# Date 2008-01-16 Time 04:07:16 PST -0800 (1200485236.15 s)
#phil __OFF__

Command line arguments: "../180.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11877
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 180

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.93, 85.9581, 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: (68.845, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7541 1.96067
Completeness in resolution range: 0.953979
Completeness with d_max=infinity: 0.951015

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7541
                             d_min =   1.9607

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7541 1.96067
Completeness in resolution range: 0.953979
Completeness with d_max=infinity: 0.951015

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7545 -  4.1948 [2165/2193]  1947   218  10.1%
  bin  2:  4.1948 -  3.3423 [2060/2079]  1856   204   9.9%
  bin  3:  3.3423 -  2.9235 [2049/2070]  1845   204  10.0%
  bin  4:  2.9235 -  2.6579 [2025/2049]  1823   202  10.0%
  bin  5:  2.6579 -  2.4684 [2016/2037]  1806   210  10.4%
  bin  6:  2.4684 -  2.3234 [1999/2045]  1805   194   9.7%
  bin  7:  2.3234 -  2.2075 [1990/2022]  1794   196   9.8%
  bin  8:  2.2075 -  2.1117 [2000/2035]  1796   204  10.2%
  bin  9:  2.1117 -  2.0306 [1958/1988]  1759   199  10.2%
  bin 10:  2.0306 -  1.9607 [1327/2016]  1199   128   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/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:
        1.43 -     2.12: 14
        2.12 -     2.82: 881
        2.82 -     3.51: 4504
        3.51 -     4.21: 9459
        4.21 -     4.90: 13841
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.428 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.539 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.563 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.696 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28694 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_180/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3101   r_free= 0.3116   ksol= 0.00   Bsol= 0.00   scale= 0.986    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 6.022911                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6784 0.99   1401  157 0.2826 0.2833      6.3498       6.389|
|  2:  4.6784 -  3.7332 0.99   1347  151 0.2464 0.2304      6.4009      6.3914|
|  3:  3.7332 -  3.2671 0.99   1323  148 0.2626 0.2613      6.2958      6.3792|
|  4:  3.2671 -  2.9711 0.99   1313  135 0.2763 0.3286      6.1849       6.272|
|  5:  2.9711 -  2.7596 0.99   1307  150 0.3039 0.2980      6.0592      6.0365|
|  6:  2.7596 -  2.5978 0.98   1297  144 0.3297 0.3531      6.0225      5.9435|
|  7:  2.5978 -  2.4684 0.99   1289  153 0.3303 0.2909      5.9836      5.8909|
|  8:  2.4684 -  2.3614 0.98   1307  134 0.3377 0.3215      5.9398       5.934|
|  9:  2.3614 -  2.2708 0.98   1285  146 0.3527 0.3766      5.9089      5.9874|
| 10:  2.2708 -  2.1927 0.97   1258  140 0.3396 0.3437      5.8836      5.8513|
| 11:  2.1927 -  2.1243 0.99   1291  146 0.3481 0.3667      5.8305      5.8822|
| 12:  2.1243 -  2.0638 0.98   1271  141 0.3638 0.3501      5.8032      5.7812|
| 13:  2.0638 -  2.0096 0.97   1254  133 0.3569 0.3786      5.7092      5.6395|
| 14:  2.0096 -  1.9607 0.54    687   81 0.3942 0.3545      5.7532      5.5653|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6784  1401   157  0.78  26.89   0.87     0.79      44296.71|
|  2:  4.6784 -  3.7332  1347   151  0.84  22.37   0.99     0.92      46915.83|
|  3:  3.7332 -  3.2671  1323   148  0.81  25.68   1.01     0.97      44541.31|
|  4:  3.2671 -  2.9711  1313   135  0.79  27.89   1.01     0.96      38171.95|
|  5:  2.9711 -  2.7596  1307   150  0.74  32.05   1.01     0.94      31530.27|
|  6:  2.7596 -  2.5978  1297   144  0.73  32.81   0.99     0.94      26768.68|
|  7:  2.5978 -  2.4684  1289   153  0.74  31.87   1.01     0.96      24209.56|
|  8:  2.4684 -  2.3614  1307   134  0.73  33.10   1.04     0.96      22721.49|
|  9:  2.3614 -  2.2708  1285   146  0.71  34.95   1.03     0.96      22535.42|
| 10:  2.2708 -  2.1927  1258   140  0.70  35.46   1.07     0.95      21094.87|
| 11:  2.1927 -  2.1243  1291   146  0.70  35.79   1.04     0.96      19874.13|
| 12:  2.1243 -  2.0638  1271   141  0.70  35.89   1.07     0.99      17830.83|
| 13:  2.0638 -  2.0096  1254   133  0.68  37.38   1.07     0.95      15994.17|
| 14:  2.0096 -  1.9607   687    81  0.69  37.14   1.04     0.85      13436.06|
|alpha:            min =        0.79 max =            0.99 mean =         0.94|
|beta:             min =    13436.06 max =        46915.83 mean =     28601.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.99 mean =        31.81|
|phase err.(test): min =        0.00 max =           89.63 mean =        31.76|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.630485              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.370   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.612868              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.334   (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 |  1.428 -  1.775:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.775 -  2.122:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.122 -  2.470:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.470 -  2.817:      848 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.817 -  3.164:     2078 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.164 -  3.511:     2426 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.511 -  3.858:     4676 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.858 -  4.206:     4783 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6263 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7578 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.428 |       0.539 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3101   r_free= 0.3116   ksol= 0.00   Bsol= 0.00   scale= 0.986    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 6.022911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2951   r_free= 0.2973   ksol= 0.32   Bsol= 28.84   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.69,-2.77,-1.30,-0.00,-0.00,-0.00); trace/3= -1.13                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.997005                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.339631              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.187   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.072   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2951      final r-factor (work) = 0.1771          |
| start r-factor (free) = 0.2973      final r-factor (free) = 0.1969          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2303 = 3.34 * 0.50 * 6.0158 + 1.00 * 0.1851                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6016 = 3.34 * 0.50 * 5.7101 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1771      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.1969      final r-factor (free) = 0.2028          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8128 = 0.32 * 1.00 * 5.7101 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7464 = 0.32 * 1.00 * 5.4373 + 1.00 * 0.0261                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.25   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    62.25   16.73    None  None   None       |
|    Sol.    : 438    0      7.16    62.25   37.68    None  None   None       |
|    Mac.    : 2385   0      0.00    61.49   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.225:  251   |   5:    31.126 -  37.351:  110        |
|      1:     6.225 -  12.450: 1124   |   6:    37.351 -  43.576:  103        |
|      2:    12.450 -  18.676:  713   |   7:    43.576 -  49.802:   72        |
|      3:    18.676 -  24.901:  245   |   8:    49.802 -  56.027:   74        |
