =    0.995
peak=    3.512 closest distance to " O   HOH Z 171 " =    4.291
peak=    3.511 closest distance to " CB  VAL A 202 " =    1.545
peak=    3.505 closest distance to " CB  ALA A 291 " =    1.204
peak=    3.495 closest distance to " CB  TYR A 116 " =    0.864
peak=    3.495 closest distance to " O   HOH Z  61 " =    1.718
peak=    3.486 closest distance to " O   HOH Z 294 " =    1.609
peak=    3.480 closest distance to " CB  GLU A 152 " =    1.143
peak=    3.475 closest distance to " CB  ILE A 120 " =    1.251
peak=    3.473 closest distance to " O   SER A  87 " =    2.341
peak=    3.469 closest distance to " O   HOH Z 425 " =    1.312
peak=    3.465 closest distance to " O   HOH Z 261 " =    1.899
peak=    3.463 closest distance to " O   HOH Z 316 " =    3.109
peak=    3.462 closest distance to " CA  ALA A 233 " =    1.463
peak=    3.462 closest distance to " O   THR A 251 " =    1.155
peak=    3.462 closest distance to " O   HOH Z 213 " =    2.908
peak=    3.459 closest distance to " O   HOH Z 158 " =    3.094
peak=    3.459 closest distance to " CA  ASP A 162 " =    1.054
peak=    3.453 closest distance to " O  BHOH Z  74 " =    1.250
peak=    3.453 closest distance to " O   HOH Z 359 " =    1.531
peak=    3.452 closest distance to " O   HOH Z 391 " =    2.951
peak=    3.452 closest distance to " O   HOH Z 405 " =    1.405
peak=    3.449 closest distance to " O   HOH Z 371 " =    2.781
peak=    3.445 closest distance to " CB  THR A  31 " =    1.548
peak=    3.443 closest distance to " CB  ARG A 102 " =    0.758
peak=    3.440 closest distance to " OH  TYR A 214 " =    1.300
peak=    3.439 closest distance to " CA  ALA A 158 " =    1.175
peak=    3.435 closest distance to " OG1 THR A 279 " =    1.341
peak=    3.432 closest distance to " O   HOH Z 422 " =    2.682
peak=    3.425 closest distance to " CD1 LEU A  96 " =    0.745
peak=    3.423 closest distance to " CG2 ILE A  20 " =    1.471
peak=    3.422 closest distance to " N   TYR A  15 " =    0.786
peak=    3.419 closest distance to " CA  ILE A 263 " =    1.117
peak=    3.416 closest distance to " NZ  LYS A 117 " =    3.040
peak=    3.411 closest distance to " O   ASN A  74 " =    2.026
peak=    3.411 closest distance to " CG2 ILE A 151 " =    0.918
peak=    3.406 closest distance to " CG  ARG A 138 " =    1.376
peak=    3.406 closest distance to " CA  ASN A 215 " =    1.102
peak=    3.402 closest distance to " O   HOH Z 365 " =    2.857
peak=    3.401 closest distance to " O   HOH Z  63 " =    1.865
peak=    3.401 closest distance to " CB  SER A 273 " =    0.910
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.277
peak=    3.395 closest distance to " CG  GLU A  37 " =    0.824
peak=    3.390 closest distance to " O   HOH Z 368 " =    1.949
peak=    3.387 closest distance to " CA  ILE A 106 " =    0.826
peak=    3.387 closest distance to " O   HOH Z 172 " =    3.010
peak=    3.380 closest distance to " O   HOH Z 153 " =    3.900
peak=    3.376 closest distance to " CB  ARG A 138 " =    1.031
peak=    3.374 closest distance to " O   HOH Z 302 " =    2.015
peak=    3.373 closest distance to " CA  ALA A 100 " =    1.054
peak=    3.372 closest distance to " O   HOH Z  69 " =    0.909
peak=    3.370 closest distance to " CA  ALA A 154 " =    1.141
peak=    3.357 closest distance to " CG1 VAL A 153 " =    0.898
peak=    3.353 closest distance to " O   HOH Z 325 " =    2.267
peak=    3.351 closest distance to " O   HOH Z 211 " =    1.134
peak=    3.341 closest distance to " N   VAL A 296 " =    1.725
peak=    3.340 closest distance to " OE2 GLU A  53 " =    1.975
peak=    3.334 closest distance to " O   HOH Z 258 " =    2.094
peak=    3.334 closest distance to " CA  ARG A 102 " =    1.154
peak=    3.333 closest distance to " CA  ASN A 217 " =    1.245
peak=    3.333 closest distance to " CA  PRO A 280 " =    1.264
peak=    3.326 closest distance to " CB  ALA A 299 " =    0.997
peak=    3.324 closest distance to " CB  ALA A  43 " =    0.790
peak=    3.322 closest distance to " CG2AVAL A  72 " =    1.628
peak=    3.320 closest distance to " O   HOH Z   5 " =    2.317
peak=    3.316 closest distance to " O   HOH Z   2 " =    1.520
peak=    3.314 closest distance to " O   HOH Z 389 " =    1.878
peak=    3.306 closest distance to " N   ARG A 156 " =    1.370
peak=    3.305 closest distance to " ND2BASN A 224 " =    0.902
