# Date 2008-01-16 Time 05:12:53 PST -0800 (1200489173.45 s)
#phil __OFF__

Command line arguments: "../640.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14831
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 640

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97102
Completeness in resolution range: 0.967167
Completeness with d_max=infinity: 0.964215

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9710

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97102
Completeness in resolution range: 0.967167
Completeness with d_max=infinity: 0.964215

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2175 [2117/2143]  1907   210   9.9%
  bin  2:  4.2175 -  3.3601 [2048/2067]  1842   206  10.1%
  bin  3:  3.3601 -  2.9391 [2014/2033]  1810   204  10.1%
  bin  4:  2.9391 -  2.6720 [1998/2028]  1803   195   9.8%
  bin  5:  2.6720 -  2.4814 [1981/2000]  1784   197   9.9%
  bin  6:  2.4814 -  2.3357 [1971/1996]  1769   202  10.2%
  bin  7:  2.3357 -  2.2191 [1967/1995]  1769   198  10.1%
  bin  8:  2.2191 -  2.1228 [1960/1996]  1769   191   9.7%
  bin  9:  2.1228 -  2.0413 [1967/2009]  1770   197  10.0%
  bin 10:  2.0413 -  1.9710 [1566/1987]  1407   159  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 31
        2.42 -     3.04: 2222
        3.04 -     3.66: 4782
        3.66 -     4.28: 9117
        4.28 -     4.90: 12493
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.060 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.105 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.107 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28640 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_640/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 85.09415 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: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3506   r_free= 0.3469   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.100980                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7040 0.99   1383  154 0.2996 0.2967      6.3844       6.339|
|  2:  4.7040 -  3.7532 0.99   1335  146 0.2803 0.2641      6.5087      6.4717|
|  3:  3.7532 -  3.2846 0.99   1290  144 0.3043 0.3143      6.4042      6.5332|
|  4:  3.2846 -  2.9869 0.99   1292  147 0.3130 0.3414      6.2948      6.3009|
|  5:  2.9869 -  2.7742 0.99   1292  142 0.3558 0.3307      6.1639      6.1078|
|  6:  2.7742 -  2.6116 0.99   1283  143 0.3673 0.3742      6.1031      6.1068|
|  7:  2.6116 -  2.4814 0.99   1271  136 0.3757 0.3432      6.0717      6.0172|
|  8:  2.4814 -  2.3738 0.98   1266  149 0.3875 0.3871      6.0424      6.0653|
|  9:  2.3738 -  2.2828 0.98   1274  137 0.3837 0.3735      5.9802      5.9009|
| 10:  2.2828 -  2.2043 0.99   1259  141 0.3895 0.3947      5.9518      5.9937|
| 11:  2.2043 -  2.1356 0.98   1259  135 0.4173 0.4025      5.9343      5.9705|
| 12:  2.1356 -  2.0747 0.97   1243  142 0.4029 0.4069      5.8643       5.892|
| 13:  2.0747 -  2.0202 1.00   1259  141 0.4056 0.4028      5.7716      5.7383|
| 14:  2.0202 -  1.9710 0.71    924  102 0.4389 0.4057      5.7871      5.6456|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7040  1383   154  0.78  26.93   0.86     0.80      45169.86|
|  2:  4.7040 -  3.7532  1335   146  0.82  23.95   0.97     0.91      54236.00|
|  3:  3.7532 -  3.2846  1290   144  0.78  28.61   1.00     0.96      55443.48|
|  4:  3.2846 -  2.9869  1292   147  0.74  32.38   1.00     0.93      49908.45|
|  5:  2.9869 -  2.7742  1292   142  0.69  36.64   0.97     0.89      40739.46|
|  6:  2.7742 -  2.6116  1283   143  0.68  37.39   0.99     0.88      35983.19|
|  7:  2.6116 -  2.4814  1271   136  0.68  37.65   0.99     0.90      32291.48|
|  8:  2.4814 -  2.3738  1266   149  0.66  39.08   0.99     0.89      30085.16|
|  9:  2.3738 -  2.2828  1274   137  0.67  38.25   1.02     0.88      26956.08|
| 10:  2.2828 -  2.2043  1259   141  0.64  40.84   1.03     0.88      26692.81|
| 11:  2.2043 -  2.1356  1259   135  0.61  43.03   1.04     0.88      26151.10|
| 12:  2.1356 -  2.0747  1243   142  0.62  42.80   1.05     0.89      24836.80|
| 13:  2.0747 -  2.0202  1259   141  0.61  43.76   1.04     0.87      20777.61|
| 14:  2.0202 -  1.9710   924   102  0.64  40.96   1.02     0.83      15748.75|
|alpha:            min =        0.80 max =            0.96 mean =         0.89|
|beta:             min =    15748.75 max =        55443.48 mean =     35239.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.97 mean =        36.36|
|phase err.(test): min =        0.00 max =           89.84 mean =        36.51|
|-----------------------------------------------------------------------------|

============================== 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 = 5.646713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.793   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.856722              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.129   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       27 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      208 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2014 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1904 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2878 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4680 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4437 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5697 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6796 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.219 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    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: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3506   r_free= 0.3469   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.100980                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3359   r_free= 0.3306   ksol= 0.33   Bsol= 32.48   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-0.13,0.92,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.086621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.704126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.770   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.419372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.029   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3359      final r-factor (work) = 0.1847          |
