# Date 2008-01-16 Time 03:44:18 PST -0800 (1200483858.42 s)
#phil __OFF__

Command line arguments: "../27.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 695
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 27

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95072
Completeness in resolution range: 0.95268
Completeness with d_max=infinity: 0.949724

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7180
                             d_min =   1.9507

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95072
Completeness in resolution range: 0.95268
Completeness with d_max=infinity: 0.949724

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7184 -  4.1738 [2162/2189]  1943   219  10.1%
  bin  2:  4.1738 -  3.3254 [2069/2085]  1865   204   9.9%
  bin  3:  3.3254 -  2.9087 [2048/2067]  1843   205  10.0%
  bin  4:  2.9087 -  2.6445 [2029/2059]  1823   206  10.2%
  bin  5:  2.6445 -  2.4558 [2003/2022]  1806   197   9.8%
  bin  6:  2.4558 -  2.3116 [2017/2042]  1814   203  10.1%
  bin  7:  2.3116 -  2.1963 [2004/2038]  1810   194   9.7%
  bin  8:  2.1963 -  2.1009 [1975/2006]  1770   205  10.4%
  bin  9:  2.1009 -  2.0203 [1982/2023]  1787   195   9.8%
  bin 10:  2.0203 -  1.9507 [1300/2031]  1169   131  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 19
        1.99 -     2.71: 226
        2.71 -     3.44: 4707
        3.44 -     4.17: 9606
        4.17 -     4.90: 14457
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.258 3.040 -x+1,y-1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.451 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.503 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.511 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.607 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29010 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.22605 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4284   r_free= 0.4202   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235950                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6550 0.99   1404  154 0.3423 0.3324      6.4916      6.4845|
|  2:  4.6550 -  3.7144 0.99   1348  154 0.3520 0.3312      6.6938      6.6749|
|  3:  3.7144 -  3.2506 0.99   1319  145 0.3951 0.4023      6.6074      6.6738|
|  4:  3.2506 -  2.9560 0.99   1318  140 0.4035 0.4305      6.4636      6.5334|
|  5:  2.9560 -  2.7456 0.99   1311  147 0.4453 0.3975      6.3064      6.2777|
|  6:  2.7456 -  2.5847 0.99   1295  148 0.4641 0.4758      6.2367      6.1866|
|  7:  2.5847 -  2.4558 0.99   1285  143 0.4654 0.4264      6.2071      6.1092|
|  8:  2.4558 -  2.3494 0.98   1294  143 0.4712 0.4957      6.1581      6.1942|
|  9:  2.3494 -  2.2593 0.98   1293  145 0.4859 0.4709      6.0853      6.1275|
| 10:  2.2593 -  2.1816 0.98   1272  137 0.4852 0.4576      6.0926       6.027|
| 11:  2.1816 -  2.1136 0.99   1289  147 0.4771 0.4916      6.0137      6.0272|
| 12:  2.1136 -  2.0533 0.97   1274  140 0.4820 0.4675      5.9485      6.0117|
| 13:  2.0533 -  1.9994 0.99   1264  138 0.4934 0.4542      5.8691      5.7983|
| 14:  1.9994 -  1.9507 0.51    664   78 0.5117 0.5014      5.8922      5.7706|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6550  1404   154  0.72  32.32   0.85     0.76      64380.69|
|  2:  4.6550 -  3.7144  1348   154  0.74  31.76   0.95     0.85      90044.95|
|  3:  3.7144 -  3.2506  1319   145  0.65  39.90   0.96     0.84      96218.55|
|  4:  3.2506 -  2.9560  1318   140  0.58  45.33   0.97     0.79      86553.05|
|  5:  2.9560 -  2.7456  1311   147  0.52  50.16   0.93     0.73      66424.83|
|  6:  2.7456 -  2.5847  1295   148  0.52  50.20   0.91     0.73      55693.51|
|  7:  2.5847 -  2.4558  1285   143  0.51  51.23   0.96     0.70      50972.36|
|  8:  2.4558 -  2.3494  1294   143  0.47  54.22   0.95     0.67      48751.52|
|  9:  2.3494 -  2.2593  1293   145  0.47  54.68   0.94     0.69      45865.89|
| 10:  2.2593 -  2.1816  1272   137  0.48  53.76   0.98     0.71      40427.33|
| 11:  2.1816 -  2.1136  1289   147  0.47  54.59   0.97     0.72      38319.98|
| 12:  2.1136 -  2.0533  1274   140  0.45  56.64   0.99     0.69      35840.73|
| 13:  2.0533 -  1.9994  1264   138  0.39  61.20   1.00     0.61      33106.19|
| 14:  1.9994 -  1.9507   664    78  0.37  62.11   0.98     0.49      27607.86|
|alpha:            min =        0.49 max =            0.85 mean =         0.72|
|beta:             min =    27607.86 max =        96218.55 mean =     57090.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.21|
|phase err.(test): min =        0.00 max =           89.98 mean =        48.99|
|-----------------------------------------------------------------------------|

============================== 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 = 8.727491              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.169   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.529976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.988   (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 |  1.258 -  1.622:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.622 -  1.986:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.986 -  2.350:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.350 -  2.715:      187 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.715 -  3.079:     2329 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.079 -  3.443:     2378 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.443 -  3.807:     4233 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.807 -  4.172:     5373 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.172 -  4.536:     6494 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.536 -  4.900:     7963 |
|-----------------------------------------------------------------------------|
|-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 |        0.219 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.258 |       1.063 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4284   r_free= 0.4202   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4181   r_free= 0.4123   ksol= 0.33   Bsol= 20.00   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,1.41,-1.71,0.00,-0.00,-0.00); trace/3= 0.15                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.224159                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.434612              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.950   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.865258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.728   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4181      final r-factor (work) = 0.2851          |
| start r-factor (free) = 0.4123      final r-factor (free) = 0.3191          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3621 = 7.43 * 0.50 * 6.2259 + 1.00 * 0.2185                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6097 = 7.43 * 0.50 * 6.0501 + 1.00 * 0.1196                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2851      final r-factor (work) = 0.2566          |
| start r-factor (free) = 0.3191      final r-factor (free) = 0.3300          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2409 = 0.87 * 1.00 * 6.0501 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0849 = 0.87 * 1.00 * 5.8589 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   18.46    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   18.46    None  None   None       |
|    Sol.    : 438    0      2.24    93.01   40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    86.56   14.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.301:  861   |   5:    46.505 -  55.806:  103        |
|      1:     9.301 -  18.602:  981   |   6:    55.806 -  65.107:   59        |
|      2:    18.602 -  27.903:  433   |   7:    65.107 -  74.408:   37        |
|      3:    27.903 -  37.204:  213   |   8:    74.408 -  83.710:    9        |
