# Date 2008-01-16 Time 05:31:32 PST -0800 (1200490292.21 s)
#phil __OFF__

Command line arguments: "../771.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7542
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 771

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 84.6622, 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: 3.24, 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: (70.6012, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96117
Completeness in resolution range: 0.949217
Completeness with d_max=infinity: 0.946374

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96117
Completeness in resolution range: 0.949217
Completeness with d_max=infinity: 0.946374

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1971 [2168/2197]  1954   214   9.9%
  bin  2:  4.1971 -  3.3435 [2073/2089]  1863   210  10.1%
  bin  3:  3.3435 -  2.9245 [2049/2068]  1843   206  10.1%
  bin  4:  2.9245 -  2.6587 [2046/2076]  1848   198   9.7%
  bin  5:  2.6587 -  2.4691 [2038/2057]  1834   204  10.0%
  bin  6:  2.4691 -  2.3241 [2014/2050]  1806   208  10.3%
  bin  7:  2.3241 -  2.2081 [1985/2018]  1784   201  10.1%
  bin  8:  2.2081 -  2.1122 [2002/2036]  1806   196   9.8%
  bin  9:  2.1122 -  2.0311 [1983/2011]  1784   199  10.0%
  bin 10:  2.0311 -  1.9612 [1231/2035]  1108   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 29
        2.42 -     3.04: 2217
        3.04 -     3.66: 4752
        3.66 -     4.28: 9121
        4.28 -     4.90: 12475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.804 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.844 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.932 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  22 " - " O   HOH Z 320 "  2.069 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28589 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_771/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3490   r_free= 0.3504   ksol= 0.00   Bsol= 0.00   scale= 0.967    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.105326                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.3001 0.2971      6.3921      6.3859|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.2808 0.2612      6.5159      6.4619|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.3094 0.3173      6.4119      6.5537|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.3104 0.3243      6.2847      6.2803|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.3557 0.3299      6.1664      6.1289|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.3755 0.3812      6.1082      6.1355|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.3660 0.3497       6.069        6.04|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.3879 0.3767      6.0293      6.0233|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.3741 0.3859      5.9707      5.9268|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.3984 0.4409      5.9618      6.0548|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.3983 0.4399      5.9184      5.9809|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.4013 0.4177      5.8482      5.9052|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.4094 0.4087      5.7702      5.7126|
| 14:  2.0101 -  1.9612 0.47    606   71 0.4616 0.4417      5.7917       5.703|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.78  26.86   0.86     0.80      44843.11|
|  2:  4.6815 -  3.7348  1359   145  0.82  24.53   0.97     0.91      55397.63|
|  3:  3.7348 -  3.2683  1321   154  0.77  29.47   0.99     0.95      56706.02|
|  4:  3.2683 -  2.9721  1332   147  0.73  32.96   1.01     0.92      50733.22|
|  5:  2.9721 -  2.7605  1312   143  0.67  38.27   0.97     0.87      42201.76|
|  6:  2.7605 -  2.5986  1300   145  0.66  39.34   0.98     0.85      37662.09|
|  7:  2.5986 -  2.4691  1315   141  0.66  38.95   1.00     0.87      34001.50|
|  8:  2.4691 -  2.3620  1273   151  0.65  40.41   0.98     0.88      31189.22|
|  9:  2.3620 -  2.2714  1299   148  0.65  40.40   1.03     0.87      28742.98|
| 10:  2.2714 -  2.1933  1280   134  0.61  43.56   1.03     0.85      29488.92|
| 11:  2.1933 -  2.1249  1281   141  0.59  45.37   1.05     0.83      28905.17|
| 12:  2.1249 -  2.0643  1265   139  0.58  46.33   1.04     0.85      27452.29|
| 13:  2.0643 -  2.0101  1284   143  0.56  47.24   1.03     0.82      23184.96|
| 14:  2.0101 -  1.9612   606    71  0.56  47.94   1.00     0.73      19735.40|
|alpha:            min =        0.73 max =            0.95 mean =         0.86|
|beta:             min =    19735.40 max =        56706.02 mean =     37322.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.95 mean =        38.15|
|phase err.(test): min =        0.00 max =           89.99 mean =        38.35|
|-----------------------------------------------------------------------------|

============================== 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 = 3.648196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.883389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.548   (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 |  1.804 -  2.113:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.113 -  2.423:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.423 -  2.733:      202 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.733 -  3.042:     2015 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.042 -  3.352:     1893 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.352 -  3.662:     2859 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.971:     4674 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.971 -  4.281:     4447 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.590:     5670 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.590 -  4.900:     6805 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.804 |       0.262 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3490   r_free= 0.3504   ksol= 0.00   Bsol= 0.00   scale= 0.967    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.105326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3338   r_free= 0.3344   ksol= 0.33   Bsol= 34.12   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.37,2.51,-0.00,0.00,0.00); trace/3= -0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.089972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.936437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.403   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.547   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3338      final r-factor (work) = 0.2242          |
| start r-factor (free) = 0.3344      final r-factor (free) = 0.2501          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1071 = 2.94 * 0.50 * 6.0892 + 1.00 * 0.1668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6739 = 2.94 * 0.50 * 5.8595 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2242      final r-factor (work) = 0.2089          |
| start r-factor (free) = 0.2501      final r-factor (free) = 0.2575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5158 = 0.43 * 1.00 * 5.8595 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4598 = 0.43 * 1.00 * 5.6792 + 1.00 * 0.0273                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.89   16.79    None  None   None       |
|    all(noH): 2823   0      0.00    68.89   16.79    None  None   None       |
|    Sol.    : 438    0      4.26    62.35   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    68.89   12.95    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 -   6.889:  374   |   5:    34.443 -  41.332:  124        |
|      1:     6.889 -  13.777: 1203   |   6:    41.332 -  48.220:   94        |
|      2:    13.777 -  20.666:  596   |   7:    48.220 -  55.109:   71        |
|      3:    20.666 -  27.554:  194   |   8:    55.109 -  61.997:   35        |