| start r-factor (free) = 0.3306      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4802 = 4.70 * 0.50 * 6.0868 + 1.00 * 0.1636                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6652 = 4.70 * 0.50 * 5.7807 + 1.00 * 0.0685                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1847      final r-factor (work) = 0.1694          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.2154          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4304 = 0.42 * 1.00 * 5.7807 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3047 = 0.42 * 1.00 * 5.4740 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.65   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    71.65   17.20    None  None   None       |
|    Sol.    : 438    0      7.39    71.65   39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    66.58   13.11    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 -   7.165:  365   |   5:    35.827 -  42.992:  122        |
|      1:     7.165 -  14.331: 1344   |   6:    42.992 -  50.157:   90        |
|      2:    14.331 -  21.496:  492   |   7:    50.157 -  57.323:   79        |
|      3:    21.496 -  28.661:  176   |   8:    57.323 -  64.488:   41        |
|      4:    28.661 -  35.827:  101   |   9:    64.488 -  71.653:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1694 r_free = 0.2154             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1691 r_free = 0.2154             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1691   r_free= 0.2154   ksol= 0.33   Bsol= 32.48   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-0.13,0.92,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.488725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2123   ksol= 0.31   Bsol= 38.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.22,-1.32,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.478553                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.714345              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.172  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.2123      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7742 = 1.71 * 0.50 * 5.4898 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6569 = 1.71 * 0.50 * 5.3779 + 1.00 * 0.0471                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1312      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1718      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0882 = 0.20 * 1.00 * 5.3779 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0594 = 0.20 * 1.00 * 5.2428 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.72    71.94   16.99    None  None   None       |
|    all(noH): 2823   0      1.72    71.94   16.99    None  None   None       |
|    Sol.    : 438    0      6.59    70.81   38.78    None  None   None       |
|    Mac.    : 2385   0      1.72    71.94   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.717 -   8.740:  651   |   5:    36.831 -  43.854:  123        |
|      1:     8.740 -  15.762: 1260   |   6:    43.854 -  50.876:   84        |
|      2:    15.762 -  22.785:  369   |   7:    50.876 -  57.899:   70        |
|      3:    22.785 -  29.808:  124   |   8:    57.899 -  64.922:   26        |
|      4:    29.808 -  36.831:  102   |   9:    64.922 -  71.945:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1259 r_free = 0.1641             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1257 r_free = 0.1642             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1642   ksol= 0.31   Bsol= 38.74   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.22,-1.32,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219225                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1645   ksol= 0.32   Bsol= 38.74   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.44,-1.55,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219531                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.143497              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.798  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.550  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6652 = 2.14 * 0.50 * 5.2419 + 1.00 * 0.0471                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5928 = 2.14 * 0.50 * 5.1661 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4980 = 0.48 * 1.00 * 5.1661 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4753 = 0.48 * 1.00 * 5.1174 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    78.48   17.02    None  None   None       |
|    all(noH): 2823   0      1.17    78.48   17.02    None  None   None       |
|    Sol.    : 438    0      5.57    75.40   39.35    None  None   None       |
|    Mac.    : 2385   0      1.17    78.48   12.92    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:     1.166 -   8.897:  717   |   5:    39.824 -  47.556:  113        |
|      1:     8.897 -  16.629: 1279   |   6:    47.556 -  55.288:   87        |
|      2:    16.629 -  24.361:  320   |   7:    55.288 -  63.019:   49        |
|      3:    24.361 -  32.093:  118   |   8:    63.019 -  70.751:   23        |
|      4:    32.093 -  39.824:  110   |   9:    70.751 -  78.483:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1523             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1524             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1524   ksol= 0.32   Bsol= 38.74   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.44,-1.55,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115487                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1524   ksol= 0.32   Bsol= 38.74   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.46,-1.62,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.115243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.471623              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.796  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.977142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.753  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3798 = 2.47 * 0.50 * 5.1171 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3632 = 2.47 * 0.50 * 5.0999 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9915 = 0.98 * 1.00 * 5.0999 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9874 = 0.98 * 1.00 * 5.0949 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    91.48   17.04    None  None   None       |