|      4:    37.204 -  46.505:  124   |   9:    83.710 -  93.011:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2566 r_free = 0.3300             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2564 r_free = 0.3303             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2564   r_free= 0.3303   ksol= 0.33   Bsol= 20.00   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,1.41,-1.71,0.00,-0.00,-0.00); trace/3= 0.15                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.873548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2524   r_free= 0.3263   ksol= 0.33   Bsol= 41.32   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,-1.03,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.860262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.881273              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.056   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.224373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.249  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2524      final r-factor (work) = 0.1806          |
| start r-factor (free) = 0.3263      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4123 = 4.88 * 0.50 * 5.8561 + 1.00 * 0.1196                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0690 = 4.88 * 0.50 * 5.7387 + 1.00 * 0.0628                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1806      final r-factor (work) = 0.1621          |
| start r-factor (free) = 0.2344      final r-factor (free) = 0.2119          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3026 = 0.22 * 1.00 * 5.7387 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2425 = 0.22 * 1.00 * 5.5013 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.27   17.40    None  None   None       |
|    all(noH): 2823   0      0.00    84.27   17.40    None  None   None       |
|    Sol.    : 438    0      6.26    83.34   39.41    None  None   None       |
|    Mac.    : 2385   0      0.00    84.27   13.36    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 -   8.427:  629   |   5:    42.134 -  50.561:  107        |
|      1:     8.427 -  16.854: 1316   |   6:    50.561 -  58.988:   83        |
|      2:    16.854 -  25.281:  346   |   7:    58.988 -  67.415:   32        |
|      3:    25.281 -  33.708:  152   |   8:    67.415 -  75.842:    8        |
|      4:    33.708 -  42.134:  145   |   9:    75.842 -  84.269:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1621 r_free = 0.2119             target_work(ml) = 5.456         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1618 r_free = 0.2114             target_work(ml) = 5.454         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1618   r_free= 0.2114   ksol= 0.33   Bsol= 41.32   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,-1.03,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.454470                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1616   r_free= 0.2105   ksol= 0.32   Bsol= 41.32   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.98,-1.17,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.450102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.029847              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.135751              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.476  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1616      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6492 = 2.03 * 0.50 * 5.5042 + 1.00 * 0.0628                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4949 = 2.03 * 0.50 * 5.3638 + 1.00 * 0.0511                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1292          |
| start r-factor (free) = 0.1779      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7363 = 0.14 * 1.00 * 5.3638 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7241 = 0.14 * 1.00 * 5.2672 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.06   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    84.06   17.18    None  None   None       |
|    Sol.    : 438    0      3.43    82.13   39.01    None  None   None       |
|    Mac.    : 2385   0      0.00    84.06   13.17    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 -   8.407:  571   |   5:    42.032 -  50.439:  107        |
|      1:     8.407 -  16.813: 1419   |   6:    50.439 -  58.845:   84        |
|      2:    16.813 -  25.219:  318   |   7:    58.845 -  67.252:   31        |
|      3:    25.219 -  33.626:  139   |   8:    67.252 -  75.658:    7        |
|      4:    33.626 -  42.032:  143   |   9:    75.658 -  84.065:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1292 r_free = 0.1720             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1290 r_free = 0.1720             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1290   r_free= 0.1720   ksol= 0.32   Bsol= 41.32   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.98,-1.17,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.248929                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1714   ksol= 0.32   Bsol= 41.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.55,-1.34,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.246741                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.204112              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.374  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.496312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.169  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1714      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8560 = 2.20 * 0.50 * 5.2673 + 1.00 * 0.0511                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7907 = 2.20 * 0.50 * 5.2027 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5933 = 0.50 * 1.00 * 5.2027 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5661 = 0.50 * 1.00 * 5.1538 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    89.95   17.30    None  None   None       |
|    all(noH): 2823   0      0.81    89.95   17.30    None  None   None       |
|    Sol.    : 438    0      3.71    84.36   40.43    None  None   None       |
|    Mac.    : 2385   0      0.81    89.95   13.05    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:     0.809 -   9.724:  938   |   5:    45.381 -  54.296:   94        |
|      1:     9.724 -  18.638: 1184   |   6:    54.296 -  63.210:   76        |
|      2:    18.638 -  27.553:  242   |   7:    63.210 -  72.125:   28        |
|      3:    27.553 -  36.467:  124   |   8:    72.125 -  81.039:    6        |
|      4:    36.467 -  45.381:  127   |   9:    81.039 -  89.953:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1579             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1579             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1579   ksol= 0.32   Bsol= 41.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.55,-1.34,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1579   ksol= 0.32   Bsol= 41.31   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.48,-1.17,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.772174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.256  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.512  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6239 = 1.77 * 0.50 * 5.1539 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6066 = 1.77 * 0.50 * 5.1402 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0202 = 0.39 * 1.00 * 5.1402 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0186 = 0.39 * 1.00 * 5.1361 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    91.05   17.13    None  None   None       |
|    all(noH): 2823   0      0.84    91.05   17.13    None  None   None       |
|    Sol.    : 438    0      4.91    84.47   40.09    None  None   None       |
|    Mac.    : 2385   0      0.84    91.05   12.91    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:     0.843 -   9.864:  997   |   5:    45.948 -  54.969:   99        |