|      4:    27.554 -  34.443:  130   |   9:    61.997 -  68.886:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2089 r_free = 0.2575             target_work(ml) = 5.691         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2084 r_free = 0.2577             target_work(ml) = 5.690         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2084   r_free= 0.2577   ksol= 0.33   Bsol= 34.12   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.37,2.51,-0.00,0.00,0.00); trace/3= -0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.689800                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2071   r_free= 0.2556   ksol= 0.32   Bsol= 34.12   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.61,-0.41,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.684294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.167295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.064   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.614   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2071      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2556      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0671 = 3.17 * 0.50 * 5.6807 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8368 = 3.17 * 0.50 * 5.5449 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.1876      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6166 = 0.29 * 1.00 * 5.5449 + 1.00 * 0.0229                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5340 = 0.29 * 1.00 * 5.3108 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    68.21   17.00    None  None   None       |
|    all(noH): 2823   0      1.63    68.21   17.00    None  None   None       |
|    Sol.    : 438    0      5.87    68.21   38.76    None  None   None       |
|    Mac.    : 2385   0      1.63    64.05   13.01    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:     1.626 -   8.285:  554   |   5:    34.920 -  41.579:  101        |
|      1:     8.285 -  14.944: 1276   |   6:    41.579 -  48.237:  108        |
|      2:    14.944 -  21.602:  396   |   7:    48.237 -  54.896:   78        |
|      3:    21.602 -  28.261:  149   |   8:    54.896 -  61.555:   47        |
|      4:    28.261 -  34.920:  101   |   9:    61.555 -  68.213:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1327 r_free = 0.1758             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1324 r_free = 0.1756             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1324   r_free= 0.1756   ksol= 0.32   Bsol= 34.12   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.61,-0.41,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.275320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1744   ksol= 0.32   Bsol= 38.84   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.53,-1.43,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.271128                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.648468              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.385  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.709238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.363  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0863 = 2.65 * 0.50 * 5.3092 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9588 = 2.65 * 0.50 * 5.2108 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7033 = 0.71 * 1.00 * 5.2108 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6532 = 0.71 * 1.00 * 5.1387 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.22   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    83.22   17.23    None  None   None       |
|    Sol.    : 438    0      2.93    76.47   40.04    None  None   None       |
|    Mac.    : 2385   0      0.00    83.22   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.322:  582   |   5:    41.610 -  49.932:  114        |
|      1:     8.322 -  16.644: 1392   |   6:    49.932 -  58.254:   89        |
|      2:    16.644 -  24.966:  347   |   7:    58.254 -  66.576:   40        |
|      3:    24.966 -  33.288:  126   |   8:    66.576 -  74.898:   19        |
|      4:    33.288 -  41.610:  109   |   9:    74.898 -  83.220:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1559             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1558             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1558   ksol= 0.32   Bsol= 38.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.53,-1.43,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1556   ksol= 0.32   Bsol= 41.37   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.54,-1.77,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132020                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.783463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.991  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.494341              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.285  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2094 = 2.78 * 0.50 * 5.1384 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1824 = 2.78 * 0.50 * 5.1143 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5368 = 0.49 * 1.00 * 5.1143 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5327 = 0.49 * 1.00 * 5.1061 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    89.27   17.03    None  None   None       |
|    all(noH): 2823   0      0.99    89.27   17.03    None  None   None       |
|    Sol.    : 438    0      3.62    78.75   39.37    None  None   None       |
|    Mac.    : 2385   0      0.99    89.27   12.93    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:     0.993 -   9.821:  982   |   5:    45.133 -  53.961:  104        |
|      1:     9.821 -  18.649: 1142   |   6:    53.961 -  62.789:   51        |
|      2:    18.649 -  27.477:  241   |   7:    62.789 -  71.617:   23        |
|      3:    27.477 -  36.305:  138   |   8:    71.617 -  80.445:   11        |
|      4:    36.305 -  45.133:  127   |   9:    80.445 -  89.273:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1059 r_free = 0.1538             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1058 r_free = 0.1537             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1537   ksol= 0.32   Bsol= 41.37   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.54,-1.77,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1535   ksol= 0.32   Bsol= 43.39   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.38,-1.71,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.568183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.558  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.106850              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.184  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1060      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0690 = 1.57 * 0.50 * 5.1071 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0647 = 1.57 * 0.50 * 5.1192 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5555 = 0.11 * 1.00 * 5.1192 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5551 = 0.11 * 1.00 * 5.1349 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.05    85.52   16.44    None  None   None       |
|    all(noH): 2823   0      2.05    85.52   16.44    None  None   None       |
|    Sol.    : 438    0      5.74    77.68   36.60    None  None   None       |
|    Mac.    : 2385   0      2.05    85.52   12.73    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:     2.048 -  10.395: 1108   |   5:    43.783 -  52.131:   98        |
|      1:    10.395 -  18.742: 1060   |   6:    52.131 -  60.478:   47        |
|      2:    18.742 -  27.089:  226   |   7:    60.478 -  68.825:   16        |
|      3:    27.089 -  35.436:  139   |   8:    68.825 -  77.172:    6        |
