# Date 2008-01-16 Time 05:10:57 PST -0800 (1200489057.81 s)
#phil __OFF__

Command line arguments: "../624.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9932
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 624

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 87.6859, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (70.25, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.96317
Completeness in resolution range: 0.937766
Completeness with d_max=infinity: 0.934991

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9632

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: (70.25, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.96317
Completeness in resolution range: 0.937766
Completeness with d_max=infinity: 0.934991

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2017 [2192/2217]  1972   220  10.0%
  bin  2:  4.2017 -  3.3471 [2108/2128]  1899   209   9.9%
  bin  3:  3.3471 -  2.9275 [2082/2101]  1875   207   9.9%
  bin  4:  2.9275 -  2.6615 [2057/2087]  1846   211  10.3%
  bin  5:  2.6615 -  2.4716 [2057/2076]  1859   198   9.6%
  bin  6:  2.4716 -  2.3264 [2044/2069]  1836   208  10.2%
  bin  7:  2.3264 -  2.2103 [2002/2030]  1799   203  10.1%
  bin  8:  2.2103 -  2.1144 [2041/2077]  1832   209  10.2%
  bin  9:  2.1144 -  2.0332 [2022/2064]  1829   193   9.5%
  bin 10:  2.0332 -  1.9632 [ 984/2040]   883   101  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.78 -     2.41: 38
        2.41 -     3.03: 2124
        3.03 -     3.65: 4683
        3.65 -     4.28: 9108
        4.28 -     4.90: 12419
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.785 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.870 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28367 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_624/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/model_refine_001.geo

CPU time processing inputs: 9.62


============================ 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 = 70.25 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4264   r_free= 0.4277   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.241939                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6869 0.99   1423  157 0.3469 0.3321      6.5277      6.4702|
|  2:  4.6869 -  3.7389 0.99   1374  154 0.3537 0.3601      6.7315      6.6699|
|  3:  3.7389 -  3.2718 0.99   1343  149 0.3847 0.3660      6.6023       6.603|
|  4:  3.2718 -  2.9752 0.99   1343  150 0.4159 0.4511      6.4794      6.5283|
|  5:  2.9752 -  2.7633 0.99   1317  149 0.4533 0.4011      6.3135      6.2955|
|  6:  2.7633 -  2.6013 0.99   1326  144 0.4517 0.4870      6.2177      6.1684|
|  7:  2.6013 -  2.4716 0.99   1325  142 0.4564 0.4475      6.1984       6.147|
|  8:  2.4716 -  2.3644 0.98   1303  152 0.4838 0.4979      6.1538      6.1525|
|  9:  2.3644 -  2.2737 0.98   1294  143 0.4643 0.5078      6.0901      6.1419|
| 10:  2.2737 -  2.1955 1.00   1313  148 0.4892 0.4788      6.0638      6.0703|
| 11:  2.1955 -  2.1271 0.98   1305  145 0.4786 0.5054      6.0087      6.0136|
| 12:  2.1271 -  2.0664 0.98   1281  137 0.4810 0.4464      5.9311      5.9499|
| 13:  2.0664 -  2.0122 0.96   1267  144 0.4720 0.4713      5.8551      5.7928|
| 14:  2.0122 -  1.9632 0.32    416   45 0.5306 0.5222      5.8853      5.8642|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6869  1423   157  0.77  28.40   0.83     0.81      52739.64|
|  2:  4.6869 -  3.7389  1374   154  0.76  29.78   0.92     0.87      82799.62|
|  3:  3.7389 -  3.2718  1343   149  0.66  38.72   0.95     0.84      90574.04|
|  4:  3.2718 -  2.9752  1343   150  0.59  44.87   0.93     0.78      84810.68|
|  5:  2.9752 -  2.7633  1317   149  0.52  50.45   0.92     0.72      65051.51|
|  6:  2.7633 -  2.6013  1326   144  0.50  52.43   0.91     0.68      58372.69|
|  7:  2.6013 -  2.4716  1325   142  0.47  54.74   0.94     0.63      54762.04|
|  8:  2.4716 -  2.3644  1303   152  0.43  57.68   0.93     0.61      52362.27|
|  9:  2.3644 -  2.2737  1294   143  0.43  57.63   0.96     0.61      48415.38|
| 10:  2.2737 -  2.1955  1313   148  0.43  57.79   0.95     0.61      43052.65|
| 11:  2.1955 -  2.1271  1305   145  0.41  59.00   0.97     0.63      43243.63|
| 12:  2.1271 -  2.0664  1281   137  0.40  60.03   0.96     0.62      39542.72|
| 13:  2.0664 -  2.0122  1267   144  0.37  62.09   0.97     0.61      35036.38|
| 14:  2.0122 -  1.9632   416    45  0.43  57.61   0.97     0.61      26696.56|
|alpha:            min =        0.61 max =            0.87 mean =         0.69|
|beta:             min =    26696.56 max =        90574.04 mean =     57287.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.94 mean =        50.15|
|phase err.(test): min =        0.00 max =           89.91 mean =        50.72|
|-----------------------------------------------------------------------------|