|      1:     9.864 -  18.885: 1146   |   6:    54.969 -  63.990:   61        |
|      2:    18.885 -  27.906:  228   |   7:    63.990 -  73.011:   26        |
|      3:    27.906 -  36.927:  128   |   8:    73.011 -  82.032:    6        |
|      4:    36.927 -  45.948:  128   |   9:    82.032 -  91.053:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1562             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1563             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1563   ksol= 0.32   Bsol= 41.31   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.48,-1.17,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137438                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6550 0.99   1404  154 0.0999 0.1253      5.3942      5.5313|
|  2:  4.6550 -  3.7144 0.99   1348  154 0.0858 0.1171      5.4413      5.6316|
|  3:  3.7144 -  3.2506 0.99   1319  145 0.1069 0.1519      5.4676      5.8354|
|  4:  3.2506 -  2.9560 0.99   1318  140 0.1184 0.1582      5.4297      5.5819|
|  5:  2.9560 -  2.7456 0.99   1311  147 0.1263 0.1676      5.2966      5.5285|
|  6:  2.7456 -  2.5847 0.99   1295  148 0.1213 0.1859      5.1873      5.4426|
|  7:  2.5847 -  2.4558 0.99   1285  143 0.1219 0.1531      5.1486      5.2977|
|  8:  2.4558 -  2.3494 0.98   1294  143 0.1156 0.1637      5.0727      5.2972|
|  9:  2.3494 -  2.2593 0.98   1293  145 0.1177 0.1888      5.0177      5.3501|
| 10:  2.2593 -  2.1816 0.98   1272  137 0.1089 0.1613      4.9403      5.1343|
| 11:  2.1816 -  2.1136 0.99   1289  147 0.1101 0.1786      4.9141      5.2886|
| 12:  2.1136 -  2.0533 0.97   1274  140 0.1125 0.1561      4.8801      5.1459|
| 13:  2.0533 -  1.9994 0.99   1264  138 0.1112 0.1814      4.7805      5.0339|
| 14:  1.9994 -  1.9507 0.51    664   78 0.0973 0.1745      4.6522      4.9499|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6550  1404   154  0.94   9.16   0.99     0.96       7251.59|
|  2:  4.6550 -  3.7144  1348   154  0.95   7.88   1.03     1.02       9030.61|
|  3:  3.7144 -  3.2506  1319   145  0.93  11.26   1.04     1.03      10119.76|
|  4:  3.2506 -  2.9560  1318   140  0.93  12.93   1.02     1.01       9779.45|
|  5:  2.9560 -  2.7456  1311   147  0.91  15.29   1.01     0.98       7883.81|
|  6:  2.7456 -  2.5847  1295   148  0.90  15.81   0.99     0.96       6703.30|
|  7:  2.5847 -  2.4558  1285   143  0.91  15.19   0.99     0.95       5895.58|
|  8:  2.4558 -  2.3494  1294   143  0.91  15.17   1.00     0.98       5380.31|
|  9:  2.3494 -  2.2593  1293   145  0.91  15.28   1.01     0.98       4873.25|
| 10:  2.2593 -  2.1816  1272   137  0.90  15.77   1.01     0.96       4299.87|
| 11:  2.1816 -  2.1136  1289   147  0.90  15.99   1.01     0.98       4256.51|
| 12:  2.1136 -  2.0533  1274   140  0.91  15.61   1.02     1.02       3998.24|
| 13:  2.0533 -  1.9994  1264   138  0.90  15.90   1.01     0.99       3310.06|
| 14:  1.9994 -  1.9507   664    78  0.92  13.85   0.99     0.96       2529.64|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2529.64 max =        10119.76 mean =      6259.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1563   ksol= 0.32   Bsol= 41.53   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.38,-1.00,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1563   ksol= 0.32   Bsol= 41.53   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.38,-1.00,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137419                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6550 0.99   1404  154 0.0999 0.1254      5.3947      5.5319|
|  2:  4.6550 -  3.7144 0.99   1348  154 0.0859 0.1171      5.4418      5.6318|
|  3:  3.7144 -  3.2506 0.99   1319  145 0.1069 0.1520      5.4678      5.8356|
|  4:  3.2506 -  2.9560 0.99   1318  140 0.1184 0.1582      5.4297      5.5816|
|  5:  2.9560 -  2.7456 0.99   1311  147 0.1263 0.1676      5.2965      5.5283|
|  6:  2.7456 -  2.5847 0.99   1295  148 0.1213 0.1857       5.187      5.4418|
|  7:  2.5847 -  2.4558 0.99   1285  143 0.1219 0.1531      5.1485      5.2977|
|  8:  2.4558 -  2.3494 0.98   1294  143 0.1156 0.1637      5.0724       5.297|
|  9:  2.3494 -  2.2593 0.98   1293  145 0.1177 0.1887      5.0178      5.3499|
| 10:  2.2593 -  2.1816 0.98   1272  137 0.1089 0.1613      4.9403      5.1345|
| 11:  2.1816 -  2.1136 0.99   1289  147 0.1101 0.1787      4.9141      5.2887|
| 12:  2.1136 -  2.0533 0.97   1274  140 0.1125 0.1562      4.8799       5.146|
| 13:  2.0533 -  1.9994 0.99   1264  138 0.1112 0.1813      4.7803      5.0329|
| 14:  1.9994 -  1.9507 0.51    664   78 0.0973 0.1744      4.6516      4.9495|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6550  1404   154  0.94   9.17   0.99     0.96       7258.39|
|  2:  4.6550 -  3.7144  1348   154  0.95   7.88   1.03     1.02       9038.22|
|  3:  3.7144 -  3.2506  1319   145  0.93  11.26   1.04     1.04      10123.93|
|  4:  3.2506 -  2.9560  1318   140  0.93  12.93   1.02     1.01       9778.33|
|  5:  2.9560 -  2.7456  1311   147  0.91  15.29   1.01     0.98       7878.92|
|  6:  2.7456 -  2.5847  1295   148  0.90  15.80   0.99     0.97       6700.03|
|  7:  2.5847 -  2.4558  1285   143  0.91  15.19   1.00     0.95       5892.16|
|  8:  2.4558 -  2.3494  1294   143  0.91  15.17   1.01     0.98       5377.28|
|  9:  2.3494 -  2.2593  1293   145  0.91  15.29   1.01     0.99       4872.85|
| 10:  2.2593 -  2.1816  1272   137  0.90  15.77   1.01     0.97       4299.84|
| 11:  2.1816 -  2.1136  1289   147  0.90  16.00   1.01     0.98       4258.20|
| 12:  2.1136 -  2.0533  1274   140  0.91  15.62   1.03     1.02       3997.83|
| 13:  2.0533 -  1.9994  1264   138  0.90  15.89   1.02     1.00       3307.81|
| 14:  1.9994 -  1.9507   664    78  0.92  13.83   1.00     0.96       2525.46|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2525.46 max =        10123.93 mean =      6259.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    91.02   17.10    None  None   None       |
|    all(noH): 2823   0      0.81    91.02   17.10    None  None   None       |
|    Sol.    : 438    0      4.89    84.44   40.06    None  None   None       |
|    Mac.    : 2385   0      0.81    91.02   12.88    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:     0.814 -   9.835:  997   |   5:    45.919 -  54.940:   99        |
|      1:     9.835 -  18.856: 1146   |   6:    54.940 -  63.961:   61        |
|      2:    18.856 -  27.877:  228   |   7:    63.961 -  72.982:   26        |
|      3:    27.877 -  36.898:  128   |   8:    72.982 -  82.003:    6        |
|      4:    36.898 -  45.919:  128   |   9:    82.003 -  91.024:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 286         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 3.885
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 286
   mapped sites are within: 0.735 - 3.885

peak=    9.212 closest distance to " O   HOH Z 178 " =    1.102
peak=    6.423 closest distance to " O   HOH Z 142 " =    1.879
peak=    5.879 closest distance to " O   HOH Z 375 " =    1.336
peak=    5.878 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.867 closest distance to " NE2 GLN A  11 " =    1.205
peak=    5.648 closest distance to " O   HOH Z 236 " =    1.531
peak=    5.588 closest distance to " O   HOH Z 126 " =    1.956
peak=    5.478 closest distance to " CG  PRO A  54 " =    1.299
peak=    5.407 closest distance to " NH2 ARG A  56 " =    2.069
peak=    5.319 closest distance to " O   HOH Z 417 " =    1.864
peak=    5.114 closest distance to " CG  PRO A 213 " =    1.317
peak=    4.956 closest distance to " O   HOH Z 112 " =    1.379
peak=    4.691 closest distance to " CG  PRO A  90 " =    1.166
peak=    4.686 closest distance to " O   HOH Z 371 " =    1.865
peak=    4.682 closest distance to " CB  PRO A  54 " =    0.984
peak=    4.639 closest distance to " O   HOH Z 403 " =    1.887
peak=    4.608 closest distance to " O   HOH Z 427 " =    2.756
peak=    4.599 closest distance to " O   HOH Z 189 " =    2.095