peak=    3.304 closest distance to " O   HOH Z 273 " =    2.780
peak=    3.301 closest distance to " O   HOH Z 402 " =    1.439
peak=    3.300 closest distance to " O   HOH Z 124 " =    1.936
peak=    3.300 closest distance to " CA  MET A  40 " =    1.224
peak=    3.298 closest distance to " CE3 TRP A  85 " =    0.976
peak=    3.297 closest distance to " CB  PRO A 198 " =    1.055
peak=    3.292 closest distance to " O   HOH Z 183 " =    1.473
peak=    3.289 closest distance to " CA  GLN A  94 " =    0.763
peak=    3.287 closest distance to " CG2 VAL A 197 " =    1.053
peak=    3.284 closest distance to " O   HOH Z 280 " =    3.012
peak=    3.282 closest distance to " CG  GLN A 144 " =    0.840
peak=    3.282 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.277 closest distance to " O   HOH Z 290 " =    1.116
peak=    3.276 closest distance to " O   HOH Z 233 " =    1.456
peak=    3.275 closest distance to " O   HOH Z 218 " =    4.660
peak=    3.274 closest distance to " O   HOH Z  88 " =    3.405
peak=    3.273 closest distance to " O   HOH Z 116 " =    1.834
peak=    3.270 closest distance to " CB  HIS A  86 " =    0.901
peak=    3.266 closest distance to " CB  THR A  82 " =    1.314
peak=    3.262 closest distance to " CB  GLN A  89 " =    1.249
peak=    3.259 closest distance to " CA  MET A 105 " =    0.931
peak=    3.259 closest distance to " CA  ASP A 124 " =    0.771
peak=    3.257 closest distance to " CB  TRP A 179 " =    1.504
peak=    3.249 closest distance to " OG1 THR A 264 " =    0.726
peak=    3.247 closest distance to " O   HOH Z 185 " =    1.834
peak=    3.246 closest distance to " O   HOH Z 120 " =    3.431
peak=    3.244 closest distance to " CA  SER A  95 " =    0.959
peak=    3.244 closest distance to " NE2 GLN A  73 " =    4.010
peak=    3.243 closest distance to " O   HOH Z 371 " =    1.877
peak=    3.243 closest distance to " O   HOH Z 251 " =    1.727
peak=    3.243 closest distance to " O   HOH Z 218 " =    1.580
peak=    3.243 closest distance to " CA  GLU A  46 " =    1.091
peak=    3.240 closest distance to " CB  LYS A 117 " =    1.204
peak=    3.235 closest distance to " O   THR A 294 " =    1.031
peak=    3.233 closest distance to " O   HOH Z  90 " =    2.255
peak=    3.232 closest distance to " NE  ARG A  79 " =    1.118
peak=    3.228 closest distance to " O   HOH Z 132 " =    2.665
peak=    3.227 closest distance to " CE3 TRP A 150 " =    1.035
peak=    3.225 closest distance to " OD2 ASP A 286 " =    3.301
peak=    3.222 closest distance to " O   HOH Z 409 " =    2.580
peak=    3.222 closest distance to " CA  GLY A 136 " =    1.000
peak=    3.217 closest distance to " CG1 ILE A 151 " =    1.087
peak=    3.214 closest distance to " O   HOH Z   9 " =    1.824
peak=    3.214 closest distance to " CB  PHE A 204 " =    1.075
peak=    3.211 closest distance to " O   MET A 105 " =    1.832
peak=    3.209 closest distance to " CB  SER A  62 " =    0.826
peak=    3.208 closest distance to " CB  ASP A 140 " =    1.005
peak=    3.203 closest distance to " CA  ALA A 160 " =    1.154
peak=    3.201 closest distance to " O   THR A 182 " =    1.408
peak=    3.197 closest distance to " CB  ALA A   1 " =    4.703
peak=    3.192 closest distance to " CA  PRO A  54 " =    1.047
peak=    3.191 closest distance to " OD1 ASN A  69 " =    2.560
peak=    3.190 closest distance to " CB  PRO A 243 " =    1.375
peak=    3.188 closest distance to " NE AARG A 275 " =    1.327
peak=    3.184 closest distance to " CB AVAL A  41 " =    1.220
peak=    3.183 closest distance to " O   HOH Z 298 " =    2.667
peak=    3.182 closest distance to " O   HOH Z  49 " =    1.042
peak=    3.180 closest distance to " CB  ASN A 173 " =    1.129
peak=    3.177 closest distance to " CA  ARG A 159 " =    1.345
peak=    3.177 closest distance to " O   HOH Z 128 " =    2.386
peak=    3.175 closest distance to " O   HOH Z 392 " =    3.041
peak=    3.173 closest distance to " O   CYS A 168 " =    1.252
peak=    3.169 closest distance to " OG BSER A  99 " =    2.242
peak=    3.167 closest distance to " CG  ARG A 159 " =    0.862
peak=    3.167 closest distance to " N   SER A 135 " =    1.268
peak=    3.166 closest distance to " OG BSER A 134 " =    2.809
peak=    3.165 closest distance to " O   HOH Z  94 " =    2.481
peak=    3.163 closest distance to " N   ASN A  39 " =    1.310
