# Date 2008-01-16 Time 04:43:47 PST -0800 (1200487427.39 s)
#phil __OFF__

Command line arguments: "../436.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10766
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 436

-------------------------------------------------------------------------------
  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: (69.5475, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.9807
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.95083

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9236
                             d_min =   1.9807

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: (69.5475, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.9807
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.95083

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9240 -  4.2378 [2167/2194]  1948   219  10.1%
  bin  2:  4.2378 -  3.3765 [2061/2077]  1858   203   9.8%
  bin  3:  3.3765 -  2.9534 [2053/2072]  1847   206  10.0%
  bin  4:  2.9534 -  2.6851 [2023/2053]  1823   200   9.9%
  bin  5:  2.6851 -  2.4936 [2005/2024]  1800   205  10.2%
  bin  6:  2.4936 -  2.3472 [2015/2051]  1814   201  10.0%
  bin  7:  2.3472 -  2.2300 [1987/2020]  1793   194   9.8%
  bin  8:  2.2300 -  2.1332 [1988/2023]  1784   204  10.3%
  bin  9:  2.1332 -  2.0513 [1976/2003]  1782   194   9.8%
  bin 10:  2.0513 -  1.9807 [1314/2021]  1181   133  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2198
        3.04 -     3.66: 4636
        3.66 -     4.28: 9031
        4.28 -     4.90: 12348
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.864 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.979 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.045 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  2.083 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28227 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_436/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 69.5475 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2925   r_free= 0.2837   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.945361                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.2587 0.2672      6.2885      6.2828|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.2194 0.1973      6.2838      6.2316|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.2551 0.2343      6.2374      6.2184|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.2691 0.2994      6.1082      6.1627|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.3033 0.2426      5.9973      5.8801|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.3111 0.3345      5.9246      5.8978|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.3013 0.2685      5.8718      5.8003|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.3250 0.3027      5.9009      5.8372|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.3248 0.2900       5.805      5.7219|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.3323 0.3018      5.8359      5.6882|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.3377 0.3475      5.7748      5.8129|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.3391 0.3640      5.7052       5.839|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.3521 0.3388      5.6588      5.5975|
| 14:  2.0301 -  1.9807 0.53    683   77 0.3482 0.3405      5.6238      5.5501|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.80  25.22   0.87     0.81      39528.27|
|  2:  4.7264 -  3.7714  1350   153  0.87  19.25   0.99     0.93      35521.73|
|  3:  3.7714 -  3.3005  1317   146  0.85  21.20   1.00     0.97      31402.62|
|  4:  3.3005 -  3.0015  1309   137  0.83  23.66   1.00     0.95      27771.39|
|  5:  3.0015 -  2.7878  1309   152  0.77  28.72   1.01     0.93      23647.76|
|  6:  2.7878 -  2.6244  1302   144  0.77  29.52   1.01     0.93      20609.61|
|  7:  2.6244 -  2.4936  1287   146  0.78  28.36   1.03     0.95      17895.33|
|  8:  2.4936 -  2.3855  1303   141  0.79  27.37   1.02     0.97      16203.02|
|  9:  2.3855 -  2.2940  1283   145  0.79  27.82   1.04     0.99      14645.71|
| 10:  2.2940 -  2.2151  1270   138  0.78  29.16   1.07     0.99      14456.70|
| 11:  2.2151 -  2.1460  1281   145  0.76  30.98   1.04     1.01      15343.89|
| 12:  2.1460 -  2.0849  1276   137  0.73  33.46   1.06     1.00      15825.32|
| 13:  2.0849 -  2.0301  1258   143  0.71  34.71   1.05     0.98      14576.70|
| 14:  2.0301 -  1.9807   683    77  0.72  34.04   1.05     0.94      11871.89|
|alpha:            min =        0.81 max =            1.01 mean =         0.95|
|beta:             min =    11871.89 max =        39528.27 mean =     21920.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           90.00 mean =        27.82|
|phase err.(test): min =        0.00 max =           89.91 mean =        27.53|
|-----------------------------------------------------------------------------|

============================== 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 = 4.474772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.574   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.453496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.342   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2010 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1847 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2789 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4650 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4381 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5631 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6717 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.194 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2925   r_free= 0.2837   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.945361                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2790   r_free= 0.2698   ksol= 0.32   Bsol= 50.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.89,0.49,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.915910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.081341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.198   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2790      final r-factor (work) = 0.1480          |
| start r-factor (free) = 0.2698      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2813 = 4.08 * 0.50 * 5.9380 + 1.00 * 0.1639                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4495 = 4.08 * 0.50 * 5.5776 + 1.00 * 0.0674                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1480      final r-factor (work) = 0.1398          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1663          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4583 = 0.26 * 1.00 * 5.5776 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5704 = 0.26 * 1.00 * 5.2788 + 1.00 * 0.1975                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.73   16.22    None  None   None       |
|    all(noH): 2823   0      0.00    81.73   16.22    None  None   None       |
|    Sol.    : 438    0      7.07    62.68   37.05    None  None   None       |
|    Mac.    : 2385   0      0.00    81.73   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.173:  450   |   5:    40.866 -  49.039:  100        |
|      1:     8.173 -  16.346: 1594   |   6:    49.039 -  57.212:   74        |
|      2:    16.346 -  24.520:  313   |   7:    57.212 -  65.385:   23        |
|      3:    24.520 -  32.693:  147   |   8:    65.385 -  73.559:    0        |