============================== 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 = 14.771397             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.903   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.857166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.752   (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 |  1.785 -  2.096:       13 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.096 -  2.408:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.408 -  2.719:      168 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.719 -  3.031:     1956 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.031 -  3.342:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.342 -  3.654:     2792 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.654 -  3.965:     4710 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.965 -  4.277:     4398 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.277 -  4.588:     5650 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6769 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.785 |       0.361 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4264   r_free= 0.4277   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.241939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4137   r_free= 0.4193   ksol= 0.34   Bsol= 41.57   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,2.70,1.70,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.231807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.036467             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.903   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.908274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4137      final r-factor (work) = 0.2757          |
| start r-factor (free) = 0.4193      final r-factor (free) = 0.3152          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6403 = 12.04 * 0.50 * 6.2254 + 1.00 * 0.1746                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.5399 = 12.04 * 0.50 * 6.0478 + 1.00 * 0.1430                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2757      final r-factor (work) = 0.2516          |
| start r-factor (free) = 0.3152      final r-factor (free) = 0.3229          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4993 = 0.91 * 1.00 * 6.0478 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3585 = 0.91 * 1.00 * 5.8459 + 1.00 * 0.0488                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.05   17.45    None  None   None       |
|    all(noH): 2823   0      0.00    66.05   17.45    None  None   None       |
|    Sol.    : 438    0      2.30    66.05   39.12    None  None   None       |
|    Mac.    : 2385   0      0.00    64.40   13.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.605:  475   |   5:    33.024 -  39.628:  107        |
|      1:     6.605 -  13.210:  881   |   6:    39.628 -  46.233:  119        |
|      2:    13.210 -  19.814:  637   |   7:    46.233 -  52.838:   91        |
|      3:    19.814 -  26.419:  286   |   8:    52.838 -  59.443:   48        |
|      4:    26.419 -  33.024:  165   |   9:    59.443 -  66.047:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2516 r_free = 0.3229             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2512 r_free = 0.3229             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2512   r_free= 0.3229   ksol= 0.34   Bsol= 41.57   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,2.70,1.70,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.856008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2484   r_free= 0.3187   ksol= 0.33   Bsol= 53.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-0.47,0.15,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.849292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.649668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.901   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.465360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.048   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2484      final r-factor (work) = 0.1794          |
| start r-factor (free) = 0.3187      final r-factor (free) = 0.2315          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6567 = 5.65 * 0.50 * 5.8461 + 1.00 * 0.1424                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2495 = 5.65 * 0.50 * 5.7268 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1794      final r-factor (work) = 0.1589          |
| start r-factor (free) = 0.2315      final r-factor (free) = 0.2167          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4276 = 1.47 * 1.00 * 5.7268 + 1.00 * 0.0358                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0603 = 1.47 * 1.00 * 5.4911 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.72   18.26    None  None   None       |
|    all(noH): 2823   0      0.00    90.72   18.26    None  None   None       |
|    Sol.    : 438    0      5.39    90.72   45.55    None  None   None       |
|    Mac.    : 2385   0      0.00    87.61   13.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.072:  887   |   5:    45.358 -  54.429:  105        |
|      1:     9.072 -  18.143: 1115   |   6:    54.429 -  63.501:   78        |
|      2:    18.143 -  27.215:  298   |   7:    63.501 -  72.572:   70        |
|      3:    27.215 -  36.286:  144   |   8:    72.572 -  81.644:   26        |
|      4:    36.286 -  45.358:   96   |   9:    81.644 -  90.715:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1589 r_free = 0.2167             target_work(ml) = 5.457         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1588 r_free = 0.2165             target_work(ml) = 5.457         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1588   r_free= 0.2165   ksol= 0.33   Bsol= 53.39   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-0.47,0.15,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.456886                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1585   r_free= 0.2159   ksol= 0.33   Bsol= 61.69   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.48,-0.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.451834                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.015525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.864  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671917              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.589  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1585      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.2159      final r-factor (free) = 0.1846          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0952 = 4.02 * 0.50 * 5.4902 + 1.00 * 0.0722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8565 = 4.02 * 0.50 * 5.3746 + 1.00 * 0.0656                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1846      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6250 = 0.67 * 1.00 * 5.3746 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5486 = 0.67 * 1.00 * 5.2642 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.66   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    92.66   17.71    None  None   None       |
|    Sol.    : 438    0      2.11    92.66   44.56    None  None   None       |
|    Mac.    : 2385   0      0.00    88.98   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.266:  960   |   5:    46.331 -  55.597:   91        |
|      1:     9.266 -  18.532: 1138   |   6:    55.597 -  64.863:   86        |
|      2:    18.532 -  27.799:  255   |   7:    64.863 -  74.130:   51        |
|      3:    27.799 -  37.065:  122   |   8:    74.130 -  83.396:   22        |
|      4:    37.065 -  46.331:   93   |   9:    83.396 -  92.662:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1747             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1237 r_free = 0.1747             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1747   ksol= 0.33   Bsol= 61.69   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.48,-0.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1745   ksol= 0.32   Bsol= 61.69   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-1.98,-0.27,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233496                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.825215              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.354  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.156712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.603  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5029 = 2.83 * 0.50 * 5.2649 + 1.00 * 0.0656                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4228 = 2.83 * 0.50 * 5.2100 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0378 = 1.16 * 1.00 * 5.2100 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9972 = 1.16 * 1.00 * 5.1751 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.36   17.39    None  None   None       |
|    all(noH): 2823   0      0.00    94.36   17.39    None  None   None       |