|      4:    35.436 -  43.783:  118   |   9:    77.172 -  85.519:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1537             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1535             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1535   ksol= 0.32   Bsol= 43.39   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.38,-1.71,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130578                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.0998 0.1257      5.3874      5.5403|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.0870 0.1090      5.4421      5.6227|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.1058 0.1528      5.4621      5.8425|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.1180 0.1489      5.4418      5.5753|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.1288 0.1694      5.2999      5.4977|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.1191 0.1734      5.1812      5.4192|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.1209 0.1546       5.135      5.3309|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.1141 0.1693      5.0281      5.2867|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.1148 0.1799      5.0048      5.2975|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.1130 0.1644      4.9479      5.1862|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.1160 0.1768      4.9326      5.2594|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.1071 0.1553      4.8486      5.0603|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.1157 0.1731      4.7607      5.0376|
| 14:  2.0101 -  1.9612 0.47    606   71 0.1000 0.1438      4.6077      4.8426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.94   8.74   0.98     0.95       6827.54|
|  2:  4.6815 -  3.7348  1359   145  0.95   7.82   1.02     1.01       8797.76|
|  3:  3.7348 -  3.2683  1321   154  0.93  11.29   1.02     1.02      10133.33|
|  4:  3.2683 -  2.9721  1332   147  0.92  13.41   1.01     0.99      10154.09|
|  5:  2.9721 -  2.7605  1312   143  0.90  15.55   0.99     0.96       7803.19|
|  6:  2.7605 -  2.5986  1300   145  0.91  15.23   0.98     0.96       6555.99|
|  7:  2.5986 -  2.4691  1315   141  0.91  14.57   0.99     0.96       5657.62|
|  8:  2.4691 -  2.3620  1273   151  0.91  14.82   1.00     0.98       4879.30|
|  9:  2.3620 -  2.2714  1299   148  0.92  14.56   1.01     0.99       4676.67|
| 10:  2.2714 -  2.1933  1280   134  0.90  15.26   1.00     0.96       4170.48|
| 11:  2.1933 -  2.1249  1281   141  0.90  15.81   1.00     0.97       4178.80|
| 12:  2.1249 -  2.0643  1265   139  0.92  14.48   1.01     1.00       3759.75|
| 13:  2.0643 -  2.0101  1284   143  0.91  15.59   1.01     1.01       3034.62|
| 14:  2.0101 -  1.9612   606    71  0.92  13.57   0.99     0.97       2203.01|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2203.01 max =        10154.09 mean =      6103.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.02 mean =        13.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1536   ksol= 0.32   Bsol= 40.54   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.28,-1.64,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1536   ksol= 0.32   Bsol= 40.54   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.28,-1.64,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130989                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.0997 0.1256      5.3877      5.5392|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.0867 0.1088      5.4396      5.6207|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.1056 0.1526      5.4606      5.8412|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.1179 0.1489      5.4419      5.5759|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.1290 0.1697      5.3011      5.4991|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.1192 0.1739      5.1826      5.4211|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.1210 0.1550      5.1365      5.3326|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.1143 0.1696      5.0296      5.2889|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.1149 0.1797      5.0056      5.2968|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.1132 0.1647      4.9487      5.1878|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.1161 0.1769      4.9333      5.2597|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.1071 0.1555      4.8491      5.0608|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.1158 0.1732      4.7614      5.0388|
| 14:  2.0101 -  1.9612 0.47    606   71 0.1001 0.1439      4.6083      4.8433|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.94   8.73   0.98     0.95       6828.29|
|  2:  4.6815 -  3.7348  1359   145  0.95   7.82   1.02     1.01       8779.61|
|  3:  3.7348 -  3.2683  1321   154  0.93  11.27   1.02     1.02      10106.87|
|  4:  3.2683 -  2.9721  1332   147  0.92  13.41   1.01     0.99      10154.90|
|  5:  2.9721 -  2.7605  1312   143  0.90  15.57   0.99     0.96       7816.55|
|  6:  2.7605 -  2.5986  1300   145  0.91  15.26   0.98     0.96       6577.25|
|  7:  2.5986 -  2.4691  1315   141  0.91  14.60   0.99     0.96       5680.39|
|  8:  2.4691 -  2.3620  1273   151  0.91  14.85   1.00     0.98       4894.52|
|  9:  2.3620 -  2.2714  1299   148  0.92  14.57   1.01     0.99       4685.87|
| 10:  2.2714 -  2.1933  1280   134  0.90  15.27   1.00     0.96       4175.43|
| 11:  2.1933 -  2.1249  1281   141  0.90  15.83   1.00     0.97       4185.19|
| 12:  2.1249 -  2.0643  1265   139  0.92  14.50   1.01     1.00       3766.05|
| 13:  2.0643 -  2.0101  1284   143  0.91  15.60   1.01     1.01       3040.34|
| 14:  2.0101 -  1.9612   606    71  0.92  13.58   0.99     0.97       2206.53|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2206.53 max =        10154.90 mean =      6108.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.79 mean =        13.58|
|phase err.(test): min =        0.00 max =           89.11 mean =        13.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.97    85.45   16.36    None  None   None       |
|    all(noH): 2823   0      1.97    85.45   16.36    None  None   None       |
|    Sol.    : 438    0      5.66    77.61   36.53    None  None   None       |
|    Mac.    : 2385   0      1.97    85.45   12.66    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:     1.974 -  10.321: 1108   |   5:    43.710 -  52.057:   98        |
|      1:    10.321 -  18.668: 1060   |   6:    52.057 -  60.404:   47        |
|      2:    18.668 -  27.015:  226   |   7:    60.404 -  68.751:   16        |
|      3:    27.015 -  35.362:  139   |   8:    68.751 -  77.098:    6        |
|      4:    35.362 -  43.710:  118   |   9:    77.098 -  85.445:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.519 - 4.557
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 306
   mapped sites are within: 0.703 - 4.557

peak=    5.917 closest distance to " NH2 ARG A  56 " =    2.166
peak=    5.602 closest distance to " CG  PRO A  54 " =    1.291
peak=    5.564 closest distance to " O   HOH Z 126 " =    1.916
peak=    5.387 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.360 closest distance to " CB  GLN A 223 " =    1.430
peak=    5.226 closest distance to " CB  SER A  63 " =    1.229
peak=    5.225 closest distance to " CG  PRO A 213 " =    1.234
peak=    5.176 closest distance to " CB  ARG A 275 " =    0.876
peak=    4.893 closest distance to " CG  PRO A  90 " =    1.156
peak=    4.757 closest distance to " CB  PRO A  54 " =    0.893
peak=    4.742 closest distance to " O   HOH Z 236 " =    1.936
peak=    4.731 closest distance to " O   HOH Z 193 " =    1.930
peak=    4.729 closest distance to " O   HOH Z 144 " =    1.702
peak=    4.727 closest distance to " O   HOH Z 232 " =    2.243
peak=    4.724 closest distance to " CB  GLN A 183 " =    1.186
peak=    4.653 closest distance to " C   PRO A 198 " =    1.547
peak=    4.586 closest distance to " CB  GLU A 128 " =    1.022
peak=    4.562 closest distance to " CB  ASN A 148 " =    1.489
peak=    4.509 closest distance to " ND2 ASN A 187 " =    1.582
peak=    4.500 closest distance to " CB  LEU A 228 " =    1.116
peak=    4.499 closest distance to " CB  SER A   3 " =    1.388
peak=    4.491 closest distance to " CG  PRO A 198 " =    1.321
peak=    4.488 closest distance to " CB  GLU A 152 " =    1.170
peak=    4.445 closest distance to " O   HOH Z  15 " =    2.187
peak=    4.402 closest distance to " O   HOH Z 189 " =    1.715