|    all(noH): 2823   0      0.84    91.48   17.04    None  None   None       |
|    Sol.    : 438    0      6.22    83.24   39.72    None  None   None       |
|    Mac.    : 2385   0      0.84    91.48   12.87    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:     0.841 -   9.905: 1024   |   5:    46.159 -  55.223:   98        |
|      1:     9.905 -  18.968: 1116   |   6:    55.223 -  64.286:   52        |
|      2:    18.968 -  28.032:  229   |   7:    64.286 -  73.350:   20        |
|      3:    28.032 -  37.095:  144   |   8:    73.350 -  82.413:   13        |
|      4:    37.095 -  46.159:  124   |   9:    82.413 -  91.477:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1535             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1054 r_free = 0.1535             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1535   ksol= 0.32   Bsol= 38.74   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.46,-1.62,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1534   ksol= 0.32   Bsol= 42.03   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.30,-1.45,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.142376              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.455  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402381              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.927  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1053      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5190 = 2.14 * 0.50 * 5.0956 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5201 = 2.14 * 0.50 * 5.1016 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1058      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0618 = 0.40 * 1.00 * 5.1016 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0625 = 0.40 * 1.00 * 5.1048 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    92.89   16.70    None  None   None       |
|    all(noH): 2823   0      0.82    92.89   16.70    None  None   None       |
|    Sol.    : 438    0      6.08    85.34   38.71    None  None   None       |
|    Mac.    : 2385   0      0.82    92.89   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.820 -  10.027: 1081   |   5:    46.853 -  56.059:   99        |
|      1:    10.027 -  19.233: 1089   |   6:    56.059 -  65.266:   47        |
|      2:    19.233 -  28.440:  215   |   7:    65.266 -  74.472:   10        |
|      3:    28.440 -  37.646:  145   |   8:    74.472 -  83.679:    9        |
|      4:    37.646 -  46.853:  124   |   9:    83.679 -  92.885:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1059 r_free = 0.1539             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1059 r_free = 0.1539             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1539   ksol= 0.32   Bsol= 42.03   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.30,-1.45,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.103808                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7040 0.99   1383  154 0.0972 0.1242      5.3593      5.5104|
|  2:  4.7040 -  3.7532 0.99   1335  146 0.0827 0.1082      5.4115      5.6068|
|  3:  3.7532 -  3.2846 0.99   1290  144 0.1006 0.1522      5.4443      5.8629|
|  4:  3.2846 -  2.9869 0.99   1292  147 0.1156 0.1526      5.4288      5.5673|
|  5:  2.9869 -  2.7742 0.99   1292  142 0.1231 0.1718      5.2798      5.5221|
|  6:  2.7742 -  2.6116 0.99   1283  143 0.1114 0.1646       5.161      5.3552|
|  7:  2.6116 -  2.4814 0.99   1271  136 0.1185 0.1614      5.1136      5.3741|
|  8:  2.4814 -  2.3738 0.98   1266  149 0.1084 0.1668      5.0093      5.3054|
|  9:  2.3738 -  2.2828 0.98   1274  137 0.1104 0.1725      4.9939      5.2737|
| 10:  2.2828 -  2.2043 0.99   1259  141 0.1035 0.1738        4.91      5.2196|
| 11:  2.2043 -  2.1356 0.98   1259  135 0.1069 0.1639      4.9127      5.2191|
| 12:  2.1356 -  2.0747 0.97   1243  142 0.1048 0.1605      4.8422      5.1406|
| 13:  2.0747 -  2.0202 1.00   1259  141 0.1065 0.1787      4.7613      5.0855|
| 14:  2.0202 -  1.9710 0.71    924  102 0.1008 0.1638      4.6321      4.8755|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7040  1383   154  0.94   8.68   0.98     0.96       6528.45|
|  2:  4.7040 -  3.7532  1335   146  0.95   7.65   1.02     1.01       8635.13|
|  3:  3.7532 -  3.2846  1290   144  0.94  10.88   1.03     1.02       9949.62|
|  4:  3.2846 -  2.9869  1292   147  0.92  13.37   1.01     1.00      10061.55|
|  5:  2.9869 -  2.7742  1292   142  0.90  15.33   0.99     0.96       7715.37|
|  6:  2.7742 -  2.6116  1283   143  0.91  14.91   0.99     0.96       6535.34|
|  7:  2.6116 -  2.4814  1271   136  0.91  14.82   0.99     0.96       5626.43|
|  8:  2.4814 -  2.3738  1266   149  0.92  14.17   0.99     0.97       4765.60|
|  9:  2.3738 -  2.2828  1274   137  0.92  14.39   1.01     0.98       4617.58|
| 10:  2.2828 -  2.2043  1259   141  0.91  14.66   1.00     0.96       4006.84|
| 11:  2.2043 -  2.1356  1259   135  0.90  16.16   1.00     0.96       4244.22|
| 12:  2.1356 -  2.0747  1243   142  0.92  14.16   1.01     0.99       3714.49|
| 13:  2.0747 -  2.0202  1259   141  0.91  15.47   1.01     1.00       3210.17|
| 14:  2.0202 -  1.9710   924   102  0.92  14.06   0.98     0.95       2395.85|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2395.85 max =        10061.55 mean =      5959.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.41|