|    Sol.    : 438    0      0.60    94.36   43.44    None  None   None       |
|    Mac.    : 2385   0      0.00    94.36   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.436: 1022   |   5:    47.179 -  56.615:   94        |
|      1:     9.436 -  18.872: 1113   |   6:    56.615 -  66.051:   65        |
|      2:    18.872 -  28.307:  231   |   7:    66.051 -  75.486:   45        |
|      3:    28.307 -  37.743:  132   |   8:    75.486 -  84.922:   20        |
|      4:    37.743 -  47.179:   93   |   9:    84.922 -  94.358:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1642             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1642             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1642   ksol= 0.32   Bsol= 61.69   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-1.98,-0.27,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171131                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1642   ksol= 0.32   Bsol= 58.20   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.06,-0.27,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.323674              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.419  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.546295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.449  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0754 = 2.32 * 0.50 * 5.1747 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0610 = 2.32 * 0.50 * 5.1652 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9979 = 1.55 * 1.00 * 5.1652 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9864 = 1.55 * 1.00 * 5.1576 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.92   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    99.92   17.12    None  None   None       |
|    Sol.    : 438    0      1.88    94.66   42.54    None  None   None       |
|    Mac.    : 2385   0      0.00    99.92   12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.992: 1180   |   5:    49.959 -  59.951:   85        |
|      1:     9.992 -  19.984: 1015   |   6:    59.951 -  69.942:   59        |
|      2:    19.984 -  29.975:  197   |   7:    69.942 -  79.934:   30        |
|      3:    29.975 -  39.967:  139   |   8:    79.934 -  89.926:   14        |
|      4:    39.967 -  49.959:   98   |   9:    89.926 -  99.918:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1616             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1617             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1617   ksol= 0.32   Bsol= 58.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.06,-0.27,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158271                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6869 0.99   1423  157 0.0938 0.1268      5.3551      5.5668|
|  2:  4.6869 -  3.7389 0.99   1374  154 0.0819 0.1135      5.4198      5.6362|
|  3:  3.7389 -  3.2718 0.99   1343  149 0.1069 0.1525      5.4775      5.8199|
|  4:  3.2718 -  2.9752 0.99   1343  150 0.1238 0.1773       5.464      5.6427|
|  5:  2.9752 -  2.7633 0.99   1317  149 0.1335 0.1752      5.3354      5.5703|
|  6:  2.7633 -  2.6013 0.99   1326  144 0.1243 0.1966       5.216      5.4983|
|  7:  2.6013 -  2.4716 0.99   1325  142 0.1306 0.1559      5.1932      5.3115|
|  8:  2.4716 -  2.3644 0.98   1303  152 0.1178 0.1660      5.0765       5.346|
|  9:  2.3644 -  2.2737 0.98   1294  143 0.1179 0.1833      5.0429      5.3338|
| 10:  2.2737 -  2.1955 1.00   1313  148 0.1099 0.1790      4.9343      5.2345|
| 11:  2.1955 -  2.1271 0.98   1305  145 0.1125 0.1896      4.9481      5.3392|
| 12:  2.1271 -  2.0664 0.98   1281  137 0.1162 0.1737      4.8878      5.1589|
| 13:  2.0664 -  2.0122 0.96   1267  144 0.1081 0.1717      4.7914      5.0158|
| 14:  2.0122 -  1.9632 0.32    416   45 0.1005 0.1678      4.6797      4.9414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6869  1423   157  0.94   9.20   0.97     0.94       7076.83|
|  2:  4.6869 -  3.7389  1374   154  0.95   7.86   1.02     1.00       9117.11|
|  3:  3.7389 -  3.2718  1343   149  0.93  11.64   1.03     1.03      10648.65|
|  4:  3.2718 -  2.9752  1343   150  0.91  14.37   1.01     0.99      10775.41|
|  5:  2.9752 -  2.7633  1317   149  0.90  16.08   1.00     0.98       8631.16|
|  6:  2.7633 -  2.6013  1326   144  0.89  16.99   0.98     0.96       7298.97|
|  7:  2.6013 -  2.4716  1325   142  0.90  16.00   0.99     0.96       6516.35|
|  8:  2.4716 -  2.3644  1303   152  0.90  15.79   0.99     0.96       5513.08|
|  9:  2.3644 -  2.2737  1294   143  0.90  15.89   0.99     0.96       5213.06|
| 10:  2.2737 -  2.1955  1313   148  0.90  15.63   1.00     0.96       4262.95|
| 11:  2.1955 -  2.1271  1305   145  0.90  16.28   0.98     0.93       4381.49|
| 12:  2.1271 -  2.0664  1281   137  0.91  15.96   1.01     1.01       4075.83|
| 13:  2.0664 -  2.0122  1267   144  0.89  17.16   0.99     0.97       3571.29|
| 14:  2.0122 -  1.9632   416    45  0.92  14.02   0.98     0.95       2759.37|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2759.37 max =        10775.41 mean =      6647.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.45|
|phase err.(test): min =        0.00 max =           89.36 mean =        13.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1616   ksol= 0.32   Bsol= 57.10   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.96,-0.08,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1616   ksol= 0.32   Bsol= 57.10   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.96,-0.08,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158320                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6869 0.99   1423  157 0.0938 0.1269      5.3558      5.5681|
|  2:  4.6869 -  3.7389 0.99   1374  154 0.0819 0.1134        5.42      5.6356|
|  3:  3.7389 -  3.2718 0.99   1343  149 0.1069 0.1525      5.4773        5.82|
|  4:  3.2718 -  2.9752 0.99   1343  150 0.1239 0.1774      5.4641      5.6428|
|  5:  2.9752 -  2.7633 0.99   1317  149 0.1335 0.1752      5.3353        5.57|
|  6:  2.7633 -  2.6013 0.99   1326  144 0.1243 0.1966      5.2158      5.4984|
|  7:  2.6013 -  2.4716 0.99   1325  142 0.1307 0.1560      5.1935       5.312|
|  8:  2.4716 -  2.3644 0.98   1303  152 0.1178 0.1660      5.0766      5.3458|
|  9:  2.3644 -  2.2737 0.98   1294  143 0.1179 0.1831       5.043      5.3333|
| 10:  2.2737 -  2.1955 1.00   1313  148 0.1099 0.1792      4.9346      5.2354|
| 11:  2.1955 -  2.1271 0.98   1305  145 0.1124 0.1897      4.9483      5.3399|
| 12:  2.1271 -  2.0664 0.98   1281  137 0.1161 0.1735      4.8876      5.1581|
| 13:  2.0664 -  2.0122 0.96   1267  144 0.1081 0.1715      4.7907      5.0145|
| 14:  2.0122 -  1.9632 0.32    416   45 0.1005 0.1676      4.6789      4.9404|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6869  1423   157  0.94   9.21   0.97     0.94       7086.47|
|  2:  4.6869 -  3.7389  1374   154  0.95   7.87   1.02     1.01       9124.29|
|  3:  3.7389 -  3.2718  1343   149  0.93  11.64   1.04     1.03      10649.09|
|  4:  3.2718 -  2.9752  1343   150  0.91  14.38   1.02     0.99      10775.96|
|  5:  2.9752 -  2.7633  1317   149  0.90  16.08   1.01     0.99       8628.44|
|  6:  2.7633 -  2.6013  1326   144  0.89  16.99   0.99     0.96       7296.62|
|  7:  2.6013 -  2.4716  1325   142  0.90  16.01   1.00     0.96       6518.46|
|  8:  2.4716 -  2.3644  1303   152  0.90  15.80   1.00     0.97       5512.30|
|  9:  2.3644 -  2.2737  1294   143  0.90  15.90   1.00     0.96       5214.88|
| 10:  2.2737 -  2.1955  1313   148  0.90  15.64   1.01     0.97       4267.19|
| 11:  2.1955 -  2.1271  1305   145  0.90  16.30   0.98     0.93       4387.84|
| 12:  2.1271 -  2.0664  1281   137  0.91  15.97   1.02     1.02       4076.94|
| 13:  2.0664 -  2.0122  1267   144  0.89  17.15   1.00     0.98       3566.01|
| 14:  2.0122 -  1.9632   416    45  0.92  14.00   0.98     0.96       2752.54|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2752.54 max =        10775.96 mean =      6648.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.45|
|phase err.(test): min =        0.00 max =           89.34 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.92   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    99.92   17.12    None  None   None       |
|    Sol.    : 438    0      1.88    94.66   42.54    None  None   None       |
|    Mac.    : 2385   0      0.00    99.92   12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.995: 1180   |   5:    49.962 -  59.954:   85        |
|      1:     9.995 -  19.987: 1015   |   6:    59.954 -  69.945:   59        |
|      2:    19.987 -  29.978:  197   |   7:    69.945 -  79.937:   30        |
|      3:    29.978 -  39.970:  139   |   8:    79.937 -  89.929:   14        |
|      4:    39.970 -  49.962:   98   |   9:    89.929 -  99.921:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 4.668
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 300
   mapped sites are within: 0.712 - 4.668