|      4:    24.901 -  31.126:  110   |   9:    56.027 -  62.252:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2028             target_work(ml) = 5.449         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1626 r_free = 0.2028             target_work(ml) = 5.448         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2028   ksol= 0.32   Bsol= 28.84   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.69,-2.77,-1.30,-0.00,-0.00,-0.00); trace/3= -1.13                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.448153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1583   r_free= 0.1982   ksol= 0.32   Bsol= 36.74   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.82,-1.75,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.430153                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.597746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.066   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191553              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.539   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1583      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1982      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1347 = 2.60 * 0.50 * 5.4415 + 1.00 * 0.0668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9632 = 2.60 * 0.50 * 5.3176 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0518 = 0.19 * 1.00 * 5.3176 + 1.00 * 0.0332                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0000 = 0.19 * 1.00 * 5.1836 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    73.78   16.77    None  None   None       |
|    all(noH): 2823   0      1.39    73.78   16.77    None  None   None       |
|    Sol.    : 438    0      6.28    67.24   37.60    None  None   None       |
|    Mac.    : 2385   0      1.39    73.78   12.94    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:     1.386 -   8.625:  619   |   5:    37.581 -  44.821:  121        |
|      1:     8.625 -  15.864: 1297   |   6:    44.821 -  52.060:  101        |
|      2:    15.864 -  23.103:  374   |   7:    52.060 -  59.299:   53        |
|      3:    23.103 -  30.342:  123   |   8:    59.299 -  66.538:   14        |
|      4:    30.342 -  37.581:  116   |   9:    66.538 -  73.777:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1579             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1578             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1578   ksol= 0.32   Bsol= 36.74   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.82,-1.75,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1568   ksol= 0.32   Bsol= 38.47   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.45,-1.49,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.979615              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.049  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.330  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7769 = 2.98 * 0.50 * 5.1823 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7039 = 2.98 * 0.50 * 5.1250 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2792 = 0.25 * 1.00 * 5.1250 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2737 = 0.25 * 1.00 * 5.1020 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    75.68   16.66    None  None   None       |
|    all(noH): 2823   0      1.73    75.68   16.66    None  None   None       |
|    Sol.    : 438    0      4.29    68.34   37.58    None  None   None       |
|    Mac.    : 2385   0      1.73    75.68   12.82    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:     1.732 -   9.127:  782   |   5:    38.705 -  46.100:  119        |
|      1:     9.127 -  16.521: 1207   |   6:    46.100 -  53.494:   96        |
|      2:    16.521 -  23.916:  322   |   7:    53.494 -  60.889:   42        |
|      3:    23.916 -  31.310:  122   |   8:    60.889 -  68.283:   14        |
|      4:    31.310 -  38.705:  114   |   9:    68.283 -  75.678:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1514             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1514             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1514   ksol= 0.32   Bsol= 38.47   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.45,-1.49,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100740                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1513   ksol= 0.32   Bsol= 40.14   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.29,-1.33,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.550741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.282  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.178584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.227  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0244 = 1.55 * 0.50 * 5.1019 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0158 = 1.55 * 0.50 * 5.1111 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1515      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9200 = 0.18 * 1.00 * 5.1111 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9202 = 0.18 * 1.00 * 5.1134 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    75.90   16.49    None  None   None       |
|    all(noH): 2823   0      1.68    75.90   16.49    None  None   None       |
|    Sol.    : 438    0      5.80    68.33   37.17    None  None   None       |
|    Mac.    : 2385   0      1.68    75.90   12.70    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:     1.676 -   9.098:  784   |   5:    38.786 -  46.208:  117        |
|      1:     9.098 -  16.520: 1217   |   6:    46.208 -  53.629:   94        |
|      2:    16.520 -  23.942:  317   |   7:    53.629 -  61.051:   35        |
|      3:    23.942 -  31.364:  126   |   8:    61.051 -  68.473:   14        |
|      4:    31.364 -  38.786:  115   |   9:    68.473 -  75.895:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1514             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1514             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1514   ksol= 0.32   Bsol= 40.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.29,-1.33,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113563                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1514   ksol= 0.32   Bsol= 40.14   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.13,-1.19,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.315928              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.885  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.802591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.793  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4174 = 1.32 * 0.50 * 5.1137 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4155 = 1.32 * 0.50 * 5.1182 + 1.00 * 0.0479                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1149 = 0.80 * 1.00 * 5.1182 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1148 = 0.80 * 1.00 * 5.1163 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    85.10   16.74    None  None   None       |
|    all(noH): 2823   0      0.61    85.10   16.74    None  None   None       |
|    Sol.    : 438    0      5.45    74.98   38.77    None  None   None       |
|    Mac.    : 2385   0      0.61    85.10   12.70    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:     0.607 -   9.056:  836   |   5:    42.851 -  51.300:  108        |
|      1:     9.056 -  17.505: 1241   |   6:    51.300 -  59.749:   82        |
|      2:    17.505 -  25.953:  271   |   7:    59.749 -  68.198:   25        |
|      3:    25.953 -  34.402:  126   |   8:    68.198 -  76.646:    9        |