|      4:    32.693 -  40.866:  121   |   9:    73.559 -  81.732:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1398 r_free = 0.1663             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1665             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1665   ksol= 0.32   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.89,0.49,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.278687                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1652   ksol= 0.32   Bsol= 53.11   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-2.51,-1.01,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.278904                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.291873              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.612  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.060877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.463   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1386      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1502          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4920 = 1.29 * 0.50 * 5.3018 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4247 = 1.29 * 0.50 * 5.2213 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1502      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5788 = 1.06 * 1.00 * 5.2213 + 1.00 * 0.0396                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4679 = 1.06 * 1.00 * 5.1455 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    81.43   17.19    None  None   None       |
|    all(noH): 2823   0      0.74    81.43   17.19    None  None   None       |
|    Sol.    : 438    0      2.41    75.15   40.03    None  None   None       |
|    Mac.    : 2385   0      0.74    81.43   12.99    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:     0.740 -   8.809:  707   |   5:    41.085 -  49.154:   98        |
|      1:     8.809 -  16.878: 1319   |   6:    49.154 -  57.223:   90        |
|      2:    16.878 -  24.947:  295   |   7:    57.223 -  65.292:   48        |
|      3:    24.947 -  33.016:  119   |   8:    65.292 -  73.361:   26        |
|      4:    33.016 -  41.085:  116   |   9:    73.361 -  81.430:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1540             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1540             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1540   ksol= 0.32   Bsol= 53.11   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-2.51,-1.01,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159553                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1537   ksol= 0.33   Bsol= 56.48   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.21,-0.94,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159374                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.238794              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.253  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.562  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8128 = 2.24 * 0.50 * 5.1464 + 1.00 * 0.0520                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8037 = 2.24 * 0.50 * 5.1292 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1200 = 0.22 * 1.00 * 5.1292 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1182 = 0.22 * 1.00 * 5.1278 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    81.29   16.61    None  None   None       |
|    all(noH): 2823   0      1.34    81.29   16.61    None  None   None       |
|    Sol.    : 438    0      3.69    72.49   37.86    None  None   None       |
|    Mac.    : 2385   0      1.34    81.29   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.344 -   9.339:  874   |   5:    41.318 -  49.313:   98        |
|      1:     9.339 -  17.334: 1187   |   6:    49.313 -  57.308:   77        |
|      2:    17.334 -  25.329:  287   |   7:    57.308 -  65.303:   35        |
|      3:    25.329 -  33.324:  119   |   8:    65.303 -  73.298:   10        |
|      4:    33.324 -  41.318:  134   |   9:    73.298 -  81.293:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1520             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1520             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1520   ksol= 0.33   Bsol= 56.48   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.21,-0.94,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122100                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1512   ksol= 0.33   Bsol= 56.48   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.05,-0.80,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.314360              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.888  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.107907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.511  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4325 = 1.31 * 0.50 * 5.1287 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4221 = 1.31 * 0.50 * 5.1300 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5613 = 0.11 * 1.00 * 5.1300 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5616 = 0.11 * 1.00 * 5.1452 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.83    78.03   16.12    None  None   None       |
|    all(noH): 2823   0      1.83    78.03   16.12    None  None   None       |
|    Sol.    : 438    0      5.72    69.23   35.84    None  None   None       |
|    Mac.    : 2385   0      1.83    78.03   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.830 -   9.450:  898   |   5:    39.930 -  47.551:   96        |
|      1:     9.450 -  17.070: 1170   |   6:    47.551 -  55.171:   70        |
|      2:    17.070 -  24.690:  283   |   7:    55.171 -  62.791:   27        |
|      3:    24.690 -  32.310:  127   |   8:    62.791 -  70.411:    9        |
|      4:    32.310 -  39.930:  141   |   9:    70.411 -  78.031:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1532             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1532             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1532   ksol= 0.33   Bsol= 56.48   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.05,-0.80,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1532   ksol= 0.33   Bsol= 56.48   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.03,-0.78,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145402                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.519723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.053  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.685635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.877  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9603 = 1.52 * 0.50 * 5.1452 + 1.00 * 0.0507                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9579 = 1.52 * 0.50 * 5.1372 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.0773 = 4.69 * 1.00 * 5.1372 + 1.00 * 0.0064                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.0380 = 4.69 * 1.00 * 5.1281 + 1.00 * 0.0094                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.46   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    85.46   16.66    None  None   None       |
|    Sol.    : 438    0      5.42    75.30   39.10    None  None   None       |
|    Mac.    : 2385   0      0.00    85.46   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.546:  742   |   5:    42.730 -  51.276:  117        |
|      1:     8.546 -  17.092: 1315   |   6:    51.276 -  59.822:   78        |
|      2:    17.092 -  25.638:  284   |   7:    59.822 -  68.368:   33        |
|      3:    25.638 -  34.184:  129   |   8:    68.368 -  76.914:   12        |