peak=    6.351 closest distance to " NE2 GLN A  11 " =    1.263
peak=    5.589 closest distance to " O   HOH Z 144 " =    1.917
peak=    5.538 closest distance to " NH2 ARG A  56 " =    2.158
peak=    5.521 closest distance to " O   HOH Z 287 " =    2.055
peak=    5.444 closest distance to " O   HOH Z 423 " =    2.013
peak=    5.406 closest distance to " CG  PRO A  54 " =    1.329
peak=    5.361 closest distance to " O   HOH Z   9 " =    1.745
peak=    5.355 closest distance to " O   HOH Z 375 " =    1.183
peak=    5.313 closest distance to " O   HOH Z 417 " =    2.253
peak=    5.242 closest distance to " O   HOH Z 126 " =    2.061
peak=    5.110 closest distance to " O   HOH Z  63 " =    1.651
peak=    4.897 closest distance to " O   HOH Z 232 " =    2.256
peak=    4.885 closest distance to " CB  GLN A 223 " =    1.515
peak=    4.836 closest distance to " CG  PRO A 213 " =    1.273
peak=    4.720 closest distance to " CB  PRO A  54 " =    1.045
peak=    4.673 closest distance to " O   HOH Z 371 " =    2.060
peak=    4.633 closest distance to " CB  ARG A 190 " =    1.627
peak=    4.632 closest distance to " CA  TYR A  30 " =    0.988
peak=    4.607 closest distance to " O   HOH Z 427 " =    2.730
peak=    4.535 closest distance to " O   HOH Z 380 " =    1.921
peak=    4.528 closest distance to " CB  SER A  63 " =    1.306
peak=    4.488 closest distance to " O   HOH Z 298 " =    2.000
peak=    4.477 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.467 closest distance to " CB  ASN A 148 " =    1.420
peak=    4.327 closest distance to " CG2 VAL A 257 " =    0.842
peak=    4.312 closest distance to " CG  PRO A 198 " =    1.302
peak=    4.283 closest distance to " O   HOH Z   1 " =    1.832
peak=    4.251 closest distance to " O   HOH Z   7 " =    1.414
peak=    4.242 closest distance to " CD  ARG A  66 " =    2.174
peak=    4.188 closest distance to " O   HOH Z 327 " =    1.674
peak=    4.184 closest distance to " O   HOH Z   2 " =    1.456
peak=    4.173 closest distance to " CB  ARG A  79 " =    1.362
peak=    4.169 closest distance to " CD  ARG A 159 " =    0.806
peak=    4.153 closest distance to " CB  ARG A 275 " =    0.952
peak=    4.144 closest distance to " O   HOH Z 345 " =    1.920
peak=    4.098 closest distance to " O   HOH Z 406 " =    1.605
peak=    4.096 closest distance to " O   HOH Z  78 " =    1.513
peak=    4.094 closest distance to " OG BSER A 164 " =    2.232
peak=    4.067 closest distance to " CG  TRP A 179 " =    2.127
peak=    4.061 closest distance to " CB  GLU A 277 " =    3.641
peak=    4.054 closest distance to " O   HOH Z 425 " =    1.395
peak=    4.048 closest distance to " O   HOH Z 290 " =    0.954
peak=    4.046 closest distance to " CB  VAL A 265 " =    1.317
peak=    4.042 closest distance to " O   HOH Z  57 " =    2.316
peak=    4.039 closest distance to " O   HOH Z 316 " =    3.059
peak=    4.016 closest distance to " O   HOH Z 371 " =    1.892
peak=    4.010 closest distance to " O   HOH Z 209 " =    2.225
peak=    4.010 closest distance to " O   HOH Z 437 " =    1.608
peak=    3.998 closest distance to " O   HOH Z 133 " =    2.624
peak=    3.994 closest distance to " ND2 ASN A 187 " =    1.482
peak=    3.984 closest distance to " CB  LEU A 228 " =    1.077
peak=    3.975 closest distance to " CZ  PHE A 218 " =    1.040
peak=    3.958 closest distance to " OD1 ASN A  69 " =    2.550
peak=    3.922 closest distance to " O   HOH Z 368 " =    3.695
peak=    3.897 closest distance to " CB  SER A 212 " =    1.136
peak=    3.886 closest distance to " O   HOH Z   1 " =    1.640
peak=    3.879 closest distance to " CB  TRP A 266 " =    1.107
peak=    3.876 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.875 closest distance to " O   HOH Z 158 " =    2.950
peak=    3.872 closest distance to " O   PRO A 198 " =    1.533
peak=    3.871 closest distance to " CG  LEU A 167 " =    1.278
peak=    3.864 closest distance to " O   HOH Z 214 " =    2.254
peak=    3.864 closest distance to " O   HOH Z 145 " =    2.265
peak=    3.860 closest distance to " NH1AARG A 145 " =    1.208
peak=    3.835 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    3.819 closest distance to " CD2 TRP A 179 " =    1.290
peak=    3.812 closest distance to " NZ  LYS A 117 " =    2.926
peak=    3.805 closest distance to " O   HOH Z  97 " =    2.136
peak=    3.805 closest distance to " O   SER A  87 " =    2.214
peak=    3.795 closest distance to " O   HOH Z  61 " =    1.546
peak=    3.794 closest distance to " CB  SER A 216 " =    0.937
peak=    3.794 closest distance to " O   HOH Z 405 " =    1.382
peak=    3.783 closest distance to " O   HOH Z 171 " =    2.831
peak=    3.780 closest distance to " O   HOH Z 128 " =    2.178
peak=    3.759 closest distance to " O   HOH Z 394 " =    1.754
peak=    3.756 closest distance to " O   HOH Z 236 " =    1.384
peak=    3.756 closest distance to " CB  ASN A  39 " =    0.988
peak=    3.756 closest distance to " O   HOH Z 352 " =    1.791
peak=    3.754 closest distance to " NH2AARG A 190 " =    1.874
peak=    3.748 closest distance to " CE  LYS A  76 " =    0.833
peak=    3.748 closest distance to " O   HOH Z 116 " =    3.113
peak=    3.737 closest distance to " O   HOH Z 359 " =    1.391
peak=    3.727 closest distance to " CB  ARG A  79 " =    0.907
peak=    3.726 closest distance to " CA  SER A  87 " =    1.038
peak=    3.720 closest distance to " CD2 LEU A 297 " =    0.964
peak=    3.720 closest distance to " CG  PRO A 243 " =    1.071
peak=    3.718 closest distance to " CB  LYS A 117 " =    1.228
peak=    3.715 closest distance to " O   HOH Z 422 " =    2.607
peak=    3.709 closest distance to " O   HOH Z  40 " =    2.201
peak=    3.705 closest distance to " OG  SER A  62 " =    2.950
peak=    3.699 closest distance to " CB  GLN A  88 " =    1.248
peak=    3.690 closest distance to " CB  GLU A 128 " =    0.957
peak=    3.682 closest distance to " ND2 ASN A 249 " =    0.839
peak=    3.681 closest distance to " O   HOH Z 357 " =    2.021
peak=    3.678 closest distance to " O   HOH Z 272 " =    1.799
peak=    3.678 closest distance to " O   HOH Z 362 " =    2.070
peak=    3.665 closest distance to " O   HOH Z 346 " =    1.637
peak=    3.662 closest distance to " CB  THR A  31 " =    1.790
peak=    3.655 closest distance to " CB  ALA A 114 " =    1.391
peak=    3.651 closest distance to " CA  MET A 105 " =    0.913
peak=    3.648 closest distance to " O   HOH Z 250 " =    1.478
peak=    3.642 closest distance to " O   HOH Z  49 " =    1.142
peak=    3.640 closest distance to " O  BHOH Z  74 " =    1.230
peak=    3.637 closest distance to " O   HOH Z 371 " =    3.172
peak=    3.633 closest distance to " CB  THR A 157 " =    1.153
peak=    3.624 closest distance to " CB  TYR A 169 " =    0.908
peak=    3.619 closest distance to " CG  LYS A  76 " =    1.978
peak=    3.612 closest distance to " CB  VAL A 202 " =    1.602
peak=    3.603 closest distance to " O   HOH Z 389 " =    1.856
peak=    3.602 closest distance to " CA  ALA A 160 " =    0.896
peak=    3.596 closest distance to " O   HOH Z 193 " =    1.670
peak=    3.594 closest distance to " CE  LYS A 119 " =    1.157
peak=    3.594 closest distance to " O   HOH Z 180 " =    2.143
peak=    3.579 closest distance to " O   HOH Z 222 " =    2.309
peak=    3.573 closest distance to " N   GLN A 278 " =    1.302
peak=    3.571 closest distance to " CB  ASP A 124 " =    0.812
peak=    3.571 closest distance to " O   HOH Z 167 " =    1.741
peak=    3.567 closest distance to " CA  ARG A 195 " =    1.245
peak=    3.563 closest distance to " O   HOH Z  88 " =    3.713
peak=    3.562 closest distance to " O   HOH Z  44 " =    1.764
peak=    3.556 closest distance to " CB  ALA A 114 " =    0.818
peak=    3.554 closest distance to " CA  ARG A 102 " =    1.121
peak=    3.552 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.549 closest distance to " CB  SER A   3 " =    1.313
peak=    3.543 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.535 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.535 closest distance to " O   HOH Z 189 " =    2.612
peak=    3.534 closest distance to " CA  SER A  95 " =    0.982
peak=    3.532 closest distance to " NE2 GLN A  73 " =    3.813
peak=    3.530 closest distance to " O   HOH Z 175 " =    2.189
peak=    3.525 closest distance to " CB  ILE A 120 " =    1.409
peak=    3.521 closest distance to " CB  SER A  62 " =    1.119
peak=    3.521 closest distance to " CB  GLU A 152 " =    1.304
peak=    3.517 closest distance to " CA  ASN A 127 " =    1.105
peak=    3.515 closest distance to " O   HOH Z 386 " =    2.864
peak=    3.514 closest distance to " O   HOH Z 274 " =    2.163
peak=    3.508 closest distance to " O   HOH Z  44 " =    2.816
peak=    3.506 closest distance to " O   ASN A  74 " =    1.513
peak=    3.499 closest distance to " O   HOH Z 403 " =    1.419
peak=    3.498 closest distance to " O   HOH Z 132 " =    2.379
peak=    3.495 closest distance to " NH2BARG A 145 " =    2.069
peak=    3.492 closest distance to " CB  SER A  26 " =    1.797
peak=    3.491 closest distance to " CA  ILE A 234 " =    1.027
peak=    3.490 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.488 closest distance to " O   HOH Z  59 " =    1.584
peak=    3.483 closest distance to " O   HOH Z   3 " =    2.014
peak=    3.481 closest distance to " CA  ALA A 158 " =    1.173
peak=    3.474 closest distance to " OG BSER A  99 " =    2.362