|      4:    34.402 -  42.851:  120   |   9:    76.646 -  85.095:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1534             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1535             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1535   ksol= 0.32   Bsol= 40.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.13,-1.19,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122638                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6784 0.99   1401  157 0.1001 0.1260      5.3795      5.5415|
|  2:  4.6784 -  3.7332 0.99   1347  151 0.0843 0.1087      5.4222      5.6085|
|  3:  3.7332 -  3.2671 0.99   1323  148 0.1036 0.1503       5.451      5.8287|
|  4:  3.2671 -  2.9711 0.99   1313  135 0.1148 0.1505      5.4164      5.5695|
|  5:  2.9711 -  2.7596 0.99   1307  150 0.1254 0.1614      5.2827       5.482|
|  6:  2.7596 -  2.5978 0.98   1297  144 0.1195 0.1941      5.1814      5.4608|
|  7:  2.5978 -  2.4684 0.99   1289  153 0.1166 0.1509      5.1203      5.2974|
|  8:  2.4684 -  2.3614 0.98   1307  134 0.1108 0.1616      5.0468      5.2753|
|  9:  2.3614 -  2.2708 0.98   1285  146 0.1144 0.1877      4.9951      5.3232|
| 10:  2.2708 -  2.1927 0.97   1258  140 0.1100 0.1513      4.9398       5.125|
| 11:  2.1927 -  2.1243 0.99   1291  146 0.1081 0.1769         4.9      5.2464|
| 12:  2.1243 -  2.0638 0.98   1271  141 0.1067 0.1620      4.8388      5.1424|
| 13:  2.0638 -  2.0096 0.97   1254  133 0.1092 0.1730      4.7769      5.0399|
| 14:  2.0096 -  1.9607 0.54    687   81 0.1047 0.1716      4.6988      4.9369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6784  1401   157  0.94   8.82   0.98     0.96       6708.30|
|  2:  4.6784 -  3.7332  1347   151  0.95   7.66   1.02     1.01       8612.36|
|  3:  3.7332 -  3.2671  1323   148  0.94  10.93   1.03     1.02       9940.90|
|  4:  3.2671 -  2.9711  1313   135  0.93  12.72   1.01     1.01       9667.42|
|  5:  2.9711 -  2.7596  1307   150  0.90  15.28   1.00     0.97       7724.81|
|  6:  2.7596 -  2.5978  1297   144  0.90  15.92   0.98     0.95       6674.10|
|  7:  2.5978 -  2.4684  1289   153  0.91  14.82   0.99     0.95       5695.81|
|  8:  2.4684 -  2.3614  1307   134  0.92  14.32   1.00     0.98       5140.52|
|  9:  2.3614 -  2.2708  1285   146  0.91  15.09   1.00     0.97       4653.12|
| 10:  2.2708 -  2.1927  1258   140  0.90  15.34   1.00     0.96       4250.89|
| 11:  2.1927 -  2.1243  1291   146  0.91  15.61   0.99     0.96       4121.84|
| 12:  2.1243 -  2.0638  1271   141  0.92  14.77   1.01     1.00       3697.82|
| 13:  2.0638 -  2.0096  1254   133  0.91  15.79   1.00     0.99       3317.30|
| 14:  2.0096 -  1.9607   687    81  0.91  15.12   0.98     0.93       2719.54|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2719.54 max =         9940.90 mean =      6071.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.62|
|phase err.(test): min =        0.00 max =           88.97 mean =        13.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1534   ksol= 0.32   Bsol= 41.65   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.90,-0.99,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1534   ksol= 0.32   Bsol= 41.65   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.90,-0.99,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122484                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6784 0.99   1401  157 0.1000 0.1261      5.3797      5.5422|
|  2:  4.6784 -  3.7332 0.99   1347  151 0.0845 0.1088      5.4234      5.6086|
|  3:  3.7332 -  3.2671 0.99   1323  148 0.1036 0.1503      5.4513      5.8291|
|  4:  3.2671 -  2.9711 0.99   1313  135 0.1148 0.1502       5.416      5.5685|
|  5:  2.9711 -  2.7596 0.99   1307  150 0.1252 0.1613       5.282      5.4814|
|  6:  2.7596 -  2.5978 0.98   1297  144 0.1194 0.1940       5.181      5.4599|
|  7:  2.5978 -  2.4684 0.99   1289  153 0.1166 0.1507      5.1197      5.2966|
|  8:  2.4684 -  2.3614 0.98   1307  134 0.1107 0.1614      5.0462      5.2744|
|  9:  2.3614 -  2.2708 0.98   1285  146 0.1144 0.1879      4.9949      5.3238|
| 10:  2.2708 -  2.1927 0.97   1258  140 0.1100 0.1512      4.9397      5.1242|
| 11:  2.1927 -  2.1243 0.99   1291  146 0.1080 0.1769      4.8998      5.2464|
| 12:  2.1243 -  2.0638 0.98   1271  141 0.1067 0.1620      4.8386      5.1424|
| 13:  2.0638 -  2.0096 0.97   1254  133 0.1092 0.1730      4.7765      5.0398|
| 14:  2.0096 -  1.9607 0.54    687   81 0.1047 0.1716      4.6987      4.9368|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6784  1401   157  0.94   8.82   0.98     0.96       6701.11|
|  2:  4.6784 -  3.7332  1347   151  0.95   7.67   1.02     1.01       8618.15|
|  3:  3.7332 -  3.2671  1323   148  0.94  10.94   1.03     1.03       9945.48|
|  4:  3.2671 -  2.9711  1313   135  0.93  12.70   1.02     1.01       9656.87|
|  5:  2.9711 -  2.7596  1307   150  0.90  15.27   1.00     0.97       7715.38|
|  6:  2.7596 -  2.5978  1297   144  0.90  15.91   0.99     0.96       6665.60|
|  7:  2.5978 -  2.4684  1289   153  0.91  14.80   0.99     0.96       5684.62|
|  8:  2.4684 -  2.3614  1307   134  0.92  14.31   1.01     0.98       5131.74|
|  9:  2.3614 -  2.2708  1285   146  0.91  15.09   1.01     0.98       4647.58|
| 10:  2.2708 -  2.1927  1258   140  0.90  15.34   1.00     0.97       4249.21|
| 11:  2.1927 -  2.1243  1291   146  0.91  15.60   1.00     0.97       4118.23|
| 12:  2.1243 -  2.0638  1271   141  0.92  14.76   1.02     1.01       3696.04|
| 13:  2.0638 -  2.0096  1254   133  0.91  15.80   1.01     1.00       3316.22|
| 14:  2.0096 -  1.9607   687    81  0.91  15.12   0.99     0.94       2719.01|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2719.01 max =         9945.48 mean =      6066.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.59    85.08   16.72    None  None   None       |
|    all(noH): 2823   0      0.59    85.08   16.72    None  None   None       |
|    Sol.    : 438    0      5.43    74.96   38.75    None  None   None       |
|    Mac.    : 2385   0      0.59    85.08   12.68    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:     0.587 -   9.036:  836   |   5:    42.831 -  51.280:  108        |
|      1:     9.036 -  17.485: 1241   |   6:    51.280 -  59.729:   82        |
|      2:    17.485 -  25.934:  271   |   7:    59.729 -  68.178:   25        |
|      3:    25.934 -  34.382:  126   |   8:    68.178 -  76.627:    9        |
|      4:    34.382 -  42.831:  120   |   9:    76.627 -  85.075:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 283         
Filter by distance & map next to the model:
   mapped sites are within: 0.422 - 4.349
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 278 from: 283
   mapped sites are within: 0.713 - 4.349

peak=    5.868 closest distance to " CB  ARG A 275 " =    0.979
peak=    5.438 closest distance to " O   HOH Z 142 " =    1.748
peak=    5.413 closest distance to " CG  PRO A  90 " =    1.167
peak=    5.320 closest distance to " O   HOH Z 126 " =    1.920
peak=    5.294 closest distance to " CG  PRO A  54 " =    1.253
peak=    5.075 closest distance to " CB  GLN A 223 " =    1.420
peak=    4.946 closest distance to " CG  PRO A 213 " =    1.291
peak=    4.942 closest distance to " CA  TYR A  30 " =    0.911
peak=    4.912 closest distance to " NE2 GLN A  11 " =    1.064
peak=    4.881 closest distance to " O   HOH Z  78 " =    1.816
peak=    4.849 closest distance to " CB  SER A  63 " =    1.165
peak=    4.842 closest distance to " NH2 ARG A  56 " =    2.112
peak=    4.789 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.694 closest distance to " O   HOH Z 232 " =    2.415
peak=    4.663 closest distance to " O   HOH Z 402 " =    1.449
peak=    4.627 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.566 closest distance to " O   HOH Z 287 " =    2.084
peak=    4.530 closest distance to " CB  PRO A  54 " =    1.005
peak=    4.513 closest distance to " CG  PRO A 243 " =    1.065
peak=    4.486 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.475 closest distance to " O   HOH Z 272 " =    1.837
peak=    4.475 closest distance to " O   HOH Z 427 " =    2.805