|      4:    34.184 -  42.730:  110   |   9:    76.914 -  85.460:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1556             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1556             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1556   ksol= 0.33   Bsol= 56.48   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.03,-0.78,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135117                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.0993 0.1258      5.3869      5.5217|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.0854 0.1072       5.431      5.5961|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.1044 0.1510      5.4581      5.8443|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.1173 0.1502      5.4221      5.5819|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.1290 0.1570      5.2982      5.4744|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.1221 0.2064      5.1978      5.4984|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.1224 0.1569      5.1477      5.3028|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.1108 0.1643      5.0534      5.3058|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.1186 0.1909      5.0252      5.3405|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.1102 0.1558       4.951      5.1321|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.1114 0.1805      4.9239       5.281|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.1099 0.1690      4.8694      5.2048|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.1076 0.1760      4.7774      5.0205|
| 14:  2.0301 -  1.9807 0.53    683   77 0.0976 0.1798      4.6611      4.9621|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.94   9.05   0.97     0.94       7042.89|
|  2:  4.7264 -  3.7714  1350   153  0.95   7.69   1.01     0.99       8676.54|
|  3:  3.7714 -  3.3005  1317   146  0.94  10.82   1.02     1.01       9825.61|
|  4:  3.3005 -  3.0015  1309   137  0.93  12.88   1.00     0.99       9665.26|
|  5:  3.0015 -  2.7878  1309   152  0.91  15.28   0.99     0.96       7776.89|
|  6:  2.7878 -  2.6244  1302   144  0.90  16.08   0.97     0.95       6817.77|
|  7:  2.6244 -  2.4936  1287   146  0.91  15.09   0.98     0.94       5890.65|
|  8:  2.4936 -  2.3855  1303   141  0.91  14.64   0.98     0.96       5226.89|
|  9:  2.3855 -  2.2940  1283   145  0.91  15.56   0.99     0.95       4936.78|
| 10:  2.2940 -  2.2151  1270   138  0.90  15.82   0.98     0.94       4398.96|
| 11:  2.2151 -  2.1460  1281   145  0.90  15.90   0.98     0.94       4297.59|
| 12:  2.1460 -  2.0849  1276   137  0.91  15.38   0.99     0.99       3947.69|
| 13:  2.0849 -  2.0301  1258   143  0.90  16.05   0.98     0.96       3375.43|
| 14:  2.0301 -  1.9807   683    77  0.92  14.38   0.95     0.91       2538.95|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2538.95 max =         9825.61 mean =      6186.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1555   ksol= 0.32   Bsol= 56.48   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.76,-0.54,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135090                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1555   ksol= 0.32   Bsol= 56.48   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.76,-0.54,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135090                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.0992 0.1260       5.386      5.5218|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.0855 0.1073      5.4319      5.5967|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.1044 0.1511      5.4584      5.8446|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.1173 0.1502      5.4219      5.5819|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.1289 0.1569      5.2979      5.4739|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.1220 0.2064      5.1976      5.4985|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.1224 0.1569      5.1477      5.3028|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.1108 0.1642      5.0535      5.3056|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.1186 0.1910      5.0253      5.3404|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.1102 0.1558       4.951      5.1321|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.1114 0.1804      4.9239      5.2809|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.1099 0.1689      4.8691       5.204|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.1075 0.1761      4.7774      5.0207|
| 14:  2.0301 -  1.9807 0.53    683   77 0.0976 0.1797      4.6616      4.9621|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.94   9.04   0.97     0.94       7023.48|
|  2:  4.7264 -  3.7714  1350   153  0.95   7.69   1.01     1.00       8677.64|
|  3:  3.7714 -  3.3005  1317   146  0.94  10.83   1.02     1.02       9835.52|
|  4:  3.3005 -  3.0015  1309   137  0.93  12.88   1.01     1.00       9663.93|
|  5:  3.0015 -  2.7878  1309   152  0.91  15.28   0.99     0.96       7774.31|
|  6:  2.7878 -  2.6244  1302   144  0.90  16.08   0.98     0.96       6814.11|
|  7:  2.6244 -  2.4936  1287   146  0.91  15.10   0.99     0.95       5889.26|
|  8:  2.4936 -  2.3855  1303   141  0.91  14.64   1.00     0.97       5225.60|
|  9:  2.3855 -  2.2940  1283   145  0.91  15.56   1.00     0.96       4936.79|
| 10:  2.2940 -  2.2151  1270   138  0.90  15.82   1.00     0.96       4395.40|
| 11:  2.2151 -  2.1460  1281   145  0.90  15.90   0.99     0.95       4294.50|
| 12:  2.1460 -  2.0849  1276   137  0.91  15.38   1.01     1.00       3945.46|
| 13:  2.0849 -  2.0301  1258   143  0.90  16.06   1.00     0.98       3375.36|
| 14:  2.0301 -  1.9807   683    77  0.92  14.39   0.97     0.92       2539.68|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2539.68 max =         9835.52 mean =      6184.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.61 mean =        13.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.46   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    85.46   16.67    None  None   None       |
|    Sol.    : 438    0      5.42    75.30   39.11    None  None   None       |
|    Mac.    : 2385   0      0.00    85.46   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.549:  742   |   5:    42.733 -  51.279:  117        |
|      1:     8.549 -  17.095: 1315   |   6:    51.279 -  59.825:   78        |
|      2:    17.095 -  25.641:  284   |   7:    59.825 -  68.371:   33        |
|      3:    25.641 -  34.187:  129   |   8:    68.371 -  76.917:   12        |
|      4:    34.187 -  42.733:  110   |   9:    76.917 -  85.463:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.597 - 5.417
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 288
   mapped sites are within: 0.707 - 5.417

peak=    5.662 closest distance to " NH2 ARG A  56 " =    2.268
peak=    5.571 closest distance to " CB  ARG A 275 " =    0.960
peak=    5.354 closest distance to " CB  GLN A 223 " =    1.413
peak=    5.162 closest distance to " CG  PRO A  54 " =    1.299
peak=    5.042 closest distance to " O   HOH Z 232 " =    2.418
peak=    4.913 closest distance to " O   HOH Z 126 " =    1.884
peak=    4.782 closest distance to " CA  TYR A  30 " =    0.900
peak=    4.774 closest distance to " CB  SER A  63 " =    1.177
peak=    4.735 closest distance to " O   HOH Z 142 " =    1.636
peak=    4.701 closest distance to " CG  PRO A  90 " =    1.206
peak=    4.682 closest distance to " CG  PRO A 213 " =    1.227
peak=    4.635 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.602 closest distance to " CB  PRO A  54 " =    0.961
peak=    4.522 closest distance to " CB  GLU A 152 " =    1.181
peak=    4.509 closest distance to " O   HOH Z 250 " =    1.480
peak=    4.498 closest distance to " C   PRO A 198 " =    1.522
peak=    4.486 closest distance to " CB  ARG A 190 " =    1.702
peak=    4.485 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.453 closest distance to " O   HOH Z 298 " =    1.831
peak=    4.436 closest distance to " NE2 GLN A  11 " =    1.030
peak=    4.407 closest distance to " CB  ASN A 148 " =    1.479
peak=    4.399 closest distance to " CB  ARG A  79 " =    1.369