peak=    3.472 closest distance to " CD BLYS A 290 " =    1.124
peak=    3.472 closest distance to " O   HOH Z  10 " =    1.666
peak=    3.468 closest distance to " O   HOH Z 258 " =    2.133
peak=    3.468 closest distance to " O   HOH Z  17 " =    1.548
peak=    3.464 closest distance to " CD1 LEU A 300 " =    1.057
peak=    3.463 closest distance to " O   HOH Z 425 " =    1.969
peak=    3.441 closest distance to " O   HOH Z  78 " =    2.010
peak=    3.439 closest distance to " CB  ASN A 110 " =    1.035
peak=    3.438 closest distance to " CB  PRO A  90 " =    1.152
peak=    3.437 closest distance to " CB  ALA A   1 " =    4.668
peak=    3.434 closest distance to " O   HOH Z 344 " =    3.110
peak=    3.429 closest distance to " O   HOH Z 368 " =    1.941
peak=    3.422 closest distance to " N   CYS A 260 " =    0.856
peak=    3.421 closest distance to " O   HOH Z 172 " =    2.342
peak=    3.418 closest distance to " O   HOH Z 286 " =    2.074
peak=    3.418 closest distance to " O   HOH Z 369 " =    1.701
peak=    3.412 closest distance to " CA  GLY A 241 " =    3.938
peak=    3.410 closest distance to " CA  VAL A 125 " =    1.099
peak=    3.409 closest distance to " CB  ASP A 140 " =    0.998
peak=    3.406 closest distance to " N   TYR A 116 " =    1.478
peak=    3.404 closest distance to " O   HOH Z  90 " =    2.101
peak=    3.400 closest distance to " O   HOH Z 392 " =    1.135
peak=    3.399 closest distance to " O   HOH Z  30 " =    1.777
peak=    3.397 closest distance to " O   HOH Z  68 " =    2.013
peak=    3.396 closest distance to " O   HOH Z 227 " =    1.837
peak=    3.394 closest distance to " N   PHE A 130 " =    1.195
peak=    3.392 closest distance to " O   HOH Z 218 " =    1.688
peak=    3.390 closest distance to " O   HOH Z 126 " =    1.440
peak=    3.388 closest distance to " O   HOH Z 432 " =    1.850
peak=    3.384 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.383 closest distance to " CA  ALA A 299 " =    0.875
peak=    3.381 closest distance to " O   HOH Z 234 " =    3.703
peak=    3.379 closest distance to " CB  MET A  47 " =    1.105
peak=    3.372 closest distance to " O   HOH Z 352 " =    1.314
peak=    3.371 closest distance to " CA  ALA A  51 " =    1.003
peak=    3.367 closest distance to " CB  ARG A 138 " =    0.879
peak=    3.366 closest distance to " CB  GLU A  46 " =    1.049
peak=    3.364 closest distance to " O   HOH Z 225 " =    1.487
peak=    3.361 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.359 closest distance to " O   HOH Z  88 " =    3.000
peak=    3.352 closest distance to " CB  ASN A 142 " =    0.925
peak=    3.349 closest distance to " CG  GLN A  89 " =    1.524
peak=    3.346 closest distance to " O   HOH Z 298 " =    2.487
peak=    3.343 closest distance to " CB  ARG A 139 " =    1.138
peak=    3.342 closest distance to " CA  ALA A 129 " =    1.227
peak=    3.341 closest distance to " O   HOH Z 336 " =    1.851
peak=    3.336 closest distance to " OD1BASN A 224 " =    2.379
peak=    3.333 closest distance to " CB  TYR A 116 " =    0.906
peak=    3.328 closest distance to " CG2 ILE A 120 " =    1.268
peak=    3.327 closest distance to " O   HOH Z 365 " =    2.761
peak=    3.327 closest distance to " O   TYR A 116 " =    1.311
peak=    3.326 closest distance to " O   HOH Z 325 " =    2.078
peak=    3.322 closest distance to " CD  ARG A 138 " =    0.835
peak=    3.319 closest distance to " O   HOH Z 145 " =    1.256
peak=    3.319 closest distance to " N   ALA A   1 " =    2.038
peak=    3.313 closest distance to " O   HOH Z 421 " =    2.137
peak=    3.309 closest distance to " O   HOH Z 147 " =    1.719
peak=    3.308 closest distance to " CE1 TYR A 186 " =    1.362
peak=    3.307 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.304 closest distance to " CE3 TRP A  85 " =    0.895
peak=    3.302 closest distance to " O   CYS A 168 " =    1.375
peak=    3.294 closest distance to " N   SER A  97 " =    0.862
peak=    3.293 closest distance to " CB  ASP A 191 " =    1.284
peak=    3.291 closest distance to " CA  LYS A 290 " =    1.294
peak=    3.289 closest distance to " CG2 VAL A 197 " =    1.003
peak=    3.285 closest distance to " O   HOH Z 291 " =    1.507
peak=    3.277 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.272 closest distance to " CB  GLN A  89 " =    1.370
peak=    3.270 closest distance to " O   HOH Z 265 " =    1.847
peak=    3.269 closest distance to " O   HOH Z 130 " =    3.634
peak=    3.267 closest distance to " N   ASN A 127 " =    1.365
peak=    3.266 closest distance to " O   HOH Z 119 " =    4.247
peak=    3.265 closest distance to " O   HOH Z 181 " =    2.134
peak=    3.265 closest distance to " O   HOH Z 373 " =    1.409
peak=    3.262 closest distance to " CB  MET A  40 " =    0.851
peak=    3.262 closest distance to " CA  ASP A 124 " =    0.712
peak=    3.261 closest distance to " CB  LEU A 300 " =    0.880
peak=    3.261 closest distance to " CB  ALA A  21 " =    1.986
peak=    3.260 closest distance to " CA  PHE A 283 " =    1.412
peak=    3.257 closest distance to " CD2 LEU A 255 " =    1.534
peak=    3.255 closest distance to " O   HOH Z 128 " =    1.899
peak=    3.253 closest distance to " O   HOH Z 213 " =    2.501
peak=    3.251 closest distance to " CA  GLU A  46 " =    0.845
peak=    3.247 closest distance to " O   HOH Z 130 " =    2.213
peak=    3.246 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.244 closest distance to " O   HOH Z 244 " =    1.679
peak=    3.243 closest distance to " CB  SER A 210 " =    0.802
peak=    3.240 closest distance to " CA  THR A 221 " =    1.007
peak=    3.239 closest distance to " CA  ASN A 215 " =    1.147
peak=    3.238 closest distance to " CA  GLY A 136 " =    1.060
peak=    3.237 closest distance to " O   HOH Z 185 " =    1.807
peak=    3.232 closest distance to " CA  MET A  40 " =    1.218
peak=    3.231 closest distance to " O   THR A 220 " =    1.446
peak=    3.229 closest distance to " NE2 HIS A 207 " =    1.193
peak=    3.227 closest distance to " O   HOH Z 193 " =    2.177
peak=    3.224 closest distance to " CB  SER A  97 " =    0.864
peak=    3.210 closest distance to " O  BHOH Z 338 " =    2.429
peak=    3.208 closest distance to " O   HOH Z 299 " =    4.365
peak=    3.206 closest distance to " CB  TRP A 150 " =    1.137
peak=    3.206 closest distance to " O   HOH Z  85 " =    2.147
peak=    3.206 closest distance to " CB  PHE A 204 " =    0.894
peak=    3.205 closest distance to " O   HOH Z 280 " =    2.904
peak=    3.199 closest distance to " CB  SER A  99 " =    0.849
peak=    3.197 closest distance to " CB  ASN A 215 " =    1.043
peak=    3.196 closest distance to " O   HOH Z 109 " =    2.329
peak=    3.195 closest distance to " CA  ALA A 233 " =    1.041
peak=    3.191 closest distance to " O   HOH Z 430 " =    1.618
peak=    3.190 closest distance to " O   HOH Z 423 " =    1.612
peak=    3.189 closest distance to " O   HOH Z 116 " =    1.664
peak=    3.186 closest distance to " O   MET A 105 " =    1.792
peak=    3.186 closest distance to " CZ  PHE A  38 " =    1.178
peak=    3.186 closest distance to " O   HOH Z 302 " =    1.631
peak=    3.184 closest distance to " O   HOH Z 394 " =    3.913
peak=    3.174 closest distance to " O   HOH Z 156 " =    2.642
peak=    3.173 closest distance to " CE3 TRP A 150 " =    1.093
peak=    3.172 closest distance to " O   HOH Z 294 " =    1.464
peak=    3.165 closest distance to " CG1BVAL A  72 " =    1.548
peak=    3.158 closest distance to " O   HOH Z 343 " =    3.289
peak=    3.157 closest distance to " O   HOH Z 233 " =    1.749
peak=    3.148 closest distance to " CG1 ILE A 151 " =    1.049
peak=    3.144 closest distance to " CD1AILE A 234 " =    0.910
peak=    3.144 closest distance to " CA  PRO A 280 " =    1.310
peak=    3.139 closest distance to " NE1 TRP A  92 " =    1.658
peak=    3.132 closest distance to " O   HOH Z 128 " =    2.073
peak=    3.128 closest distance to " CA  ARG A  36 " =    1.012
peak=    3.128 closest distance to " O   GLN A 278 " =    1.457
peak=    3.126 closest distance to " OG  SER A  62 " =    2.832
peak=    3.122 closest distance to " O   HOH Z 188 " =    1.432
peak=    3.110 closest distance to " CB  ALA A 248 " =    0.920
peak=    3.104 closest distance to " O   HOH Z 132 " =    3.571
peak=    3.103 closest distance to " N   ARG A 156 " =    1.319
peak=    3.102 closest distance to " OE2 GLU A  44 " =    1.182
peak=    3.099 closest distance to " O   HOH Z 426 " =    1.892
peak=    3.097 closest distance to " NH1BARG A 145 " =    1.171
peak=    3.092 closest distance to " CB  ASP A 171 " =    0.726
peak=    3.090 closest distance to " N   VAL A 296 " =    1.691
peak=    3.087 closest distance to " N   TYR A  15 " =    1.066
peak=    3.086 closest distance to " O   HOH Z 260 " =    2.308
peak=    3.080 closest distance to " O   ARG A 145 " =    1.683
peak=    3.074 closest distance to " NH1 ARG A 138 " =    1.002
peak=    3.051 closest distance to " CB  VAL A 265 " =    1.922
peak=    3.049 closest distance to " O   HOH Z 285 " =    2.138
peak=    3.044 closest distance to " O   THR A 294 " =    1.112
peak=    3.035 closest distance to " O   ASN A 209 " =    1.317
peak=    3.029 closest distance to " O   HOH Z 359 " =    4.238
peak=    3.023 closest distance to " CA  GLY A  35 " =    1.086
peak=    3.018 closest distance to " CB  ARG A  79 " =    0.842