peak=    3.160 closest distance to " N   ASN A 127 " =    1.223
peak=    3.160 closest distance to " O   HOH Z 305 " =    3.657
peak=    3.159 closest distance to " OD1 ASP A 171 " =    1.181
peak=    3.151 closest distance to " O   HOH Z 327 " =    1.907
peak=    3.146 closest distance to " O   HOH Z  66 " =    2.335
peak=    3.145 closest distance to " NH1 ARG A 138 " =    1.023
peak=    3.143 closest distance to " CG  LYS A 119 " =    1.099
peak=    3.140 closest distance to " O   HOH Z 437 " =    1.233
peak=    3.126 closest distance to " O   HOH Z 145 " =    1.542
peak=    3.124 closest distance to " O   HOH Z  59 " =    1.843
peak=    3.123 closest distance to " CB  ASN A 215 " =    1.181
peak=    3.121 closest distance to " CA  THR A 221 " =    0.976
peak=    3.117 closest distance to " O   SER A 164 " =    1.412
peak=    3.116 closest distance to " OG  SER A  62 " =    2.817
peak=    3.112 closest distance to " OE1 GLN A 240 " =    1.574
peak=    3.112 closest distance to " CD1 ILE A 106 " =    0.843
peak=    3.112 closest distance to " CD1AILE A 234 " =    0.919
peak=    3.109 closest distance to " N   GLN A 278 " =    1.458
peak=    3.108 closest distance to " CA  ALA A 299 " =    0.989
peak=    3.106 closest distance to " CD2 LEU A   5 " =    1.456
peak=    3.105 closest distance to " O   ASN A 209 " =    1.349
peak=    3.104 closest distance to " N   CYS A 260 " =    0.837
peak=    3.097 closest distance to " O   HOH Z 147 " =    1.798
peak=    3.088 closest distance to " OE2 GLU A  53 " =    1.169
peak=    3.087 closest distance to " O   HOH Z  80 " =    1.607
peak=    3.081 closest distance to " O   HOH Z 417 " =    3.720
peak=    3.080 closest distance to " CB  VAL A 265 " =    1.991
peak=    3.077 closest distance to " O   HOH Z 344 " =    3.190
peak=    3.074 closest distance to " CB  GLN A 103 " =    0.982
peak=    3.074 closest distance to " CA  ARG A 156 " =    1.153
peak=    3.068 closest distance to " O   HOH Z 369 " =    1.723
peak=    3.067 closest distance to " CB  LEU A 300 " =    0.920
peak=    3.061 closest distance to " O   HOH Z 380 " =    5.022
peak=    3.056 closest distance to " N   ASP A 162 " =    1.179
peak=    3.044 closest distance to " O   HOH Z 213 " =    2.150
peak=    3.015 closest distance to " CB  PRO A 163 " =    4.283
peak=    3.004 closest distance to " O   HOH Z 438 " =    2.770

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 5.696
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 208
   mapped sites are within: 0.819 - 5.696

peak=   -4.567 closest distance to " CD  ARG A  14 " =    3.498
peak=   -4.387 closest distance to " O   HOH Z 377 " =    2.007
peak=   -4.318 closest distance to " CG2 ILE A  49 " =    2.811
peak=   -4.293 closest distance to " O   PRO A 198 " =    1.228
peak=   -4.286 closest distance to " OG BSER A 134 " =    1.383
peak=   -4.206 closest distance to " CB  ALA A  43 " =    2.603
peak=   -4.198 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -4.164 closest distance to " O   HOH Z 231 " =    2.233
peak=   -4.133 closest distance to " CZ3 TRP A 179 " =    1.230
peak=   -4.106 closest distance to " CG1 VAL A 250 " =    2.683
peak=   -4.089 closest distance to " CB  PRO A 243 " =    2.653
peak=   -4.070 closest distance to " CE BMET A  47 " =    1.329
peak=   -4.061 closest distance to " CD2 TYR A 293 " =    1.961
peak=   -4.026 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.000 closest distance to " O   TYR A 247 " =    2.926
peak=   -3.997 closest distance to " O   HOH Z 290 " =    0.976
peak=   -3.960 closest distance to " N   ALA A  43 " =    2.541
peak=   -3.945 closest distance to " O   HOH Z 351 " =    1.360
peak=   -3.928 closest distance to " OG  SER A  97 " =    2.271
peak=   -3.926 closest distance to " CD  GLN A  58 " =    0.853
peak=   -3.888 closest distance to " O   HOH Z 295 " =    1.753
peak=   -3.843 closest distance to " O   HOH Z  38 " =    1.559
peak=   -3.829 closest distance to " O   HOH Z  73 " =    2.205
peak=   -3.801 closest distance to " ND2 ASN A 249 " =    2.206
peak=   -3.784 closest distance to " CG  MET A 105 " =    0.966
peak=   -3.777 closest distance to " CD  GLN A  88 " =    0.850
peak=   -3.771 closest distance to " O   HOH Z  60 " =    1.139
peak=   -3.757 closest distance to " CG1 VAL A 112 " =    3.035
peak=   -3.753 closest distance to " O   ALA A  10 " =    1.720