peak=    4.392 closest distance to " OD1 ASN A  69 " =    2.605
peak=    4.365 closest distance to " O   HOH Z 234 " =    3.712
peak=    4.282 closest distance to " O   HOH Z 427 " =    2.843
peak=    4.262 closest distance to " O   HOH Z  78 " =    1.737
peak=    4.247 closest distance to " OD2 ASP A 286 " =    2.825
peak=    4.245 closest distance to " O   HOH Z 368 " =    1.810
peak=    4.225 closest distance to " O   HOH Z 344 " =    3.000
peak=    4.218 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.216 closest distance to " CG  PRO A 243 " =    1.089
peak=    4.188 closest distance to " O   HOH Z 369 " =    1.885
peak=    4.146 closest distance to " CA  THR A 264 " =    0.865
peak=    4.122 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.116 closest distance to " O   HOH Z 316 " =    3.044
peak=    4.096 closest distance to " O   HOH Z 352 " =    1.872
peak=    4.081 closest distance to " CG  PRO A 280 " =    0.726
peak=    4.025 closest distance to " CB  SER A 216 " =    0.730
peak=    4.025 closest distance to " CB  TYR A 169 " =    0.767
peak=    4.013 closest distance to " O   HOH Z 303 " =    2.025
peak=    3.990 closest distance to " CA  TYR A  30 " =    0.979
peak=    3.981 closest distance to " O   HOH Z  10 " =    1.897
peak=    3.979 closest distance to " O   HOH Z  44 " =    1.790
peak=    3.978 closest distance to " O   HOH Z  21 " =    1.677
peak=    3.971 closest distance to " CA  ASN A 215 " =    1.162
peak=    3.967 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.935 closest distance to " O   HOH Z 108 " =    1.346
peak=    3.919 closest distance to " O   HOH Z  97 " =    1.944
peak=    3.914 closest distance to " O   HOH Z  66 " =    2.136
peak=    3.911 closest distance to " CG2 VAL A 257 " =    0.965
peak=    3.910 closest distance to " O   HOH Z  54 " =    1.683
peak=    3.906 closest distance to " CB  VAL A 265 " =    1.228
peak=    3.884 closest distance to " O   HOH Z  61 " =    1.566
peak=    3.883 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.880 closest distance to " O   HOH Z 207 " =    1.832
peak=    3.861 closest distance to " CB  LEU A 143 " =    1.097
peak=    3.854 closest distance to " NZ  LYS A 117 " =    3.295
peak=    3.853 closest distance to " O   HOH Z 144 " =    2.265
peak=    3.850 closest distance to " NH1AARG A 145 " =    1.110
peak=    3.847 closest distance to " O   HOH Z  88 " =    3.126
peak=    3.837 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.832 closest distance to " CB  TRP A 179 " =    1.322
peak=    3.827 closest distance to " O   SER A  87 " =    2.264
peak=    3.794 closest distance to " O   HOH Z  59 " =    1.968
peak=    3.793 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.792 closest distance to " CD1 LEU A 300 " =    1.304
peak=    3.780 closest distance to " O   HOH Z   6 " =    2.136
peak=    3.774 closest distance to " CA  THR A 221 " =    0.943
peak=    3.765 closest distance to " CB  ARG A  79 " =    1.299
peak=    3.759 closest distance to " O   HOH Z  78 " =    2.052
peak=    3.749 closest distance to " O   HOH Z 209 " =    2.185
peak=    3.747 closest distance to " O   HOH Z 368 " =    3.649
peak=    3.742 closest distance to " CA  ASP A 124 " =    0.728
peak=    3.730 closest distance to " O   HOH Z 346 " =    1.739
peak=    3.728 closest distance to " O   HOH Z   3 " =    1.832
peak=    3.716 closest distance to " O   HOH Z 389 " =    1.873
peak=    3.715 closest distance to " O   HOH Z 128 " =    2.126
peak=    3.709 closest distance to " O   HOH Z 158 " =    3.110
peak=    3.707 closest distance to " NH1BARG A 145 " =    1.313
peak=    3.706 closest distance to " O   HOH Z 295 " =    1.516
peak=    3.704 closest distance to " O   HOH Z 132 " =    2.401
peak=    3.697 closest distance to " CG1BVAL A  72 " =    1.536
peak=    3.691 closest distance to " O   HOH Z  93 " =    2.370
peak=    3.687 closest distance to " O   HOH Z 371 " =    2.994
peak=    3.682 closest distance to " O   HOH Z 273 " =    2.598
peak=    3.671 closest distance to " O   HOH Z  40 " =    1.573
peak=    3.656 closest distance to " O   HOH Z 261 " =    2.011
peak=    3.646 closest distance to " O   HOH Z   9 " =    2.050
peak=    3.637 closest distance to " O   HOH Z   1 " =    1.874
peak=    3.631 closest distance to " O   HOH Z 426 " =    1.549
peak=    3.630 closest distance to " O   HOH Z 214 " =    2.023
peak=    3.630 closest distance to " CG  LEU A 167 " =    1.189
peak=    3.629 closest distance to " CB  TRP A 266 " =    0.943
peak=    3.629 closest distance to " CE  LYS A  76 " =    0.924
peak=    3.618 closest distance to " CB  ARG A 190 " =    1.702
peak=    3.613 closest distance to " CB  TYR A 169 " =    0.854
peak=    3.610 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.597 closest distance to " CD BLYS A 290 " =    1.239
peak=    3.593 closest distance to " CD  ARG A 159 " =    0.711
peak=    3.587 closest distance to " CB  VAL A 202 " =    1.615
peak=    3.577 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.571 closest distance to " O   HOH Z  50 " =    1.518
peak=    3.568 closest distance to " O   HOH Z 133 " =    1.557
peak=    3.562 closest distance to " O   HOH Z 173 " =    1.807
peak=    3.560 closest distance to " O   HOH Z 425 " =    1.314
peak=    3.551 closest distance to " NH2 ARG A 156 " =    1.215
peak=    3.548 closest distance to " CA  GLY A 241 " =    3.821
peak=    3.538 closest distance to " O   HOH Z 402 " =    1.511
peak=    3.534 closest distance to " O   HOH Z 227 " =    2.152
peak=    3.532 closest distance to " O   HOH Z 407 " =    2.435
peak=    3.531 closest distance to " O   HOH Z 419 " =    1.938
peak=    3.530 closest distance to " CG  ARG A  66 " =    2.478
peak=    3.529 closest distance to " CA  ALA A 233 " =    1.291
peak=    3.528 closest distance to " N   ASN A  39 " =    1.165
peak=    3.527 closest distance to " CZ  PHE A 218 " =    1.001
peak=    3.526 closest distance to " CD2 LEU A 255 " =    1.370
peak=    3.524 closest distance to " O   HOH Z 134 " =    1.335
peak=    3.512 closest distance to " O   HOH Z 263 " =    2.252
peak=    3.506 closest distance to " O   HOH Z 250 " =    1.432
peak=    3.503 closest distance to " NH2BARG A 145 " =    2.013
peak=    3.502 closest distance to " O   HOH Z 135 " =    1.638
peak=    3.501 closest distance to " O   HOH Z 281 " =    4.557
peak=    3.494 closest distance to " NH2AARG A 190 " =    1.219
peak=    3.489 closest distance to " O   HOH Z 263 " =    1.641
peak=    3.481 closest distance to " OE1 GLU A 277 " =    1.918
peak=    3.479 closest distance to " CG2 ILE A 120 " =    1.221
peak=    3.479 closest distance to " O   HOH Z 329 " =    3.612
peak=    3.475 closest distance to " CA  ALA A  51 " =    0.874
peak=    3.475 closest distance to " O   HOH Z  43 " =    1.827
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.472 closest distance to " O   MET A 105 " =    1.759
peak=    3.468 closest distance to " O   HOH Z 163 " =    1.827
peak=    3.464 closest distance to " CB  ALA A 291 " =    1.266
peak=    3.464 closest distance to " CG2 THR A 221 " =    1.085
peak=    3.464 closest distance to " O   HOH Z 409 " =    2.760
peak=    3.462 closest distance to " O   HOH Z 175 " =    2.073
peak=    3.460 closest distance to " O   HOH Z 108 " =    2.057
peak=    3.457 closest distance to " CZ2 TRP A 179 " =    1.721
peak=    3.456 closest distance to " O   HOH Z 280 " =    1.846
peak=    3.456 closest distance to " CD  LYS A 166 " =    1.248
peak=    3.452 closest distance to " O   HOH Z 197 " =    3.034
peak=    3.451 closest distance to " CG  GLU A 277 " =    2.247
peak=    3.444 closest distance to " O   HOH Z 124 " =    1.401
peak=    3.436 closest distance to " O   HOH Z 163 " =    1.987
peak=    3.434 closest distance to " O   HOH Z 353 " =    2.632
peak=    3.433 closest distance to " O   HOH Z 219 " =    2.088
peak=    3.431 closest distance to " CA  SER A  87 " =    0.914
peak=    3.426 closest distance to " O   HOH Z 147 " =    1.711