peak=    4.561 closest distance to " O   HOH Z 287 " =    1.719
peak=    4.543 closest distance to " CB  GLN A 223 " =    1.549
peak=    4.536 closest distance to " CG  ARG A  66 " =    2.474
peak=    4.500 closest distance to " O   HOH Z  78 " =    1.693
peak=    4.498 closest distance to " NZ  LYS A 117 " =    3.003
peak=    4.491 closest distance to " O   HOH Z 193 " =    1.587
peak=    4.486 closest distance to " CG2 VAL A 257 " =    0.874
peak=    4.477 closest distance to " O   HOH Z 369 " =    2.276
peak=    4.434 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.408 closest distance to " CB  ASN A 148 " =    1.406
peak=    4.402 closest distance to " O   HOH Z 232 " =    2.408
peak=    4.393 closest distance to " O   HOH Z 402 " =    1.425
peak=    4.390 closest distance to " O   HOH Z 272 " =    1.830
peak=    4.382 closest distance to " OG ASER A 258 " =    2.991
peak=    4.377 closest distance to " C   PRO A 198 " =    1.534
peak=    4.362 closest distance to " CB  SER A  63 " =    1.202
peak=    4.354 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.350 closest distance to " ND2 ASN A 187 " =    1.428
peak=    4.323 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.313 closest distance to " O   HOH Z 419 " =    2.272
peak=    4.293 closest distance to " O   SER A  87 " =    2.239
peak=    4.275 closest distance to " O   HOH Z 425 " =    2.051
peak=    4.251 closest distance to " O   HOH Z 327 " =    1.647
peak=    4.235 closest distance to " O   HOH Z 209 " =    2.215
peak=    4.233 closest distance to " CB  GLU A 152 " =    1.263
peak=    4.184 closest distance to " O   HOH Z 416 " =    2.351
peak=    4.171 closest distance to " OG BSER A 164 " =    2.153
peak=    4.162 closest distance to " O   HOH Z  44 " =    1.860
peak=    4.157 closest distance to " O   HOH Z 346 " =    1.645
peak=    4.139 closest distance to " O   HOH Z  93 " =    2.323
peak=    4.127 closest distance to " O   HOH Z 203 " =    1.779
peak=    4.058 closest distance to " CD2 TRP A 179 " =    1.322
peak=    4.027 closest distance to " O  BHOH Z  74 " =    1.292
peak=    4.027 closest distance to " CG  PRO A 198 " =    1.277
peak=    4.016 closest distance to " O   HOH Z 298 " =    1.852
peak=    4.005 closest distance to " CB  THR A  31 " =    1.626
peak=    3.995 closest distance to " O   HOH Z 128 " =    1.968
peak=    3.992 closest distance to " O   HOH Z 132 " =    2.021
peak=    3.982 closest distance to " O   HOH Z   9 " =    2.260
peak=    3.981 closest distance to " CG  TRP A 179 " =    2.118
peak=    3.972 closest distance to " CB  GLU A 128 " =    1.034
peak=    3.929 closest distance to " O   HOH Z 368 " =    3.574
peak=    3.926 closest distance to " O   HOH Z 380 " =    1.652
peak=    3.904 closest distance to " CB  ARG A 190 " =    1.764
peak=    3.888 closest distance to " O   HOH Z 234 " =    3.444
peak=    3.875 closest distance to " O   HOH Z 250 " =    1.529
peak=    3.872 closest distance to " CA  ASN A 215 " =    0.974
peak=    3.872 closest distance to " O   HOH Z 394 " =    1.637
peak=    3.860 closest distance to " CB  SER A   3 " =    1.204
peak=    3.827 closest distance to " NZ  LYS A 119 " =    2.592
peak=    3.823 closest distance to " O   HOH Z 365 " =    2.568
peak=    3.822 closest distance to " CG AARG A 275 " =    1.070
peak=    3.821 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.813 closest distance to " O   HOH Z 407 " =    1.300
peak=    3.802 closest distance to " O   HOH Z 353 " =    2.517
peak=    3.800 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.791 closest distance to " O   HOH Z  97 " =    2.002
peak=    3.785 closest distance to " N   ASN A  39 " =    1.186
peak=    3.780 closest distance to " CB  VAL A 265 " =    1.231
peak=    3.768 closest distance to " O   HOH Z  10 " =    1.825
peak=    3.764 closest distance to " N   PHE A 130 " =    1.263
peak=    3.759 closest distance to " CA  ALA A  84 " =    1.224
peak=    3.741 closest distance to " O   HOH Z   1 " =    1.976
peak=    3.740 closest distance to " CB  ARG A  79 " =    1.375
peak=    3.735 closest distance to " O   HOH Z 357 " =    1.841
peak=    3.734 closest distance to " O   HOH Z 344 " =    3.170
peak=    3.733 closest distance to " O   HOH Z 425 " =    1.314
peak=    3.731 closest distance to " O   HOH Z  24 " =    1.685
peak=    3.726 closest distance to " O   HOH Z 128 " =    2.048
peak=    3.723 closest distance to " O   HOH Z 213 " =    1.628
peak=    3.707 closest distance to " NH1AARG A 145 " =    1.176
peak=    3.702 closest distance to " CB  ILE A 120 " =    1.403
peak=    3.692 closest distance to " CB  ARG A 139 " =    1.061
peak=    3.691 closest distance to " CA  ALA A 299 " =    0.936
peak=    3.689 closest distance to " O   HOH Z 144 " =    1.988
peak=    3.688 closest distance to " O   HOH Z   1 " =    1.528
peak=    3.688 closest distance to " O   HOH Z 173 " =    2.170
peak=    3.686 closest distance to " CB  SER A  26 " =    1.711
peak=    3.681 closest distance to " O   HOH Z 389 " =    1.605
peak=    3.676 closest distance to " O   HOH Z 286 " =    2.353
peak=    3.668 closest distance to " CB  TRP A 266 " =    1.208
peak=    3.664 closest distance to " O   HOH Z 257 " =    1.979
peak=    3.659 closest distance to " CD2 LEU A 297 " =    1.033
peak=    3.657 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.653 closest distance to " O   HOH Z 375 " =    2.109
peak=    3.652 closest distance to " O   HOH Z  66 " =    2.173
peak=    3.644 closest distance to " O   HOH Z  61 " =    1.688
peak=    3.634 closest distance to " O   HOH Z 234 " =    1.973
peak=    3.632 closest distance to " O   HOH Z 336 " =    1.804
peak=    3.629 closest distance to " O   HOH Z   3 " =    1.979
peak=    3.625 closest distance to " CB  LEU A 300 " =    1.021
peak=    3.625 closest distance to " CA  ASN A 127 " =    1.044
peak=    3.622 closest distance to " O   HOH Z 146 " =    1.621
peak=    3.615 closest distance to " CG2 ILE A 120 " =    1.183
peak=    3.613 closest distance to " CD  GLN A 194 " =    1.502
peak=    3.607 closest distance to " CG  MET A 185 " =    1.292
peak=    3.595 closest distance to " O   HOH Z 248 " =    1.519
peak=    3.594 closest distance to " O   HOH Z 227 " =    1.860
peak=    3.590 closest distance to " O   HOH Z 345 " =    3.172
peak=    3.575 closest distance to " SD AMET A  47 " =    0.934
peak=    3.562 closest distance to " O   HOH Z 272 " =    2.177
peak=    3.559 closest distance to " O   HOH Z 371 " =    3.143
peak=    3.557 closest distance to " O   HOH Z 305 " =    3.531
peak=    3.557 closest distance to " CA  ARG A 195 " =    1.304
peak=    3.554 closest distance to " CE  LYS A 119 " =    1.231
peak=    3.546 closest distance to " O   HOH Z  88 " =    2.365
peak=    3.536 closest distance to " O   HOH Z 245 " =    1.400
peak=    3.529 closest distance to " O   HOH Z 416 " =    1.063
peak=    3.523 closest distance to " O   HOH Z  85 " =    1.312
peak=    3.507 closest distance to " O   HOH Z 403 " =    1.306
peak=    3.506 closest distance to " CB  GLN A  89 " =    1.399
peak=    3.497 closest distance to " O   HOH Z 193 " =    1.955
peak=    3.491 closest distance to " O   HOH Z 244 " =    1.762
peak=    3.489 closest distance to " O   HOH Z  43 " =    1.844
peak=    3.485 closest distance to " O   HOH Z 423 " =    1.360
peak=    3.484 closest distance to " CG  MET A 113 " =    0.916
peak=    3.483 closest distance to " O   HOH Z 153 " =    1.619
peak=    3.482 closest distance to " N   GLU A   2 " =    1.401
peak=    3.482 closest distance to " CB  LYS A 117 " =    1.198
peak=    3.480 closest distance to " O   HOH Z 145 " =    2.365
peak=    3.480 closest distance to " O   HOH Z   6 " =    2.122
peak=    3.480 closest distance to " CG2BVAL A  41 " =    0.796
peak=    3.475 closest distance to " O   HOH Z 126 " =    1.477
peak=    3.475 closest distance to " O   HOH Z 368 " =    1.968
peak=    3.473 closest distance to " O   HOH Z 106 " =    2.849