|phase err.(test): min =        0.00 max =           89.71 mean =        12.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1538   ksol= 0.32   Bsol= 44.35   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.14,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1538   ksol= 0.32   Bsol= 44.35   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.14,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105041                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7040 0.99   1383  154 0.0972 0.1252      5.3682       5.503|
|  2:  4.7040 -  3.7532 0.99   1335  146 0.0836 0.1087      5.4169      5.6049|
|  3:  3.7532 -  3.2846 0.99   1290  144 0.1012 0.1517      5.4454      5.8564|
|  4:  3.2846 -  2.9869 0.99   1292  147 0.1157 0.1519      5.4284      5.5686|
|  5:  2.9869 -  2.7742 0.99   1292  142 0.1235 0.1710      5.2811      5.5181|
|  6:  2.7742 -  2.6116 0.99   1283  143 0.1115 0.1642      5.1621      5.3538|
|  7:  2.6116 -  2.4814 0.99   1271  136 0.1187 0.1619      5.1134      5.3781|
|  8:  2.4814 -  2.3738 0.98   1266  149 0.1083 0.1669      5.0096      5.3028|
|  9:  2.3738 -  2.2828 0.98   1274  137 0.1105 0.1728      4.9938      5.2755|
| 10:  2.2828 -  2.2043 0.99   1259  141 0.1034 0.1736      4.9095      5.2181|
| 11:  2.2043 -  2.1356 0.98   1259  135 0.1069 0.1639      4.9118      5.2187|
| 12:  2.1356 -  2.0747 0.97   1243  142 0.1047 0.1605      4.8419      5.1414|
| 13:  2.0747 -  2.0202 1.00   1259  141 0.1064 0.1791      4.7618      5.0869|
| 14:  2.0202 -  1.9710 0.71    924  102 0.1007 0.1638      4.6321       4.876|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7040  1383   154  0.94   8.68   0.98     0.95       6600.13|
|  2:  4.7040 -  3.7532  1335   146  0.95   7.64   1.03     1.02       8616.94|
|  3:  3.7532 -  3.2846  1290   144  0.94  10.84   1.03     1.02       9876.13|
|  4:  3.2846 -  2.9869  1292   147  0.92  13.37   1.02     1.01      10033.36|
|  5:  2.9869 -  2.7742  1292   142  0.90  15.31   1.00     0.97       7701.01|
|  6:  2.7742 -  2.6116  1283   143  0.91  14.94   0.99     0.97       6550.96|
|  7:  2.6116 -  2.4814  1271   136  0.91  14.79   1.00     0.96       5614.24|
|  8:  2.4814 -  2.3738  1266   149  0.92  14.18   1.00     0.98       4775.55|
|  9:  2.3738 -  2.2828  1274   137  0.92  14.39   1.01     0.99       4616.52|
| 10:  2.2828 -  2.2043  1259   141  0.91  14.65   1.01     0.97       4006.46|
| 11:  2.2043 -  2.1356  1259   135  0.90  16.14   1.01     0.97       4232.71|
| 12:  2.1356 -  2.0747  1243   142  0.92  14.16   1.01     1.00       3714.98|
| 13:  2.0747 -  2.0202  1259   141  0.91  15.50   1.02     1.01       3220.07|
| 14:  2.0202 -  1.9710   924   102  0.92  14.09   0.99     0.96       2401.74|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2401.74 max =        10033.36 mean =      5956.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.83 mean =        13.41|
|phase err.(test): min =        0.00 max =           89.86 mean =        12.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    92.86   16.68    None  None   None       |
|    all(noH): 2823   0      0.79    92.86   16.68    None  None   None       |
|    Sol.    : 438    0      6.06    85.31   38.68    None  None   None       |
|    Mac.    : 2385   0      0.79    92.86   12.63    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:     0.793 -   9.999: 1081   |   5:    46.825 -  56.032:   99        |
|      1:     9.999 -  19.206: 1089   |   6:    56.032 -  65.238:   47        |
|      2:    19.206 -  28.412:  215   |   7:    65.238 -  74.445:   10        |
|      3:    28.412 -  37.619:  145   |   8:    74.445 -  83.651:    9        |
|      4:    37.619 -  46.825:  124   |   9:    83.651 -  92.858:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.503 - 4.532
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 289
   mapped sites are within: 0.720 - 4.532

peak=    5.909 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.862 closest distance to " NH2 ARG A  56 " =    2.198
peak=    5.654 closest distance to " O   HOH Z 144 " =    1.738
peak=    5.615 closest distance to " CG  PRO A  54 " =    1.257
peak=    5.575 closest distance to " O   HOH Z 126 " =    1.926
peak=    5.205 closest distance to " CG  PRO A 213 " =    1.237
peak=    5.151 closest distance to " CB  ARG A 275 " =    0.879
peak=    5.050 closest distance to " CB  GLN A 223 " =    1.463
peak=    5.005 closest distance to " CB  SER A  63 " =    1.201
peak=    4.822 closest distance to " CB  GLN A 183 " =    1.225
peak=    4.757 closest distance to " O   HOH Z 232 " =    2.344
peak=    4.649 closest distance to " O   HOH Z  78 " =    1.736
peak=    4.638 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.543 closest distance to " O   HOH Z  15 " =    2.344
peak=    4.538 closest distance to " C   PRO A 198 " =    1.482
peak=    4.522 closest distance to " O   HOH Z 427 " =    2.788
peak=    4.501 closest distance to " CG  PRO A  90 " =    1.080
peak=    4.465 closest distance to " OD1 ASN A  69 " =    2.614
peak=    4.446 closest distance to " ND2 ASN A 187 " =    1.479
peak=    4.442 closest distance to " CB  GLU A 152 " =    1.228
peak=    4.432 closest distance to " O   HOH Z 193 " =    1.824
peak=    4.404 closest distance to " O   HOH Z 298 " =    1.846
peak=    4.403 closest distance to " CB  ASN A 148 " =    1.389
peak=    4.354 closest distance to " O   HOH Z 236 " =    2.127
peak=    4.298 closest distance to " O   HOH Z 369 " =    2.124
peak=    4.286 closest distance to " CB  SER A   3 " =    1.322
peak=    4.280 closest distance to " O   HOH Z 272 " =    1.808
peak=    4.260 closest distance to " CB  ARG A  79 " =    1.377
peak=    4.228 closest distance to " O   HOH Z 203 " =    1.833
peak=    4.222 closest distance to " CB  LEU A 228 " =    1.098
peak=    4.212 closest distance to " O   HOH Z 234 " =    3.623
peak=    4.210 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.204 closest distance to " O   HOH Z 344 " =    3.110
peak=    4.192 closest distance to " CB  GLU A 128 " =    1.045
peak=    4.188 closest distance to " CG  ARG A  66 " =    2.459
peak=    4.179 closest distance to " NZ  LYS A 117 " =    3.263
peak=    4.159 closest distance to " O   HOH Z 316 " =    3.053