peak=   -3.736 closest distance to " CD2 PHE A 192 " =    1.983
peak=   -3.730 closest distance to " CE2 TYR A  30 " =    2.716
peak=   -3.720 closest distance to " O   HOH Z  69 " =    2.049
peak=   -3.717 closest distance to " O   HOH Z 411 " =    5.453
peak=   -3.708 closest distance to " O   HOH Z 407 " =    3.186
peak=   -3.684 closest distance to " O   HOH Z 191 " =    5.696
peak=   -3.673 closest distance to " O   HOH Z   9 " =    1.769
peak=   -3.667 closest distance to " O   HOH Z 357 " =    2.112
peak=   -3.662 closest distance to " CD1 LEU A 255 " =    2.978
peak=   -3.662 closest distance to " CB  ALA A   9 " =    2.450
peak=   -3.660 closest distance to " O   HOH Z 359 " =    3.150
peak=   -3.651 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.646 closest distance to " CA  GLY A 241 " =    3.311
peak=   -3.630 closest distance to " O   HOH Z 216 " =    1.063
peak=   -3.627 closest distance to " O   HOH Z 372 " =    2.434
peak=   -3.625 closest distance to " O   HOH Z 412 " =    4.412
peak=   -3.620 closest distance to " O   PRO A 163 " =    1.901
peak=   -3.608 closest distance to " C   HIS A 108 " =    1.171
peak=   -3.600 closest distance to " O   HOH Z 131 " =    4.023
peak=   -3.600 closest distance to " CG  GLN A 223 " =    2.218
peak=   -3.597 closest distance to " O   HOH Z 394 " =    1.573
peak=   -3.589 closest distance to " CA  GLY A 133 " =    2.066
peak=   -3.581 closest distance to " OD1 ASP A 171 " =    1.635
peak=   -3.579 closest distance to " CG2 THR A  18 " =    2.819
peak=   -3.558 closest distance to " CD  ARG A  79 " =    1.147
peak=   -3.553 closest distance to " CE2 PHE A  61 " =    2.745
peak=   -3.550 closest distance to " CA  ASP A 298 " =    1.136
peak=   -3.544 closest distance to " CG2 ILE A  20 " =    2.993
peak=   -3.543 closest distance to " O   HOH Z 111 " =    1.652
peak=   -3.535 closest distance to " O   VAL A  67 " =    2.654
peak=   -3.534 closest distance to " O   GLY A  17 " =    1.152
peak=   -3.532 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.526 closest distance to " CG2 ILE A 263 " =    2.411
peak=   -3.523 closest distance to " CG  PRO A 198 " =    1.881
peak=   -3.523 closest distance to " CD2 PHE A  61 " =    2.146
peak=   -3.520 closest distance to " O   ILE A 106 " =    2.061
peak=   -3.519 closest distance to " CG  ARG A 269 " =    2.536
peak=   -3.514 closest distance to " CE  MET A 105 " =    2.409
peak=   -3.512 closest distance to " O   HOH Z 185 " =    2.278
peak=   -3.511 closest distance to " CB  ASN A  39 " =    2.240
peak=   -3.510 closest distance to " NH2AARG A 275 " =    5.583
peak=   -3.498 closest distance to " OD2 ASP A  27 " =    1.615
peak=   -3.485 closest distance to " O   GLU A 152 " =    1.399
peak=   -3.481 closest distance to " CA  GLY A 203 " =    2.461
peak=   -3.471 closest distance to " OE1 GLN A  88 " =    1.118
peak=   -3.465 closest distance to " O   HOH Z  52 " =    1.504
peak=   -3.462 closest distance to " N   THR A  52 " =    1.712
peak=   -3.460 closest distance to " O   VAL A 189 " =    2.635
peak=   -3.459 closest distance to " O   HOH Z 198 " =    1.576
peak=   -3.435 closest distance to " O   HOH Z 389 " =    2.180
peak=   -3.432 closest distance to " N   THR A 157 " =    1.576
peak=   -3.431 closest distance to " O   ARG A 145 " =    1.548
peak=   -3.429 closest distance to " CE3 TRP A 150 " =    2.222
peak=   -3.421 closest distance to " ND2 ASN A  45 " =    2.087
peak=   -3.420 closest distance to " CA  ASP A  27 " =    2.464
peak=   -3.417 closest distance to " CG2 THR A 178 " =    2.327
peak=   -3.417 closest distance to " O   HOH Z 103 " =    1.744
peak=   -3.406 closest distance to " CB  ALA A 291 " =    2.298
peak=   -3.405 closest distance to " CD2 LEU A 143 " =    2.605
peak=   -3.398 closest distance to " CG  GLU A 277 " =    1.280
peak=   -3.397 closest distance to " O   HOH Z 313 " =    1.764
peak=   -3.397 closest distance to " O   HOH Z 298 " =    2.464
peak=   -3.395 closest distance to " O   HOH Z 102 " =    1.502
peak=   -3.394 closest distance to " O   HOH Z 275 " =    1.798
peak=   -3.389 closest distance to " OH  TYR A 172 " =    1.838
peak=   -3.385 closest distance to " O   HOH Z 281 " =    2.762
peak=   -3.383 closest distance to " O   HOH Z 174 " =    2.583
peak=   -3.365 closest distance to " CB  ALA A 100 " =    2.306