peak=    4.469 closest distance to " O   HOH Z 209 " =    2.246
peak=    4.440 closest distance to " C   PRO A 198 " =    1.513
peak=    4.385 closest distance to " CB  ASN A 148 " =    1.475
peak=    4.320 closest distance to " O   HOH Z 234 " =    3.594
peak=    4.310 closest distance to " O   HOH Z 250 " =    1.494
peak=    4.296 closest distance to " ND2 ASN A 187 " =    1.414
peak=    4.296 closest distance to " O   HOH Z  97 " =    2.471
peak=    4.276 closest distance to " CD2 TRP A 179 " =    1.377
peak=    4.276 closest distance to " O   HOH Z 298 " =    1.810
peak=    4.263 closest distance to " NZ  LYS A 117 " =    3.126
peak=    4.240 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.221 closest distance to " O   SER A  87 " =    2.219
peak=    4.221 closest distance to " O   HOH Z  97 " =    1.944
peak=    4.195 closest distance to " O   HOH Z 303 " =    2.022
peak=    4.193 closest distance to " CG2 VAL A 257 " =    0.861
peak=    4.192 closest distance to " O   HOH Z  54 " =    1.753
peak=    4.188 closest distance to " O   HOH Z  43 " =    1.996
peak=    4.182 closest distance to " O   HOH Z 193 " =    1.772
peak=    4.168 closest distance to " O   HOH Z 346 " =    1.674
peak=    4.151 closest distance to " CB  ARG A 190 " =    1.733
peak=    4.143 closest distance to " CB  ARG A  79 " =    1.287
peak=    4.116 closest distance to " CB  VAL A 265 " =    1.243
peak=    4.112 closest distance to " CG1 ILE A  33 " =    1.265
peak=    4.093 closest distance to " O   HOH Z 128 " =    1.914
peak=    4.073 closest distance to " OG ASER A 258 " =    3.043
peak=    4.065 closest distance to " O   HOH Z  15 " =    2.210
peak=    4.042 closest distance to " O   HOH Z 344 " =    3.032
peak=    4.032 closest distance to " CA  ARG A  36 " =    1.005
peak=    4.025 closest distance to " CB  GLU A 128 " =    1.076
peak=    4.019 closest distance to " CA  ALA A  21 " =    1.098
peak=    4.016 closest distance to " O   HOH Z 389 " =    1.826
peak=    4.003 closest distance to " CB  TYR A 169 " =    0.769
peak=    3.985 closest distance to " O   HOH Z 203 " =    1.728
peak=    3.978 closest distance to " CG2 ILE A 120 " =    1.187
peak=    3.965 closest distance to " O   HOH Z 403 " =    1.765
peak=    3.953 closest distance to " O   HOH Z 416 " =    2.593
peak=    3.923 closest distance to " OD1 ASN A  69 " =    2.547
peak=    3.920 closest distance to " O   HOH Z 189 " =    2.042
peak=    3.917 closest distance to " CB  SER A   3 " =    1.238
peak=    3.915 closest distance to " CA  ASN A 215 " =    1.102
peak=    3.912 closest distance to " O   HOH Z 327 " =    1.612
peak=    3.908 closest distance to " CB  LEU A 228 " =    1.064
peak=    3.907 closest distance to " O   HOH Z  59 " =    1.959
peak=    3.906 closest distance to " NH2BARG A 145 " =    2.048
peak=    3.905 closest distance to " O   HOH Z 423 " =    1.951
peak=    3.892 closest distance to " CG  ARG A  66 " =    2.528
peak=    3.885 closest distance to " O   HOH Z 392 " =    2.919
peak=    3.876 closest distance to " O   HOH Z   6 " =    2.301
peak=    3.867 closest distance to " O   HOH Z  44 " =    1.848
peak=    3.866 closest distance to " O   HOH Z 128 " =    2.157
peak=    3.861 closest distance to " N   ASN A  39 " =    1.199
peak=    3.857 closest distance to " CB  TRP A 266 " =    1.023
peak=    3.850 closest distance to " O   HOH Z  40 " =    1.790
peak=    3.812 closest distance to " CZ  PHE A 218 " =    1.052
peak=    3.810 closest distance to " OD2 ASP A 286 " =    2.762
peak=    3.803 closest distance to " CB  ARG A  79 " =    0.869
peak=    3.792 closest distance to " O   HOH Z 173 " =    2.045
peak=    3.773 closest distance to " CD2 LEU A 297 " =    0.948
peak=    3.767 closest distance to " CG AARG A 275 " =    1.066
peak=    3.756 closest distance to " CB  SER A  26 " =    1.643
peak=    3.755 closest distance to " O   HOH Z  61 " =    1.612
peak=    3.751 closest distance to " O   HOH Z  68 " =    2.107
peak=    3.736 closest distance to " CB  THR A  31 " =    1.583
peak=    3.735 closest distance to " O   HOH Z 280 " =    2.941
peak=    3.724 closest distance to " O   HOH Z 132 " =    2.680
peak=    3.717 closest distance to " O   HOH Z 126 " =    2.101
peak=    3.715 closest distance to " CG1BVAL A  72 " =    1.518
peak=    3.714 closest distance to " O   HOH Z 227 " =    1.552
peak=    3.697 closest distance to " CB  VAL A 202 " =    1.513
peak=    3.687 closest distance to " O   HOH Z 368 " =    2.027
peak=    3.683 closest distance to " CE  LYS A  76 " =    0.787
peak=    3.674 closest distance to " N   TYR A 116 " =    1.567
peak=    3.665 closest distance to " CD  ARG A 269 " =    1.032
peak=    3.661 closest distance to " O   HOH Z  88 " =    2.635
peak=    3.647 closest distance to " CB  TRP A 179 " =    1.126
peak=    3.642 closest distance to " O   HOH Z 421 " =    1.692
peak=    3.632 closest distance to " CB  GLU A 277 " =    3.511
peak=    3.630 closest distance to " O   HOH Z 144 " =    2.135
peak=    3.619 closest distance to " O   HOH Z 172 " =    3.520
peak=    3.615 closest distance to " CB  ILE A 120 " =    1.279
peak=    3.606 closest distance to " O   HOH Z 368 " =    3.638
peak=    3.604 closest distance to " O   HOH Z  19 " =    2.214
peak=    3.600 closest distance to " CB  ALA A 291 " =    1.254
peak=    3.597 closest distance to " O   HOH Z 371 " =    3.144
peak=    3.593 closest distance to " O   HOH Z 158 " =    2.934
peak=    3.589 closest distance to " CG2 ILE A  20 " =    1.409
peak=    3.588 closest distance to " O   HOH Z 245 " =    1.309
peak=    3.587 closest distance to " O   HOH Z 250 " =    1.923
peak=    3.580 closest distance to " O   HOH Z 417 " =    3.249
peak=    3.558 closest distance to " CA  ALA A  84 " =    1.211
peak=    3.553 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.549 closest distance to " CG2BVAL A  41 " =    0.829
peak=    3.547 closest distance to " O   HOH Z 193 " =    1.959
peak=    3.541 closest distance to " O   HOH Z 291 " =    1.465
peak=    3.538 closest distance to " NH1AARG A 145 " =    1.227
peak=    3.537 closest distance to " O   HOH Z 132 " =    2.394
peak=    3.535 closest distance to " O   HOH Z 426 " =    1.495
peak=    3.530 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.529 closest distance to " CA  GLY A  80 " =    0.815
peak=    3.528 closest distance to " O   HOH Z 214 " =    2.246
peak=    3.524 closest distance to " O   HOH Z 265 " =    2.351
peak=    3.511 closest distance to " CA  MET A  40 " =    1.077
peak=    3.510 closest distance to " O   HOH Z 337 " =    3.531
peak=    3.507 closest distance to " CA  MET A 105 " =    1.042
peak=    3.484 closest distance to " CB  ASN A 110 " =    1.070
peak=    3.482 closest distance to " CG  LYS A  76 " =    1.006
peak=    3.481 closest distance to " CG  GLN A  77 " =    2.201
peak=    3.477 closest distance to " O   HOH Z  10 " =    1.821
peak=    3.474 closest distance to " NZ  LYS A 119 " =    1.470
peak=    3.466 closest distance to " O   HOH Z 371 " =    1.517
peak=    3.459 closest distance to " O   HOH Z 357 " =    1.867
peak=    3.449 closest distance to " N   ARG A 156 " =    1.286
peak=    3.444 closest distance to " O   HOH Z 305 " =    3.553
peak=    3.442 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.438 closest distance to " CB  PRO A 198 " =    1.123
peak=    3.438 closest distance to " CB  ASP A 140 " =    0.960
peak=    3.435 closest distance to " O   HOH Z 359 " =    1.476
peak=    3.428 closest distance to " O   HOH Z 187 " =    2.202
peak=    3.427 closest distance to " O   HOH Z 365 " =    2.826
peak=    3.419 closest distance to " CD  LYS A 119 " =    1.326
peak=    3.419 closest distance to " O   HOH Z 411 " =    3.835
peak=    3.417 closest distance to " CB  ALA A 114 " =    1.076
peak=    3.417 closest distance to " O   HOH Z   9 " =    2.185
peak=    3.416 closest distance to " O   ALA A   1 " =    1.694