peak=    3.425 closest distance to " CB  PRO A 198 " =    0.854
peak=    3.425 closest distance to " O   HOH Z 327 " =    1.770
peak=    3.424 closest distance to " O   HOH Z 403 " =    1.721
peak=    3.424 closest distance to " CB  SER A 141 " =    1.016
peak=    3.423 closest distance to " O   HOH Z 248 " =    1.731
peak=    3.421 closest distance to " O   ALA A   1 " =    1.498
peak=    3.421 closest distance to " OG BSER A 164 " =    2.427
peak=    3.419 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.417 closest distance to " N   ARG A 156 " =    1.266
peak=    3.411 closest distance to " O   HOH Z  40 " =    2.400
peak=    3.405 closest distance to " O   HOH Z 234 " =    1.778
peak=    3.400 closest distance to " CD1 ILE A 106 " =    0.924
peak=    3.396 closest distance to " O   HOH Z 411 " =    1.786
peak=    3.393 closest distance to " O   HOH Z 183 " =    1.498
peak=    3.391 closest distance to " CB  GLN A  88 " =    1.213
peak=    3.388 closest distance to " O   HOH Z 125 " =    2.230
peak=    3.385 closest distance to " CB  ILE A 120 " =    1.204
peak=    3.385 closest distance to " O   HOH Z 245 " =    1.409
peak=    3.382 closest distance to " OG  SER A  22 " =    2.700
peak=    3.378 closest distance to " O   HOH Z 292 " =    1.814
peak=    3.375 closest distance to " CB  MET A  47 " =    1.052
peak=    3.374 closest distance to " OD1BASN A 224 " =    2.250
peak=    3.374 closest distance to " CG  MET A 113 " =    1.166
peak=    3.374 closest distance to " CD2 TRP A 179 " =    1.349
peak=    3.372 closest distance to " O   HOH Z 193 " =    1.687
peak=    3.370 closest distance to " CA  ASP A 140 " =    1.139
peak=    3.368 closest distance to " CB  ALA A  34 " =    0.916
peak=    3.365 closest distance to " CB  SER A 212 " =    1.171
peak=    3.359 closest distance to " CA  ASP A 162 " =    1.106
peak=    3.353 closest distance to " O   HOH Z 425 " =    1.911
peak=    3.351 closest distance to " CD  ARG A 269 " =    0.982
peak=    3.349 closest distance to " CG  ARG A 159 " =    0.839
peak=    3.347 closest distance to " O   HOH Z 406 " =    1.655
peak=    3.345 closest distance to " CD  PRO A 243 " =    1.494
peak=    3.342 closest distance to " O   ASN A 209 " =    1.285
peak=    3.341 closest distance to " CG2AVAL A 121 " =    2.347
peak=    3.338 closest distance to " OG  SER A 206 " =    1.308
peak=    3.331 closest distance to " O   HOH Z 366 " =    3.006
peak=    3.318 closest distance to " CB  SER A  62 " =    1.230
peak=    3.317 closest distance to " O   HOH Z 287 " =    1.874
peak=    3.315 closest distance to " CG  MET A 185 " =    1.173
peak=    3.315 closest distance to " O   HOH Z  85 " =    2.190
peak=    3.312 closest distance to " CA  MET A  40 " =    1.099
peak=    3.308 closest distance to " O   HOH Z 291 " =    1.577
peak=    3.306 closest distance to " CA  VAL A 126 " =    0.972
peak=    3.306 closest distance to " N   ASN A 127 " =    1.249
peak=    3.305 closest distance to " CG AARG A 275 " =    1.078
peak=    3.303 closest distance to " O   HOH Z 374 " =    2.546
peak=    3.296 closest distance to " CD2 HIS A  81 " =    1.297
peak=    3.294 closest distance to " O   HOH Z 261 " =    2.000
peak=    3.294 closest distance to " CD2 LEU A 297 " =    0.922
peak=    3.294 closest distance to " O   HOH Z 258 " =    1.827
peak=    3.293 closest distance to " CB  ARG A  79 " =    0.851
peak=    3.291 closest distance to " CE BMET A  47 " =    1.428
peak=    3.288 closest distance to " OD1 ASP A 231 " =    1.806
peak=    3.282 closest distance to " CA  ILE A 234 " =    0.898
peak=    3.281 closest distance to " CB  GLU A 277 " =    3.500
peak=    3.281 closest distance to " N   PHE A 130 " =    1.311
peak=    3.281 closest distance to " O   HOH Z 284 " =    3.075
peak=    3.279 closest distance to " OD1 ASP A 238 " =    1.025
peak=    3.278 closest distance to " O   HOH Z   1 " =    1.728
peak=    3.276 closest distance to " O   HOH Z 336 " =    1.955
peak=    3.269 closest distance to " O   HOH Z 345 " =    3.414
peak=    3.267 closest distance to " O   HOH Z 271 " =    2.210
peak=    3.265 closest distance to " O   HOH Z 334 " =    1.461
peak=    3.265 closest distance to " CB  GLU A 152 " =    1.394
peak=    3.264 closest distance to " O   HOH Z 175 " =    2.138
peak=    3.264 closest distance to " O   ALA A 165 " =    1.380
peak=    3.259 closest distance to " N   GLN A 278 " =    0.930
peak=    3.257 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.256 closest distance to " NZ  LYS A  76 " =    1.216
peak=    3.254 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.249 closest distance to " CB  ALA A  71 " =    1.380
peak=    3.248 closest distance to " O   TRP A 274 " =    1.794
peak=    3.247 closest distance to " CG  GLN A  89 " =    1.482
peak=    3.242 closest distance to " CD  LYS A 119 " =    1.351
peak=    3.240 closest distance to " O   HOH Z  48 " =    1.354
peak=    3.237 closest distance to " O   HOH Z 180 " =    2.098
peak=    3.236 closest distance to " OG  SER A  97 " =    3.551
peak=    3.235 closest distance to " O   HOH Z 299 " =    4.310
peak=    3.234 closest distance to " O   HOH Z 423 " =    1.919
peak=    3.230 closest distance to " O   HOH Z 313 " =    1.625
peak=    3.228 closest distance to " O   HOH Z 435 " =    1.911
peak=    3.226 closest distance to " CG1 VAL A 153 " =    0.894
peak=    3.225 closest distance to " O   HOH Z 151 " =    2.115
peak=    3.225 closest distance to " O   HOH Z 337 " =    3.700
peak=    3.223 closest distance to " O   HOH Z 247 " =    1.285
peak=    3.217 closest distance to " O   HOH Z  73 " =    1.563
peak=    3.216 closest distance to " CD BARG A 102 " =    1.254
peak=    3.214 closest distance to " O   HOH Z 188 " =    2.024
peak=    3.208 closest distance to " O   HOH Z  40 " =    1.897
peak=    3.207 closest distance to " CG  LYS A  76 " =    0.963
peak=    3.207 closest distance to " O   GLY A 229 " =    1.619
peak=    3.205 closest distance to " CB  ASN A 215 " =    1.053
peak=    3.203 closest distance to " CA  ALA A 291 " =    0.975
peak=    3.198 closest distance to " CG1 ILE A 151 " =    0.926
peak=    3.197 closest distance to " CA  ALA A 248 " =    1.274
peak=    3.188 closest distance to " O   HOH Z 437 " =    1.679
peak=    3.185 closest distance to " O   HOH Z 216 " =    2.409
peak=    3.184 closest distance to " O   HOH Z 379 " =    1.847
peak=    3.183 closest distance to " N   CYS A 260 " =    0.717
peak=    3.182 closest distance to " CG2BVAL A  41 " =    0.813
peak=    3.180 closest distance to " O   HOH Z 387 " =    3.190
peak=    3.173 closest distance to " ND1 HIS A  81 " =    1.610
peak=    3.172 closest distance to " ND1 HIS A  86 " =    1.709
peak=    3.169 closest distance to " CB  ALA A 114 " =    1.221
peak=    3.169 closest distance to " O   HOH Z  49 " =    2.084
peak=    3.168 closest distance to " CA  LYS A 290 " =    1.370
peak=    3.165 closest distance to " O   HOH Z 433 " =    1.888
peak=    3.163 closest distance to " O   HOH Z 367 " =    3.602
peak=    3.160 closest distance to " CB  LEU A 255 " =    0.770
peak=    3.154 closest distance to " O   HOH Z 172 " =    3.369
peak=    3.154 closest distance to " CG BARG A 275 " =    1.504
peak=    3.153 closest distance to " N   TYR A  15 " =    0.756
peak=    3.151 closest distance to " CA  LEU A 282 " =    1.157
peak=    3.147 closest distance to " O   HOH Z 227 " =    1.573
peak=    3.147 closest distance to " CG  MET A 185 " =    1.066
peak=    3.142 closest distance to " CB  LYS A 193 " =    0.935
peak=    3.141 closest distance to " O   HOH Z  66 " =    1.910
peak=    3.141 closest distance to " O   HOH Z 291 " =    1.864
peak=    3.139 closest distance to " CA  TYR A 186 " =    1.464
peak=    3.136 closest distance to " OD1 ASN A 217 " =    1.675
peak=    3.136 closest distance to " O   GLY A 147 " =    1.178
peak=    3.135 closest distance to " O   ALA A   1 " =    1.630
peak=    3.134 closest distance to " CB  THR A 157 " =    1.044
peak=    3.132 closest distance to " CA  VAL A  41 " =    0.856