peak=    3.472 closest distance to " CB  ASN A 110 " =    0.984
peak=    3.467 closest distance to " NH2AARG A 190 " =    1.852
peak=    3.464 closest distance to " OD1 ASN A  69 " =    2.360
peak=    3.461 closest distance to " O   HOH Z 423 " =    2.438
peak=    3.453 closest distance to " CB  ALA A 114 " =    1.075
peak=    3.451 closest distance to " CE  LYS A  76 " =    0.833
peak=    3.450 closest distance to " CB  ALA A 114 " =    1.421
peak=    3.440 closest distance to " O   ASN A  74 " =    1.531
peak=    3.430 closest distance to " NH1BARG A 145 " =    1.270
peak=    3.429 closest distance to " O   HOH Z 261 " =    1.559
peak=    3.429 closest distance to " CB  LEU A 228 " =    1.098
peak=    3.427 closest distance to " O   HOH Z 227 " =    2.049
peak=    3.425 closest distance to " CA  ALA A 233 " =    0.957
peak=    3.415 closest distance to " NE2 GLN A  73 " =    3.718
peak=    3.413 closest distance to " OD2 ASP A 286 " =    2.580
peak=    3.403 closest distance to " O   HOH Z  43 " =    2.434
peak=    3.402 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.400 closest distance to " NZ  LYS A 117 " =    1.431
peak=    3.399 closest distance to " NH1 ARG A  14 " =    1.211
peak=    3.396 closest distance to " NH2BARG A 145 " =    2.095
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.226
peak=    3.392 closest distance to " O   HOH Z 104 " =    1.308
peak=    3.390 closest distance to " CG1BVAL A  72 " =    1.380
peak=    3.389 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.386 closest distance to " CG  LEU A 101 " =    1.103
peak=    3.376 closest distance to " N   TRP A 150 " =    1.566
peak=    3.376 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.370 closest distance to " CB  TYR A 169 " =    0.985
peak=    3.363 closest distance to " O   HOH Z 222 " =    2.358
peak=    3.354 closest distance to " O   HOH Z 109 " =    2.066
peak=    3.354 closest distance to " O   HOH Z 188 " =    2.203
peak=    3.354 closest distance to " O   HOH Z 158 " =    2.896
peak=    3.352 closest distance to " O   HOH Z  88 " =    2.459
peak=    3.348 closest distance to " OG BSER A  99 " =    2.484
peak=    3.346 closest distance to " O   HOH Z 141 " =    1.678
peak=    3.346 closest distance to " N   GLN A 278 " =    1.232
peak=    3.344 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.342 closest distance to " CB  TRP A 179 " =    1.171
peak=    3.340 closest distance to " O   HOH Z   2 " =    1.555
peak=    3.339 closest distance to " OD1BASN A 224 " =    2.217
peak=    3.332 closest distance to " CB  GLU A 277 " =    3.501
peak=    3.329 closest distance to " O   HOH Z 437 " =    1.652
peak=    3.327 closest distance to " O   HOH Z  80 " =    2.353
peak=    3.327 closest distance to " OG BSER A 258 " =    3.085
peak=    3.325 closest distance to " CA  ALA A 129 " =    1.456
peak=    3.322 closest distance to " O   HOH Z 422 " =    2.511
peak=    3.320 closest distance to " CB  THR A 157 " =    1.153
peak=    3.319 closest distance to " O   HOH Z  40 " =    1.481
peak=    3.316 closest distance to " O   HOH Z 194 " =    1.979
peak=    3.316 closest distance to " O   HOH Z 284 " =    2.854
peak=    3.316 closest distance to " O   HOH Z 415 " =    3.485
peak=    3.316 closest distance to " O   HOH Z 421 " =    1.763
peak=    3.315 closest distance to " O   HOH Z 291 " =    1.451
peak=    3.310 closest distance to " O   HOH Z  53 " =    2.385
peak=    3.310 closest distance to " CG2 VAL A 232 " =    0.898
peak=    3.304 closest distance to " O   HOH Z 423 " =    1.832
peak=    3.300 closest distance to " O   HOH Z 124 " =    1.235
peak=    3.296 closest distance to " CA  ASN A 217 " =    1.076
peak=    3.290 closest distance to " O   HOH Z 388 " =    1.965
peak=    3.289 closest distance to " CB  SER A  62 " =    1.364
peak=    3.288 closest distance to " CG1 ILE A 120 " =    1.206
peak=    3.287 closest distance to " O   HOH Z 302 " =    1.617
peak=    3.286 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.284 closest distance to " CB  THR A  52 " =    0.913
peak=    3.282 closest distance to " O   HOH Z  47 " =    1.470
peak=    3.282 closest distance to " CB  ARG A 219 " =    0.798
peak=    3.282 closest distance to " CE ALYS A 290 " =    1.157
peak=    3.279 closest distance to " CB  ALA A 248 " =    1.365
peak=    3.273 closest distance to " O   HOH Z  80 " =    1.853
peak=    3.264 closest distance to " CG  GLU A 277 " =    1.998
peak=    3.259 closest distance to " O  BHOH Z 338 " =    2.292
peak=    3.259 closest distance to " CB  ALA A  10 " =    1.350
peak=    3.258 closest distance to " CG  GLN A  58 " =    1.014
peak=    3.257 closest distance to " OG  SER A  62 " =    2.763
peak=    3.257 closest distance to " NH1BARG A 190 " =    1.964
peak=    3.254 closest distance to " O   HOH Z  50 " =    1.890
peak=    3.253 closest distance to " O   HOH Z 329 " =    3.885
peak=    3.252 closest distance to " CD1 ILE A 263 " =    1.451
peak=    3.248 closest distance to " CB  PHE A 130 " =    0.899
peak=    3.246 closest distance to " NE  ARG A  24 " =    1.939
peak=    3.245 closest distance to " CG  LYS A  76 " =    1.779
peak=    3.242 closest distance to " O   HOH Z  59 " =    1.487
peak=    3.241 closest distance to " O   HOH Z 299 " =    2.338
peak=    3.240 closest distance to " N   ASP A 162 " =    1.085
peak=    3.239 closest distance to " NE  ARG A  14 " =    1.174
peak=    3.239 closest distance to " CA  MET A 105 " =    0.901
peak=    3.239 closest distance to " O   HOH Z 426 " =    1.802
peak=    3.235 closest distance to " O   HOH Z 342 " =    0.793
peak=    3.234 closest distance to " O   HOH Z 298 " =    2.434
peak=    3.232 closest distance to " N   TYR A 116 " =    1.560
peak=    3.230 closest distance to " CB  SER A 273 " =    0.895
peak=    3.230 closest distance to " NH1 ARG A 138 " =    1.232
peak=    3.229 closest distance to " O   ARG A 145 " =    1.774
peak=    3.227 closest distance to " O   HOH Z  51 " =    1.775
peak=    3.225 closest distance to " O   HOH Z 327 " =    1.732
peak=    3.224 closest distance to " O   HOH Z 406 " =    1.681
peak=    3.222 closest distance to " NE2 GLN A 223 " =    1.951
peak=    3.218 closest distance to " CB  ALA A 291 " =    1.210
peak=    3.215 closest distance to " CB  THR A 279 " =    1.705
peak=    3.210 closest distance to " CB  LYS A 290 " =    1.020
peak=    3.210 closest distance to " O   HOH Z  35 " =    2.459
peak=    3.206 closest distance to " O   HOH Z  48 " =    1.553
peak=    3.204 closest distance to " O   HOH Z 411 " =    3.716
peak=    3.201 closest distance to " O   HOH Z 153 " =    3.652
peak=    3.197 closest distance to " O   HOH Z  21 " =    1.804
peak=    3.192 closest distance to " O   HOH Z  59 " =    1.959
peak=    3.189 closest distance to " O   HOH Z  94 " =    1.899
peak=    3.188 closest distance to " CG2 THR A 294 " =    1.571
peak=    3.183 closest distance to " CA  ASP A 140 " =    1.162
peak=    3.181 closest distance to " CA  LEU A 300 " =    1.070
peak=    3.181 closest distance to " O   HOH Z 433 " =    1.923
peak=    3.176 closest distance to " N   HIS A  86 " =    1.730
peak=    3.176 closest distance to " O   HOH Z 373 " =    1.507
peak=    3.174 closest distance to " CB  VAL A 126 " =    1.158
peak=    3.168 closest distance to " CB  TYR A 116 " =    0.894
peak=    3.161 closest distance to " CA  ALA A  21 " =    1.081
peak=    3.156 closest distance to " O   HOH Z  44 " =    2.933
peak=    3.153 closest distance to " O   HOH Z  85 " =    2.226
peak=    3.150 closest distance to " CB  SER A 276 " =    1.293
peak=    3.143 closest distance to " O   HOH Z  71 " =    1.997
peak=    3.141 closest distance to " CA  GLY A  80 " =    0.735
peak=    3.140 closest distance to " O   HOH Z 147 " =    1.727
peak=    3.135 closest distance to " N   CYS A 260 " =    0.836
peak=    3.123 closest distance to " O   HOH Z 271 " =    2.173
peak=    3.119 closest distance to " CA  ASN A 176 " =    1.456