peak=    3.412 closest distance to " CB  SER A  62 " =    1.405
peak=    3.409 closest distance to " C   ILE A 106 " =    1.896
peak=    3.406 closest distance to " ND2 ASN A 110 " =    1.720
peak=    3.406 closest distance to " O   HOH Z 180 " =    2.261
peak=    3.399 closest distance to " O   HOH Z 148 " =    3.309
peak=    3.397 closest distance to " CA  ASP A 162 " =    1.112
peak=    3.396 closest distance to " CB  GLU A  46 " =    1.027
peak=    3.394 closest distance to " O   HOH Z 299 " =    4.349
peak=    3.388 closest distance to " CB  GLN A  88 " =    1.130
peak=    3.387 closest distance to " CG  MET A 113 " =    0.965
peak=    3.385 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.382 closest distance to " O   HOH Z  61 " =    1.459
peak=    3.379 closest distance to " CD1 ILE A 106 " =    0.887
peak=    3.378 closest distance to " CA  ARG A 195 " =    1.169
peak=    3.377 closest distance to " CB  SER A 141 " =    1.095
peak=    3.377 closest distance to " O   HOH Z  21 " =    1.802
peak=    3.365 closest distance to " O   TRP A 274 " =    1.958
peak=    3.360 closest distance to " CB  ARG A 139 " =    0.916
peak=    3.358 closest distance to " O   HOH Z 406 " =    1.482
peak=    3.348 closest distance to " CA  THR A 221 " =    0.968
peak=    3.348 closest distance to " OG BSER A 164 " =    2.239
peak=    3.346 closest distance to " O   HOH Z   1 " =    1.910
peak=    3.340 closest distance to " CA  ASP A 140 " =    1.103
peak=    3.340 closest distance to " O   HOH Z 247 " =    1.344
peak=    3.338 closest distance to " O   HOH Z 185 " =    1.698
peak=    3.333 closest distance to " CG1 ILE A 120 " =    1.099
peak=    3.331 closest distance to " CZ2 TRP A 179 " =    1.703
peak=    3.331 closest distance to " N   PHE A 130 " =    1.233
peak=    3.327 closest distance to " CA  ALA A  43 " =    1.237
peak=    3.325 closest distance to " CB  HIS A 108 " =    0.857
peak=    3.324 closest distance to " CA  ASN A 176 " =    1.120
peak=    3.318 closest distance to " O   HOH Z 261 " =    1.672
peak=    3.317 closest distance to " CG  GLU A 277 " =    2.132
peak=    3.316 closest distance to " OH  TYR A 116 " =    1.027
peak=    3.313 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.313 closest distance to " CB  GLN A 278 " =    0.857
peak=    3.311 closest distance to " O   THR A 220 " =    1.269
peak=    3.311 closest distance to " CE  LYS A 119 " =    1.180
peak=    3.305 closest distance to " O   HOH Z 433 " =    1.764
peak=    3.302 closest distance to " O   HOH Z  80 " =    1.742
peak=    3.300 closest distance to " CG2 VAL A  78 " =    0.896
peak=    3.295 closest distance to " CB  SER A 212 " =    1.058
peak=    3.290 closest distance to " CG2 ILE A 239 " =    0.713
peak=    3.288 closest distance to " O   HOH Z 279 " =    2.125
peak=    3.286 closest distance to " O   HOH Z  49 " =    2.123
peak=    3.275 closest distance to " O   HOH Z  66 " =    2.113
peak=    3.272 closest distance to " CB  SER A  62 " =    0.930
peak=    3.272 closest distance to " CA  THR A 264 " =    0.855
peak=    3.272 closest distance to " CB  MET A  47 " =    0.996
peak=    3.271 closest distance to " O   HOH Z 286 " =    2.213
peak=    3.268 closest distance to " CG  MET A 185 " =    1.148
peak=    3.267 closest distance to " O   HOH Z 425 " =    1.974
peak=    3.267 closest distance to " CD1AILE A 234 " =    0.943
peak=    3.264 closest distance to " O   HOH Z  94 " =    2.014
peak=    3.264 closest distance to " O   HOH Z  71 " =    2.148
peak=    3.264 closest distance to " CD1 LEU A  96 " =    0.748
peak=    3.263 closest distance to " CA  ALA A  51 " =    0.861
peak=    3.262 closest distance to " CB  ASN A 215 " =    1.123
peak=    3.262 closest distance to " O   HOH Z 257 " =    2.072
peak=    3.261 closest distance to " NH2 ARG A 219 " =    1.940
peak=    3.260 closest distance to " O  BHOH Z 338 " =    2.307
peak=    3.260 closest distance to " O   HOH Z 124 " =    1.235
peak=    3.255 closest distance to " O   HOH Z 336 " =    1.648
peak=    3.252 closest distance to " CB  ALA A  34 " =    1.041
peak=    3.247 closest distance to " CA  ALA A 291 " =    0.794
peak=    3.245 closest distance to " O   HOH Z  35 " =    2.472
peak=    3.242 closest distance to " O   HOH Z 403 " =    1.296
peak=    3.242 closest distance to " O   HOH Z 313 " =    1.906
peak=    3.241 closest distance to " CB  VAL A 126 " =    1.083
peak=    3.240 closest distance to " CG  GLN A  11 " =    1.619
peak=    3.237 closest distance to " CD2 HIS A  81 " =    1.082
peak=    3.231 closest distance to " CA  LYS A 290 " =    1.214
peak=    3.230 closest distance to " O   HOH Z 380 " =    1.963
peak=    3.229 closest distance to " O   HOH Z 393 " =    3.319
peak=    3.227 closest distance to " O   HOH Z 329 " =    3.874
peak=    3.227 closest distance to " O   HOH Z 273 " =    2.693
peak=    3.224 closest distance to " O   HOH Z 423 " =    3.110
peak=    3.224 closest distance to " O   HOH Z 248 " =    1.597
peak=    3.219 closest distance to " CG  ARG A 269 " =    1.199
peak=    3.218 closest distance to " O   SER A 164 " =    1.117
peak=    3.217 closest distance to " CD  ARG A  36 " =    1.016
peak=    3.217 closest distance to " CB  TYR A 116 " =    0.767
peak=    3.215 closest distance to " O   HOH Z 435 " =    1.849
peak=    3.215 closest distance to " O   HOH Z  64 " =    2.269
peak=    3.214 closest distance to " O   HOH Z 342 " =    0.828
peak=    3.202 closest distance to " O   HOH Z  44 " =    3.318
peak=    3.201 closest distance to " CD1 LEU A 300 " =    1.342
peak=    3.201 closest distance to " O   HOH Z 353 " =    2.621
peak=    3.201 closest distance to " CA  ILE A 234 " =    0.918
peak=    3.198 closest distance to " CD  LYS A 166 " =    1.236
peak=    3.197 closest distance to " NZ  LYS A  76 " =    1.531
peak=    3.190 closest distance to " OG  SER A  62 " =    2.772
peak=    3.189 closest distance to " CA  SER A 146 " =    1.790
peak=    3.187 closest distance to " O   HOH Z 302 " =    1.872
peak=    3.186 closest distance to " CE1 HIS A 108 " =    1.175
peak=    3.186 closest distance to " C   TYR A 214 " =    1.457
peak=    3.180 closest distance to " O   HOH Z  47 " =    1.511
peak=    3.174 closest distance to " O   HOH Z 219 " =    2.031
peak=    3.173 closest distance to " O   HOH Z 109 " =    2.393
peak=    3.171 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.168 closest distance to " CE ALYS A 290 " =    1.271
peak=    3.168 closest distance to " OE2 GLU A  53 " =    2.082
peak=    3.157 closest distance to " CB  ARG A 269 " =    0.758
peak=    3.157 closest distance to " O   HOH Z 367 " =    3.675
peak=    3.153 closest distance to " CB  SER A 273 " =    0.855
peak=    3.147 closest distance to " O   HOH Z  88 " =    2.499
peak=    3.144 closest distance to " O   HOH Z 345 " =    3.122
peak=    3.141 closest distance to " CG2 VAL A 202 " =    1.136
peak=    3.133 closest distance to " CD  LYS A  76 " =    1.954
peak=    3.133 closest distance to " OH  TYR A  30 " =    1.010
peak=    3.127 closest distance to " CB  GLN A 103 " =    0.827
peak=    3.127 closest distance to " O   HOH Z 325 " =    2.507
peak=    3.121 closest distance to " CA  ARG A 159 " =    1.324
peak=    3.115 closest distance to " CB  LYS A 290 " =    1.165
peak=    3.114 closest distance to " O   HOH Z  47 " =    1.687
peak=    3.113 closest distance to " CA  ALA A 299 " =    0.972
peak=    3.108 closest distance to " O   HOH Z 380 " =    1.946
peak=    3.107 closest distance to " O   HOH Z 298 " =    2.656
peak=    3.099 closest distance to " O   HOH Z  89 " =    1.936
peak=    3.095 closest distance to " N   VAL A 265 " =    1.131
peak=    3.095 closest distance to " O   HOH Z 234 " =    2.245
peak=    3.091 closest distance to " O   HOH Z 409 " =    3.087
peak=    3.091 closest distance to " CG2 VAL A 197 " =    1.037
peak=    3.088 closest distance to " CB  ASP A 191 " =    1.151