peak=    4.156 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.156 closest distance to " O   HOH Z 303 " =    2.156
peak=    4.104 closest distance to " CG2 VAL A 257 " =    0.908
peak=    4.086 closest distance to " O   HOH Z 144 " =    2.258
peak=    4.085 closest distance to " O   HOH Z 368 " =    1.912
peak=    4.062 closest distance to " OG BSER A 164 " =    2.306
peak=    4.028 closest distance to " CB  TYR A 169 " =    0.748
peak=    4.021 closest distance to " O   HOH Z  78 " =    2.090
peak=    4.006 closest distance to " CB  VAL A 265 " =    1.344
peak=    3.997 closest distance to " OD2 ASP A 286 " =    2.786
peak=    3.987 closest distance to " O   HOH Z  40 " =    1.724
peak=    3.969 closest distance to " O   HOH Z 189 " =    1.965
peak=    3.955 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.954 closest distance to " O   HOH Z  59 " =    1.742
peak=    3.948 closest distance to " O   HOH Z   9 " =    2.044
peak=    3.946 closest distance to " O   HOH Z  43 " =    1.817
peak=    3.930 closest distance to " O   HOH Z  61 " =    1.603
peak=    3.928 closest distance to " O   HOH Z 419 " =    2.028
peak=    3.927 closest distance to " CB  ARG A 139 " =    0.985
peak=    3.915 closest distance to " CG  PRO A 243 " =    1.082
peak=    3.908 closest distance to " CA  THR A 264 " =    0.832
peak=    3.895 closest distance to " CA  ASN A 215 " =    1.183
peak=    3.883 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.879 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.875 closest distance to " O   SER A  87 " =    2.233
peak=    3.868 closest distance to " O   HOH Z  66 " =    2.169
peak=    3.863 closest distance to " O   HOH Z 346 " =    1.691
peak=    3.859 closest distance to " CB  TRP A 179 " =    1.282
peak=    3.835 closest distance to " O   HOH Z 132 " =    2.369
peak=    3.820 closest distance to " O   HOH Z   1 " =    1.903
peak=    3.810 closest distance to " O   HOH Z  93 " =    2.272
peak=    3.805 closest distance to " O   HOH Z 250 " =    1.396
peak=    3.798 closest distance to " CB  ARG A 190 " =    1.646
peak=    3.792 closest distance to " NH1BARG A 145 " =    1.292
peak=    3.781 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.774 closest distance to " O   HOH Z  44 " =    1.799
peak=    3.772 closest distance to " CB  SER A 216 " =    0.768
peak=    3.763 closest distance to " O   HOH Z 209 " =    2.183
peak=    3.756 closest distance to " O   HOH Z   3 " =    1.886
peak=    3.751 closest distance to " O   HOH Z 403 " =    1.687
peak=    3.737 closest distance to " O   MET A 105 " =    1.766
peak=    3.737 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.736 closest distance to " O   HOH Z 207 " =    1.768
peak=    3.723 closest distance to " O   HOH Z 371 " =    2.917
peak=    3.716 closest distance to " CB  TRP A 266 " =    0.994
peak=    3.715 closest distance to " CD BLYS A 290 " =    1.268
peak=    3.712 closest distance to " O   HOH Z 214 " =    2.086
peak=    3.706 closest distance to " O   HOH Z  54 " =    1.672
peak=    3.706 closest distance to " O   HOH Z  21 " =    1.717
peak=    3.685 closest distance to " CB  TYR A 169 " =    0.805
peak=    3.677 closest distance to " O   HOH Z 193 " =    1.691
peak=    3.671 closest distance to " O   HOH Z 426 " =    1.634
peak=    3.667 closest distance to " CA  ALA A  21 " =    1.120
peak=    3.667 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.665 closest distance to " CE  LYS A  76 " =    0.829
peak=    3.659 closest distance to " O   HOH Z 392 " =    3.151
peak=    3.658 closest distance to " O   HOH Z 402 " =    1.426
peak=    3.657 closest distance to " O   HOH Z 425 " =    2.025
peak=    3.655 closest distance to " O   HOH Z 158 " =    3.066
peak=    3.638 closest distance to " O   HOH Z 425 " =    1.231
peak=    3.628 closest distance to " O   HOH Z 409 " =    2.620
peak=    3.621 closest distance to " NH1AARG A 145 " =    1.105
peak=    3.613 closest distance to " O   HOH Z 291 " =    1.566
peak=    3.607 closest distance to " O   HOH Z 407 " =    2.252
peak=    3.607 closest distance to " O   HOH Z 295 " =    1.545
peak=    3.606 closest distance to " CA  ALA A 233 " =    1.134
peak=    3.595 closest distance to " CB  LEU A 143 " =    1.116
peak=    3.589 closest distance to " O   HOH Z 273 " =    2.625
peak=    3.570 closest distance to " CA  MET A  40 " =    1.076
peak=    3.563 closest distance to " O   HOH Z  88 " =    2.962
peak=    3.538 closest distance to " O   HOH Z 219 " =    2.204
peak=    3.537 closest distance to " O   HOH Z 147 " =    1.754
peak=    3.533 closest distance to " CB  SER A  62 " =    1.220
peak=    3.528 closest distance to " CB  ALA A 291 " =    1.349
peak=    3.525 closest distance to " O   HOH Z 261 " =    2.117
peak=    3.523 closest distance to " N   PHE A 130 " =    1.290
peak=    3.523 closest distance to " O   HOH Z 183 " =    1.378
peak=    3.521 closest distance to " O   HOH Z  64 " =    2.264
peak=    3.521 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.520 closest distance to " CD2 TRP A 179 " =    1.362
peak=    3.508 closest distance to " CD2 LEU A 255 " =    1.504
peak=    3.498 closest distance to " O   HOH Z   1 " =    1.710
peak=    3.498 closest distance to " O   HOH Z 124 " =    1.363
peak=    3.495 closest distance to " O   HOH Z 173 " =    1.795
peak=    3.494 closest distance to " O   HOH Z  50 " =    1.550
peak=    3.491 closest distance to " O   HOH Z 353 " =    2.655
peak=    3.491 closest distance to " O   HOH Z 245 " =    1.304
peak=    3.491 closest distance to " O   HOH Z 327 " =    1.591
peak=    3.485 closest distance to " CB  THR A 157 " =    1.045
peak=    3.483 closest distance to " CD1 LEU A 300 " =    1.278
peak=    3.476 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.475 closest distance to " CG  LEU A 167 " =    1.175
peak=    3.475 closest distance to " O   HOH Z 234 " =    1.774
peak=    3.473 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.472 closest distance to " O   HOH Z 227 " =    2.179
peak=    3.471 closest distance to " ND1 HIS A  86 " =    1.828