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.743 - 5.950
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 213
   mapped sites are within: 0.743 - 5.950

peak=   -4.701 closest distance to " O   HOH Z 377 " =    1.975
peak=   -4.560 closest distance to " CD  ARG A  14 " =    3.350
peak=   -4.338 closest distance to " OG BSER A 134 " =    1.431
peak=   -4.281 closest distance to " CB  ALA A  43 " =    2.558
peak=   -4.253 closest distance to " CB  PRO A 243 " =    2.624
peak=   -4.120 closest distance to " CD  ARG A 156 " =    2.072
peak=   -4.119 closest distance to " C   HIS A 108 " =    1.204
peak=   -4.111 closest distance to " CA  GLY A  98 " =    1.781
peak=   -4.076 closest distance to " CG  GLN A 223 " =    2.081
peak=   -4.068 closest distance to " CE2 PHE A 218 " =    2.444
peak=   -4.063 closest distance to " O   HOH Z 231 " =    2.139
peak=   -4.054 closest distance to " O   HOH Z 131 " =    4.001
peak=   -4.014 closest distance to " OD1 ASP A 191 " =    1.805
peak=   -4.004 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.984 closest distance to " O   HOH Z 351 " =    1.595
peak=   -3.963 closest distance to " ND2 ASN A 249 " =    2.196
peak=   -3.961 closest distance to " O   SER A 135 " =    1.463
peak=   -3.960 closest distance to " O   HOH Z 266 " =    5.004
peak=   -3.959 closest distance to " O   HOH Z 372 " =    2.552
peak=   -3.951 closest distance to " O   HOH Z  65 " =    1.143
peak=   -3.935 closest distance to " O   HOH Z 198 " =    1.880
peak=   -3.921 closest distance to " O   HOH Z 185 " =    2.151
peak=   -3.902 closest distance to " CD2 TYR A 293 " =    1.791
peak=   -3.882 closest distance to " CD1 LEU A 255 " =    2.869
peak=   -3.876 closest distance to " O   HOH Z  60 " =    2.329
peak=   -3.852 closest distance to " N   THR A 157 " =    1.520
peak=   -3.837 closest distance to " CD2 PHE A  61 " =    1.987
peak=   -3.824 closest distance to " CG2 THR A  18 " =    2.814
peak=   -3.788 closest distance to " CG2 ILE A  49 " =    2.706
peak=   -3.776 closest distance to " O   SER A  22 " =    2.586
peak=   -3.760 closest distance to " O   ARG A 145 " =    1.356
peak=   -3.758 closest distance to " CB  ALA A 291 " =    2.215
peak=   -3.749 closest distance to " CE  MET A 105 " =    2.494
peak=   -3.726 closest distance to " O   HOH Z 298 " =    2.406
peak=   -3.701 closest distance to " O   VAL A  67 " =    2.602
peak=   -3.689 closest distance to " CE BMET A  47 " =    1.303
peak=   -3.683 closest distance to " O   HOH Z 407 " =    3.064
peak=   -3.678 closest distance to " ND2 ASN A 187 " =    1.437
peak=   -3.676 closest distance to " OG  SER A  87 " =    1.286
peak=   -3.671 closest distance to " O   HOH Z  73 " =    2.037
peak=   -3.661 closest distance to " CG  GLN A  58 " =    1.052
peak=   -3.641 closest distance to " O   PHE A 218 " =    1.416
peak=   -3.638 closest distance to " O   PRO A 243 " =    2.438
peak=   -3.637 closest distance to " CB  PHE A 192 " =    1.833
peak=   -3.626 closest distance to " O   HOH Z 389 " =    2.069
peak=   -3.616 closest distance to " O   HOH Z 152 " =    4.766
peak=   -3.615 closest distance to " CB  TYR A  15 " =    2.236
peak=   -3.614 closest distance to " CB  ALA A 158 " =    1.755
peak=   -3.613 closest distance to " CG2 THR A 178 " =    2.204
peak=   -3.612 closest distance to " O   ALA A  10 " =    1.684
peak=   -3.602 closest distance to " CB  ASN A  39 " =    2.287
peak=   -3.589 closest distance to " O   HOH Z 348 " =    2.252
peak=   -3.587 closest distance to " N   ALA A  43 " =    2.655
peak=   -3.585 closest distance to " CZ3 TRP A 179 " =    1.270
peak=   -3.560 closest distance to " CG2 ILE A  20 " =    2.923
peak=   -3.556 closest distance to " O   HOH Z  60 " =    1.836
peak=   -3.548 closest distance to " CB  ALA A   9 " =    2.368
peak=   -3.545 closest distance to " CA  GLY A 203 " =    2.380
peak=   -3.543 closest distance to " CE2 TYR A  30 " =    2.636
peak=   -3.541 closest distance to " CG1 VAL A 112 " =    3.063
peak=   -3.528 closest distance to " O   HOH Z  52 " =    1.381
peak=   -3.525 closest distance to " CZ2 TRP A 274 " =    0.993
peak=   -3.524 closest distance to " CZ  PHE A  59 " =    1.477
peak=   -3.519 closest distance to " CA  GLY A 241 " =    2.208
peak=   -3.511 closest distance to " CB  PRO A 213 " =    2.232
peak=   -3.508 closest distance to " O   HOH Z 174 " =    2.607
peak=   -3.507 closest distance to " ND2 ASN A  60 " =    4.075
peak=   -3.498 closest distance to " O   HOH Z 134 " =    3.649
peak=   -3.493 closest distance to " CD2 LEU A 237 " =    2.825
peak=   -3.493 closest distance to " O   SER A  95 " =    1.462
peak=   -3.481 closest distance to " CE1 PHE A  59 " =    2.126
peak=   -3.480 closest distance to " CG  PHE A 283 " =    2.593
peak=   -3.479 closest distance to " O   PRO A 198 " =    1.366
peak=   -3.479 closest distance to " O   HOH Z 140 " =    1.406
peak=   -3.475 closest distance to " NE2 GLN A 278 " =    1.661
peak=   -3.465 closest distance to " NE  ARG A  36 " =    1.974
peak=   -3.462 closest distance to " CB  ALA A 248 " =    2.333
peak=   -3.459 closest distance to " ND2 ASN A  45 " =    2.087
peak=   -3.454 closest distance to " O   HOH Z 352 " =    2.129
peak=   -3.454 closest distance to " CG2BVAL A  41 " =    1.137
peak=   -3.452 closest distance to " O   HOH Z 286 " =    1.843
peak=   -3.449 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.449 closest distance to " O   HOH Z   1 " =    1.447
peak=   -3.448 closest distance to " O   HOH Z 412 " =    4.223
peak=   -3.441 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.440 closest distance to " CA  GLY A 133 " =    1.986
peak=   -3.439 closest distance to " NH2 ARG A  79 " =    2.185
peak=   -3.437 closest distance to " CB  TRP A  85 " =    2.399
peak=   -3.427 closest distance to " O   HOH Z 211 " =    1.407
peak=   -3.425 closest distance to " O   PRO A 163 " =    1.986
peak=   -3.424 closest distance to " O   HOH Z 313 " =    1.762
peak=   -3.419 closest distance to " O   ALA A 180 " =    1.118
peak=   -3.418 closest distance to " CD2 PHE A 225 " =    1.167
peak=   -3.409 closest distance to " O   HOH Z 290 " =    1.135
peak=   -3.405 closest distance to " CB  ALA A 131 " =    1.950
peak=   -3.405 closest distance to " CE3 TRP A 274 " =    2.317
peak=   -3.404 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.399 closest distance to " ND2 ASN A 285 " =    2.129
peak=   -3.393 closest distance to " O   HOH Z 253 " =    3.879
peak=   -3.389 closest distance to " C   ALA A 114 " =    2.271
peak=   -3.381 closest distance to " CG2 ILE A 263 " =    2.301
peak=   -3.376 closest distance to " CG1 VAL A 250 " =    2.624
peak=   -3.374 closest distance to " O   HOH Z 317 " =    1.349
peak=   -3.373 closest distance to " CB  PRO A  54 " =    2.408
peak=   -3.373 closest distance to " O   HOH Z  39 " =    1.095