peak=    3.130 closest distance to " C   TYR A 214 " =    1.443
peak=    3.127 closest distance to " CB  MET A  40 " =    0.892
peak=    3.124 closest distance to " CE BLYS A 290 " =    1.171
peak=    3.123 closest distance to " O   HOH Z 286 " =    2.417
peak=    3.121 closest distance to " CA  ARG A  36 " =    1.044
peak=    3.121 closest distance to " CG  GLN A 144 " =    1.088
peak=    3.120 closest distance to " O   HOH Z 357 " =    1.777
peak=    3.120 closest distance to " CB  TYR A 116 " =    0.876
peak=    3.120 closest distance to " O   HOH Z  83 " =    1.897
peak=    3.114 closest distance to " CA  ALA A  43 " =    1.167
peak=    3.110 closest distance to " CA  ALA A 299 " =    0.921
peak=    3.106 closest distance to " CA  ALA A 154 " =    0.970
peak=    3.106 closest distance to " O   HOH Z  49 " =    2.360
peak=    3.097 closest distance to " O   HOH Z 403 " =    1.343
peak=    3.095 closest distance to " CZ3 TRP A 123 " =    1.237
peak=    3.085 closest distance to " CA  ASP A 191 " =    0.739
peak=    3.085 closest distance to " CB  GLN A 103 " =    0.788
peak=    3.084 closest distance to " O   HOH Z 110 " =    1.504
peak=    3.072 closest distance to " CB  ASP A 140 " =    0.703
peak=    3.072 closest distance to " O   HOH Z 359 " =    3.960
peak=    3.069 closest distance to " CZ  PHE A 192 " =    0.974
peak=    3.060 closest distance to " NZ  LYS A 119 " =    1.178
peak=    3.049 closest distance to " CB  ARG A 138 " =    0.975
peak=    3.044 closest distance to " CA  ALA A 158 " =    1.076
peak=    3.030 closest distance to " O   HOH Z  87 " =    2.091
peak=    3.016 closest distance to " O   HOH Z 383 " =    1.618

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 5.303
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 189
   mapped sites are within: 0.734 - 5.303

peak=   -4.709 closest distance to " O   HOH Z 290 " =    1.032
peak=   -4.579 closest distance to " CB  PRO A 243 " =    2.613
peak=   -4.301 closest distance to " O   PRO A 198 " =    1.224
peak=   -4.268 closest distance to " O   HOH Z 266 " =    4.374
peak=   -4.233 closest distance to " O   VAL A  67 " =    2.689
peak=   -4.227 closest distance to " CB  ALA A 161 " =    2.564
peak=   -4.113 closest distance to " CD  ARG A 156 " =    1.965
peak=   -4.092 closest distance to " CG  GLN A 223 " =    1.780
peak=   -4.078 closest distance to " O   HOH Z 198 " =    2.080
peak=   -4.021 closest distance to " C   ALA A 158 " =    1.282
peak=   -4.018 closest distance to " ND2 ASN A  45 " =    1.053
peak=   -4.012 closest distance to " SG  CYS A 254 " =    3.253
peak=   -3.985 closest distance to " CB  CYS A 201 " =    2.658
peak=   -3.951 closest distance to " N   ALA A  43 " =    2.394
peak=   -3.951 closest distance to " CE2 TYR A  30 " =    2.853
peak=   -3.950 closest distance to " O   HOH Z 377 " =    1.847
peak=   -3.940 closest distance to " O   HOH Z 185 " =    2.294
peak=   -3.920 closest distance to " O   HOH Z 351 " =    1.408
peak=   -3.918 closest distance to " CZ3 TRP A 179 " =    1.240
peak=   -3.900 closest distance to " N   GLN A  58 " =    1.850
peak=   -3.897 closest distance to " O   HOH Z 353 " =    2.225
peak=   -3.891 closest distance to " CG  PHE A 283 " =    2.738
peak=   -3.867 closest distance to " C   HIS A 108 " =    1.125
peak=   -3.851 closest distance to " CG  ASP A 231 " =    0.756
peak=   -3.821 closest distance to " O   HOH Z  43 " =    1.679
peak=   -3.807 closest distance to " CA  GLY A  98 " =    1.938
peak=   -3.788 closest distance to " CD1 LEU A 228 " =    2.253
peak=   -3.785 closest distance to " O   HOH Z  52 " =    1.241
peak=   -3.783 closest distance to " O   PRO A 163 " =    1.958
peak=   -3.782 closest distance to " CE  MET A 105 " =    2.035
peak=   -3.769 closest distance to " O   HOH Z 118 " =    2.963
peak=   -3.769 closest distance to " O   HOH Z 231 " =    1.933
peak=   -3.767 closest distance to " OXT GLY A 302 " =    2.654
peak=   -3.765 closest distance to " CZ  TYR A 169 " =    1.635
peak=   -3.757 closest distance to " CB  ASN A  39 " =    2.107
peak=   -3.736 closest distance to " O   HOH Z  13 " =    1.292
peak=   -3.726 closest distance to " CD2 LEU A 300 " =    2.822
peak=   -3.725 closest distance to " OE1 GLN A  88 " =    1.075
peak=   -3.723 closest distance to " O   HOH Z 407 " =    3.154
peak=   -3.722 closest distance to " O   VAL A  67 " =    2.651
peak=   -3.713 closest distance to " O   VAL A 153 " =    2.358
peak=   -3.711 closest distance to " O   HOH Z 435 " =    2.730
peak=   -3.708 closest distance to " CG1 VAL A 112 " =    2.885
peak=   -3.700 closest distance to " O   HOH Z  47 " =    1.484
peak=   -3.686 closest distance to " CG  GLU A 152 " =    0.838
peak=   -3.683 closest distance to " O   HOH Z 210 " =    0.837
peak=   -3.677 closest distance to " O   GLY A 196 " =    1.057
peak=   -3.677 closest distance to " O   HOH Z 126 " =    1.856
peak=   -3.667 closest distance to " NH2AARG A 275 " =    5.303
peak=   -3.641 closest distance to " OG BSER A 134 " =    1.237
peak=   -3.636 closest distance to " O   HOH Z 222 " =    1.049
peak=   -3.635 closest distance to " O   HOH Z 388 " =    1.982
peak=   -3.633 closest distance to " N   ASP A 286 " =    2.398
peak=   -3.611 closest distance to " O   HOH Z  11 " =    1.792
peak=   -3.610 closest distance to " CD1 LEU A 101 " =    2.447
peak=   -3.585 closest distance to " O   ALA A 161 " =    1.494
peak=   -3.582 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.581 closest distance to " O   HOH Z 389 " =    1.809
peak=   -3.576 closest distance to " O   HOH Z 211 " =    1.567
peak=   -3.564 closest distance to " CB  PRO A 163 " =    2.635
peak=   -3.560 closest distance to " CD1 PHE A  59 " =    1.822
peak=   -3.553 closest distance to " NH2 ARG A  79 " =    1.869
peak=   -3.551 closest distance to " O   SER A 135 " =    1.508
peak=   -3.547 closest distance to " OG  SER A  97 " =    2.148
peak=   -3.544 closest distance to " CG  MET A 105 " =    0.942
peak=   -3.542 closest distance to " O   HOH Z 313 " =    2.034
peak=   -3.536 closest distance to " O   HOH Z 198 " =    1.151
peak=   -3.520 closest distance to " N   ALA A 248 " =    1.605
peak=   -3.517 closest distance to " O   HOH Z 395 " =    5.171
peak=   -3.501 closest distance to " CG  LYS A 193 " =    2.267
peak=   -3.496 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.495 closest distance to " OG BSER A 134 " =    1.678
peak=   -3.488 closest distance to " N   SER A 212 " =    1.813
peak=   -3.485 closest distance to " CZ  PHE A  59 " =    1.525
peak=   -3.483 closest distance to " CD2 LEU A 237 " =    2.737
peak=   -3.468 closest distance to " OD2 ASP A 171 " =    2.335
peak=   -3.466 closest distance to " O   HOH Z 311 " =    3.480
peak=   -3.457 closest distance to " O   HOH Z  63 " =    1.460
peak=   -3.432 closest distance to " C   LEU A 143 " =    1.195
peak=   -3.425 closest distance to " O   VAL A 174 " =    2.031
peak=   -3.422 closest distance to " O   HOH Z  10 " =    1.412
peak=   -3.420 closest distance to " OD1 ASP A 191 " =    1.663
peak=   -3.411 closest distance to " O   HOH Z  11 " =    2.019
peak=   -3.389 closest distance to " N   GLY A  23 " =    2.177
peak=   -3.388 closest distance to " CE3 TRP A 123 " =    1.237
peak=   -3.387 closest distance to " CB  ALA A 291 " =    2.189
peak=   -3.387 closest distance to " NH1 ARG A 195 " =    2.520
peak=   -3.379 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.377 closest distance to " CG  LEU A  83 " =    1.862
peak=   -3.377 closest distance to " CE  MET A  93 " =    1.081
peak=   -3.374 closest distance to " CA  GLY A 203 " =    2.227
peak=   -3.371 closest distance to " O   HOH Z 417 " =    2.461
peak=   -3.356 closest distance to " CG1 VAL A 197 " =    2.228
peak=   -3.356 closest distance to " CE  LYS A  76 " =    2.801
peak=   -3.355 closest distance to " O   HOH Z 385 " =    2.012
peak=   -3.353 closest distance to " O   HOH Z 298 " =    1.182
peak=   -3.351 closest distance to " CB  ALA A 291 " =    2.333
peak=   -3.344 closest distance to " CD1 ILE A 239 " =    2.059