peak=    4.376 closest distance to " O   HOH Z 369 " =    2.364
peak=    4.356 closest distance to " O   HOH Z  78 " =    1.671
peak=    4.335 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.292 closest distance to " O   HOH Z 402 " =    1.422
peak=    4.264 closest distance to " O   HOH Z 287 " =    1.991
peak=    4.209 closest distance to " O   HOH Z  15 " =    2.158
peak=    4.208 closest distance to " CA  ARG A  36 " =    1.044
peak=    4.180 closest distance to " O   HOH Z 303 " =    2.074
peak=    4.159 closest distance to " CG  PRO A 243 " =    1.010
peak=    4.156 closest distance to " CB  TRP A 266 " =    0.999
peak=    4.145 closest distance to " CA  ASN A 215 " =    1.091
peak=    4.136 closest distance to " O   SER A  87 " =    2.211
peak=    4.135 closest distance to " O   HOH Z 427 " =    2.978
peak=    4.131 closest distance to " O   HOH Z  40 " =    1.836
peak=    4.123 closest distance to " O   HOH Z 209 " =    2.253
peak=    4.098 closest distance to " O   HOH Z 158 " =    3.051
peak=    4.098 closest distance to " CG2 VAL A 257 " =    0.861
peak=    4.094 closest distance to " CD2 TRP A 179 " =    1.345
peak=    4.093 closest distance to " CB  TYR A 169 " =    0.738
peak=    4.083 closest distance to " O   HOH Z 392 " =    2.938
peak=    4.078 closest distance to " O   HOH Z  61 " =    1.635
peak=    4.076 closest distance to " ND2 ASN A 187 " =    1.448
peak=    4.074 closest distance to " CE  LYS A  76 " =    0.860
peak=    4.067 closest distance to " CB  VAL A 265 " =    1.219
peak=    4.058 closest distance to " O   HOH Z 189 " =    2.608
peak=    4.054 closest distance to " CB  LEU A 228 " =    1.074
peak=    4.049 closest distance to " O   HOH Z 346 " =    1.687
peak=    4.037 closest distance to " O   HOH Z 234 " =    3.728
peak=    4.026 closest distance to " O   HOH Z 272 " =    1.842
peak=    3.952 closest distance to " O   HOH Z  43 " =    1.940
peak=    3.952 closest distance to " O   HOH Z 423 " =    1.972
peak=    3.925 closest distance to " OD1 ASN A  69 " =    2.593
peak=    3.908 closest distance to " O   HOH Z 193 " =    1.802
peak=    3.901 closest distance to " O   HOH Z 214 " =    2.090
peak=    3.893 closest distance to " O   HOH Z 265 " =    2.257
peak=    3.889 closest distance to " NZ  LYS A 117 " =    3.202
peak=    3.884 closest distance to " O   HOH Z  63 " =    2.136
peak=    3.878 closest distance to " O   HOH Z 403 " =    1.676
peak=    3.878 closest distance to " CB  ARG A  79 " =    0.919
peak=    3.874 closest distance to " CB  GLU A 277 " =    3.622
peak=    3.869 closest distance to " O   HOH Z  19 " =    2.224
peak=    3.853 closest distance to " OG ASER A 258 " =    3.103
peak=    3.780 closest distance to " O   HOH Z 389 " =    1.844
peak=    3.779 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.771 closest distance to " CB  GLU A  46 " =    1.023
peak=    3.767 closest distance to " CB  THR A  31 " =    1.564
peak=    3.763 closest distance to " O   HOH Z 203 " =    1.662
peak=    3.754 closest distance to " CG  ARG A  66 " =    2.460
peak=    3.754 closest distance to " O   HOH Z  97 " =    2.465
peak=    3.751 closest distance to " CB  GLU A 128 " =    1.051
peak=    3.749 closest distance to " CG2 ILE A 120 " =    1.052
peak=    3.740 closest distance to " CB  ASN A  39 " =    0.901
peak=    3.736 closest distance to " O   HOH Z  59 " =    2.104
peak=    3.735 closest distance to " O   HOH Z 368 " =    2.105
peak=    3.733 closest distance to " O   HOH Z 128 " =    2.024
peak=    3.732 closest distance to " CA  ARG A 195 " =    1.240
peak=    3.725 closest distance to " O   HOH Z 180 " =    2.202
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.489
peak=    3.703 closest distance to " O  BHOH Z 338 " =    2.263
peak=    3.692 closest distance to " CD  ARG A 269 " =    0.975
peak=    3.689 closest distance to " CB  ALA A 291 " =    1.265
peak=    3.681 closest distance to " CG2AVAL A  72 " =    1.703
peak=    3.677 closest distance to " CB  ASP A 140 " =    1.031
peak=    3.676 closest distance to " N   HIS A 108 " =    1.942
peak=    3.673 closest distance to " CD2 LEU A 297 " =    0.874
peak=    3.673 closest distance to " O   HOH Z 313 " =    1.964
peak=    3.662 closest distance to " O   HOH Z 280 " =    2.929
peak=    3.662 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.659 closest distance to " CD  LYS A 166 " =    1.262
peak=    3.659 closest distance to " O   HOH Z 261 " =    1.794
peak=    3.646 closest distance to " O   HOH Z 147 " =    1.807
peak=    3.643 closest distance to " O   HOH Z 411 " =    3.934
peak=    3.642 closest distance to " CE1 TYR A 186 " =    1.305
peak=    3.638 closest distance to " CD1 LEU A  96 " =    0.739
peak=    3.624 closest distance to " N   ASN A  39 " =    1.248
peak=    3.616 closest distance to " O   HOH Z  97 " =    1.993
peak=    3.613 closest distance to " O   HOH Z 365 " =    2.842
peak=    3.608 closest distance to " O   HOH Z 368 " =    3.656
peak=    3.606 closest distance to " O   HOH Z 291 " =    1.564
peak=    3.605 closest distance to " NH1AARG A 145 " =    1.235
peak=    3.604 closest distance to " O   HOH Z 403 " =    1.406
peak=    3.602 closest distance to " O   HOH Z 407 " =    2.536
peak=    3.594 closest distance to " CB  ASN A 110 " =    1.146
peak=    3.592 closest distance to " CA  ALA A  51 " =    0.867
peak=    3.592 closest distance to " O   HOH Z 421 " =    1.853
peak=    3.588 closest distance to " O   THR A 220 " =    1.212
peak=    3.581 closest distance to " O   HOH Z 406 " =    1.525
peak=    3.579 closest distance to " O   HOH Z 227 " =    1.288
peak=    3.573 closest distance to " N   TYR A 116 " =    1.523
peak=    3.568 closest distance to " CB  ALA A 114 " =    1.061
peak=    3.564 closest distance to " CB  SER A   3 " =    1.226
peak=    3.562 closest distance to " O   HOH Z  21 " =    1.826
peak=    3.550 closest distance to " O   HOH Z  44 " =    1.776
peak=    3.549 closest distance to " O   HOH Z  54 " =    1.661
peak=    3.533 closest distance to " CB  PHE A 204 " =    0.707
peak=    3.530 closest distance to " O   ASN A  74 " =    1.475
peak=    3.527 closest distance to " CG AARG A 275 " =    1.114
peak=    3.524 closest distance to " CG  MET A 185 " =    1.104
peak=    3.521 closest distance to " ND2 ASN A 249 " =    0.918
peak=    3.519 closest distance to " CG  GLU A  37 " =    0.938
peak=    3.511 closest distance to " O   HOH Z 353 " =    2.657
peak=    3.508 closest distance to " O   HOH Z 327 " =    1.604
peak=    3.505 closest distance to " CG2 ILE A  20 " =    1.428
peak=    3.500 closest distance to " OG BSER A 164 " =    2.277
peak=    3.498 closest distance to " O   HOH Z 344 " =    3.114
peak=    3.492 closest distance to " CB  TRP A 179 " =    1.331
peak=    3.492 closest distance to " N   ARG A 156 " =    1.379
peak=    3.482 closest distance to " O   HOH Z 128 " =    2.173
peak=    3.481 closest distance to " O   HOH Z 185 " =    1.773
peak=    3.479 closest distance to " CA  ASN A 217 " =    1.223
peak=    3.473 closest distance to " O   HOH Z 371 " =    3.213
peak=    3.468 closest distance to " NE2 GLN A  77 " =    3.220
peak=    3.464 closest distance to " CB  SER A 212 " =    1.047
peak=    3.463 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.461 closest distance to " O   HOH Z   1 " =    2.005
peak=    3.459 closest distance to " O   ALA A 165 " =    1.519
peak=    3.459 closest distance to " CA  MET A 105 " =    1.029
peak=    3.450 closest distance to " O   HOH Z 172 " =    3.642
peak=    3.449 closest distance to " CD1AILE A 234 " =    0.908
peak=    3.448 closest distance to " O   HOH Z 245 " =    1.285
peak=    3.440 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.439 closest distance to " CZ2 TRP A 179 " =    1.746