peak=   -3.363 closest distance to " O   HOH Z 100 " =    1.103
peak=   -3.359 closest distance to " O   PHE A 218 " =    1.484
peak=   -3.358 closest distance to " O   HOH Z 140 " =    1.309
peak=   -3.356 closest distance to " OH  TYR A 247 " =    2.207
peak=   -3.355 closest distance to " NE2 GLN A 194 " =    1.911
peak=   -3.355 closest distance to " O   HOH Z 128 " =    2.631
peak=   -3.350 closest distance to " O   SER A  22 " =    2.694
peak=   -3.347 closest distance to " OD1 ASN A 148 " =    1.343
peak=   -3.344 closest distance to " CG  LEU A 282 " =    2.421
peak=   -3.342 closest distance to " CD2 HIS A 207 " =    2.163
peak=   -3.342 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.341 closest distance to " CB  HIS A  86 " =    1.138
peak=   -3.340 closest distance to " C   MET A 188 " =    1.478
peak=   -3.337 closest distance to " CB  GLN A  11 " =    1.675
peak=   -3.334 closest distance to " O   HOH Z 252 " =    4.025
peak=   -3.334 closest distance to " CG  GLU A  53 " =    1.314
peak=   -3.329 closest distance to " CA  GLY A  98 " =    1.911
peak=   -3.329 closest distance to " N   SER A 212 " =    1.972
peak=   -3.327 closest distance to " CB  ALA A 129 " =    2.379
peak=   -3.326 closest distance to " O   TYR A 186 " =    1.664
peak=   -3.323 closest distance to " NE2 GLN A 278 " =    1.611
peak=   -3.318 closest distance to " N   ASP A 171 " =    2.566
peak=   -3.313 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.312 closest distance to " CB  TRP A  85 " =    2.491
peak=   -3.309 closest distance to " CB  ASP A 286 " =    2.149
peak=   -3.308 closest distance to " CB  PRO A 163 " =    2.480
peak=   -3.307 closest distance to " O   HOH Z  10 " =    1.423
peak=   -3.305 closest distance to " O   HOH Z 100 " =    0.886
peak=   -3.305 closest distance to " CA  SER A 135 " =    1.219
peak=   -3.305 closest distance to " O   HOH Z 241 " =    1.316
peak=   -3.304 closest distance to " O   HOH Z 215 " =    1.402
peak=   -3.301 closest distance to " CZ  PHE A 155 " =    1.234
peak=   -3.300 closest distance to " CG  LEU A 167 " =    0.944
peak=   -3.291 closest distance to " N   ASP A 191 " =    1.246
peak=   -3.289 closest distance to " O   HOH Z  64 " =    1.346
peak=   -3.285 closest distance to " O   GLN A 240 " =    2.156
peak=   -3.282 closest distance to " O   ARG A  56 " =    1.772
peak=   -3.278 closest distance to " C   ASN A 285 " =    2.398
peak=   -3.277 closest distance to " O   HOH Z 108 " =    1.474
peak=   -3.277 closest distance to " O   HOH Z 166 " =    2.243
peak=   -3.269 closest distance to " O   HOH Z 421 " =    3.011
peak=   -3.267 closest distance to " ND2 ASN A  60 " =    4.104
peak=   -3.265 closest distance to " O   HOH Z 231 " =    1.217
peak=   -3.262 closest distance to " CE1 TYR A 247 " =    2.836
peak=   -3.261 closest distance to " OG BSER A 134 " =    1.860
peak=   -3.257 closest distance to " O   HOH Z 275 " =    1.501
peak=   -3.252 closest distance to " O   HOH Z 429 " =    1.864
peak=   -3.250 closest distance to " O   HOH Z 426 " =    1.593
peak=   -3.248 closest distance to " O   HOH Z 384 " =    3.030
peak=   -3.245 closest distance to " NZ  LYS A 166 " =    1.099
peak=   -3.245 closest distance to " N   SER A 141 " =    1.874
peak=   -3.245 closest distance to " O   HOH Z  51 " =    1.537
peak=   -3.244 closest distance to " O   HOH Z 417 " =    2.990
peak=   -3.236 closest distance to " O   ALA A  34 " =    2.522
peak=   -3.235 closest distance to " O   GLY A 211 " =    1.241
peak=   -3.231 closest distance to " CD  GLU A 236 " =    1.121
peak=   -3.229 closest distance to " CD1 TRP A  70 " =    1.096
peak=   -3.227 closest distance to " O   HOH Z 118 " =    1.347
peak=   -3.226 closest distance to " ND2 ASN A  45 " =    1.239
peak=   -3.224 closest distance to " O   ALA A   7 " =    1.507
peak=   -3.223 closest distance to " O   HOH Z 368 " =    1.637
peak=   -3.218 closest distance to " O   HOH Z  65 " =    1.212
peak=   -3.215 closest distance to " NH2 ARG A  79 " =    1.573
peak=   -3.214 closest distance to " O   HOH Z 326 " =    5.106
peak=   -3.213 closest distance to " CB  ALA A  10 " =    2.272
peak=   -3.206 closest distance to " O   HOH Z  22 " =    2.362
peak=   -3.199 closest distance to " O   HOH Z 219 " =    4.175
peak=   -3.195 closest distance to " C   LYS A  76 " =    1.397