peak=   -3.320 closest distance to " O   GLY A 211 " =    1.446
peak=   -3.316 closest distance to " O   HOH Z  38 " =    1.599
peak=   -3.309 closest distance to " O   HOH Z  98 " =    2.328
peak=   -3.307 closest distance to " CD  LYS A 289 " =    2.471
peak=   -3.306 closest distance to " CD1 TYR A 247 " =    2.773
peak=   -3.305 closest distance to " O   HOH Z 102 " =    1.728
peak=   -3.304 closest distance to " CG1 VAL A 250 " =    2.711
peak=   -3.303 closest distance to " O   PRO A 198 " =    1.155
peak=   -3.301 closest distance to " CD1 ILE A 239 " =    2.534
peak=   -3.294 closest distance to " N   MET A 105 " =    2.855
peak=   -3.293 closest distance to " CB  TYR A  15 " =    2.182
peak=   -3.289 closest distance to " CG  GLU A 277 " =    1.137
peak=   -3.285 closest distance to " O   HOH Z  93 " =    1.850
peak=   -3.284 closest distance to " O   GLN A 240 " =    2.074
peak=   -3.284 closest distance to " OG  SER A 245 " =    0.895
peak=   -3.283 closest distance to " O   HOH Z  15 " =    1.670
peak=   -3.282 closest distance to " N   HIS A 115 " =    2.050
peak=   -3.282 closest distance to " N   GLN A 122 " =    1.470
peak=   -3.281 closest distance to " O   HOH Z 148 " =    3.349
peak=   -3.279 closest distance to " OG  SER A   3 " =    1.527
peak=   -3.275 closest distance to " CD2 LEU A 300 " =    2.839
peak=   -3.267 closest distance to " O   HOH Z 250 " =    1.448
peak=   -3.267 closest distance to " CB  ASP A 132 " =    2.224
peak=   -3.267 closest distance to " CA  GLY A 241 " =    2.301
peak=   -3.262 closest distance to " O   HOH Z 100 " =    0.771
peak=   -3.261 closest distance to " CA  ASP A  27 " =    2.417
peak=   -3.260 closest distance to " ND2 ASN A 187 " =    1.475
peak=   -3.259 closest distance to " CD  GLN A  88 " =    0.734
peak=   -3.257 closest distance to " CA  TRP A 274 " =    1.513
peak=   -3.253 closest distance to " SG ACYS A 201 " =    1.956
peak=   -3.253 closest distance to " O   HOH Z 317 " =    2.564
peak=   -3.244 closest distance to " O   HOH Z 193 " =    1.845
peak=   -3.243 closest distance to " N   ALA A 226 " =    2.053
peak=   -3.235 closest distance to " OD1 ASN A 148 " =    1.717
peak=   -3.229 closest distance to " CG  ARG A 269 " =    2.406
peak=   -3.229 closest distance to " CG2 ILE A 263 " =    2.267
peak=   -3.228 closest distance to " OG1 THR A 178 " =    1.284
peak=   -3.226 closest distance to " OXT GLY A 302 " =    3.475
peak=   -3.225 closest distance to " CG1BVAL A  41 " =    2.923
peak=   -3.224 closest distance to " O   HOH Z  51 " =    1.227
peak=   -3.221 closest distance to " O   HOH Z 423 " =    1.017
peak=   -3.220 closest distance to " CD2 PHE A 192 " =    2.124
peak=   -3.218 closest distance to " NH1AARG A 275 " =    1.773
peak=   -3.216 closest distance to " CB  ASP A 286 " =    2.152
peak=   -3.215 closest distance to " CB  CYS A 254 " =    2.422
peak=   -3.215 closest distance to " CE3 TRP A 150 " =    1.930
peak=   -3.215 closest distance to " CE3 TRP A 274 " =    2.507
peak=   -3.213 closest distance to " O   HOH Z 385 " =    1.975
peak=   -3.211 closest distance to " O   HOH Z  44 " =    2.138
peak=   -3.206 closest distance to " O   HOH Z  24 " =    1.469
peak=   -3.202 closest distance to " O   ALA A  51 " =    1.433
peak=   -3.202 closest distance to " O   HOH Z  71 " =    1.054
peak=   -3.200 closest distance to " O   HOH Z 298 " =    2.587
peak=   -3.199 closest distance to " OH  TYR A 247 " =    2.085
peak=   -3.198 closest distance to " O   HOH Z 166 " =    1.393
peak=   -3.198 closest distance to " OE1 GLN A 223 " =    1.692
peak=   -3.187 closest distance to " O   HOH Z 281 " =    3.205
peak=   -3.173 closest distance to " CG  ASN A 301 " =    1.914
peak=   -3.170 closest distance to " N   VAL A 189 " =    1.646
peak=   -3.166 closest distance to " O   SER A 146 " =    1.046
peak=   -3.159 closest distance to " CB  ALA A 248 " =    2.397
peak=   -3.158 closest distance to " NE2 GLN A  58 " =    1.222
peak=   -3.155 closest distance to " CG  TRP A 266 " =    1.825
peak=   -3.152 closest distance to " C   GLN A 205 " =    2.020
peak=   -3.148 closest distance to " O   HOH Z 426 " =    1.603
peak=   -3.141 closest distance to " CG  ASP A  50 " =    2.379
peak=   -3.137 closest distance to " O   HOH Z 281 " =    2.789
peak=   -3.135 closest distance to " O   HOH Z  60 " =    2.314
peak=   -3.127 closest distance to " O   HOH Z 390 " =    2.443
peak=   -3.124 closest distance to " O   HOH Z 322 " =    1.534
peak=   -3.117 closest distance to " O   ASN A 249 " =    1.517
peak=   -3.115 closest distance to " CG  PRO A 163 " =    2.517
peak=   -3.108 closest distance to " CD2 TYR A 293 " =    2.023
peak=   -3.105 closest distance to " CG  GLU A   2 " =    2.024
peak=   -3.105 closest distance to " O   HOH Z 196 " =    2.146
peak=   -3.102 closest distance to " O   HOH Z 265 " =    2.072
peak=   -3.099 closest distance to " N   ALA A 248 " =    2.492
peak=   -3.099 closest distance to " CZ  PHE A 130 " =    0.788
peak=   -3.093 closest distance to " ND2 ASN A 249 " =    2.325
peak=   -3.089 closest distance to " CG  GLU A 152 " =    1.300
peak=   -3.085 closest distance to " OG  SER A  97 " =    2.210
peak=   -3.082 closest distance to " O   HOH Z 111 " =    1.283
peak=   -3.075 closest distance to " CB  TRP A  85 " =    2.578
peak=   -3.070 closest distance to " OD1 ASP A 171 " =    1.580
peak=   -3.055 closest distance to " C   PHE A 218 " =    1.520
peak=   -3.039 closest distance to " OD2 ASP A 270 " =    1.470
peak=   -3.035 closest distance to " OD1 ASN A 249 " =    1.304
peak=   -3.018 closest distance to " O   HOH Z 111 " =    2.414

================= 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    :  0.3490 0.3504   6.105326e+00   6.112161e+00
   1_bss:  0.3338 0.3344   6.089972e+00   6.080360e+00
   1_xyz:  0.2242 0.2501   5.729518e+00   5.831056e+00
   1_adp:  0.2089 0.2575   5.691136e+00   5.855977e+00
   1_occ:  0.2084 0.2577   5.689800e+00   5.855288e+00
   2_bss:  0.2071 0.2556   5.684294e+00   5.849410e+00
   2_xyz:  0.1455 0.1876   5.354347e+00   5.552213e+00
   2_adp:  0.1327 0.1758   5.276300e+00   5.486519e+00
   2_occ:  0.1324 0.1756   5.275320e+00   5.485711e+00
   3_bss:  0.1321 0.1744   5.271128e+00   5.481415e+00
   3_xyz:  0.1151 0.1574   5.153628e+00   5.384040e+00
   3_adp:  0.1113 0.1559   5.133257e+00   5.372343e+00
   3_occ:  0.1113 0.1558   5.132872e+00   5.372046e+00
   4_bss:  0.1112 0.1556   5.132020e+00   5.371351e+00
   4_xyz:  0.1066 0.1536   5.108927e+00   5.362096e+00
   4_adp:  0.1059 0.1538   5.107258e+00   5.363065e+00
   4_occ:  0.1058 0.1537   5.107122e+00   5.363119e+00
   5_bss:  0.1060 0.1535   5.109164e+00   5.363608e+00
   5_xyz:  0.1083 0.1545   5.124717e+00   5.372658e+00
   5_adp:  0.1105 0.1537   5.130635e+00   5.366989e+00
   5_occ:  0.1104 0.1535   5.130578e+00   5.367273e+00
   5_bss:  0.1104 0.1536   5.130989e+00   5.367735e+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:  0.326  34.125  -2.681  -2.372   2.513  -0.000   0.000   0.000
   1_xyz:  0.326  34.125  -2.681  -2.372   2.513  -0.000   0.000   0.000
   1_adp:  0.326  34.125  -2.681  -2.372   2.513  -0.000   0.000   0.000
   1_occ:  0.326  34.125  -2.681  -2.372   2.513  -0.000   0.000   0.000
   2_bss:  0.317  34.125  -2.604  -2.608  -0.407  -0.000  -0.000  -0.000
   2_xyz:  0.317  34.125  -2.604  -2.608  -0.407  -0.000  -0.000  -0.000
   2_adp:  0.317  34.125  -2.604  -2.608  -0.407  -0.000  -0.000  -0.000
   2_occ:  0.317  34.125  -2.604  -2.608  -0.407  -0.000  -0.000  -0.000
   3_bss:  0.319  38.836  -2.475  -2.534  -1.433  -0.000  -0.000  -0.000
   3_xyz:  0.319  38.836  -2.475  -2.534  -1.433  -0.000  -0.000  -0.000
   3_adp:  0.319  38.836  -2.475  -2.534  -1.433  -0.000  -0.000  -0.000
   3_occ:  0.319  38.836  -2.475  -2.534  -1.433  -0.000  -0.000  -0.000
   4_bss:  0.320  41.367  -2.522  -2.539  -1.765  -0.000  -0.000  -0.000
   4_xyz:  0.320  41.367  -2.522  -2.539  -1.765  -0.000  -0.000  -0.000
   4_adp:  0.320  41.367  -2.522  -2.539  -1.765  -0.000  -0.000  -0.000