peak=   -3.373 closest distance to " O   HOH Z 111 " =    1.972
peak=   -3.369 closest distance to " CG  ASN A  39 " =    1.724
peak=   -3.369 closest distance to " CD1 LEU A 101 " =    2.221
peak=   -3.364 closest distance to " CB  ASP A  27 " =    2.418
peak=   -3.352 closest distance to " CB  ALA A 114 " =    2.460
peak=   -3.350 closest distance to " OG BSER A 134 " =    1.732
peak=   -3.350 closest distance to " O   GLU A 152 " =    1.404
peak=   -3.349 closest distance to " CB  ALA A 248 " =    2.102
peak=   -3.343 closest distance to " CD1 ILE A 239 " =    2.322
peak=   -3.342 closest distance to " CE2 PHE A  61 " =    2.624
peak=   -3.339 closest distance to " CD1 PHE A  59 " =    2.064
peak=   -3.336 closest distance to " ND2 ASN A  45 " =    1.213
peak=   -3.333 closest distance to " OD1 ASN A 187 " =    1.626
peak=   -3.331 closest distance to " O   HOH Z 191 " =    5.520
peak=   -3.329 closest distance to " CG  ARG A 269 " =    2.460
peak=   -3.325 closest distance to " NH2AARG A 275 " =    5.285
peak=   -3.321 closest distance to " CB  ASP A 171 " =    2.291
peak=   -3.321 closest distance to " CB  ALA A 291 " =    1.924
peak=   -3.320 closest distance to " O   TYR A 186 " =    1.622
peak=   -3.318 closest distance to " O   HOH Z 318 " =    1.821
peak=   -3.312 closest distance to " O   HOH Z 103 " =    1.669
peak=   -3.308 closest distance to " CA  ASN A 127 " =    1.316
peak=   -3.302 closest distance to " O   HOH Z  38 " =    1.785
peak=   -3.302 closest distance to " OH  TYR A 172 " =    1.875
peak=   -3.301 closest distance to " OD1 ASP A 171 " =    1.574
peak=   -3.299 closest distance to " O   HOH Z  15 " =    1.568
peak=   -3.297 closest distance to " O   HOH Z 292 " =    1.524
peak=   -3.296 closest distance to " O   HOH Z   9 " =    1.684
peak=   -3.293 closest distance to " CG  LEU A  83 " =    1.998
peak=   -3.293 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.291 closest distance to " OE1 GLN A 183 " =    1.550
peak=   -3.285 closest distance to " O   HOH Z 147 " =    2.007
peak=   -3.282 closest distance to " O   HOH Z  63 " =    2.318
peak=   -3.270 closest distance to " O   HOH Z 281 " =    2.696
peak=   -3.270 closest distance to " OE1 GLN A  88 " =    1.234
peak=   -3.268 closest distance to " O   HOH Z 359 " =    3.264
peak=   -3.258 closest distance to " CB  ALA A  10 " =    2.270
peak=   -3.257 closest distance to " OD2 ASP A 191 " =    1.394
peak=   -3.252 closest distance to " O   ALA A 161 " =    1.569
peak=   -3.251 closest distance to " O   HOH Z 283 " =    5.950
peak=   -3.251 closest distance to " OD1 ASN A 148 " =    1.522
peak=   -3.250 closest distance to " O   HOH Z  49 " =    1.232
peak=   -3.248 closest distance to " CB  CYS A 254 " =    2.133
peak=   -3.240 closest distance to " CA  GLY A  57 " =    2.153
peak=   -3.237 closest distance to " O   HOH Z 384 " =    3.059
peak=   -3.232 closest distance to " CD  LYS A 289 " =    2.343
peak=   -3.229 closest distance to " O   VAL A 189 " =    2.556
peak=   -3.225 closest distance to " O   HOH Z 114 " =    2.859
peak=   -3.218 closest distance to " CG  GLN A 240 " =    2.311
peak=   -3.217 closest distance to " O   HOH Z 216 " =    1.535
peak=   -3.211 closest distance to " CA  GLY A 241 " =    3.057
peak=   -3.210 closest distance to " O   HOH Z 100 " =    1.314
peak=   -3.209 closest distance to " O   HOH Z 166 " =    1.949
peak=   -3.209 closest distance to " O   HOH Z  90 " =    2.478
peak=   -3.208 closest distance to " O   HOH Z 166 " =    1.200
peak=   -3.208 closest distance to " CG  PRO A 163 " =    2.735
peak=   -3.199 closest distance to " CB  PRO A 163 " =    2.475
peak=   -3.199 closest distance to " OE2 GLU A 152 " =    1.218
peak=   -3.196 closest distance to " O   GLN A 240 " =    1.866
peak=   -3.196 closest distance to " N   SER A 212 " =    1.993
peak=   -3.191 closest distance to " O   HOH Z  60 " =    1.536
peak=   -3.191 closest distance to " O   HOH Z 165 " =    2.364
peak=   -3.186 closest distance to " N   GLN A  58 " =    1.352
peak=   -3.184 closest distance to " O   HOH Z 339 " =    1.873
peak=   -3.183 closest distance to " CE3 TRP A 150 " =    2.271
peak=   -3.183 closest distance to " O   HOH Z 200 " =    3.467
peak=   -3.182 closest distance to " O   HOH Z 218 " =    3.777
peak=   -3.182 closest distance to " NE1 TRP A 266 " =    1.980
peak=   -3.175 closest distance to " O   HOH Z 295 " =    1.746
peak=   -3.173 closest distance to " OD2 ASP A 171 " =    1.775
peak=   -3.171 closest distance to " N   LYS A 166 " =    1.742
peak=   -3.170 closest distance to " CG2 ILE A 151 " =    2.574
peak=   -3.167 closest distance to " C   LEU A 222 " =    0.743
peak=   -3.163 closest distance to " O   ALA A 292 " =    2.120
peak=   -3.163 closest distance to " O   HOH Z 337 " =    1.621
peak=   -3.162 closest distance to " NH2 ARG A 219 " =    1.759
peak=   -3.155 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.153 closest distance to " O   HOH Z 374 " =    1.802
peak=   -3.146 closest distance to " CD2 TYR A 293 " =    2.102
peak=   -3.144 closest distance to " O   VAL A 174 " =    2.252
peak=   -3.143 closest distance to " C   LEU A 143 " =    1.215
peak=   -3.141 closest distance to " OG  SER A  63 " =    1.264
peak=   -3.141 closest distance to " N   ALA A 248 " =    1.459
peak=   -3.139 closest distance to " NH1AARG A 275 " =    1.938
peak=   -3.137 closest distance to " O   ILE A  49 " =    1.675
peak=   -3.137 closest distance to " N   ASP A 171 " =    2.413
peak=   -3.136 closest distance to " CD2 HIS A 207 " =    2.277
peak=   -3.133 closest distance to " OG1 THR A  82 " =    1.887
peak=   -3.132 closest distance to " CG1 VAL A 112 " =    2.564
peak=   -3.132 closest distance to " CB  ASP A 286 " =    2.296
peak=   -3.132 closest distance to " O   ASN A 249 " =    1.628
peak=   -3.126 closest distance to " SG BCYS A 201 " =    2.019
peak=   -3.125 closest distance to " ND2BASN A 224 " =    1.706
peak=   -3.123 closest distance to " O   HOH Z 346 " =    1.762
peak=   -3.114 closest distance to " O   ALA A  51 " =    1.269
peak=   -3.104 closest distance to " O   HOH Z 189 " =    2.027
peak=   -3.103 closest distance to " CB  GLN A  11 " =    1.882
peak=   -3.095 closest distance to " N   VAL A 232 " =    2.162
peak=   -3.094 closest distance to " CZ  PHE A  16 " =    2.254
peak=   -3.088 closest distance to " CB  ALA A   7 " =    2.027
peak=   -3.085 closest distance to " O   TRP A  70 " =    1.429
peak=   -3.085 closest distance to " CB  SER A 210 " =    1.112
peak=   -3.077 closest distance to " CD2 PHE A 130 " =    2.960
peak=   -3.076 closest distance to " O   HOH Z  68 " =    1.384
peak=   -3.050 closest distance to " O   HOH Z 350 " =    1.869
peak=   -3.035 closest distance to " O   HOH Z 377 " =    1.346
peak=   -3.025 closest distance to " O   HOH Z 193 " =    1.586
peak=   -3.018 closest distance to " CA  GLY A 133 " =    2.205