peak=   -3.194 closest distance to " O   HOH Z 364 " =    1.447
peak=   -3.182 closest distance to " CD  PRO A 213 " =    2.101
peak=   -3.182 closest distance to " SG BCYS A 201 " =    2.091
peak=   -3.179 closest distance to " CB  PRO A  54 " =    2.613
peak=   -3.179 closest distance to " CA  GLY A 287 " =    1.349
peak=   -3.179 closest distance to " CB  ALA A 291 " =    1.913
peak=   -3.171 closest distance to " CB  ALA A 158 " =    1.677
peak=   -3.160 closest distance to " CG2 VAL A 189 " =    1.966
peak=   -3.155 closest distance to " O   HOH Z 134 " =    3.286
peak=   -3.154 closest distance to " CG2 THR A 178 " =    2.273
peak=   -3.150 closest distance to " O   ASP A  27 " =    1.846
peak=   -3.148 closest distance to " OXT GLY A 302 " =    3.197
peak=   -3.140 closest distance to " O   HOH Z 348 " =    2.202
peak=   -3.131 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.128 closest distance to " CB  ALA A 114 " =    2.585
peak=   -3.126 closest distance to " O   VAL A 189 " =    1.599
peak=   -3.124 closest distance to " O   HOH Z 193 " =    1.278
peak=   -3.120 closest distance to " CD2 LEU A 222 " =    2.230
peak=   -3.118 closest distance to " O   TRP A  70 " =    1.459
peak=   -3.117 closest distance to " CG1AVAL A  41 " =    2.752
peak=   -3.116 closest distance to " O   HOH Z 340 " =    1.778
peak=   -3.114 closest distance to " O   ARG A  56 " =    4.349
peak=   -3.112 closest distance to " N   GLN A 223 " =    0.923
peak=   -3.106 closest distance to " ND2 ASN A  60 " =    2.036
peak=   -3.106 closest distance to " O   HOH Z 364 " =    2.533
peak=   -3.105 closest distance to " O   HOH Z 191 " =    3.254
peak=   -3.104 closest distance to " ND2BASN A 224 " =    1.768
peak=   -3.099 closest distance to " O   HOH Z 114 " =    1.416
peak=   -3.099 closest distance to " CZ  PHE A  38 " =    1.094
peak=   -3.090 closest distance to " CG  TRP A 266 " =    1.705
peak=   -3.084 closest distance to " O   HOH Z 171 " =    2.325
peak=   -3.083 closest distance to " CG1 VAL A 197 " =    2.300
peak=   -3.078 closest distance to " CA  GLY A 241 " =    2.887
peak=   -3.077 closest distance to " O   HOH Z 187 " =    1.658
peak=   -3.074 closest distance to " O   HOH Z  60 " =    1.294
peak=   -3.072 closest distance to " CB  ASP A  65 " =    1.670
peak=   -3.071 closest distance to " CD  GLN A 223 " =    0.819
peak=   -3.067 closest distance to " CD1 ILE A 239 " =    2.507
peak=   -3.055 closest distance to " CA  GLY A  57 " =    1.998
peak=   -3.030 closest distance to " SD  MET A 188 " =    2.392

================= 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    :  0.4266 0.4172   6.232499e+00   6.210608e+00
   1_bss:  0.4150 0.4106   6.220769e+00   6.196385e+00
   1_xyz:  0.2552 0.2885   5.829125e+00   5.913307e+00
   1_adp:  0.2335 0.2943   5.781854e+00   5.937270e+00
   1_occ:  0.2332 0.2940   5.781074e+00   5.937285e+00
   2_bss:  0.2311 0.2921   5.779586e+00   5.937279e+00
   2_xyz:  0.1806 0.2321   5.556247e+00   5.736890e+00
   2_adp:  0.1669 0.2203   5.495759e+00   5.692639e+00
   2_occ:  0.1668 0.2205   5.495618e+00   5.693082e+00
   3_bss:  0.1667 0.2203   5.494825e+00   5.692715e+00
   3_xyz:  0.1366 0.1871   5.320609e+00   5.545823e+00
   3_adp:  0.1301 0.1793   5.275599e+00   5.502722e+00
   3_occ:  0.1299 0.1792   5.275294e+00   5.502702e+00
   4_bss:  0.1302 0.1791   5.275192e+00   5.502133e+00
   4_xyz:  0.1245 0.1717   5.235886e+00   5.465345e+00
   4_adp:  0.1265 0.1678   5.239243e+00   5.449873e+00
   4_occ:  0.1264 0.1676   5.238538e+00   5.449689e+00
   5_bss:  0.1261 0.1674   5.237914e+00   5.449602e+00
   5_xyz:  0.1222 0.1652   5.217926e+00   5.441069e+00
   5_adp:  0.1202 0.1661   5.210910e+00   5.444334e+00
   5_occ:  0.1201 0.1661   5.210811e+00   5.444313e+00
   5_bss:  0.1201 0.1660   5.210883e+00   5.444374e+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:  0.315  54.727  -2.194  -1.151   5.228  -0.000   0.000   0.000
   1_xyz:  0.315  54.727  -2.194  -1.151   5.228  -0.000   0.000   0.000
   1_adp:  0.315  54.727  -2.194  -1.151   5.228  -0.000   0.000   0.000
   1_occ:  0.315  54.727  -2.194  -1.151   5.228  -0.000   0.000   0.000
   2_bss:  0.338  73.382  -2.440  -2.241   1.556  -0.000   0.000   0.000
   2_xyz:  0.338  73.382  -2.440  -2.241   1.556  -0.000   0.000   0.000
   2_adp:  0.338  73.382  -2.440  -2.241   1.556  -0.000   0.000   0.000