peak=    3.119 closest distance to " O   HOH Z  28 " =    1.833
peak=    3.117 closest distance to " CA  ARG A  36 " =    0.965
peak=    3.110 closest distance to " O   HOH Z  40 " =    1.697
peak=    3.108 closest distance to " CA  THR A 264 " =    0.806
peak=    3.106 closest distance to " OE1 GLU A  46 " =    1.475
peak=    3.092 closest distance to " CB  GLN A 278 " =    0.795
peak=    3.087 closest distance to " O   HOH Z 251 " =    1.648
peak=    3.085 closest distance to " OG1 THR A 221 " =    1.266
peak=    3.080 closest distance to " O   HOH Z 265 " =    2.158
peak=    3.047 closest distance to " CG  LEU A 167 " =    1.275
peak=    3.041 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.038 closest distance to " N   TRP A 150 " =    1.047
peak=    3.032 closest distance to " CE BLYS A 290 " =    0.911

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 5.833
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.723 - 5.833

peak=   -4.663 closest distance to " O   PRO A 198 " =    1.219
peak=   -4.476 closest distance to " CG  GLN A  58 " =    1.015
peak=   -4.458 closest distance to " O   HOH Z 372 " =    2.463
peak=   -4.409 closest distance to " CD1 LEU A 255 " =    2.781
peak=   -4.373 closest distance to " CA  VAL A  67 " =    2.900
peak=   -4.280 closest distance to " O   ALA A 161 " =    1.613
peak=   -4.278 closest distance to " O   HOH Z 387 " =    2.638
peak=   -4.253 closest distance to " C   HIS A 108 " =    1.167
peak=   -4.167 closest distance to " OG BSER A 134 " =    1.341
peak=   -4.099 closest distance to " O   HOH Z 290 " =    1.013
peak=   -4.093 closest distance to " CD  ARG A  14 " =    3.281
peak=   -4.082 closest distance to " CG  PHE A 283 " =    2.587
peak=   -4.035 closest distance to " O   HOH Z 266 " =    4.916
peak=   -4.024 closest distance to " CD  ARG A 156 " =    2.072
peak=   -4.022 closest distance to " OD2 ASP A 191 " =    1.386
peak=   -4.015 closest distance to " CB  PHE A 192 " =    1.879
peak=   -4.007 closest distance to " O   HOH Z 377 " =    2.018
peak=   -3.998 closest distance to " N   GLN A  58 " =    1.617
peak=   -3.972 closest distance to " O   HOH Z 429 " =    1.968
peak=   -3.953 closest distance to " O   VAL A  67 " =    2.550
peak=   -3.937 closest distance to " OG  SER A   3 " =    1.574
peak=   -3.921 closest distance to " O   HOH Z 351 " =    1.475
peak=   -3.888 closest distance to " OXT GLY A 302 " =    2.875
peak=   -3.871 closest distance to " O   HOH Z 198 " =    1.514
peak=   -3.833 closest distance to " CG  GLN A 223 " =    1.578
peak=   -3.804 closest distance to " CG1 VAL A 112 " =    2.898
peak=   -3.779 closest distance to " ND2 ASN A  45 " =    1.002
peak=   -3.777 closest distance to " CG  GLN A  58 " =    1.265
peak=   -3.775 closest distance to " O   HOH Z 185 " =    2.168
peak=   -3.775 closest distance to " CE  MET A 105 " =    2.278
peak=   -3.747 closest distance to " O   HOH Z 362 " =    5.833
peak=   -3.720 closest distance to " O   HOH Z 313 " =    1.689
peak=   -3.716 closest distance to " O   SER A  22 " =    2.303
peak=   -3.706 closest distance to " O   HOH Z 211 " =    1.692
peak=   -3.696 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.693 closest distance to " CB  ASN A  39 " =    2.248
peak=   -3.662 closest distance to " N   ALA A 248 " =    1.676
peak=   -3.656 closest distance to " O   SER A  95 " =    1.374
peak=   -3.655 closest distance to " CB  PHE A 208 " =    2.178
peak=   -3.653 closest distance to " O   PRO A 198 " =    1.199
peak=   -3.649 closest distance to " O   HOH Z  13 " =    1.577
peak=   -3.636 closest distance to " OD1 ASP A 171 " =    1.533
peak=   -3.633 closest distance to " O   HOH Z 231 " =    2.249
peak=   -3.632 closest distance to " CD2 PHE A 225 " =    1.259
peak=   -3.628 closest distance to " O   HOH Z 139 " =    5.027
peak=   -3.610 closest distance to " O   HOH Z 119 " =    2.330
peak=   -3.599 closest distance to " CB  ALA A 244 " =    2.025
peak=   -3.593 closest distance to " C   ALA A 158 " =    1.391
peak=   -3.592 closest distance to " CZ  PHE A  59 " =    1.383
peak=   -3.590 closest distance to " O   HOH Z 165 " =    2.218
peak=   -3.583 closest distance to " O   HOH Z 256 " =    1.357
peak=   -3.583 closest distance to " O   HOH Z 314 " =    1.584
peak=   -3.581 closest distance to " OD2 ASP A  50 " =    1.597
peak=   -3.575 closest distance to " O   SER A 146 " =    1.039
peak=   -3.575 closest distance to " O   PRO A 243 " =    2.570
peak=   -3.573 closest distance to " OD2 ASP A 171 " =    2.172
peak=   -3.571 closest distance to " O   SER A 135 " =    1.431
peak=   -3.568 closest distance to " O   HOH Z 140 " =    1.848
peak=   -3.568 closest distance to " O   TRP A  70 " =    1.415
peak=   -3.564 closest distance to " ND2 ASN A  39 " =    1.308
peak=   -3.563 closest distance to " O   HOH Z  90 " =    2.294
peak=   -3.561 closest distance to " OD1 ASN A 148 " =    1.541
peak=   -3.560 closest distance to " CB  GLN A  55 " =    1.414
peak=   -3.554 closest distance to " CB  PRO A 163 " =    2.555
peak=   -3.544 closest distance to " O   HOH Z  52 " =    1.344
peak=   -3.533 closest distance to " O   HOH Z 423 " =    2.278
peak=   -3.528 closest distance to " ND2 ASN A  45 " =    1.572
peak=   -3.527 closest distance to " O   HOH Z  63 " =    1.646
peak=   -3.526 closest distance to " CZ  TYR A 169 " =    1.830
peak=   -3.524 closest distance to " NE2 GLN A  55 " =    1.332
peak=   -3.517 closest distance to " C   ALA A 114 " =    2.298
peak=   -3.516 closest distance to " O   HOH Z  11 " =    1.764
peak=   -3.512 closest distance to " O   HOH Z 389 " =    1.955
peak=   -3.508 closest distance to " CD1 LEU A 101 " =    2.282
peak=   -3.502 closest distance to " CB  TRP A  85 " =    2.390
peak=   -3.491 closest distance to " CB  ALA A 291 " =    2.112
peak=   -3.483 closest distance to " O   HOH Z  60 " =    1.874
peak=   -3.481 closest distance to " N   ALA A  43 " =    2.388
peak=   -3.477 closest distance to " NE  ARG A 156 " =    1.880
peak=   -3.476 closest distance to " CB  SER A 210 " =    1.225
peak=   -3.473 closest distance to " N   ASN A 127 " =    1.362
peak=   -3.471 closest distance to " CG  PRO A 243 " =    1.629
peak=   -3.466 closest distance to " O   HOH Z 250 " =    1.254
peak=   -3.457 closest distance to " O   HOH Z 407 " =    2.323
peak=   -3.456 closest distance to " OE1 GLN A 183 " =    1.384
peak=   -3.455 closest distance to " CG1 VAL A 268 " =    2.391
peak=   -3.452 closest distance to " CE2 TYR A  30 " =    2.728
peak=   -3.451 closest distance to " OD1 ASP A 191 " =    1.372
peak=   -3.442 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.439 closest distance to " CA  GLY A  98 " =    1.782
peak=   -3.428 closest distance to " O   VAL A 189 " =    2.542
peak=   -3.425 closest distance to " O   HOH Z 298 " =    2.400
peak=   -3.425 closest distance to " O   HOH Z 131 " =    4.094
peak=   -3.420 closest distance to " CD  ARG A 139 " =    1.361
peak=   -3.418 closest distance to " CD1 PHE A  59 " =    2.017
peak=   -3.412 closest distance to " CE3 TRP A 274 " =    2.195
peak=   -3.409 closest distance to " CG1 VAL A 230 " =    1.956
peak=   -3.405 closest distance to " O   HOH Z 427 " =    1.499
peak=   -3.400 closest distance to " O   HOH Z 421 " =    2.889
peak=   -3.399 closest distance to " CB  ALA A 131 " =    1.980
peak=   -3.397 closest distance to " CE1 TYR A 169 " =    2.532
peak=   -3.388 closest distance to " CG2 ILE A  49 " =    2.734
peak=   -3.386 closest distance to " O   HOH Z  24 " =    1.292
peak=   -3.379 closest distance to " CA  GLY A 241 " =    2.207
peak=   -3.375 closest distance to " CB  ALA A  43 " =    2.309
peak=   -3.373 closest distance to " NH1AARG A 275 " =    1.856
peak=   -3.373 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.371 closest distance to " N   ASP A 286 " =    2.060
peak=   -3.370 closest distance to " O   SER A 210 " =    1.983
peak=   -3.366 closest distance to " CA  GLY A 133 " =    2.067