================= 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    :  0.4264 0.4277   6.241939e+00   6.228830e+00
   1_bss:  0.4137 0.4193   6.231807e+00   6.215685e+00
   1_xyz:  0.2757 0.3152   5.905706e+00   5.992661e+00
   1_adp:  0.2516 0.3229   5.856465e+00   6.016097e+00
   1_occ:  0.2512 0.3229   5.856008e+00   6.016101e+00
   2_bss:  0.2484 0.3187   5.849292e+00   6.009647e+00
   2_xyz:  0.1794 0.2315   5.548230e+00   5.746542e+00
   2_adp:  0.1589 0.2167   5.457379e+00   5.681084e+00
   2_occ:  0.1588 0.2165   5.456886e+00   5.680731e+00
   3_bss:  0.1585 0.2159   5.451834e+00   5.676094e+00
   3_xyz:  0.1305 0.1846   5.284557e+00   5.528791e+00
   3_adp:  0.1237 0.1747   5.233842e+00   5.474789e+00
   3_occ:  0.1237 0.1747   5.233700e+00   5.474542e+00
   4_bss:  0.1240 0.1745   5.233496e+00   5.472927e+00
   4_xyz:  0.1165 0.1656   5.182478e+00   5.430085e+00
   4_adp:  0.1142 0.1642   5.171214e+00   5.422493e+00
   4_occ:  0.1141 0.1642   5.171131e+00   5.422448e+00
   5_bss:  0.1141 0.1642   5.170898e+00   5.422229e+00
   5_xyz:  0.1125 0.1618   5.160495e+00   5.414027e+00
   5_adp:  0.1118 0.1616   5.157980e+00   5.414099e+00
   5_occ:  0.1117 0.1617   5.158271e+00   5.414548e+00
   5_bss:  0.1117 0.1616   5.158320e+00   5.414538e+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:  0.336  41.570  -3.298   2.698   1.698   0.000   0.000   0.000
   1_xyz:  0.336  41.570  -3.298   2.698   1.698   0.000   0.000   0.000
   1_adp:  0.336  41.570  -3.298   2.698   1.698   0.000   0.000   0.000
   1_occ:  0.336  41.570  -3.298   2.698   1.698   0.000   0.000   0.000
   2_bss:  0.332  53.392  -2.548  -0.466   0.147  -0.000   0.000   0.000
   2_xyz:  0.332  53.392  -2.548  -0.466   0.147  -0.000   0.000   0.000
   2_adp:  0.332  53.392  -2.548  -0.466   0.147  -0.000   0.000   0.000
   2_occ:  0.332  53.392  -2.548  -0.466   0.147  -0.000   0.000   0.000
   3_bss:  0.328  61.688  -2.250  -1.475  -0.117  -0.000  -0.000  -0.000
   3_xyz:  0.328  61.688  -2.250  -1.475  -0.117  -0.000  -0.000  -0.000
   3_adp:  0.328  61.688  -2.250  -1.475  -0.117  -0.000  -0.000  -0.000
   3_occ:  0.328  61.688  -2.250  -1.475  -0.117  -0.000  -0.000  -0.000
   4_bss:  0.324  61.688  -2.240  -1.978  -0.267  -0.000  -0.000  -0.000
   4_xyz:  0.324  61.688  -2.240  -1.978  -0.267  -0.000  -0.000  -0.000
   4_adp:  0.324  61.688  -2.240  -1.978  -0.267  -0.000  -0.000  -0.000
   4_occ:  0.324  61.688  -2.240  -1.978  -0.267  -0.000  -0.000  -0.000
   5_bss:  0.319  58.201  -2.133  -2.065  -0.266  -0.000  -0.000  -0.000
   5_xyz:  0.319  58.201  -2.133  -2.065  -0.266  -0.000  -0.000  -0.000
   5_adp:  0.319  58.201  -2.133  -2.065  -0.266  -0.000  -0.000  -0.000
   5_occ:  0.319  58.201  -2.133  -2.065  -0.266  -0.000  -0.000  -0.000
   5_bss:  0.318  57.102  -1.926  -1.961  -0.083  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.210 0.5184  0.6928    57291.988
   1_bss:  49.297 0.5282  0.7184    54774.839
   1_xyz:  31.913 0.7375  0.9438    25837.907
   1_adp:  33.176 0.7222  0.9267    27446.112
   1_occ:  33.236 0.7215  0.9255    27468.845
   2_bss:  32.665 0.7279  0.8930    26766.389
   2_xyz:  22.852 0.8325  0.9781    13600.056
   2_adp:  20.894 0.8526  0.9805    11843.617
   2_occ:  20.887 0.8526  0.9802    11824.887
   3_bss:  20.713 0.8542  0.9702    11638.206
   3_xyz:  17.261 0.8862  0.9882     8441.856
   3_adp:  15.928 0.8987  0.9860     7653.051
   3_occ:  15.926 0.8987  0.9858     7645.760
   4_bss:  15.898 0.8990  0.9785     7634.294
   4_xyz:  14.810 0.9083  0.9834     6881.119
   4_adp:  14.602 0.9103  0.9787     6788.433
   4_occ:  14.605 0.9102  0.9786     6786.675
   5_bss:  14.603 0.9102  0.9788     6784.760
   5_xyz:  14.415 0.9119  0.9780     6662.986
   5_adp:  14.381 0.9122  0.9713     6641.671
   5_occ:  14.393 0.9121  0.9712     6647.341
   5_bss:  14.396 0.9121  0.9770     6648.933
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7457e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7457e-01
   1_xyz:   1.653  0.013  0.109 16.429  0.007  4.110   1.4295e-01
   1_adp:   1.653  0.013  0.109 16.429  0.007  4.110   1.4295e-01
   1_occ:   1.653  0.013  0.109 16.429  0.007  4.110   1.4295e-01
   2_bss:   1.653  0.013  0.109 16.429  0.007  4.110   1.4295e-01
   2_xyz:   1.148  0.008  0.077 15.242  0.005  4.123   7.2202e-02
   2_adp:   1.148  0.008  0.077 15.242  0.005  4.123   7.2202e-02
   2_occ:   1.148  0.008  0.077 15.242  0.005  4.123   7.2202e-02
   3_bss:   1.148  0.008  0.077 15.242  0.005  4.123   7.2202e-02
   3_xyz:   1.045  0.008  0.076 15.161  0.004  4.129   6.5625e-02
   3_adp:   1.045  0.008  0.076 15.161  0.004  4.129   6.5625e-02
   3_occ:   1.045  0.008  0.076 15.161  0.004  4.129   6.5625e-02
   4_bss:   1.045  0.008  0.076 15.161  0.004  4.129   6.5625e-02
   4_xyz:   1.029  0.008  0.077 14.963  0.004  4.110   6.3181e-02
   4_adp:   1.029  0.008  0.077 14.963  0.004  4.110   6.3181e-02
   4_occ:   1.029  0.008  0.077 14.963  0.004  4.110   6.3181e-02
   5_bss:   1.029  0.008  0.077 14.963  0.004  4.110   6.3181e-02
   5_xyz:   0.991  0.007  0.075 14.842  0.004  4.112   5.9932e-02
   5_adp:   0.991  0.007  0.075 14.842  0.004  4.112   5.9932e-02
   5_occ:   0.991  0.007  0.075 14.842  0.004  4.112   5.9932e-02
   5_bss:   0.991  0.007  0.075 14.842  0.004  4.112   5.9932e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.785   2.4077e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.785   2.4077e-01
   1_xyz:  15.929  0.073  0.340 83.955  0.064  2.064   1.1929e-01
   1_adp:  15.929  0.073  0.340 83.955  0.064  2.064   1.1929e-01
   1_occ:  15.929  0.073  0.340 83.955  0.064  2.064   1.1929e-01
   2_bss:  15.929  0.073  0.340 83.955  0.064  2.064   1.1929e-01
   2_xyz:   6.786  0.041  0.294 81.486  0.043  2.308   6.5667e-02
   2_adp:   6.786  0.041  0.294 81.486  0.043  2.308   6.5667e-02
   2_occ:   6.786  0.041  0.294 81.486  0.043  2.308   6.5667e-02
   3_bss:   6.786  0.041  0.294 81.486  0.043  2.308   6.5667e-02
   3_xyz:   6.716  0.047  0.251 85.407  0.036  2.302   5.2539e-02
   3_adp:   6.716  0.047  0.251 85.407  0.036  2.302   5.2539e-02
   3_occ:   6.716  0.047  0.251 85.407  0.036  2.302   5.2539e-02
   4_bss:   6.716  0.047  0.251 85.407  0.036  2.302   5.2539e-02
   4_xyz:   6.988  0.042  0.254 83.454  0.041  2.316   4.6968e-02
   4_adp:   6.988  0.042  0.254 83.454  0.041  2.316   4.6968e-02
   4_occ:   6.988  0.042  0.254 83.454  0.041  2.316   4.6968e-02
   5_bss:   6.988  0.042  0.254 83.454  0.041  2.316   4.6968e-02
   5_xyz:   6.755  0.047  0.245 84.366  0.041  2.334   5.2847e-02
   5_adp:   6.755  0.047  0.245 84.366  0.041  2.334   5.2847e-02
   5_occ:   6.755  0.047  0.245 84.366  0.041  2.334   5.2847e-02
   5_bss:   6.755  0.047  0.245 84.366  0.041  2.334   5.2847e-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:  66.05   0.00  17.45  64.40   0.00  13.46  66.05   2.30  39.12
   1_occ:  66.05   0.00  17.45  64.40   0.00  13.46  66.05   2.30  39.12
   2_bss:  66.05   0.00  17.45  64.40   0.00  13.46  66.05   2.30  39.12
   2_xyz:  66.05   0.00  17.45  64.40   0.00  13.46  66.05   2.30  39.12
   2_adp:  90.72   0.00  18.26  87.61   0.00  13.25  90.72   5.39  45.55
   2_occ:  90.72   0.00  18.26  87.61   0.00  13.25  90.72   5.39  45.55
   3_bss:  90.72   0.00  18.26  87.61   0.00  13.25  90.72   5.39  45.55
   3_xyz:  90.72   0.00  18.26  87.61   0.00  13.25  90.72   5.39  45.55
   3_adp:  92.66   0.00  17.71  88.98   0.00  12.77  92.66   2.11  44.56
   3_occ:  92.66   0.00  17.71  88.98   0.00  12.77  92.66   2.11  44.56
   4_bss:  92.66   0.00  17.71  88.98   0.00  12.77  92.66   2.11  44.56
   4_xyz:  92.66   0.00  17.71  88.98   0.00  12.77  92.66   2.11  44.56
   4_adp:  94.36   0.00  17.39  94.36   0.00  12.61  94.36   0.60  43.44
   4_occ:  94.36   0.00  17.39  94.36   0.00  12.61  94.36   0.60  43.44
   5_bss:  94.36   0.00  17.39  94.36   0.00  12.61  94.36   0.60  43.44
   5_xyz:  94.36   0.00  17.39  94.36   0.00  12.61  94.36   0.60  43.44
   5_adp:  99.92   0.00  17.12  99.92   0.00  12.45  94.66   1.88  42.54
   5_occ:  99.92   0.00  17.12  99.92   0.00  12.45  94.66   1.88  42.54
   5_bss:  99.92   0.00  17.12  99.92   0.00  12.45  94.66   1.88  42.54
------------------------------------------------------------------------
 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:    1.483    0.020    0.495
   1_adp:    1.483    0.020    0.495
   1_occ:    1.483    0.020    0.495
   2_bss:    1.483    0.020    0.495
   2_xyz:    1.306    0.033    0.590
   2_adp:    1.306    0.033    0.590
   2_occ:    1.306    0.033    0.590
   3_bss:    1.306    0.033    0.590
   3_xyz:    1.296    0.055    0.660
   3_adp:    1.296    0.055    0.660
   3_occ:    1.296    0.055    0.660
   4_bss:    1.296    0.055    0.660
   4_xyz:    1.480    0.075    0.681
   4_adp:    1.480    0.075    0.681
   4_occ:    1.480    0.075    0.681
   5_bss:    1.480    0.075    0.681
   5_xyz:    1.515    0.087    0.693
   5_adp:    1.515    0.087    0.693
   5_occ:    1.515    0.087    0.693
   5_bss:    1.515    0.087    0.693
------------------------------------------------------------------------

CPU time actual refinement: 322.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/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_624/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_624/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.90 
  Macro-tasks:
    bulk solvent and scale       = 38.84  
    individual site refinement   = 131.06 
    weights calculation          = 29.57  
    collect and process          = 6.49   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 206.09 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 101.97 
    alpha_beta                      = 8.07   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.30 
    fmodel                         = 6.46   
    r_factors                      = 0.19   
    phase_errors                   = 10.52  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 240.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.627 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    625 calls, 101.54 s
gradients_fft:          570 calls,  97.26 s

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

# Date 2008-01-16 Time 05:16:31 PST -0800 (1200489391.61 s)
Start R-work = 0.4264, R-free = 0.4277 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.4137, R-free = 0.4193
Final R-work = 0.1117, R-free = 0.1616