peak=    3.436 closest distance to " O   HOH Z 299 " =    4.420
peak=    3.433 closest distance to " CB  SER A  62 " =    0.914
peak=    3.432 closest distance to " CG  LEU A 167 " =    1.227
peak=    3.426 closest distance to " CB  TYR A 169 " =    0.812
peak=    3.424 closest distance to " CE1 PHE A  38 " =    1.256
peak=    3.421 closest distance to " CB  ALA A 248 " =    1.344
peak=    3.420 closest distance to " O   TRP A 274 " =    1.911
peak=    3.415 closest distance to " NH2BARG A 145 " =    2.075
peak=    3.413 closest distance to " O   HOH Z 248 " =    1.584
peak=    3.413 closest distance to " CD1 LEU A 300 " =    1.230
peak=    3.407 closest distance to " O   HOH Z 359 " =    1.448
peak=    3.398 closest distance to " CB  SER A  26 " =    1.721
peak=    3.397 closest distance to " O   HOH Z 419 " =    2.060
peak=    3.396 closest distance to " O   HOH Z 325 " =    2.467
peak=    3.394 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.393 closest distance to " CB  SER A 141 " =    1.013
peak=    3.387 closest distance to " O   HOH Z 337 " =    3.567
peak=    3.380 closest distance to " CA  THR A 221 " =    1.026
peak=    3.378 closest distance to " CB  GLN A 205 " =    1.121
peak=    3.374 closest distance to " N   PHE A 130 " =    1.227
peak=    3.373 closest distance to " CB  ALA A 242 " =    0.957
peak=    3.371 closest distance to " CA  ALA A  84 " =    1.213
peak=    3.371 closest distance to " O   HOH Z  88 " =    2.494
peak=    3.369 closest distance to " CA  MET A  40 " =    1.134
peak=    3.363 closest distance to " O   HOH Z  88 " =    3.024
peak=    3.363 closest distance to " O   HOH Z 173 " =    1.960
peak=    3.358 closest distance to " CB  HIS A 108 " =    0.829
peak=    3.357 closest distance to " CB  ASN A 215 " =    1.216
peak=    3.354 closest distance to " CA  VAL A 125 " =    1.051
peak=    3.353 closest distance to " O   HOH Z 133 " =    2.849
peak=    3.351 closest distance to " OG1 THR A 294 " =    2.438
peak=    3.345 closest distance to " CA  ALA A 291 " =    0.788
peak=    3.337 closest distance to " CA  ALA A 160 " =    0.901
peak=    3.330 closest distance to " O   HOH Z 417 " =    3.153
peak=    3.329 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.327 closest distance to " CB  ASN A 142 " =    1.104
peak=    3.316 closest distance to " CD1 ILE A 106 " =    0.827
peak=    3.315 closest distance to " CB  TYR A 116 " =    0.709
peak=    3.307 closest distance to " O   HOH Z 305 " =    3.596
peak=    3.306 closest distance to " OD2 ASP A 286 " =    2.841
peak=    3.306 closest distance to " OH  TYR A 116 " =    1.043
peak=    3.305 closest distance to " CB  MET A  47 " =    1.015
peak=    3.305 closest distance to " O   HOH Z 148 " =    3.432
peak=    3.304 closest distance to " O   HOH Z   6 " =    2.236
peak=    3.301 closest distance to " CB  ARG A 139 " =    0.952
peak=    3.301 closest distance to " OG  SER A  22 " =    2.630
peak=    3.300 closest distance to " CB  PRO A  90 " =    1.056
peak=    3.297 closest distance to " O   HOH Z 426 " =    1.615
peak=    3.294 closest distance to " CA  THR A 264 " =    0.917
peak=    3.292 closest distance to " O   HOH Z 261 " =    1.997
peak=    3.289 closest distance to " CA  ALA A  21 " =    1.130
peak=    3.283 closest distance to " CG  GLN A  11 " =    1.490
peak=    3.280 closest distance to " CA  SER A  87 " =    1.062
peak=    3.279 closest distance to " O   HOH Z 393 " =    3.249
peak=    3.279 closest distance to " CA  ASN A 176 " =    1.205
peak=    3.274 closest distance to " CB  PRO A 198 " =    1.159
peak=    3.266 closest distance to " O   HOH Z 357 " =    2.013
peak=    3.263 closest distance to " CA  ASP A 140 " =    1.136
peak=    3.262 closest distance to " O   HOH Z 193 " =    2.066
peak=    3.261 closest distance to " O   HOH Z 329 " =    3.997
peak=    3.260 closest distance to " CB  LYS A 290 " =    1.085
peak=    3.254 closest distance to " CG1 VAL A 153 " =    0.976
peak=    3.253 closest distance to " O   THR A 251 " =    1.130
peak=    3.252 closest distance to " O   HOH Z 108 " =    2.709
peak=    3.246 closest distance to " CZ3 TRP A 266 " =    1.105
peak=    3.246 closest distance to " O   ASP A 124 " =    1.111
peak=    3.240 closest distance to " CA  ASP A 162 " =    1.056
peak=    3.238 closest distance to " CB  GLN A  88 " =    1.175
peak=    3.235 closest distance to " O   HOH Z 391 " =    2.925
peak=    3.235 closest distance to " CG  LYS A  76 " =    0.955
peak=    3.231 closest distance to " CA  ILE A 234 " =    0.967
peak=    3.230 closest distance to " N   GLY A  98 " =    1.082
peak=    3.223 closest distance to " CD1 ILE A 199 " =    1.033
peak=    3.223 closest distance to " O   HOH Z  66 " =    2.233
peak=    3.219 closest distance to " C   TYR A 214 " =    1.490
peak=    3.219 closest distance to " CD BLYS A 290 " =    0.979
peak=    3.218 closest distance to " O   HOH Z 383 " =    1.915
peak=    3.211 closest distance to " CE  LYS A  48 " =    1.027
peak=    3.209 closest distance to " O   HOH Z 425 " =    1.968
peak=    3.208 closest distance to " CA  TYR A 116 " =    1.386
peak=    3.205 closest distance to " O   HOH Z 273 " =    2.946
peak=    3.201 closest distance to " O   HOH Z 271 " =    2.118
peak=    3.201 closest distance to " O   HOH Z 336 " =    1.589
peak=    3.200 closest distance to " CB  GLN A 103 " =    0.861
peak=    3.199 closest distance to " O   HOH Z 171 " =    2.013
peak=    3.199 closest distance to " CG1 ILE A 120 " =    1.064
peak=    3.199 closest distance to " CA  LYS A 290 " =    1.163
peak=    3.197 closest distance to " O   HOH Z 279 " =    2.214
peak=    3.194 closest distance to " CB  PRO A 243 " =    1.583
peak=    3.190 closest distance to " CB  ALA A  34 " =    1.055
peak=    3.190 closest distance to " O   HOH Z 258 " =    2.187
peak=    3.188 closest distance to " NE2 HIS A 207 " =    1.232
peak=    3.186 closest distance to " NZ  LYS A  48 " =    1.226
peak=    3.184 closest distance to " CA  ALA A 248 " =    1.109
peak=    3.184 closest distance to " O   HOH Z 258 " =    1.622
peak=    3.183 closest distance to " CA  ALA A 154 " =    0.975
peak=    3.181 closest distance to " N   ASN A 127 " =    1.235
peak=    3.180 closest distance to " N   VAL A 126 " =    1.345
peak=    3.175 closest distance to " CA  ARG A 159 " =    1.338
peak=    3.174 closest distance to " OG BSER A  99 " =    2.344
peak=    3.173 closest distance to " CG2 ILE A 234 " =    0.799
peak=    3.173 closest distance to " O   HOH Z 213 " =    1.765
peak=    3.170 closest distance to " CG1 ILE A  49 " =    1.550
peak=    3.169 closest distance to " CG2 VAL A 197 " =    1.073
peak=    3.164 closest distance to " O   HOH Z 234 " =    1.926
peak=    3.164 closest distance to " O   HOH Z  88 " =    2.096
peak=    3.162 closest distance to " CA  ASN A 252 " =    1.915
peak=    3.160 closest distance to " O   ALA A   1 " =    1.723
peak=    3.158 closest distance to " OG1 THR A 264 " =    0.736
peak=    3.152 closest distance to " CG2 THR A 221 " =    1.156
peak=    3.148 closest distance to " CD  LYS A 119 " =    1.288
peak=    3.147 closest distance to " O   HOH Z 285 " =    1.625
peak=    3.136 closest distance to " O   HOH Z 394 " =    3.987
peak=    3.120 closest distance to " O   HOH Z  80 " =    1.688
peak=    3.119 closest distance to " O   HOH Z 380 " =    1.916
peak=    3.109 closest distance to " CG2BVAL A  41 " =    0.859
peak=    3.109 closest distance to " O   HOH Z 430 " =    5.417
peak=    3.103 closest distance to " N   ASP A 162 " =    1.097
peak=    3.101 closest distance to " O   HOH Z 345 " =    3.238
peak=    3.095 closest distance to " O   HOH Z  49 " =    2.164
peak=    3.094 closest distance to " O   HOH Z 285 " =    2.663
peak=    3.087 closest distance to " O   HOH Z 267 " =    2.000