peak=   -3.365 closest distance to " OD1 ASN A  39 " =    2.125
peak=   -3.363 closest distance to " O   PHE A 218 " =    1.439
peak=   -3.359 closest distance to " CD2 LEU A 237 " =    2.265
peak=   -3.358 closest distance to " CZ3 TRP A 179 " =    1.289
peak=   -3.346 closest distance to " O   HOH Z 377 " =    0.850
peak=   -3.343 closest distance to " O   HOH Z 388 " =    2.058
peak=   -3.341 closest distance to " OG  SER A  63 " =    1.101
peak=   -3.341 closest distance to " O   PRO A 163 " =    1.827
peak=   -3.337 closest distance to " O   ALA A  34 " =    2.241
peak=   -3.331 closest distance to " O   ALA A  10 " =    1.585
peak=   -3.326 closest distance to " O   HOH Z 183 " =    1.613
peak=   -3.325 closest distance to " O   ALA A  51 " =    1.151
peak=   -3.322 closest distance to " O   HOH Z  37 " =    1.454
peak=   -3.320 closest distance to " O   HOH Z 385 " =    1.823
peak=   -3.318 closest distance to " O   HOH Z 137 " =    1.396
peak=   -3.316 closest distance to " CD2 TYR A 293 " =    1.919
peak=   -3.309 closest distance to " O  BHOH Z 338 " =    1.543
peak=   -3.308 closest distance to " O   VAL A 174 " =    2.143
peak=   -3.307 closest distance to " CZ2 TRP A 274 " =    0.967
peak=   -3.302 closest distance to " O   ILE A 120 " =    1.484
peak=   -3.300 closest distance to " O   HOH Z 282 " =    1.211
peak=   -3.291 closest distance to " O   HOH Z  15 " =    1.536
peak=   -3.286 closest distance to " O   HOH Z 148 " =    1.776
peak=   -3.282 closest distance to " CG2 VAL A 296 " =    1.863
peak=   -3.281 closest distance to " OH  TYR A 172 " =    1.741
peak=   -3.278 closest distance to " CG  ASP A 231 " =    0.723
peak=   -3.268 closest distance to " CG  LEU A  83 " =    2.052
peak=   -3.256 closest distance to " NE2 GLN A 278 " =    1.686
peak=   -3.256 closest distance to " CB  ASP A 286 " =    2.236
peak=   -3.254 closest distance to " O   VAL A 125 " =    2.180
peak=   -3.253 closest distance to " O   HOH Z 134 " =    3.364
peak=   -3.249 closest distance to " OE1 GLN A  88 " =    1.135
peak=   -3.242 closest distance to " OG  SER A 245 " =    1.361
peak=   -3.237 closest distance to " CB  ALA A   7 " =    2.022
peak=   -3.233 closest distance to " NE  ARG A  36 " =    1.915
peak=   -3.233 closest distance to " OG1 THR A  82 " =    1.845
peak=   -3.233 closest distance to " O   HOH Z 193 " =    1.861
peak=   -3.229 closest distance to " O   HOH Z 288 " =    1.230
peak=   -3.228 closest distance to " C   ASP A 231 " =    2.497
peak=   -3.227 closest distance to " OG  SER A  63 " =    1.322
peak=   -3.225 closest distance to " CD  GLU A 277 " =    1.314
peak=   -3.224 closest distance to " O   ALA A   1 " =    1.519
peak=   -3.224 closest distance to " O   ASN A  45 " =    1.848
peak=   -3.216 closest distance to " N   MET A 188 " =    1.972
peak=   -3.213 closest distance to " OG1 THR A 178 " =    1.303
peak=   -3.207 closest distance to " O   HOH Z 166 " =    1.351
peak=   -3.202 closest distance to " OH  TYR A 169 " =    0.896
peak=   -3.200 closest distance to " O   HOH Z 123 " =    2.455
peak=   -3.193 closest distance to " OD1 ASP A 191 " =    1.736
peak=   -3.190 closest distance to " O   HOH Z 298 " =    1.316
peak=   -3.190 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.186 closest distance to " CG1 VAL A 265 " =    2.671
peak=   -3.183 closest distance to " O   HOH Z  28 " =    2.309
peak=   -3.178 closest distance to " N   PHE A  59 " =    1.782
peak=   -3.172 closest distance to " CA  GLY A 203 " =    2.352
peak=   -3.170 closest distance to " O   PRO A 163 " =    1.235
peak=   -3.170 closest distance to " NH1 ARG A 195 " =    2.616
peak=   -3.170 closest distance to " OE2 GLU A 236 " =    1.750
peak=   -3.167 closest distance to " O   HOH Z 265 " =    2.149
peak=   -3.157 closest distance to " CZ  ARG A 259 " =    0.924
peak=   -3.156 closest distance to " O   MET A  40 " =    2.743
peak=   -3.153 closest distance to " N   ALA A 226 " =    1.878
peak=   -3.150 closest distance to " O   HOH Z 189 " =    1.747
peak=   -3.144 closest distance to " CG  GLN A  88 " =    0.840
peak=   -3.138 closest distance to " O   HOH Z 281 " =    2.781
peak=   -3.137 closest distance to " O   GLN A 240 " =    1.810
peak=   -3.135 closest distance to " NH1BARG A 145 " =    3.732
peak=   -3.132 closest distance to " O   HOH Z 351 " =    1.658
peak=   -3.124 closest distance to " O   HOH Z 114 " =    3.092
peak=   -3.121 closest distance to " CA  TRP A 274 " =    1.418
peak=   -3.121 closest distance to " CB  ALA A 248 " =    2.175
peak=   -3.117 closest distance to " N   GLN A  77 " =    1.685
peak=   -3.110 closest distance to " OG1 THR A 246 " =    1.374
peak=   -3.104 closest distance to " O   HOH Z 390 " =    2.462
peak=   -3.102 closest distance to " CG2BVAL A  41 " =    1.045
peak=   -3.096 closest distance to " OE2 GLU A 152 " =    1.251
peak=   -3.091 closest distance to " O   ASN A 224 " =    1.058
peak=   -3.077 closest distance to " O   HOH Z 145 " =    2.997
peak=   -3.076 closest distance to " CG  GLU A 152 " =    1.073
peak=   -3.074 closest distance to " CD1 ILE A 263 " =    2.778
peak=   -3.072 closest distance to " CE  MET A 105 " =    2.024
peak=   -3.066 closest distance to " O   LYS A  76 " =    1.795
peak=   -3.065 closest distance to " O   HOH Z  89 " =    2.724
peak=   -3.059 closest distance to " C   LEU A 143 " =    1.000
peak=   -3.053 closest distance to " CE  LYS A  76 " =    2.737
peak=   -3.029 closest distance to " CB  ASP A 132 " =    2.238
peak=   -3.011 closest distance to " CB  ASN A  39 " =    2.059

================= 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    :  0.4284 0.4202   6.235950e+00   6.227068e+00
   1_bss:  0.4181 0.4123   6.224159e+00   6.208732e+00
   1_xyz:  0.2851 0.3191   5.926456e+00   5.999049e+00
   1_adp:  0.2566 0.3300   5.873521e+00   6.027668e+00
   1_occ:  0.2564 0.3303   5.873548e+00   6.028159e+00
   2_bss:  0.2524 0.3263   5.860262e+00   6.018072e+00
   2_xyz:  0.1806 0.2344   5.551165e+00   5.745901e+00
   2_adp:  0.1621 0.2119   5.455990e+00   5.656627e+00
   2_occ:  0.1618 0.2114   5.454470e+00   5.655071e+00
   3_bss:  0.1616 0.2105   5.450102e+00   5.648985e+00
   3_xyz:  0.1336 0.1779   5.282281e+00   5.495053e+00
   3_adp:  0.1292 0.1720   5.249580e+00   5.460012e+00
   3_occ:  0.1290 0.1720   5.248929e+00   5.459541e+00
   4_bss:  0.1289 0.1714   5.246741e+00   5.456915e+00
   4_xyz:  0.1169 0.1598   5.169020e+00   5.393419e+00
   4_adp:  0.1135 0.1579   5.147327e+00   5.380727e+00
   4_occ:  0.1134 0.1579   5.147212e+00   5.380766e+00
   5_bss:  0.1134 0.1579   5.147059e+00   5.380554e+00
   5_xyz:  0.1113 0.1563   5.139197e+00   5.377583e+00
   5_adp:  0.1107 0.1562   5.137504e+00   5.379041e+00
   5_occ:  0.1106 0.1563   5.137438e+00   5.379133e+00
   5_bss:  0.1106 0.1563   5.137419e+00   5.379038e+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:  0.331  20.000   0.754   1.414  -1.715   0.000  -0.000  -0.000
   1_xyz:  0.331  20.000   0.754   1.414  -1.715   0.000  -0.000  -0.000
   1_adp:  0.331  20.000   0.754   1.414  -1.715   0.000  -0.000  -0.000
   1_occ:  0.331  20.000   0.754   1.414  -1.715   0.000  -0.000  -0.000
   2_bss:  0.333  41.317  -1.803  -0.806  -1.026  -0.000  -0.000  -0.000
   2_xyz:  0.333  41.317  -1.803  -0.806  -1.026  -0.000  -0.000  -0.000
   2_adp:  0.333  41.317  -1.803  -0.806  -1.026  -0.000  -0.000  -0.000
   2_occ:  0.333  41.317  -1.803  -0.806  -1.026  -0.000  -0.000  -0.000
   3_bss:  0.319  41.317  -2.778  -1.981  -1.168  -0.000  -0.000  -0.000
   3_xyz:  0.319  41.317  -2.778  -1.981  -1.168  -0.000  -0.000  -0.000
   3_adp:  0.319  41.317  -2.778  -1.981  -1.168  -0.000  -0.000  -0.000
   3_occ:  0.319  41.317  -2.778  -1.981  -1.168  -0.000  -0.000  -0.000
   4_bss:  0.324  41.317  -3.268  -2.551  -1.342  -0.000  -0.000  -0.000
   4_xyz:  0.324  41.317  -3.268  -2.551  -1.342  -0.000  -0.000  -0.000
   4_adp:  0.324  41.317  -3.268  -2.551  -1.342  -0.000  -0.000  -0.000