   4_occ:  0.320  41.367  -2.522  -2.539  -1.765  -0.000  -0.000  -0.000
   5_bss:  0.321  43.387  -2.372  -2.375  -1.712  -0.000  -0.000  -0.000
   5_xyz:  0.321  43.387  -2.372  -2.375  -1.712  -0.000  -0.000  -0.000
   5_adp:  0.321  43.387  -2.372  -2.375  -1.712  -0.000  -0.000  -0.000
   5_occ:  0.321  43.387  -2.372  -2.375  -1.712  -0.000  -0.000  -0.000
   5_bss:  0.321  40.535  -2.308  -2.282  -1.640  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.168 0.6670  0.8621    37320.661
   1_bss:  36.499 0.6841  0.8593    33055.149
   1_xyz:  25.171 0.8108  0.9721    16991.641
   1_adp:  26.414 0.7967  0.9624    18083.372
   1_occ:  26.425 0.7965  0.9620    18061.252
   2_bss:  26.031 0.8006  0.9317    17696.197
   2_xyz:  17.780 0.8820  0.9891     8905.142
   2_adp:  16.152 0.8969  0.9956     7857.346
   2_occ:  16.130 0.8971  0.9954     7836.187
   3_bss:  16.017 0.8981  0.9861     7774.150
   3_xyz:  13.999 0.9146  0.9923     6265.065
   3_adp:  13.727 0.9170  0.9893     6141.643
   3_occ:  13.718 0.9171  0.9892     6137.140
   4_bss:  13.702 0.9172  0.9847     6131.785
   4_xyz:  13.490 0.9190  0.9843     5995.420
   4_adp:  13.471 0.9193  0.9797     6003.030
   4_occ:  13.472 0.9193  0.9796     6003.023
   5_bss:  13.499 0.9191  0.9838     6034.693
   5_xyz:  13.647 0.9181  0.9827     6139.646
   5_adp:  13.515 0.9191  0.9814     6103.975
   5_occ:  13.518 0.9191  0.9812     6103.783
   5_bss:  13.529 0.9190  0.9811     6108.367
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6678e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6678e-01
   1_xyz:   1.096  0.008  0.068 15.180  0.004  4.108   7.0937e-02
   1_adp:   1.096  0.008  0.068 15.180  0.004  4.108   7.0937e-02
   1_occ:   1.096  0.008  0.068 15.180  0.004  4.108   7.0937e-02
   2_bss:   1.096  0.008  0.068 15.180  0.004  4.108   7.0937e-02
   2_xyz:   1.002  0.006  0.069 14.225  0.004  4.115   5.5753e-02
   2_adp:   1.002  0.006  0.069 14.225  0.004  4.115   5.5753e-02
   2_occ:   1.002  0.006  0.069 14.225  0.004  4.115   5.5753e-02
   3_bss:   1.002  0.006  0.069 14.225  0.004  4.115   5.5753e-02
   3_xyz:   0.994  0.007  0.073 14.533  0.004  4.114   5.8479e-02
   3_adp:   0.994  0.007  0.073 14.533  0.004  4.114   5.8479e-02
   3_occ:   0.994  0.007  0.073 14.533  0.004  4.114   5.8479e-02
   4_bss:   0.994  0.007  0.073 14.533  0.004  4.114   5.8479e-02
   4_xyz:   1.062  0.008  0.077 14.770  0.004  4.113   6.4640e-02
   4_adp:   1.062  0.008  0.077 14.770  0.004  4.113   6.4640e-02
   4_occ:   1.062  0.008  0.077 14.770  0.004  4.113   6.4640e-02
   5_bss:   1.062  0.008  0.077 14.770  0.004  4.113   6.4640e-02
   5_xyz:   0.913  0.005  0.068 14.354  0.004  4.112   5.0781e-02
   5_adp:   0.913  0.005  0.068 14.354  0.004  4.112   5.0781e-02
   5_occ:   0.913  0.005  0.068 14.354  0.004  4.112   5.0781e-02
   5_bss:   0.913  0.005  0.068 14.354  0.004  4.112   5.0781e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.804   2.3915e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.804   2.3915e-01
   1_xyz:   8.447  0.043  0.284 85.008  0.032  2.281   7.4959e-02
   1_adp:   8.447  0.043  0.284 85.008  0.032  2.281   7.4959e-02
   1_occ:   8.447  0.043  0.284 85.008  0.032  2.281   7.4959e-02
   2_bss:   8.447  0.043  0.284 85.008  0.032  2.281   7.4959e-02
   2_xyz:   7.118  0.031  0.247 81.374  0.030  2.369   4.9733e-02
   2_adp:   7.118  0.031  0.247 81.374  0.030  2.369   4.9733e-02
   2_occ:   7.118  0.031  0.247 81.374  0.030  2.369   4.9733e-02
   3_bss:   7.118  0.031  0.247 81.374  0.030  2.369   4.9733e-02
   3_xyz:   6.902  0.039  0.231 84.929  0.035  2.309   6.0995e-02
   3_adp:   6.902  0.039  0.231 84.929  0.035  2.309   6.0995e-02
   3_occ:   6.902  0.039  0.231 84.929  0.035  2.309   6.0995e-02
   4_bss:   6.902  0.039  0.231 84.929  0.035  2.309   6.0995e-02
   4_xyz:   6.557  0.042  0.254 82.728  0.039  2.275   5.0500e-02
   4_adp:   6.557  0.042  0.254 82.728  0.039  2.275   5.0500e-02
   4_occ:   6.557  0.042  0.254 82.728  0.039  2.275   5.0500e-02
   5_bss:   6.557  0.042  0.254 82.728  0.039  2.275   5.0500e-02
   5_xyz:   6.680  0.038  0.219 83.797  0.036  2.355   3.3305e-02
   5_adp:   6.680  0.038  0.219 83.797  0.036  2.355   3.3305e-02
   5_occ:   6.680  0.038  0.219 83.797  0.036  2.355   3.3305e-02
   5_bss:   6.680  0.038  0.219 83.797  0.036  2.355   3.3305e-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:  68.89   0.00  16.79  68.89   0.00  12.95  62.35   4.26  37.66
   1_occ:  68.89   0.00  16.79  68.89   0.00  12.95  62.35   4.26  37.66
   2_bss:  68.89   0.00  16.79  68.89   0.00  12.95  62.35   4.26  37.66
   2_xyz:  68.89   0.00  16.79  68.89   0.00  12.95  62.35   4.26  37.66
   2_adp:  68.21   1.63  17.00  64.05   1.63  13.01  68.21   5.87  38.76
   2_occ:  68.21   1.63  17.00  64.05   1.63  13.01  68.21   5.87  38.76
   3_bss:  68.21   1.63  17.00  64.05   1.63  13.01  68.21   5.87  38.76
   3_xyz:  68.21   1.63  17.00  64.05   1.63  13.01  68.21   5.87  38.76
   3_adp:  83.22   0.00  17.23  83.22   0.00  13.04  76.47   2.93  40.04
   3_occ:  83.22   0.00  17.23  83.22   0.00  13.04  76.47   2.93  40.04
   4_bss:  83.22   0.00  17.23  83.22   0.00  13.04  76.47   2.93  40.04
   4_xyz:  83.22   0.00  17.23  83.22   0.00  13.04  76.47   2.93  40.04
   4_adp:  89.27   0.99  17.03  89.27   0.99  12.93  78.75   3.62  39.37
   4_occ:  89.27   0.99  17.03  89.27   0.99  12.93  78.75   3.62  39.37
   5_bss:  89.27   0.99  17.03  89.27   0.99  12.93  78.75   3.62  39.37
   5_xyz:  89.27   0.99  17.03  89.27   0.99  12.93  78.75   3.62  39.37
   5_adp:  85.52   2.05  16.44  85.52   2.05  12.73  77.68   5.74  36.60
   5_occ:  85.52   2.05  16.44  85.52   2.05  12.73  77.68   5.74  36.60
   5_bss:  85.45   1.97  16.36  85.45   1.97  12.66  77.61   5.66  36.53
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.668    0.012    0.267
   1_adp:    1.668    0.012    0.267
   1_occ:    1.668    0.012    0.267
   2_bss:    1.668    0.012    0.267
   2_xyz:    0.992    0.035    0.390
   2_adp:    0.992    0.035    0.390
   2_occ:    0.992    0.035    0.390
   3_bss:    0.992    0.035    0.390
   3_xyz:    1.023    0.043    0.426
   3_adp:    1.023    0.043    0.426
   3_occ:    1.023    0.043    0.426
   4_bss:    1.023    0.043    0.426
   4_xyz:    1.074    0.051    0.445
   4_adp:    1.074    0.051    0.445
   4_occ:    1.074    0.051    0.445
   5_bss:    1.074    0.051    0.445
   5_xyz:    1.156    0.047    0.449
   5_adp:    1.156    0.047    0.449
   5_occ:    1.156    0.047    0.449
   5_bss:    1.156    0.047    0.449
------------------------------------------------------------------------

CPU time actual refinement: 334.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/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_771/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_771/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.08 
  Macro-tasks:
    bulk solvent and scale       = 36.31  
    individual site refinement   = 138.90 
    weights calculation          = 30.00  
    collect and process          = 6.70   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 212.02 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 107.35 
    alpha_beta                      = 8.34   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 116.82 
    fmodel                         = 6.64   
    r_factors                      = 0.21   
    phase_errors                   = 11.17  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 253.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.696 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    664 calls, 107.07 s
gradients_fft:          609 calls, 102.79 s

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

# Date 2008-01-16 Time 05:37:18 PST -0800 (1200490638.34 s)
Start R-work = 0.3490, R-free = 0.3504 (no bulk solvent and anisotropic scale)
Final R-work = 0.1361, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.3338, R-free = 0.3344
Final R-work = 0.1104, R-free = 0.1536