peak=    3.086 closest distance to " CG2 THR A 294 " =    1.582
peak=    3.083 closest distance to " NE2 GLN A  58 " =    2.611
peak=    3.080 closest distance to " CA  ARG A 102 " =    1.061
peak=    3.076 closest distance to " ND2 ASN A 249 " =    0.918
peak=    3.074 closest distance to " CD2 TYR A  30 " =    0.934
peak=    3.074 closest distance to " O   HOH Z 112 " =    2.608
peak=    3.049 closest distance to " CB  LEU A 255 " =    0.814
peak=    2.970 closest distance to " O   HOH Z 286 " =    2.421

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.859 - 5.834
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 196
   mapped sites are within: 0.859 - 5.834

peak=   -4.975 closest distance to " O   HOH Z 266 " =    4.909
peak=   -4.527 closest distance to " C   HIS A 108 " =    1.104
peak=   -4.476 closest distance to " CG  GLN A  58 " =    1.111
peak=   -4.420 closest distance to " O   VAL A  67 " =    2.611
peak=   -4.361 closest distance to " OG BSER A 134 " =    1.205
peak=   -4.353 closest distance to " SG  CYS A 254 " =    3.376
peak=   -4.323 closest distance to " O   HOH Z 372 " =    2.289
peak=   -4.274 closest distance to " O   HOH Z 198 " =    1.795
peak=   -4.263 closest distance to " CG  GLN A 223 " =    1.949
peak=   -4.206 closest distance to " CB  PRO A 243 " =    2.606
peak=   -4.148 closest distance to " CG1 VAL A 112 " =    2.778
peak=   -4.111 closest distance to " CD  ARG A 156 " =    2.041
peak=   -4.065 closest distance to " O   PRO A 198 " =    1.205
peak=   -4.056 closest distance to " O   HOH Z 377 " =    2.022
peak=   -4.044 closest distance to " OD2 ASP A 191 " =    1.391
peak=   -4.041 closest distance to " CE2 TYR A  30 " =    2.791
peak=   -4.041 closest distance to " O   HOH Z 290 " =    1.140
peak=   -4.040 closest distance to " O   HOH Z 231 " =    2.299
peak=   -4.034 closest distance to " CA  VAL A  67 " =    2.827
peak=   -3.994 closest distance to " ND2 ASN A  45 " =    0.993
peak=   -3.982 closest distance to " OXT GLY A 302 " =    2.754
peak=   -3.977 closest distance to " CB  PHE A 192 " =    1.960
peak=   -3.922 closest distance to " N   GLN A  58 " =    1.795
peak=   -3.918 closest distance to " CB  ASN A  39 " =    2.277
peak=   -3.916 closest distance to " O   HOH Z 353 " =    2.187
peak=   -3.910 closest distance to " O   HOH Z 102 " =    1.627
peak=   -3.875 closest distance to " CZ3 TRP A 179 " =    1.249
peak=   -3.864 closest distance to " OG  SER A   3 " =    1.685
peak=   -3.800 closest distance to " ND2 ASN A 187 " =    1.526
peak=   -3.799 closest distance to " O   ALA A 161 " =    1.604
peak=   -3.798 closest distance to " CZ  TYR A 169 " =    1.753
peak=   -3.790 closest distance to " CG  PHE A 283 " =    2.653
peak=   -3.776 closest distance to " O   PHE A 218 " =    1.528
peak=   -3.776 closest distance to " CD1 LEU A 101 " =    2.322
peak=   -3.773 closest distance to " O   HOH Z 407 " =    2.711
peak=   -3.771 closest distance to " N   ALA A 248 " =    1.677
peak=   -3.763 closest distance to " CB  ALA A 291 " =    2.399
peak=   -3.755 closest distance to " CD  ARG A 139 " =    1.489
peak=   -3.753 closest distance to " O   HOH Z 351 " =    1.480
peak=   -3.750 closest distance to " CB  ALA A 161 " =    2.452
peak=   -3.745 closest distance to " N   ALA A  43 " =    2.560
peak=   -3.742 closest distance to " O   HOH Z  13 " =    1.594
peak=   -3.737 closest distance to " O   HOH Z 385 " =    2.106
peak=   -3.721 closest distance to " O   HOH Z 114 " =    3.154
peak=   -3.706 closest distance to " O   HOH Z 126 " =    1.909
peak=   -3.701 closest distance to " CA  GLY A 203 " =    2.403
peak=   -3.701 closest distance to " CG2 ILE A 263 " =    2.232
peak=   -3.695 closest distance to " O   HOH Z 362 " =    5.834
peak=   -3.684 closest distance to " OD2 ASP A 171 " =    2.354
peak=   -3.683 closest distance to " CG1 VAL A  78 " =    2.975
peak=   -3.673 closest distance to " CB  ASP A 132 " =    2.248
peak=   -3.639 closest distance to " O   HOH Z 166 " =    1.543
peak=   -3.633 closest distance to " O   PRO A 163 " =    2.012
peak=   -3.628 closest distance to " O   HOH Z 185 " =    2.309
peak=   -3.616 closest distance to " O   HOH Z 211 " =    1.774
peak=   -3.601 closest distance to " O   SER A 210 " =    2.007
peak=   -3.584 closest distance to " CG  ASP A 231 " =    0.859
peak=   -3.564 closest distance to " CB  ALA A 248 " =    2.067
peak=   -3.563 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.562 closest distance to " O   HOH Z  63 " =    1.560
peak=   -3.555 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.546 closest distance to " OG  SER A  97 " =    2.101
peak=   -3.538 closest distance to " O   VAL A 174 " =    2.033
peak=   -3.528 closest distance to " OD1 ASP A 191 " =    1.555
peak=   -3.527 closest distance to " O   HOH Z 389 " =    1.757
peak=   -3.526 closest distance to " O   HOH Z 435 " =    2.740
peak=   -3.526 closest distance to " O   ARG A 145 " =    1.655
peak=   -3.526 closest distance to " OD1 ASN A  39 " =    2.186
peak=   -3.523 closest distance to " N   ASP A 286 " =    2.384
peak=   -3.519 closest distance to " CG2 THR A 178 " =    2.235
peak=   -3.515 closest distance to " CE  MET A 105 " =    2.247
peak=   -3.514 closest distance to " CD1 LEU A  25 " =    2.512
peak=   -3.504 closest distance to " O   HOH Z 165 " =    2.070
peak=   -3.501 closest distance to " O   GLN A  89 " =    1.501
peak=   -3.497 closest distance to " O   HOH Z  88 " =    4.354
peak=   -3.492 closest distance to " O   HOH Z 166 " =    1.974
peak=   -3.489 closest distance to " CZ  PHE A  59 " =    1.471
peak=   -3.482 closest distance to " O   HOH Z 313 " =    1.953
peak=   -3.474 closest distance to " C   MET A 188 " =    1.419
peak=   -3.463 closest distance to " O   HOH Z  11 " =    2.054
peak=   -3.459 closest distance to " CD1 PHE A  59 " =    1.912
peak=   -3.458 closest distance to " NH2AARG A 275 " =    5.005
peak=   -3.455 closest distance to " O   HOH Z 196 " =    2.089
peak=   -3.446 closest distance to " OD1 ASN A 148 " =    1.540
peak=   -3.443 closest distance to " CZ2 TRP A 274 " =    1.073
peak=   -3.441 closest distance to " O   ALA A  34 " =    2.281
peak=   -3.434 closest distance to " CD1 ILE A 239 " =    2.273
peak=   -3.424 closest distance to " ND2 ASN A  39 " =    1.210
peak=   -3.410 closest distance to " O   SER A  95 " =    1.504
peak=   -3.402 closest distance to " NH1 ARG A  66 " =    1.092
peak=   -3.400 closest distance to " CD2 LEU A 237 " =    2.636
peak=   -3.399 closest distance to " O   HOH Z  10 " =    1.429
peak=   -3.391 closest distance to " N   THR A  52 " =    1.692
peak=   -3.387 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.382 closest distance to " CZ  PHE A 130 " =    0.889
peak=   -3.380 closest distance to " C   ASP A 231 " =    2.540
peak=   -3.375 closest distance to " CD2 TYR A 293 " =    1.927
peak=   -3.374 closest distance to " O   HOH Z 395 " =    5.151
peak=   -3.370 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.366 closest distance to " O   SER A 135 " =    1.469
peak=   -3.366 closest distance to " OD2 ASP A  50 " =    1.495
peak=   -3.364 closest distance to " C   THR A 279 " =    1.208
peak=   -3.359 closest distance to " N   HIS A 115 " =    2.161
peak=   -3.358 closest distance to " N   ALA A 226 " =    1.937
peak=   -3.355 closest distance to " CG  GLU A 277 " =    1.207
peak=   -3.351 closest distance to " CB  ASP A 286 " =    2.136
peak=   -3.350 closest distance to " O   HOH Z 197 " =    5.003
peak=   -3.344 closest distance to " CB  PRO A 163 " =    2.442
peak=   -3.340 closest distance to " O   MET A  40 " =    2.663
peak=   -3.337 closest distance to " CB  PHE A 208 " =    2.243
peak=   -3.336 closest distance to " N   THR A 235 " =    1.389
peak=   -3.334 closest distance to " CA  GLY A 133 " =    1.898
peak=   -3.329 closest distance to " O   HOH Z 250 " =    1.374