peak=    3.083 closest distance to " N   SER A 135 " =    1.272
peak=    3.080 closest distance to " CD  ARG A  36 " =    0.980
peak=    3.077 closest distance to " O   SER A 164 " =    1.224
peak=    3.077 closest distance to " OG  SER A  62 " =    2.782
peak=    3.072 closest distance to " CD  ARG A  66 " =    2.440
peak=    3.070 closest distance to " O   HOH Z  85 " =    1.950
peak=    3.066 closest distance to " O   HOH Z  62 " =    2.182
peak=    3.059 closest distance to " CB  VAL A 126 " =    1.094
peak=    3.059 closest distance to " CB  LEU A 300 " =    0.905
peak=    3.057 closest distance to " O   HOH Z 233 " =    1.709
peak=    3.048 closest distance to " CB  ALA A 227 " =    1.127
peak=    3.036 closest distance to " O   HOH Z 417 " =    2.106
peak=    3.032 closest distance to " CB  GLN A 278 " =    0.865
peak=    3.029 closest distance to " CA  ARG A 102 " =    1.055
peak=    3.014 closest distance to " CA  GLY A  80 " =    0.817

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.808 - 5.810
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.808 - 5.810

peak=   -4.852 closest distance to " CD  GLN A  58 " =    1.031
peak=   -4.691 closest distance to " O   HOH Z 266 " =    5.309
peak=   -4.613 closest distance to " CD  ARG A  14 " =    3.460
peak=   -4.504 closest distance to " C   HIS A 108 " =    1.094
peak=   -4.421 closest distance to " CB  PRO A 243 " =    2.616
peak=   -4.353 closest distance to " O   HOH Z 231 " =    2.242
peak=   -4.325 closest distance to " O   VAL A  67 " =    2.662
peak=   -4.292 closest distance to " O   HOH Z 372 " =    2.280
peak=   -4.269 closest distance to " OG BSER A 134 " =    1.234
peak=   -4.265 closest distance to " CD  ARG A 156 " =    2.035
peak=   -4.240 closest distance to " CG  GLN A 223 " =    2.037
peak=   -4.213 closest distance to " O   HOH Z 198 " =    1.825
peak=   -4.123 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -4.091 closest distance to " O   HOH Z 377 " =    2.163
peak=   -4.042 closest distance to " CB  ALA A 161 " =    2.532
peak=   -4.033 closest distance to " CB  PHE A 192 " =    2.010
peak=   -4.027 closest distance to " O   PRO A 198 " =    1.257
peak=   -4.017 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.959 closest distance to " O   HOH Z 196 " =    2.009
peak=   -3.940 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.934 closest distance to " CA  VAL A  67 " =    2.946
peak=   -3.926 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.908 closest distance to " OXT GLY A 302 " =    2.831
peak=   -3.890 closest distance to " OD2 ASP A 191 " =    1.427
peak=   -3.885 closest distance to " CG2 ILE A 263 " =    2.318
peak=   -3.875 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -3.867 closest distance to " CB  ASN A  39 " =    2.371
peak=   -3.815 closest distance to " ND2 ASN A  45 " =    1.771
peak=   -3.810 closest distance to " CB  ASP A 132 " =    2.292
peak=   -3.799 closest distance to " CD1 LEU A 101 " =    2.398
peak=   -3.797 closest distance to " O   SER A 210 " =    2.007
peak=   -3.737 closest distance to " CA  GLY A 203 " =    2.395
peak=   -3.724 closest distance to " OD1 ASN A 148 " =    1.463
peak=   -3.720 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.718 closest distance to " O   HOH Z 290 " =    1.230
peak=   -3.714 closest distance to " O   HOH Z 389 " =    1.840
peak=   -3.708 closest distance to " CE  MET A 105 " =    2.511
peak=   -3.704 closest distance to " N   ALA A  43 " =    2.716
peak=   -3.702 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.696 closest distance to " O   HOH Z 351 " =    1.503
peak=   -3.688 closest distance to " O   HOH Z  73 " =    2.359
peak=   -3.686 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.682 closest distance to " O   HOH Z  10 " =    1.504
peak=   -3.677 closest distance to " O   HOH Z 407 " =    2.945
peak=   -3.666 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.665 closest distance to " NE2 GLN A 194 " =    1.864
peak=   -3.663 closest distance to " O   HOH Z 114 " =    3.162
peak=   -3.646 closest distance to " O   PHE A 218 " =    1.577
peak=   -3.643 closest distance to " O   HOH Z  13 " =    1.686
peak=   -3.630 closest distance to " OD2 ASP A 171 " =    2.438
peak=   -3.626 closest distance to " ND2 ASN A 187 " =    1.508
peak=   -3.625 closest distance to " O   HOH Z 353 " =    2.132
peak=   -3.621 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.589 closest distance to " CB  ALA A 248 " =    2.282
peak=   -3.586 closest distance to " CG  GLU A 277 " =    1.204
peak=   -3.583 closest distance to " CE2 PHE A  61 " =    2.585
peak=   -3.581 closest distance to " CB  ASP A 286 " =    1.804
peak=   -3.579 closest distance to " CB  ALA A 248 " =    2.228
peak=   -3.570 closest distance to " O   PRO A 163 " =    2.084
peak=   -3.569 closest distance to " CD  ARG A 195 " =    5.135
peak=   -3.566 closest distance to " O   HOH Z 292 " =    4.543
peak=   -3.548 closest distance to " CZ  TYR A 169 " =    1.768
peak=   -3.543 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -3.542 closest distance to " O   HOH Z 211 " =    1.588
peak=   -3.539 closest distance to " CG  ARG A 269 " =    2.317
peak=   -3.531 closest distance to " CD1 LEU A  25 " =    2.508
peak=   -3.529 closest distance to " N   THR A  52 " =    1.705
peak=   -3.521 closest distance to " NE2 GLN A  88 " =    1.840
peak=   -3.517 closest distance to " CD1 LEU A 255 " =    2.763
peak=   -3.502 closest distance to " N   ALA A 248 " =    1.651
peak=   -3.502 closest distance to " N   GLN A  58 " =    1.681
peak=   -3.498 closest distance to " O   HOH Z 185 " =    2.363
peak=   -3.482 closest distance to " CZ  PHE A 155 " =    1.182
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.889
peak=   -3.473 closest distance to " OD1 ASP A 171 " =    1.597
peak=   -3.470 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.469 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.464 closest distance to " O   HOH Z 394 " =    1.450
peak=   -3.460 closest distance to " CG  ASP A 231 " =    0.808
peak=   -3.457 closest distance to " O   HOH Z 102 " =    1.574
peak=   -3.456 closest distance to " ND2 ASN A 249 " =    2.392
peak=   -3.454 closest distance to " CG1 VAL A 112 " =    2.800
peak=   -3.449 closest distance to " CB  PHE A 208 " =    2.287
peak=   -3.448 closest distance to " O   HOH Z 126 " =    1.953
peak=   -3.435 closest distance to " CE3 TRP A 150 " =    2.205
peak=   -3.433 closest distance to " O   HOH Z 313 " =    1.940
peak=   -3.429 closest distance to " NH2AARG A 275 " =    5.202
peak=   -3.428 closest distance to " O   HOH Z 171 " =    1.993
peak=   -3.427 closest distance to " OD1 ASN A 187 " =    1.759
peak=   -3.418 closest distance to " O   ALA A  34 " =    2.338
peak=   -3.417 closest distance to " CG1 VAL A 250 " =    2.658
peak=   -3.412 closest distance to " O   HOH Z   6 " =    2.293
peak=   -3.412 closest distance to " CG  PHE A 283 " =    2.660
peak=   -3.407 closest distance to " CG  GLN A  11 " =    1.763
peak=   -3.405 closest distance to " CD1 ILE A 239 " =    2.328
peak=   -3.401 closest distance to " O   HOH Z 191 " =    5.810
peak=   -3.400 closest distance to " O   ALA A 161 " =    1.717
peak=   -3.394 closest distance to " CB  TYR A  15 " =    2.189
peak=   -3.394 closest distance to " O   HOH Z 165 " =    1.980
peak=   -3.384 closest distance to " CB  ALA A  43 " =    2.563
peak=   -3.379 closest distance to " O   HOH Z 421 " =    3.316
peak=   -3.376 closest distance to " O   HOH Z 357 " =    2.094
peak=   -3.368 closest distance to " O   VAL A 174 " =    2.099
peak=   -3.363 closest distance to " O   HOH Z  60 " =    2.167
peak=   -3.359 closest distance to " O   HOH Z  43 " =    1.663
peak=   -3.354 closest distance to " NH2 ARG A  79 " =    1.582