peak=    3.469 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.467 closest distance to " OG  SER A  22 " =    2.714
peak=    3.466 closest distance to " O   HOH Z 193 " =    2.010
peak=    3.462 closest distance to " O   HOH Z 411 " =    3.834
peak=    3.455 closest distance to " N   ARG A 156 " =    1.266
peak=    3.440 closest distance to " CB  ALA A  34 " =    0.959
peak=    3.439 closest distance to " O   HOH Z  97 " =    1.925
peak=    3.438 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.419 closest distance to " O   HOH Z 133 " =    1.480
peak=    3.418 closest distance to " O   HOH Z 437 " =    1.563
peak=    3.418 closest distance to " CB  GLU A 277 " =    3.529
peak=    3.413 closest distance to " O   HOH Z 180 " =    2.128
peak=    3.409 closest distance to " O   HOH Z 135 " =    1.692
peak=    3.402 closest distance to " OD1BASN A 224 " =    2.242
peak=    3.392 closest distance to " N   ASN A  39 " =    1.235
peak=    3.392 closest distance to " CA  ASP A 162 " =    1.126
peak=    3.391 closest distance to " CA  PHE A 283 " =    1.289
peak=    3.390 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.388 closest distance to " O   HOH Z 227 " =    1.740
peak=    3.386 closest distance to " CA  THR A 221 " =    0.969
peak=    3.377 closest distance to " O   ALA A   1 " =    1.691
peak=    3.377 closest distance to " CD2 LEU A 297 " =    0.901
peak=    3.375 closest distance to " O   HOH Z 366 " =    2.888
peak=    3.373 closest distance to " O   HOH Z 345 " =    3.362
peak=    3.373 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.369 closest distance to " O   HOH Z 284 " =    2.994
peak=    3.367 closest distance to " CB  SER A 212 " =    1.011
peak=    3.366 closest distance to " O   HOH Z 175 " =    2.105
peak=    3.365 closest distance to " O   HOH Z 371 " =    1.594
peak=    3.360 closest distance to " CB  TYR A 116 " =    0.809
peak=    3.359 closest distance to " O   HOH Z 435 " =    1.909
peak=    3.356 closest distance to " O   HOH Z 337 " =    3.676
peak=    3.349 closest distance to " O   HOH Z 406 " =    1.642
peak=    3.349 closest distance to " O   HOH Z 389 " =    1.809
peak=    3.349 closest distance to " O   HOH Z 336 " =    1.951
peak=    3.344 closest distance to " O   HOH Z 250 " =    1.877
peak=    3.339 closest distance to " CG1 VAL A 153 " =    0.915
peak=    3.334 closest distance to " CZ  PHE A 218 " =    0.988
peak=    3.332 closest distance to " CB  SER A  26 " =    1.549
peak=    3.329 closest distance to " O   HOH Z 163 " =    1.743
peak=    3.325 closest distance to " O   HOH Z 329 " =    3.638
peak=    3.323 closest distance to " CD  LYS A 166 " =    1.242
peak=    3.323 closest distance to " N   ASN A 127 " =    1.260
peak=    3.322 closest distance to " O   HOH Z 144 " =    1.882
peak=    3.314 closest distance to " CG  MET A 113 " =    1.145
peak=    3.308 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.296 closest distance to " CG1BVAL A  72 " =    1.411
peak=    3.294 closest distance to " O   HOH Z 286 " =    2.320
peak=    3.294 closest distance to " CZ  ARG A  14 " =    1.893
peak=    3.293 closest distance to " O   HOH Z 417 " =    1.960
peak=    3.292 closest distance to " O   HOH Z 391 " =    2.986
peak=    3.290 closest distance to " O   HOH Z 108 " =    2.187
peak=    3.287 closest distance to " O   HOH Z 305 " =    3.546
peak=    3.287 closest distance to " O   HOH Z 313 " =    1.807
peak=    3.283 closest distance to " CB  ALA A 233 " =    1.333
peak=    3.275 closest distance to " CG  GLU A 277 " =    2.083
peak=    3.267 closest distance to " O   HOH Z 172 " =    3.311
peak=    3.265 closest distance to " CG  MET A 185 " =    1.205
peak=    3.264 closest distance to " CE1 TYR A 186 " =    1.332
peak=    3.264 closest distance to " OE1 GLU A 236 " =    1.285
peak=    3.263 closest distance to " O   HOH Z 411 " =    1.746
peak=    3.262 closest distance to " OG  SER A  62 " =    2.895
peak=    3.261 closest distance to " CB  SER A 141 " =    1.020
peak=    3.260 closest distance to " O   HOH Z 163 " =    1.852
peak=    3.259 closest distance to " O   HOH Z  63 " =    1.460
peak=    3.253 closest distance to " OG  SER A 206 " =    1.333
peak=    3.245 closest distance to " N   GLN A 278 " =    1.088
peak=    3.244 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.244 closest distance to " O   HOH Z  44 " =    3.300
peak=    3.243 closest distance to " O   HOH Z 271 " =    2.315
peak=    3.242 closest distance to " O   HOH Z 128 " =    2.086
peak=    3.241 closest distance to " O   HOH Z 292 " =    1.699
peak=    3.240 closest distance to " O   HOH Z 299 " =    4.249
peak=    3.240 closest distance to " O   HOH Z 189 " =    2.079
peak=    3.234 closest distance to " O   HOH Z 125 " =    2.311
peak=    3.234 closest distance to " O   HOH Z 133 " =    2.477
peak=    3.228 closest distance to " O   HOH Z 188 " =    1.972
peak=    3.227 closest distance to " O   HOH Z  92 " =    2.508
peak=    3.221 closest distance to " CG2BVAL A  41 " =    0.882
peak=    3.218 closest distance to " CB  ALA A   1 " =    4.532
peak=    3.217 closest distance to " O   HOH Z 248 " =    1.672
peak=    3.215 closest distance to " CB  ALA A  71 " =    1.375
peak=    3.213 closest distance to " O   HOH Z 108 " =    1.138
peak=    3.211 closest distance to " O   HOH Z 303 " =    1.687
peak=    3.211 closest distance to " NZ  LYS A 119 " =    1.220
peak=    3.211 closest distance to " CB  ILE A 120 " =    1.346
peak=    3.210 closest distance to " OE1 GLN A  11 " =    2.070
peak=    3.209 closest distance to " O   HOH Z 211 " =    2.777
peak=    3.206 closest distance to " CA  ASP A 140 " =    1.157
peak=    3.204 closest distance to " CB  LYS A 117 " =    1.142
peak=    3.204 closest distance to " CB  SER A 273 " =    0.799
peak=    3.200 closest distance to " CG AARG A 275 " =    1.021
peak=    3.199 closest distance to " ND1 HIS A  81 " =    1.556
peak=    3.197 closest distance to " CE AMET A  47 " =    1.443
peak=    3.197 closest distance to " CB  ASP A 140 " =    0.866
peak=    3.197 closest distance to " CA  ARG A  36 " =    1.037
peak=    3.196 closest distance to " CD  LYS A 119 " =    1.300