peak=   -3.326 closest distance to " O   ALA A 292 " =    1.970
peak=   -3.324 closest distance to " O   HOH Z  43 " =    1.729
peak=   -3.320 closest distance to " C   LEU A 143 " =    1.017
peak=   -3.319 closest distance to " O   GLU A 152 " =    1.357
peak=   -3.317 closest distance to " O   SER A 146 " =    1.091
peak=   -3.316 closest distance to " O   HOH Z  24 " =    1.396
peak=   -3.303 closest distance to " CG  GLU A   2 " =    1.973
peak=   -3.302 closest distance to " CB  ASP A 132 " =    2.374
peak=   -3.301 closest distance to " O   TRP A  92 " =    1.730
peak=   -3.300 closest distance to " OG BSER A 134 " =    1.725
peak=   -3.299 closest distance to " CD  GLU A 236 " =    1.036
peak=   -3.299 closest distance to " O   HOH Z 423 " =    2.292
peak=   -3.297 closest distance to " OG  SER A  62 " =    1.682
peak=   -3.295 closest distance to " O   ILE A 106 " =    1.804
peak=   -3.293 closest distance to " NE2 GLN A  88 " =    1.791
peak=   -3.292 closest distance to " NH2 ARG A  79 " =    2.013
peak=   -3.291 closest distance to " O   HOH Z 427 " =    1.511
peak=   -3.289 closest distance to " O   HOH Z 421 " =    3.167
peak=   -3.288 closest distance to " O   LEU A 167 " =    1.465
peak=   -3.287 closest distance to " OD1 ASP A 191 " =    1.640
peak=   -3.276 closest distance to " O   HOH Z 369 " =    2.119
peak=   -3.276 closest distance to " OG  SER A 206 " =    1.548
peak=   -3.273 closest distance to " CD1 LEU A 228 " =    1.982
peak=   -3.266 closest distance to " O   ALA A  51 " =    1.322
peak=   -3.264 closest distance to " O   HOH Z 111 " =    3.605
peak=   -3.261 closest distance to " CD2 LEU A 300 " =    2.852
peak=   -3.260 closest distance to " O   HOH Z  37 " =    1.748
peak=   -3.256 closest distance to " CG1 VAL A 230 " =    1.959
peak=   -3.255 closest distance to " CZ  ARG A 259 " =    0.927
peak=   -3.253 closest distance to " O   HOH Z 134 " =    2.994
peak=   -3.251 closest distance to " OD1 ASP A 171 " =    1.538
peak=   -3.249 closest distance to " NH1 ARG A 195 " =    2.586
peak=   -3.244 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.244 closest distance to " CB  GLN A  11 " =    1.789
peak=   -3.238 closest distance to " NE2 GLN A  88 " =    1.098
peak=   -3.237 closest distance to " O   HOH Z 309 " =    2.566
peak=   -3.230 closest distance to " OE1 GLN A 194 " =    1.648
peak=   -3.225 closest distance to " O   HOH Z  11 " =    1.772
peak=   -3.224 closest distance to " OD2 ASP A  50 " =    2.296
peak=   -3.220 closest distance to " N   SER A 206 " =    1.820
peak=   -3.220 closest distance to " CG  GLU A  53 " =    1.467
peak=   -3.220 closest distance to " O   HOH Z 174 " =    4.115
peak=   -3.206 closest distance to " O   ASN A  45 " =    1.867
peak=   -3.203 closest distance to " CA  TRP A  70 " =    2.368
peak=   -3.203 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.199 closest distance to " CE3 TRP A 150 " =    2.134
peak=   -3.196 closest distance to " CG  PRO A 243 " =    1.648
peak=   -3.184 closest distance to " O   HOH Z 171 " =    1.994
peak=   -3.183 closest distance to " SG ACYS A 201 " =    1.987
peak=   -3.181 closest distance to " OXT GLY A 302 " =    3.313
peak=   -3.173 closest distance to " O   HOH Z 210 " =    1.082
peak=   -3.172 closest distance to " CG  ARG A 269 " =    2.232
peak=   -3.171 closest distance to " CG  TRP A 266 " =    1.949
peak=   -3.166 closest distance to " O   GLY A  75 " =    1.672
peak=   -3.151 closest distance to " O   HOH Z 111 " =    2.511
peak=   -3.148 closest distance to " CG  GLU A 152 " =    0.978
peak=   -3.145 closest distance to " O   HOH Z 414 " =    1.490
peak=   -3.144 closest distance to " OD1 ASN A 176 " =    1.336
peak=   -3.144 closest distance to " OG ASER A 134 " =    1.185
peak=   -3.143 closest distance to " O   HOH Z   6 " =    1.499
peak=   -3.140 closest distance to " CA  GLY A  57 " =    2.135
peak=   -3.138 closest distance to " OG  SER A  97 " =    1.948
peak=   -3.137 closest distance to " C   ALA A 158 " =    1.312
peak=   -3.132 closest distance to " OE2 GLU A 152 " =    1.294
peak=   -3.132 closest distance to " O   HOH Z 193 " =    2.053
peak=   -3.131 closest distance to " O   HOH Z 191 " =    5.702
peak=   -3.131 closest distance to " CA  GLY A 241 " =    3.168
peak=   -3.130 closest distance to " O   ALA A 180 " =    1.013
peak=   -3.126 closest distance to " OD1 ASN A 301 " =    1.913
peak=   -3.119 closest distance to " OE1 GLN A 183 " =    1.436
peak=   -3.117 closest distance to " O   HOH Z  71 " =    1.845
peak=   -3.116 closest distance to " O   ALA A 180 " =    1.140
peak=   -3.115 closest distance to " O   HOH Z 281 " =    2.709
peak=   -3.111 closest distance to " O   ALA A   1 " =    1.757
peak=   -3.102 closest distance to " O   HOH Z 361 " =    3.420
peak=   -3.102 closest distance to " O   HOH Z 377 " =    1.508
peak=   -3.099 closest distance to " O   HOH Z 244 " =    2.075
peak=   -3.098 closest distance to " CD  GLN A 223 " =    0.944
peak=   -3.096 closest distance to " O   ASN A 249 " =    1.406
peak=   -3.084 closest distance to " NH2 ARG A  66 " =    5.075
peak=   -3.047 closest distance to " CG1 VAL A 197 " =    2.190
peak=   -3.042 closest distance to " OG1 THR A 246 " =    1.363
peak=   -3.021 closest distance to " ND2 ASN A  60 " =    1.431

================= 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    :  0.3101 0.3116   6.022911e+00   6.015804e+00
   1_bss:  0.2951 0.2973   5.997005e+00   5.988970e+00
   1_xyz:  0.1771 0.1969   5.498497e+00   5.599097e+00
   1_adp:  0.1629 0.2028   5.449124e+00   5.627656e+00
   1_occ:  0.1626 0.2028   5.448153e+00   5.626958e+00
   2_bss:  0.1583 0.1982   5.430153e+00   5.609087e+00
   2_xyz:  0.1232 0.1627   5.208598e+00   5.417016e+00
   2_adp:  0.1173 0.1579   5.165215e+00   5.381316e+00
   2_occ:  0.1171 0.1578   5.164347e+00   5.380634e+00
   3_bss:  0.1170 0.1568   5.161196e+00   5.374050e+00
   3_xyz:  0.1078 0.1520   5.108396e+00   5.347587e+00
   3_adp:  0.1064 0.1514   5.100998e+00   5.344669e+00
   3_occ:  0.1063 0.1514   5.100740e+00   5.344656e+00
   4_bss:  0.1062 0.1513   5.100483e+00   5.344258e+00
   4_xyz:  0.1084 0.1515   5.113398e+00   5.348722e+00
   4_adp:  0.1086 0.1514   5.113373e+00   5.348398e+00
   4_occ:  0.1086 0.1514   5.113563e+00   5.348881e+00
   5_bss:  0.1085 0.1514   5.113592e+00   5.348848e+00
   5_xyz:  0.1094 0.1521   5.122007e+00   5.357463e+00
   5_adp:  0.1084 0.1534   5.122511e+00   5.366326e+00
   5_occ:  0.1084 0.1535   5.122638e+00   5.366721e+00
   5_bss:  0.1083 0.1534   5.122484e+00   5.366489e+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:  0.318  28.844   0.694  -2.775  -1.295  -0.000  -0.000  -0.000
   1_xyz:  0.318  28.844   0.694  -2.775  -1.295  -0.000  -0.000  -0.000
   1_adp:  0.318  28.844   0.694  -2.775  -1.295  -0.000  -0.000  -0.000
   1_occ:  0.318  28.844   0.694  -2.775  -1.295  -0.000  -0.000  -0.000
   2_bss:  0.319  36.741  -2.383  -2.818  -1.754  -0.000  -0.000  -0.000
   2_xyz:  0.319  36.741  -2.383  -2.818  -1.754  -0.000  -0.000  -0.000
   2_adp:  0.319  36.741  -2.383  -2.818  -1.754  -0.000  -0.000  -0.000
   2_occ:  0.319  36.741  -2.383  -2.818  -1.754  -0.000  -0.000  -0.000
   3_bss:  0.319  38.465  -2.862  -2.453  -1.488  -0.000  -0.000  -0.000
   3_xyz:  0.319  38.465  -2.862  -2.453  -1.488  -0.000  -0.000  -0.000
   3_adp:  0.319  38.465  -2.862  -2.453  -1.488  -0.000  -0.000  -0.000
   3_occ:  0.319  38.465  -2.862  -2.453  -1.488  -0.000  -0.000  -0.000
   4_bss:  0.322  40.137  -2.926  -2.289  -1.326  -0.000  -0.000  -0.000
   4_xyz:  0.322  40.137  -2.926  -2.289  -1.326  -0.000  -0.000  -0.000
   4_adp:  0.322  40.137  -2.926  -2.289  -1.326  -0.000  -0.000  -0.000
   4_occ:  0.322  40.137  -2.926  -2.289  -1.326  -0.000  -0.000  -0.000
   5_bss:  0.322  40.137  -2.886  -2.130  -1.189  -0.000  -0.000  -0.000