   2_occ:  0.338  73.382  -2.440  -2.241   1.556  -0.000   0.000   0.000
   3_bss:  0.337  78.919  -2.255  -2.207   0.578  -0.000   0.000   0.000
   3_xyz:  0.337  78.919  -2.255  -2.207   0.578  -0.000   0.000   0.000
   3_adp:  0.337  78.919  -2.255  -2.207   0.578  -0.000   0.000   0.000
   3_occ:  0.337  78.919  -2.255  -2.207   0.578  -0.000   0.000   0.000
   4_bss:  0.336  80.000  -2.234  -2.322   0.010  -0.000   0.000   0.000
   4_xyz:  0.336  80.000  -2.234  -2.322   0.010  -0.000   0.000   0.000
   4_adp:  0.336  80.000  -2.234  -2.322   0.010  -0.000   0.000   0.000
   4_occ:  0.336  80.000  -2.234  -2.322   0.010  -0.000   0.000   0.000
   5_bss:  0.322  61.898  -2.272  -2.426  -0.234  -0.000  -0.000  -0.000
   5_xyz:  0.322  61.898  -2.272  -2.426  -0.234  -0.000  -0.000  -0.000
   5_adp:  0.322  61.898  -2.272  -2.426  -0.234  -0.000  -0.000  -0.000
   5_occ:  0.322  61.898  -2.272  -2.426  -0.234  -0.000  -0.000  -0.000
   5_bss:  0.322  61.892  -2.102  -2.277  -0.118  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.938 0.5469  0.7091    52515.112
   1_bss:  46.807 0.5598  0.7464    49924.775
   1_xyz:  28.599 0.7742  0.9675    21220.201
   1_adp:  29.842 0.7596  0.9572    22590.449
   1_occ:  29.860 0.7593  0.9564    22558.508
   2_bss:  29.576 0.7629  0.9090    22484.620
   2_xyz:  22.654 0.8351  0.9638    13571.636
   2_adp:  21.162 0.8504  0.9659    12369.212
   2_occ:  21.175 0.8502  0.9655    12371.744
   3_bss:  21.126 0.8508  0.9573    12369.327
   3_xyz:  17.662 0.8829  0.9777     8908.930
   3_adp:  16.580 0.8930  0.9730     8133.525
   3_occ:  16.576 0.8931  0.9730     8132.096
   4_bss:  16.557 0.8932  0.9658     8118.290
   4_xyz:  15.590 0.9020  0.9695     7423.971
   4_adp:  15.179 0.9058  0.9672     7268.533
   4_occ:  15.180 0.9058  0.9672     7259.615
   5_bss:  15.182 0.9058  0.9628     7248.169
   5_xyz:  14.986 0.9074  0.9648     7087.490
   5_adp:  15.019 0.9071  0.9592     7089.447
   5_occ:  15.019 0.9071  0.9591     7088.177
   5_bss:  15.022 0.9071  0.9638     7089.725
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6586e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6586e-01
   1_xyz:   1.457  0.012  0.096 16.171  0.006  4.115   1.1644e-01
   1_adp:   1.457  0.012  0.096 16.171  0.006  4.115   1.1644e-01
   1_occ:   1.457  0.012  0.096 16.171  0.006  4.115   1.1644e-01
   2_bss:   1.457  0.012  0.096 16.171  0.006  4.115   1.1644e-01
   2_xyz:   0.997  0.006  0.073 14.736  0.004  4.127   5.8172e-02
   2_adp:   0.997  0.006  0.073 14.736  0.004  4.127   5.8172e-02
   2_occ:   0.997  0.006  0.073 14.736  0.004  4.127   5.8172e-02
   3_bss:   0.997  0.006  0.073 14.736  0.004  4.127   5.8172e-02
   3_xyz:   1.018  0.008  0.074 14.791  0.003  4.114   6.1006e-02
   3_adp:   1.018  0.008  0.074 14.791  0.003  4.114   6.1006e-02
   3_occ:   1.018  0.008  0.074 14.791  0.003  4.114   6.1006e-02
   4_bss:   1.018  0.008  0.074 14.791  0.003  4.114   6.1006e-02
   4_xyz:   0.938  0.007  0.071 14.485  0.003  4.119   5.3193e-02
   4_adp:   0.938  0.007  0.071 14.485  0.003  4.119   5.3193e-02
   4_occ:   0.938  0.007  0.071 14.485  0.003  4.119   5.3193e-02
   5_bss:   0.938  0.007  0.071 14.485  0.003  4.119   5.3193e-02
   5_xyz:   0.951  0.007  0.072 14.426  0.003  4.123   5.4000e-02
   5_adp:   0.951  0.007  0.072 14.426  0.003  4.123   5.4000e-02
   5_occ:   0.951  0.007  0.072 14.426  0.003  4.123   5.4000e-02
   5_bss:   0.951  0.007  0.072 14.426  0.003  4.123   5.4000e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.787   2.4321e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.787   2.4321e-01
   1_xyz:   8.663  0.059  0.326 82.475  0.051  1.988   1.1873e-01
   1_adp:   8.663  0.059  0.326 82.475  0.051  1.988   1.1873e-01
   1_occ:   8.663  0.059  0.326 82.475  0.051  1.988   1.1873e-01
   2_bss:   8.663  0.059  0.326 82.475  0.051  1.988   1.1873e-01
   2_xyz:   6.412  0.053  0.237 81.993  0.032  2.293   7.5851e-02
   2_adp:   6.412  0.053  0.237 81.993  0.032  2.293   7.5851e-02
   2_occ:   6.412  0.053  0.237 81.993  0.032  2.293   7.5851e-02
   3_bss:   6.412  0.053  0.237 81.993  0.032  2.293   7.5851e-02
   3_xyz:   7.488  0.051  0.225 83.763  0.026  2.369   4.9413e-02
   3_adp:   7.488  0.051  0.225 83.763  0.026  2.369   4.9413e-02
   3_occ:   7.488  0.051  0.225 83.763  0.026  2.369   4.9413e-02