peak=    3.195 closest distance to " C   TYR A 214 " =    1.502
peak=    3.193 closest distance to " O   HOH Z 422 " =    2.713
peak=    3.193 closest distance to " OE1 GLU A   2 " =    2.156
peak=    3.192 closest distance to " O   HOH Z 357 " =    1.817
peak=    3.191 closest distance to " O   HOH Z 266 " =    3.035
peak=    3.182 closest distance to " O   HOH Z 374 " =    2.539
peak=    3.181 closest distance to " NE2 GLN A  73 " =    3.611
peak=    3.178 closest distance to " O   GLY A  57 " =    2.524
peak=    3.176 closest distance to " O   HOH Z 222 " =    2.489
peak=    3.176 closest distance to " CG1 ILE A 151 " =    0.934
peak=    3.173 closest distance to " CG  GLN A  89 " =    1.459
peak=    3.172 closest distance to " NH2 ARG A 156 " =    1.202
peak=    3.165 closest distance to " O   HOH Z 217 " =    1.447
peak=    3.165 closest distance to " CG  LYS A  76 " =    1.002
peak=    3.164 closest distance to " CH2 TRP A  92 " =    2.127
peak=    3.163 closest distance to " CA  ASN A  74 " =    1.244
peak=    3.161 closest distance to " CD1 ILE A 106 " =    0.837
peak=    3.159 closest distance to " CD2 HIS A  81 " =    1.193
peak=    3.157 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.157 closest distance to " CB  LEU A 255 " =    0.751
peak=    3.155 closest distance to " O   HOH Z 433 " =    1.803
peak=    3.153 closest distance to " CA  ALA A 154 " =    0.949
peak=    3.153 closest distance to " O   HOH Z 153 " =    1.588
peak=    3.152 closest distance to " OG1 THR A 246 " =    3.182
peak=    3.151 closest distance to " CA  ALA A  43 " =    1.216
peak=    3.150 closest distance to " O   HOH Z 403 " =    1.328
peak=    3.140 closest distance to " O   HOH Z 285 " =    1.530
peak=    3.140 closest distance to " O   HOH Z 106 " =    2.516
peak=    3.134 closest distance to " O   HOH Z  88 " =    2.262
peak=    3.130 closest distance to " CB  VAL A 126 " =    1.056
peak=    3.128 closest distance to " CE BLYS A 290 " =    1.169
peak=    3.126 closest distance to " CB  ASN A 224 " =    0.979
peak=    3.125 closest distance to " CB  SER A 276 " =    1.098
peak=    3.124 closest distance to " CB  TRP A 179 " =    1.417
peak=    3.118 closest distance to " CB  MET A  40 " =    0.827
peak=    3.115 closest distance to " CB  GLN A 278 " =    0.848
peak=    3.114 closest distance to " CB  THR A  31 " =    1.756
peak=    3.113 closest distance to " CG  ARG A 159 " =    0.831
peak=    3.111 closest distance to " N   TYR A  15 " =    0.720
peak=    3.111 closest distance to " OG BSER A 258 " =    3.554
peak=    3.108 closest distance to " CA  ALA A 291 " =    0.914
peak=    3.107 closest distance to " CB  ASN A 215 " =    1.070
peak=    3.107 closest distance to " NH2AARG A 190 " =    1.148
peak=    3.105 closest distance to " CB  ALA A   9 " =    1.544
peak=    3.098 closest distance to " CA  ALA A  51 " =    0.904
peak=    3.094 closest distance to " CA  SER A 146 " =    1.734
peak=    3.092 closest distance to " O   HOH Z 423 " =    1.524
peak=    3.087 closest distance to " CA  ALA A 158 " =    1.119
peak=    3.087 closest distance to " CB  ARG A 138 " =    0.931
peak=    3.083 closest distance to " O   HOH Z 383 " =    1.679
peak=    3.075 closest distance to " O   HOH Z 423 " =    2.745
peak=    3.068 closest distance to " O  BHOH Z  74 " =    1.390
peak=    3.053 closest distance to " CB  LYS A 290 " =    1.263
peak=    3.036 closest distance to " CA  ALA A 299 " =    0.909
peak=    3.014 closest distance to " O   HOH Z 218 " =    2.302

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.776 - 5.237
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.776 - 5.237

peak=   -4.655 closest distance to " O   HOH Z 266 " =    4.516
peak=   -4.651 closest distance to " CB  PRO A 243 " =    2.572
peak=   -4.526 closest distance to " O   HOH Z 377 " =    1.976
peak=   -4.430 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.376 closest distance to " CD  ARG A 156 " =    1.989
peak=   -4.245 closest distance to " O   VAL A  67 " =    2.679
peak=   -4.187 closest distance to " O   HOH Z 372 " =    2.403
peak=   -4.184 closest distance to " CG  GLN A 223 " =    1.988
peak=   -4.175 closest distance to " SG  CYS A 254 " =    3.415
peak=   -4.159 closest distance to " O   PRO A 198 " =    1.279
peak=   -4.149 closest distance to " OG BSER A 134 " =    1.217
peak=   -4.109 closest distance to " O   HOH Z 290 " =    1.130
peak=   -4.024 closest distance to " O   HOH Z 198 " =    1.933
peak=   -4.018 closest distance to " O   HOH Z  43 " =    1.677
peak=   -3.994 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.988 closest distance to " CE  MET A 105 " =    2.271
peak=   -3.985 closest distance to " O   HOH Z  47 " =    1.567
peak=   -3.937 closest distance to " OXT GLY A 302 " =    2.763
peak=   -3.936 closest distance to " O   HOH Z 231 " =    2.167
peak=   -3.922 closest distance to " O   HOH Z 389 " =    1.889
peak=   -3.920 closest distance to " O   HOH Z 435 " =    2.828
peak=   -3.916 closest distance to " O   ILE A 109 " =    2.571
peak=   -3.916 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.873 closest distance to " CD1 PHE A  59 " =    1.865
peak=   -3.859 closest distance to " O   SER A 135 " =    1.465
peak=   -3.845 closest distance to " O   HOH Z 185 " =    2.204
peak=   -3.827 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.825 closest distance to " CB  ASN A  39 " =    2.220
peak=   -3.823 closest distance to " O   HOH Z  13 " =    1.414
peak=   -3.822 closest distance to " N   ALA A  43 " =    2.469
peak=   -3.814 closest distance to " CD1 LEU A 228 " =    2.183
peak=   -3.809 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.802 closest distance to " CB  ALA A 291 " =    2.147
peak=   -3.789 closest distance to " ND2 ASN A  45 " =    0.991
peak=   -3.774 closest distance to " CZ  TYR A 169 " =    1.687
peak=   -3.770 closest distance to " O   VAL A  67 " =    2.704
peak=   -3.765 closest distance to " CE2 PHE A 218 " =    2.483
peak=   -3.760 closest distance to " O   HOH Z 313 " =    1.959
peak=   -3.750 closest distance to " CE2 TYR A  30 " =    2.800