   4_occ:  0.324  41.317  -3.268  -2.551  -1.342  -0.000  -0.000  -0.000
   5_bss:  0.321  41.306  -3.137  -2.481  -1.171  -0.000  -0.000  -0.000
   5_xyz:  0.321  41.306  -3.137  -2.481  -1.171  -0.000  -0.000  -0.000
   5_adp:  0.321  41.306  -3.137  -2.481  -1.171  -0.000  -0.000  -0.000
   5_occ:  0.321  41.306  -3.137  -2.481  -1.171  -0.000  -0.000  -0.000
   5_bss:  0.320  41.526  -3.007  -2.376  -0.997  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.185 0.5324  0.7219    57082.647
   1_bss:  48.164 0.5435  0.7438    53735.116
   1_xyz:  32.411 0.7320  0.9544    26942.812
   1_adp:  34.093 0.7118  0.9354    29209.971
   1_occ:  34.138 0.7113  0.9346    29281.326
   2_bss:  33.435 0.7188  0.9008    28103.888
   2_xyz:  22.708 0.8345  0.9988    13777.018
   2_adp:  19.923 0.8629  1.0154    11331.218
   2_occ:  19.885 0.8633  1.0153    11275.602
   3_bss:  19.657 0.8651  0.9880    11007.614
   3_xyz:  16.385 0.8947  0.9993     7997.029
   3_adp:  15.555 0.9023  1.0009     7493.704
   3_occ:  15.548 0.9023  1.0007     7471.409
   4_bss:  15.479 0.9028  0.9859     7404.813
   4_xyz:  14.215 0.9131  0.9897     6454.856
   4_adp:  13.943 0.9153  0.9861     6291.809
   4_occ:  13.945 0.9153  0.9861     6290.750
   5_bss:  13.942 0.9153  0.9906     6288.402
   5_xyz:  13.826 0.9165  0.9904     6238.697
   5_adp:  13.833 0.9166  0.9856     6257.139
   5_occ:  13.836 0.9165  0.9855     6258.787
   5_bss:  13.836 0.9165  0.9894     6258.806
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.1854e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.1854e-01
   1_xyz:   1.462  0.011  0.093 15.363  0.007  4.104   1.1956e-01
   1_adp:   1.462  0.011  0.093 15.363  0.007  4.104   1.1956e-01
   1_occ:   1.462  0.011  0.093 15.363  0.007  4.104   1.1956e-01
   2_bss:   1.462  0.011  0.093 15.363  0.007  4.104   1.1956e-01
   2_xyz:   1.041  0.007  0.073 14.692  0.004  4.107   6.2848e-02
   2_adp:   1.041  0.007  0.073 14.692  0.004  4.107   6.2848e-02
   2_occ:   1.041  0.007  0.073 14.692  0.004  4.107   6.2848e-02
   3_bss:   1.041  0.007  0.073 14.692  0.004  4.107   6.2848e-02
   3_xyz:   0.918  0.005  0.064 14.502  0.004  4.110   5.1145e-02
   3_adp:   0.918  0.005  0.064 14.502  0.004  4.110   5.1145e-02
   3_occ:   0.918  0.005  0.064 14.502  0.004  4.110   5.1145e-02
   4_bss:   0.918  0.005  0.064 14.502  0.004  4.110   5.1145e-02
   4_xyz:   0.983  0.006  0.070 14.678  0.004  4.111   5.7019e-02
   4_adp:   0.983  0.006  0.070 14.678  0.004  4.111   5.7019e-02
   4_occ:   0.983  0.006  0.070 14.678  0.004  4.111   5.7019e-02
   5_bss:   0.983  0.006  0.070 14.678  0.004  4.111   5.7019e-02
   5_xyz:   0.925  0.005  0.067 14.513  0.004  4.107   5.1926e-02
   5_adp:   0.925  0.005  0.067 14.513  0.004  4.107   5.1926e-02
   5_occ:   0.925  0.005  0.067 14.513  0.004  4.107   5.1926e-02
   5_bss:   0.925  0.005  0.067 14.513  0.004  4.107   5.1926e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.258   2.4007e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.258   2.4007e-01
   1_xyz:   9.830  0.074  0.326 86.184  0.057  2.028   8.1771e-02
   1_adp:   9.830  0.074  0.326 86.184  0.057  2.028   8.1771e-02
   1_occ:   9.830  0.074  0.326 86.184  0.057  2.028   8.1771e-02
   2_bss:   9.830  0.074  0.326 86.184  0.057  2.028   8.1771e-02
   2_xyz:   6.763  0.039  0.223 79.936  0.026  2.344   5.8759e-02
   2_adp:   6.763  0.039  0.223 79.936  0.026  2.344   5.8759e-02
   2_occ:   6.763  0.039  0.223 79.936  0.026  2.344   5.8759e-02
   3_bss:   6.763  0.039  0.223 79.936  0.026  2.344   5.8759e-02
   3_xyz:   7.378  0.047  0.201 82.679  0.031  2.374   3.1933e-02
   3_adp:   7.378  0.047  0.201 82.679  0.031  2.374   3.1933e-02
   3_occ:   7.378  0.047  0.201 82.679  0.031  2.374   3.1933e-02
   4_bss:   7.378  0.047  0.201 82.679  0.031  2.374   3.1933e-02
   4_xyz:   7.245  0.042  0.216 84.060  0.042  2.295   4.0217e-02
   4_adp:   7.245  0.042  0.216 84.060  0.042  2.295   4.0217e-02
   4_occ:   7.245  0.042  0.216 84.060  0.042  2.295   4.0217e-02
   5_bss:   7.245  0.042  0.216 84.060  0.042  2.295   4.0217e-02
   5_xyz:   7.042  0.046  0.216 84.800  0.040  2.345   3.4845e-02
   5_adp:   7.042  0.046  0.216 84.800  0.040  2.345   3.4845e-02
   5_occ:   7.042  0.046  0.216 84.800  0.040  2.345   3.4845e-02
   5_bss:   7.042  0.046  0.216 84.800  0.040  2.345   3.4845e-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:  93.01   0.00  18.46  86.56   0.00  14.39  93.01   2.24  40.60
   1_occ:  93.01   0.00  18.46  86.56   0.00  14.39  93.01   2.24  40.60
   2_bss:  93.01   0.00  18.46  86.56   0.00  14.39  93.01   2.24  40.60
   2_xyz:  93.01   0.00  18.46  86.56   0.00  14.39  93.01   2.24  40.60
   2_adp:  84.27   0.00  17.40  84.27   0.00  13.36  83.34   6.26  39.41
   2_occ:  84.27   0.00  17.40  84.27   0.00  13.36  83.34   6.26  39.41
   3_bss:  84.27   0.00  17.40  84.27   0.00  13.36  83.34   6.26  39.41
   3_xyz:  84.27   0.00  17.40  84.27   0.00  13.36  83.34   6.26  39.41
   3_adp:  84.06   0.00  17.18  84.06   0.00  13.17  82.13   3.43  39.01
   3_occ:  84.06   0.00  17.18  84.06   0.00  13.17  82.13   3.43  39.01
   4_bss:  84.06   0.00  17.18  84.06   0.00  13.17  82.13   3.43  39.01
   4_xyz:  84.06   0.00  17.18  84.06   0.00  13.17  82.13   3.43  39.01
   4_adp:  89.95   0.81  17.30  89.95   0.81  13.05  84.36   3.71  40.43
   4_occ:  89.95   0.81  17.30  89.95   0.81  13.05  84.36   3.71  40.43
   5_bss:  89.95   0.81  17.30  89.95   0.81  13.05  84.36   3.71  40.43
   5_xyz:  89.95   0.81  17.30  89.95   0.81  13.05  84.36   3.71  40.43
   5_adp:  91.05   0.84  17.13  91.05   0.84  12.91  84.47   4.91  40.09
   5_occ:  91.05   0.84  17.13  91.05   0.84  12.91  84.47   4.91  40.09
   5_bss:  91.02   0.81  17.10  91.02   0.81  12.88  84.44   4.89  40.06
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.090    0.003    0.400
   1_adp:    2.090    0.003    0.400
   1_occ:    2.090    0.003    0.400
   2_bss:    2.090    0.003    0.400
   2_xyz:    1.997    0.018    0.550
   2_adp:    1.997    0.018    0.550
   2_occ:    1.997    0.018    0.550
   3_bss:    1.997    0.018    0.550
   3_xyz:    1.836    0.025    0.609
   3_adp:    1.836    0.025    0.609
   3_occ:    1.836    0.025    0.609
   4_bss:    1.836    0.025    0.609
   4_xyz:    1.709    0.041    0.639
   4_adp:    1.709    0.041    0.639
   4_occ:    1.709    0.041    0.639
   5_bss:    1.709    0.041    0.639
   5_xyz:    1.763    0.073    0.652
   5_adp:    1.763    0.073    0.652
   5_occ:    1.763    0.073    0.652
   5_bss:    1.763    0.073    0.652
------------------------------------------------------------------------

CPU time actual refinement: 347.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/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_27/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_27/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.24 
  Macro-tasks:
    bulk solvent and scale       = 41.97  
    individual site refinement   = 151.87 
    weights calculation          = 29.78  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 230.34 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 109.39 
    alpha_beta                      = 8.05   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 121.08 
    fmodel                         = 7.58   
    r_factors                      = 0.28   
    phase_errors                   = 10.83  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 260.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.788 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    663 calls, 108.95 s
gradients_fft:          608 calls, 106.51 s

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

# Date 2008-01-16 Time 03:50:19 PST -0800 (1200484219.19 s)
Start R-work = 0.4284, R-free = 0.4202 (no bulk solvent and anisotropic scale)
Final R-work = 0.1369, R-free = 0.1770 (no bulk solvent and anisotropic scale)

Start R-work = 0.4181, R-free = 0.4123
Final R-work = 0.1106, R-free = 0.1563