peak=   -3.353 closest distance to " O   ALA A 292 " =    2.029
peak=   -3.348 closest distance to " N   TYR A  68 " =    3.174
peak=   -3.345 closest distance to " O   HOH Z 311 " =    3.644
peak=   -3.343 closest distance to " OD2 ASP A  50 " =    2.153
peak=   -3.343 closest distance to " O   GLN A  89 " =    1.507
peak=   -3.339 closest distance to " O   HOH Z 177 " =    1.729
peak=   -3.335 closest distance to " C   GLY A 262 " =    1.910
peak=   -3.333 closest distance to " CG2 THR A 178 " =    2.283
peak=   -3.330 closest distance to " CD  GLN A 223 " =    1.320
peak=   -3.324 closest distance to " O   HOH Z 123 " =    2.291
peak=   -3.322 closest distance to " C   LEU A 143 " =    1.014
peak=   -3.319 closest distance to " O   HOH Z   6 " =    1.418
peak=   -3.318 closest distance to " N   ALA A 226 " =    2.009
peak=   -3.311 closest distance to " O   VAL A 189 " =    2.653
peak=   -3.311 closest distance to " CA  ILE A 263 " =    1.014
peak=   -3.306 closest distance to " C   SER A 206 " =    1.548
peak=   -3.300 closest distance to " NE2 GLN A 278 " =    1.786
peak=   -3.294 closest distance to " O   HOH Z  63 " =    1.584
peak=   -3.293 closest distance to " O   HOH Z 322 " =    1.732
peak=   -3.286 closest distance to " O   HOH Z 243 " =    1.992
peak=   -3.279 closest distance to " O   GLN A 240 " =    2.099
peak=   -3.277 closest distance to " CZ2 TRP A 274 " =    0.991
peak=   -3.276 closest distance to " CA  GLY A 241 " =    2.391
peak=   -3.275 closest distance to " CG  GLU A  53 " =    1.491
peak=   -3.273 closest distance to " C   ASP A 231 " =    2.626
peak=   -3.267 closest distance to " CD  GLU A 236 " =    1.080
peak=   -3.264 closest distance to " CA  GLY A 241 " =    3.257
peak=   -3.263 closest distance to " O   HOH Z  11 " =    1.673
peak=   -3.262 closest distance to " O   HOH Z 265 " =    2.244
peak=   -3.253 closest distance to " O   HOH Z 298 " =    1.330
peak=   -3.251 closest distance to " O   HOH Z  37 " =    1.747
peak=   -3.245 closest distance to " CG  HIS A  86 " =    1.079
peak=   -3.243 closest distance to " O   LEU A 167 " =    1.483
peak=   -3.238 closest distance to " SG ACYS A 201 " =    1.998
peak=   -3.233 closest distance to " CG  TRP A 266 " =    1.972
peak=   -3.231 closest distance to " CB  PHE A  16 " =    2.553
peak=   -3.218 closest distance to " O   LEU A 101 " =    2.100
peak=   -3.218 closest distance to " O   SER A 135 " =    1.465
peak=   -3.217 closest distance to " CB  PRO A 163 " =    2.421
peak=   -3.216 closest distance to " O   HOH Z 253 " =    3.918
peak=   -3.210 closest distance to " O   HOH Z 414 " =    1.542
peak=   -3.210 closest distance to " O   HOH Z 244 " =    1.972
peak=   -3.209 closest distance to " CB  TRP A  85 " =    2.554
peak=   -3.199 closest distance to " OG BSER A 134 " =    1.837
peak=   -3.197 closest distance to " C   MET A 188 " =    1.393
peak=   -3.187 closest distance to " CA  GLY A 133 " =    2.021
peak=   -3.185 closest distance to " NE2 GLN A 223 " =    1.392
peak=   -3.184 closest distance to " O   HOH Z 298 " =    2.499
peak=   -3.179 closest distance to " O   HOH Z 317 " =    1.514
peak=   -3.178 closest distance to " CD2 PHE A 225 " =    1.153
peak=   -3.176 closest distance to " O   MET A  40 " =    2.828
peak=   -3.173 closest distance to " CG1 VAL A 125 " =    1.911
peak=   -3.172 closest distance to " O   HOH Z  38 " =    1.611
peak=   -3.171 closest distance to " O   TRP A  70 " =    1.459
peak=   -3.171 closest distance to " O   HOH Z  71 " =    2.099
peak=   -3.161 closest distance to " CD1 ILE A 151 " =    2.429
peak=   -3.159 closest distance to " OE2 GLU A 152 " =    1.246
peak=   -3.156 closest distance to " OE1 GLN A 183 " =    1.581
peak=   -3.145 closest distance to " N   ASP A 286 " =    2.308
peak=   -3.145 closest distance to " O   SER A  95 " =    1.615
peak=   -3.145 closest distance to " O   ILE A 106 " =    1.850
peak=   -3.141 closest distance to " CG1AVAL A  41 " =    2.810
peak=   -3.136 closest distance to " CG2 VAL A 189 " =    2.187
peak=   -3.136 closest distance to " C   ALA A 158 " =    1.369
peak=   -3.129 closest distance to " O   HOH Z 134 " =    3.041
peak=   -3.126 closest distance to " O   HOH Z 166 " =    1.616
peak=   -3.125 closest distance to " CZ3 TRP A 274 " =    2.383
peak=   -3.124 closest distance to " O   HOH Z  52 " =    1.486
peak=   -3.122 closest distance to " O   HOH Z 351 " =    1.423
peak=   -3.118 closest distance to " O   HOH Z 174 " =    4.047
peak=   -3.115 closest distance to " CD2 LEU A 237 " =    2.772
peak=   -3.106 closest distance to " CD1 ILE A 199 " =    2.466
peak=   -3.103 closest distance to " CG  LEU A  83 " =    1.962
peak=   -3.094 closest distance to " O   ALA A   1 " =    1.750
peak=   -3.086 closest distance to " CE BMET A  47 " =    1.630
peak=   -3.080 closest distance to " O   GLU A 152 " =    1.683
peak=   -3.079 closest distance to " O   HOH Z 128 " =    2.606
peak=   -3.072 closest distance to " SD  MET A 188 " =    2.158
peak=   -3.058 closest distance to " ND2 ASN A  60 " =    1.342
peak=   -3.042 closest distance to " O   PRO A 198 " =    1.314
peak=   -2.908 closest distance to " CB  SER A  97 " =    2.348

================= 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    :  0.2925 0.2837   5.945361e+00   5.909990e+00
   1_bss:  0.2790 0.2698   5.915910e+00   5.875455e+00
   1_xyz:  0.1480 0.1669   5.324608e+00   5.423398e+00
   1_adp:  0.1398 0.1663   5.279887e+00   5.428498e+00
   1_occ:  0.1393 0.1665   5.278687e+00   5.429379e+00
   2_bss:  0.1386 0.1652   5.278904e+00   5.425602e+00
   2_xyz:  0.1241 0.1502   5.182231e+00   5.338845e+00
   2_adp:  0.1171 0.1540   5.159655e+00   5.362007e+00
   2_occ:  0.1170 0.1540   5.159553e+00   5.362027e+00
   3_bss:  0.1169 0.1537   5.159374e+00   5.361777e+00
   3_xyz:  0.1100 0.1536   5.127668e+00   5.362667e+00
   3_adp:  0.1100 0.1520   5.122265e+00   5.354343e+00
   3_occ:  0.1098 0.1520   5.122100e+00   5.354419e+00
   4_bss:  0.1099 0.1512   5.120660e+00   5.350401e+00
   4_xyz:  0.1121 0.1531   5.137639e+00   5.365292e+00
   4_adp:  0.1137 0.1532   5.145201e+00   5.365616e+00
   4_occ:  0.1136 0.1532   5.145345e+00   5.366071e+00
   5_bss:  0.1136 0.1532   5.145402e+00   5.366126e+00
   5_xyz:  0.1118 0.1541   5.138606e+00   5.370268e+00
   5_adp:  0.1100 0.1556   5.134996e+00   5.378830e+00
   5_occ:  0.1100 0.1556   5.135117e+00   5.379124e+00
   5_bss:  0.1098 0.1555   5.135090e+00   5.379081e+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:  0.321  50.001  -2.264  -1.892   0.495  -0.000   0.000   0.000
   1_xyz:  0.321  50.001  -2.264  -1.892   0.495  -0.000   0.000   0.000
   1_adp:  0.321  50.001  -2.264  -1.892   0.495  -0.000   0.000   0.000
   1_occ:  0.321  50.001  -2.264  -1.892   0.495  -0.000   0.000   0.000
   2_bss:  0.324  53.109  -3.286  -2.514  -1.014  -0.000  -0.000  -0.000
   2_xyz:  0.324  53.109  -3.286  -2.514  -1.014  -0.000  -0.000  -0.000
   2_adp:  0.324  53.109  -3.286  -2.514  -1.014  -0.000  -0.000  -0.000
   2_occ:  0.324  53.109  -3.286  -2.514  -1.014  -0.000  -0.000  -0.000
   3_bss:  0.327  56.479  -2.978  -2.215  -0.938  -0.000  -0.000  -0.000
   3_xyz:  0.327  56.479  -2.978  -2.215  -0.938  -0.000  -0.000  -0.000
   3_adp:  0.327  56.479  -2.978  -2.215  -0.938  -0.000  -0.000  -0.000
   3_occ:  0.327  56.479  -2.978  -2.215  -0.938  -0.000  -0.000  -0.000
   4_bss:  0.327  56.479  -2.792  -2.049  -0.803  -0.000  -0.000  -0.000
   4_xyz:  0.327  56.479  -2.792  -2.049  -0.803  -0.000  -0.000  -0.000
   4_adp:  0.327  56.479  -2.792  -2.049  -0.803  -0.000  -0.000  -0.000
   4_occ:  0.327  56.479  -2.792  -2.049  -0.803  -0.000  -0.000  -0.000
   5_bss:  0.329  56.479  -2.779  -2.034  -0.783  -0.000  -0.000  -0.000
   5_xyz:  0.329  56.479  -2.779  -2.034  -0.783  -0.000  -0.000  -0.000