   4_bss:   7.488  0.051  0.225 83.763  0.026  2.369   4.9413e-02
   4_xyz:   7.349  0.049  0.222 81.370  0.028  2.413   3.2950e-02
   4_adp:   7.349  0.049  0.222 81.370  0.028  2.413   3.2950e-02
   4_occ:   7.349  0.049  0.222 81.370  0.028  2.413   3.2950e-02
   5_bss:   7.349  0.049  0.222 81.370  0.028  2.413   3.2950e-02
   5_xyz:   7.508  0.046  0.229 83.423  0.027  2.381   3.1823e-02
   5_adp:   7.508  0.046  0.229 83.423  0.027  2.381   3.1823e-02
   5_occ:   7.508  0.046  0.229 83.423  0.027  2.381   3.1823e-02
   5_bss:   7.508  0.046  0.229 83.423  0.027  2.381   3.1823e-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: 108.04   0.00  17.28 108.04   0.00  13.27  65.78   1.46  39.10
   1_occ: 108.04   0.00  17.28 108.04   0.00  13.27  65.78   1.46  39.10
   2_bss: 108.04   0.00  17.28 108.04   0.00  13.27  65.78   1.46  39.10
   2_xyz: 108.04   0.00  17.28 108.04   0.00  13.27  65.78   1.46  39.10
   2_adp:  87.17   0.00  18.23  87.17   0.00  13.46  81.27   3.46  44.22
   2_occ:  87.17   0.00  18.23  87.17   0.00  13.46  81.27   3.46  44.22
   3_bss:  87.17   0.00  18.23  87.17   0.00  13.46  81.27   3.46  44.22
   3_xyz:  87.17   0.00  18.23  87.17   0.00  13.46  81.27   3.46  44.22
   3_adp: 102.95   0.00  18.15  85.48   0.00  13.09 102.95   0.00  45.74
   3_occ: 102.95   0.00  18.15  85.48   0.00  13.09 102.95   0.00  45.74
   4_bss: 102.95   0.00  18.15  85.48   0.00  13.09 102.95   0.00  45.74
   4_xyz: 102.95   0.00  18.15  85.48   0.00  13.09 102.95   0.00  45.74
   4_adp:  84.52   0.00  16.64  77.16   0.00  12.59  84.52   2.42  38.71
   4_occ:  84.52   0.00  16.64  77.16   0.00  12.59  84.52   2.42  38.71
   5_bss:  84.52   0.00  16.64  77.16   0.00  12.59  84.52   2.42  38.71
   5_xyz:  84.52   0.00  16.64  77.16   0.00  12.59  84.52   2.42  38.71
   5_adp:  87.66   0.22  16.79  78.32   0.22  12.55  87.66   3.78  39.87
   5_occ:  87.66   0.22  16.79  78.32   0.22  12.55  87.66   3.78  39.87
   5_bss:  87.65   0.22  16.78  78.32   0.22  12.54  87.65   3.77  39.87
------------------------------------------------------------------------
 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:    1.469    0.024    0.448
   1_adp:    1.469    0.024    0.448
   1_occ:    1.469    0.024    0.448
   2_bss:    1.469    0.024    0.448
   2_xyz:    1.286    0.057    0.501
   2_adp:    1.286    0.057    0.501
   2_occ:    1.286    0.057    0.501
   3_bss:    1.286    0.057    0.501
   3_xyz:    1.173    0.050    0.583
   3_adp:    1.173    0.050    0.583
   3_occ:    1.173    0.050    0.583
   4_bss:    1.173    0.050    0.583
   4_xyz:    1.389    0.061    0.604
   4_adp:    1.389    0.061    0.604
   4_occ:    1.389    0.061    0.604
   5_bss:    1.389    0.061    0.604
   5_xyz:    1.616    0.044    0.622
   5_adp:    1.616    0.044    0.622
   5_occ:    1.616    0.044    0.622
   5_bss:    1.616    0.044    0.622
------------------------------------------------------------------------

CPU time actual refinement: 343.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/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_890/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_890/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.90 
  Macro-tasks:
    bulk solvent and scale       = 49.65  
    individual site refinement   = 141.38 
    weights calculation          = 28.96  
    collect and process          = 6.66   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.75 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 105.69 
    alpha_beta                      = 8.24   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 115.73 
    fmodel                         = 8.24   
    r_factors                      = 0.23   
    phase_errors                   = 10.95  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 252.21 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.784 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    651 calls, 105.27 s
gradients_fft:          596 calls, 101.98 s

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

# Date 2008-01-16 Time 05:54:47 PST -0800 (1200491687.17 s)
Start R-work = 0.4266, R-free = 0.4172 (no bulk solvent and anisotropic scale)
Final R-work = 0.1421, R-free = 0.1841 (no bulk solvent and anisotropic scale)

Start R-work = 0.4150, R-free = 0.4106
Final R-work = 0.1201, R-free = 0.1660