   5_xyz:  0.322  40.137  -2.886  -2.130  -1.189  -0.000  -0.000  -0.000
   5_adp:  0.322  40.137  -2.886  -2.130  -1.189  -0.000  -0.000  -0.000
   5_occ:  0.322  40.137  -2.886  -2.130  -1.189  -0.000  -0.000  -0.000
   5_bss:  0.321  41.652  -2.701  -1.898  -0.986  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.809 0.7417  0.9372    28599.237
   1_bss:  30.563 0.7540  0.9199    25351.753
   1_xyz:  18.529 0.8765  1.0116     9922.392
   1_adp:  19.229 0.8695  1.0081    10406.578
   1_occ:  19.225 0.8695  1.0080    10394.739
   2_bss:  18.703 0.8743  0.9680     9905.899
   2_xyz:  14.784 0.9081  0.9834     6662.729
   2_adp:  14.058 0.9142  0.9826     6283.302
   2_occ:  14.045 0.9143  0.9826     6269.517
   3_bss:  13.953 0.9149  0.9842     6172.142
   3_xyz:  13.351 0.9198  0.9859     5851.159
   3_adp:  13.273 0.9206  0.9813     5838.104
   3_occ:  13.275 0.9206  0.9812     5834.545
   4_bss:  13.269 0.9206  0.9842     5830.558
   4_xyz:  13.315 0.9204  0.9838     5873.176
   4_adp:  13.288 0.9207  0.9798     5872.569
   4_occ:  13.296 0.9206  0.9797     5877.196
   5_bss:  13.298 0.9206  0.9836     5876.363
   5_xyz:  13.397 0.9200  0.9831     5977.222
   5_adp:  13.577 0.9186  0.9769     6065.197
   5_occ:  13.584 0.9186  0.9769     6069.889
   5_bss:  13.580 0.9186  0.9836     6065.515
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8505e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8505e-01
   1_xyz:   1.064  0.007  0.071 14.941  0.005  4.108   6.6840e-02
   1_adp:   1.064  0.007  0.071 14.941  0.005  4.108   6.6840e-02
   1_occ:   1.064  0.007  0.071 14.941  0.005  4.108   6.6840e-02
   2_bss:   1.064  0.007  0.071 14.941  0.005  4.108   6.6840e-02
   2_xyz:   0.983  0.006  0.071 14.606  0.004  4.111   5.6239e-02
   2_adp:   0.983  0.006  0.071 14.606  0.004  4.111   5.6239e-02
   2_occ:   0.983  0.006  0.071 14.606  0.004  4.111   5.6239e-02
   3_bss:   0.983  0.006  0.071 14.606  0.004  4.111   5.6239e-02
   3_xyz:   1.089  0.008  0.079 15.030  0.005  4.108   6.8555e-02
   3_adp:   1.089  0.008  0.079 15.030  0.005  4.108   6.8555e-02
   3_occ:   1.089  0.008  0.079 15.030  0.005  4.108   6.8555e-02
   4_bss:   1.089  0.008  0.079 15.030  0.005  4.108   6.8555e-02
   4_xyz:   0.935  0.005  0.071 14.591  0.004  4.108   5.2809e-02
   4_adp:   0.935  0.005  0.071 14.591  0.004  4.108   5.2809e-02
   4_occ:   0.935  0.005  0.071 14.591  0.004  4.108   5.2809e-02
   5_bss:   0.935  0.005  0.071 14.591  0.004  4.108   5.2809e-02
   5_xyz:   0.873  0.005  0.067 14.347  0.003  4.108   4.7911e-02
   5_adp:   0.873  0.005  0.067 14.347  0.003  4.108   4.7911e-02
   5_occ:   0.873  0.005  0.067 14.347  0.003  4.108   4.7911e-02
   5_bss:   0.873  0.005  0.067 14.347  0.003  4.108   4.7911e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.428   2.3956e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.428   2.3956e-01
   1_xyz:   6.787  0.056  0.254 85.028  0.042  2.195   9.0443e-02
   1_adp:   6.787  0.056  0.254 85.028  0.042  2.195   9.0443e-02
   1_occ:   6.787  0.056  0.254 85.028  0.042  2.195   9.0443e-02
   2_bss:   6.787  0.056  0.254 85.028  0.042  2.195   9.0443e-02
   2_xyz:   7.093  0.039  0.210 81.093  0.040  2.295   6.3826e-02
   2_adp:   7.093  0.039  0.210 81.093  0.040  2.295   6.3826e-02
   2_occ:   7.093  0.039  0.210 81.093  0.040  2.295   6.3826e-02
   3_bss:   7.093  0.039  0.210 81.093  0.040  2.295   6.3826e-02
   3_xyz:   7.351  0.050  0.262 82.278  0.039  2.299   6.4275e-02
   3_adp:   7.351  0.050  0.262 82.278  0.039  2.299   6.4275e-02
   3_occ:   7.351  0.050  0.262 82.278  0.039  2.299   6.4275e-02
   4_bss:   7.351  0.050  0.262 82.278  0.039  2.299   6.4275e-02
   4_xyz:   6.366  0.042  0.227 82.367  0.043  2.366   3.4495e-02
   4_adp:   6.366  0.042  0.227 82.367  0.043  2.366   3.4495e-02
   4_occ:   6.366  0.042  0.227 82.367  0.043  2.366   3.4495e-02
   5_bss:   6.366  0.042  0.227 82.367  0.043  2.366   3.4495e-02
   5_xyz:   6.130  0.041  0.210 83.165  0.032  2.383   2.8451e-02
   5_adp:   6.130  0.041  0.210 83.165  0.032  2.383   2.8451e-02
   5_occ:   6.130  0.041  0.210 83.165  0.032  2.383   2.8451e-02
   5_bss:   6.130  0.041  0.210 83.165  0.032  2.383   2.8451e-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:  62.25   0.00  16.73  61.49   0.00  12.88  62.25   7.16  37.68
   1_occ:  62.25   0.00  16.73  61.49   0.00  12.88  62.25   7.16  37.68
   2_bss:  62.25   0.00  16.73  61.49   0.00  12.88  62.25   7.16  37.68
   2_xyz:  62.25   0.00  16.73  61.49   0.00  12.88  62.25   7.16  37.68
   2_adp:  73.78   1.39  16.77  73.78   1.39  12.94  67.24   6.28  37.60
   2_occ:  73.78   1.39  16.77  73.78   1.39  12.94  67.24   6.28  37.60
   3_bss:  73.78   1.39  16.77  73.78   1.39  12.94  67.24   6.28  37.60
   3_xyz:  73.78   1.39  16.77  73.78   1.39  12.94  67.24   6.28  37.60
   3_adp:  75.68   1.73  16.66  75.68   1.73  12.82  68.34   4.29  37.58
   3_occ:  75.68   1.73  16.66  75.68   1.73  12.82  68.34   4.29  37.58
   4_bss:  75.68   1.73  16.66  75.68   1.73  12.82  68.34   4.29  37.58
   4_xyz:  75.68   1.73  16.66  75.68   1.73  12.82  68.34   4.29  37.58
   4_adp:  75.90   1.68  16.49  75.90   1.68  12.70  68.33   5.80  37.17
   4_occ:  75.90   1.68  16.49  75.90   1.68  12.70  68.33   5.80  37.17
   5_bss:  75.90   1.68  16.49  75.90   1.68  12.70  68.33   5.80  37.17
   5_xyz:  75.90   1.68  16.49  75.90   1.68  12.70  68.33   5.80  37.17
   5_adp:  85.10   0.61  16.74  85.10   0.61  12.70  74.98   5.45  38.77
   5_occ:  85.10   0.61  16.74  85.10   0.61  12.70  74.98   5.45  38.77
   5_bss:  85.08   0.59  16.72  85.08   0.59  12.68  74.96   5.43  38.75
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.314    0.010    0.284
   1_adp:    1.314    0.010    0.284
   1_occ:    1.314    0.010    0.284
   2_bss:    1.314    0.010    0.284
   2_xyz:    0.988    0.008    0.339
   2_adp:    0.988    0.008    0.339
   2_occ:    0.988    0.008    0.339
   3_bss:    0.988    0.008    0.339
   3_xyz:    1.023    0.010    0.366
   3_adp:    1.023    0.010    0.366
   3_occ:    1.023    0.010    0.366
   4_bss:    1.023    0.010    0.366
   4_xyz:    1.142    0.006    0.369
   4_adp:    1.142    0.006    0.369
   4_occ:    1.142    0.006    0.369
   5_bss:    1.142    0.006    0.369
   5_xyz:    1.179    0.009    0.375
   5_adp:    1.179    0.009    0.375
   5_occ:    1.179    0.009    0.375
   5_bss:    1.179    0.009    0.375
------------------------------------------------------------------------

CPU time actual refinement: 326.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/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_180/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_180/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.69 
  Macro-tasks:
    bulk solvent and scale       = 37.27  
    individual site refinement   = 140.69 
    weights calculation          = 28.43  
    collect and process          = 6.47   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 212.94 
  Micro-tasks:
    mask                            = 1.15   
    f_calc                          = 104.00 
    alpha_beta                      = 7.85   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.92 
    fmodel                         = 6.49   
    r_factors                      = 0.19   
    phase_errors                   = 11.21  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 247.22 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.523 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    672 calls, 103.71 s
gradients_fft:          617 calls, 100.49 s

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

# Date 2008-01-16 Time 04:12:54 PST -0800 (1200485574.75 s)
Start R-work = 0.3101, R-free = 0.3116 (no bulk solvent and anisotropic scale)
Final R-work = 0.1333, R-free = 0.1743 (no bulk solvent and anisotropic scale)

Start R-work = 0.2951, R-free = 0.2973
Final R-work = 0.1083, R-free = 0.1534