   5_adp:  0.329  56.479  -2.779  -2.034  -0.783  -0.000  -0.000  -0.000
   5_occ:  0.329  56.479  -2.779  -2.034  -0.783  -0.000  -0.000  -0.000
   5_bss:  0.324  56.482  -2.484  -1.761  -0.541  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.789 0.7858  0.9526    21919.519
   1_bss:  26.453 0.7983  0.9298    18902.466
   1_xyz:  14.874 0.9083  1.0071     6986.646
   1_adp:  14.990 0.9070  1.0041     7019.465
   1_occ:  15.012 0.9068  1.0037     7031.516
   2_bss:  14.906 0.9077  0.9669     6958.904
   2_xyz:  13.103 0.9223  0.9700     5809.947
   2_adp:  13.581 0.9185  0.9632     5994.131
   2_occ:  13.584 0.9185  0.9630     5993.318
   3_bss:  13.577 0.9186  0.9710     5993.139
   3_xyz:  13.546 0.9189  0.9723     6051.723
   3_adp:  13.352 0.9203  0.9677     5965.432
   3_occ:  13.354 0.9203  0.9676     5964.441
   4_bss:  13.284 0.9208  0.9731     5874.177
   4_xyz:  13.525 0.9191  0.9722     6041.431
   4_adp:  13.511 0.9192  0.9680     6067.064
   4_occ:  13.521 0.9191  0.9679     6071.461
   5_bss:  13.523 0.9191  0.9685     6073.088
   5_xyz:  13.580 0.9187  0.9687     6135.279
   5_adp:  13.777 0.9171  0.9618     6182.452
   5_occ:  13.779 0.9171  0.9617     6185.890
   5_bss:  13.779 0.9171  0.9710     6183.797
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6386e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6386e-01
   1_xyz:   1.097  0.008  0.073 15.222  0.004  4.117   6.7369e-02
   1_adp:   1.097  0.008  0.073 15.222  0.004  4.117   6.7369e-02
   1_occ:   1.097  0.008  0.073 15.222  0.004  4.117   6.7369e-02
   2_bss:   1.097  0.008  0.073 15.222  0.004  4.117   6.7369e-02
   2_xyz:   0.926  0.006  0.071 14.567  0.004  4.120   5.2117e-02
   2_adp:   0.926  0.006  0.071 14.567  0.004  4.120   5.2117e-02
   2_occ:   0.926  0.006  0.071 14.567  0.004  4.120   5.2117e-02
   3_bss:   0.926  0.006  0.071 14.567  0.004  4.120   5.2117e-02
   3_xyz:   1.013  0.008  0.078 14.755  0.004  4.123   6.2027e-02
   3_adp:   1.013  0.008  0.078 14.755  0.004  4.123   6.2027e-02
   3_occ:   1.013  0.008  0.078 14.755  0.004  4.123   6.2027e-02
   4_bss:   1.013  0.008  0.078 14.755  0.004  4.123   6.2027e-02
   4_xyz:   0.908  0.006  0.072 14.411  0.004  4.122   5.0730e-02
   4_adp:   0.908  0.006  0.072 14.411  0.004  4.122   5.0730e-02
   4_occ:   0.908  0.006  0.072 14.411  0.004  4.122   5.0730e-02
   5_bss:   0.908  0.006  0.072 14.411  0.004  4.122   5.0730e-02
   5_xyz:   0.947  0.007  0.074 14.425  0.004  4.124   5.4359e-02
   5_adp:   0.947  0.007  0.074 14.425  0.004  4.124   5.4359e-02
   5_occ:   0.947  0.007  0.074 14.425  0.004  4.124   5.4359e-02
   5_bss:   0.947  0.007  0.074 14.425  0.004  4.124   5.4359e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4138e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4138e-01
   1_xyz:   7.737  0.044  0.283 82.931  0.040  2.275   6.0657e-02
   1_adp:   7.737  0.044  0.283 82.931  0.040  2.275   6.0657e-02
   1_occ:   7.737  0.044  0.283 82.931  0.040  2.275   6.0657e-02
   2_bss:   7.737  0.044  0.283 82.931  0.040  2.275   6.0657e-02
   2_xyz:   6.410  0.036  0.224 82.137  0.039  2.398   3.6292e-02
   2_adp:   6.410  0.036  0.224 82.137  0.039  2.398   3.6292e-02
   2_occ:   6.410  0.036  0.224 82.137  0.039  2.398   3.6292e-02
   3_bss:   6.410  0.036  0.224 82.137  0.039  2.398   3.6292e-02
   3_xyz:   7.403  0.050  0.270 82.879  0.036  2.336   5.0012e-02
   3_adp:   7.403  0.050  0.270 82.879  0.036  2.336   5.0012e-02
   3_occ:   7.403  0.050  0.270 82.879  0.036  2.336   5.0012e-02
   4_bss:   7.403  0.050  0.270 82.879  0.036  2.336   5.0012e-02
   4_xyz:   6.528  0.042  0.226 82.575  0.034  2.407   3.0635e-02
   4_adp:   6.528  0.042  0.226 82.575  0.034  2.407   3.0635e-02
   4_occ:   6.528  0.042  0.226 82.575  0.034  2.407   3.0635e-02
   5_bss:   6.528  0.042  0.226 82.575  0.034  2.407   3.0635e-02
   5_xyz:   6.921  0.045  0.235 83.029  0.032  2.362   3.4976e-02
   5_adp:   6.921  0.045  0.235 83.029  0.032  2.362   3.4976e-02
   5_occ:   6.921  0.045  0.235 83.029  0.032  2.362   3.4976e-02
   5_bss:   6.921  0.045  0.235 83.029  0.032  2.362   3.4976e-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:  81.73   0.00  16.22  81.73   0.00  12.39  62.68   7.07  37.05
   1_occ:  81.73   0.00  16.22  81.73   0.00  12.39  62.68   7.07  37.05
   2_bss:  81.73   0.00  16.22  81.73   0.00  12.39  62.68   7.07  37.05
   2_xyz:  81.73   0.00  16.22  81.73   0.00  12.39  62.68   7.07  37.05
   2_adp:  81.43   0.74  17.19  81.43   0.74  12.99  75.15   2.41  40.03
   2_occ:  81.43   0.74  17.19  81.43   0.74  12.99  75.15   2.41  40.03
   3_bss:  81.43   0.74  17.19  81.43   0.74  12.99  75.15   2.41  40.03
   3_xyz:  81.43   0.74  17.19  81.43   0.74  12.99  75.15   2.41  40.03
   3_adp:  81.29   1.34  16.61  81.29   1.34  12.71  72.49   3.69  37.86
   3_occ:  81.29   1.34  16.61  81.29   1.34  12.71  72.49   3.69  37.86
   4_bss:  81.29   1.34  16.61  81.29   1.34  12.71  72.49   3.69  37.86
   4_xyz:  81.29   1.34  16.61  81.29   1.34  12.71  72.49   3.69  37.86
   4_adp:  78.03   1.83  16.12  78.03   1.83  12.50  69.23   5.72  35.84
   4_occ:  78.03   1.83  16.12  78.03   1.83  12.50  69.23   5.72  35.84
   5_bss:  78.03   1.83  16.12  78.03   1.83  12.50  69.23   5.72  35.84
   5_xyz:  78.03   1.83  16.12  78.03   1.83  12.50  69.23   5.72  35.84
   5_adp:  85.46   0.00  16.66  85.46   0.00  12.54  75.30   5.42  39.10
   5_occ:  85.46   0.00  16.66  85.46   0.00  12.54  75.30   5.42  39.10
   5_bss:  85.46   0.00  16.67  85.46   0.00  12.54  75.30   5.42  39.11
------------------------------------------------------------------------
 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:    0.661    0.019    0.261
   1_adp:    0.661    0.019    0.261
   1_occ:    0.661    0.019    0.261
   2_bss:    0.661    0.019    0.261
   2_xyz:    0.751    0.004    0.296
   2_adp:    0.751    0.004    0.296
   2_occ:    0.751    0.004    0.296
   3_bss:    0.751    0.004    0.296
   3_xyz:    1.010    0.021    0.320
   3_adp:    1.010    0.021    0.320
   3_occ:    1.010    0.021    0.320
   4_bss:    1.010    0.021    0.320
   4_xyz:    1.102    0.020    0.326
   4_adp:    1.102    0.020    0.326
   4_occ:    1.102    0.020    0.326
   5_bss:    1.102    0.020    0.326
   5_xyz:    1.182    0.024    0.333
   5_adp:    1.182    0.024    0.333
   5_occ:    1.182    0.024    0.333
   5_bss:    1.182    0.024    0.333
------------------------------------------------------------------------

CPU time actual refinement: 308.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/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_436/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_436/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 308.57 
  Macro-tasks:
    bulk solvent and scale       = 37.23  
    individual site refinement   = 126.41 
    weights calculation          = 28.78  
    collect and process          = 6.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 199.01 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 96.84  
    alpha_beta                      = 7.71   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 106.14 
    fmodel                         = 5.95   
    r_factors                      = 0.17   
    phase_errors                   = 11.33  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 230.64 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.413 micro seconds
Total CPU time: 5.36 minutes
from_scatterers_fft:    626 calls, 96.51 s
gradients_fft:          571 calls, 92.90 s

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

# Date 2008-01-16 Time 04:49:07 PST -0800 (1200487747.74 s)
Start R-work = 0.2925, R-free = 0.2837 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.2790, R-free = 0.2698
Final R-work = 0.1098, R-free = 0.1555