peak=   -3.744 closest distance to " NE  ARG A 156 " =    1.862
peak=   -3.743 closest distance to " CZ  PHE A  59 " =    1.514
peak=   -3.737 closest distance to " O   PRO A 163 " =    1.957
peak=   -3.729 closest distance to " ND2 ASN A  45 " =    1.258
peak=   -3.728 closest distance to " O   HOH Z 102 " =    1.644
peak=   -3.726 closest distance to " O   HOH Z 407 " =    3.062
peak=   -3.720 closest distance to " CA  GLY A 203 " =    2.177
peak=   -3.711 closest distance to " CD  ARG A 139 " =    1.478
peak=   -3.704 closest distance to " OG  SER A   3 " =    1.698
peak=   -3.703 closest distance to " CA  GLY A  98 " =    1.883
peak=   -3.674 closest distance to " O   HOH Z 126 " =    1.834
peak=   -3.668 closest distance to " CG  PHE A 283 " =    2.642
peak=   -3.668 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.666 closest distance to " NH1 ARG A  36 " =    2.097
peak=   -3.639 closest distance to " O   HOH Z 351 " =    1.475
peak=   -3.636 closest distance to " O   HOH Z 353 " =    2.209
peak=   -3.631 closest distance to " N   ALA A 248 " =    1.588
peak=   -3.622 closest distance to " O   HOH Z  52 " =    1.307
peak=   -3.619 closest distance to " O   ALA A 161 " =    1.552
peak=   -3.611 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.598 closest distance to " O   HOH Z  11 " =    1.833
peak=   -3.586 closest distance to " O   HOH Z 114 " =    2.983
peak=   -3.577 closest distance to " O   HOH Z 385 " =    1.966
peak=   -3.577 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.572 closest distance to " OXT GLY A 302 " =    3.523
peak=   -3.569 closest distance to " NH2 ARG A  79 " =    1.911
peak=   -3.565 closest distance to " N   ASP A 286 " =    2.382
peak=   -3.559 closest distance to " O   HOH Z  11 " =    2.051
peak=   -3.544 closest distance to " C   LEU A 143 " =    1.141
peak=   -3.532 closest distance to " O   HOH Z 298 " =    1.211
peak=   -3.528 closest distance to " O   HOH Z 211 " =    1.665
peak=   -3.516 closest distance to " O   VAL A 174 " =    2.090
peak=   -3.508 closest distance to " O   HOH Z 152 " =    5.156
peak=   -3.495 closest distance to " CB  ALA A 248 " =    1.982
peak=   -3.494 closest distance to " N   SER A 212 " =    1.921
peak=   -3.473 closest distance to " OG  SER A  97 " =    2.094
peak=   -3.469 closest distance to " O   GLY A  80 " =    2.425
peak=   -3.467 closest distance to " O   ALA A  51 " =    1.354
peak=   -3.463 closest distance to " O   HOH Z 198 " =    1.453
peak=   -3.446 closest distance to " OD1 ASN A 148 " =    1.669
peak=   -3.442 closest distance to " ND2 ASN A 187 " =    1.545
peak=   -3.437 closest distance to " OD2 ASP A 171 " =    2.326
peak=   -3.435 closest distance to " CD2 LEU A 237 " =    2.706
peak=   -3.431 closest distance to " OD1 ASP A 191 " =    1.816
peak=   -3.431 closest distance to " O   SER A  95 " =    1.452
peak=   -3.427 closest distance to " O   HOH Z  63 " =    1.546
peak=   -3.425 closest distance to " CD2 PHE A 192 " =    2.000
peak=   -3.421 closest distance to " CD1 LEU A 101 " =    2.290
peak=   -3.419 closest distance to " O   HOH Z  51 " =    1.247
peak=   -3.419 closest distance to " O   HOH Z  93 " =    1.959
peak=   -3.419 closest distance to " OE1 GLN A  88 " =    1.131
peak=   -3.412 closest distance to " NH2BARG A 275 " =    1.869
peak=   -3.410 closest distance to " O   PRO A 243 " =    2.507
peak=   -3.404 closest distance to " OD1 ASP A 171 " =    1.584
peak=   -3.401 closest distance to " CD2 LEU A 300 " =    2.868
peak=   -3.396 closest distance to " OD2 ASP A 191 " =    1.475
peak=   -3.392 closest distance to " CB  ASP A 132 " =    2.316
peak=   -3.391 closest distance to " CB  CYS A 254 " =    2.287
peak=   -3.383 closest distance to " O   HOH Z  44 " =    2.176
peak=   -3.373 closest distance to " O   HOH Z 193 " =    1.751
peak=   -3.373 closest distance to " CB  ALA A 131 " =    2.012
peak=   -3.371 closest distance to " SG ACYS A 201 " =    1.903
peak=   -3.371 closest distance to " OG BSER A 134 " =    1.611
peak=   -3.360 closest distance to " O   HOH Z 348 " =    1.747
peak=   -3.357 closest distance to " O   HOH Z 263 " =    2.869
peak=   -3.355 closest distance to " NH1 ARG A 195 " =    2.591
peak=   -3.353 closest distance to " O   HOH Z 250 " =    1.435
peak=   -3.343 closest distance to " O   HOH Z 417 " =    2.386
peak=   -3.339 closest distance to " OD2 ASP A  50 " =    1.487
peak=   -3.338 closest distance to " CG  GLU A   2 " =    2.033
peak=   -3.333 closest distance to " CE3 TRP A 150 " =    2.024
peak=   -3.331 closest distance to " CD  ARG A  36 " =    1.950
peak=   -3.327 closest distance to " O   ASN A 249 " =    1.484
peak=   -3.326 closest distance to " NH2AARG A 275 " =    5.237
peak=   -3.320 closest distance to " CB  ALA A 291 " =    2.384
peak=   -3.320 closest distance to " CG2 VAL A 189 " =    2.005
peak=   -3.316 closest distance to " CA  GLY A 133 " =    1.924
peak=   -3.313 closest distance to " O   HOH Z  60 " =    2.374
peak=   -3.312 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.312 closest distance to " CA  TRP A 274 " =    1.535
peak=   -3.311 closest distance to " O   HOH Z  24 " =    1.366
peak=   -3.301 closest distance to " O   GLY A  80 " =    2.355
peak=   -3.295 closest distance to " O   HOH Z  38 " =    1.648
peak=   -3.292 closest distance to " O   HOH Z 388 " =    1.997
peak=   -3.291 closest distance to " OH  TYR A 214 " =    1.224
peak=   -3.291 closest distance to " O   HOH Z 166 " =    1.423
peak=   -3.286 closest distance to " O   HOH Z 140 " =    1.986
peak=   -3.279 closest distance to " O   HOH Z  10 " =    1.374
peak=   -3.274 closest distance to " OE1 GLN A 223 " =    1.880
peak=   -3.270 closest distance to " CB  PRO A 163 " =    2.498
peak=   -3.269 closest distance to " O   VAL A 153 " =    2.271
peak=   -3.269 closest distance to " O   HOH Z 385 " =    1.858
peak=   -3.268 closest distance to " CB  ALA A 248 " =    2.353
peak=   -3.255 closest distance to " CE3 TRP A 274 " =    2.371
peak=   -3.255 closest distance to " CB  ASP A 132 " =    2.242
peak=   -3.251 closest distance to " O   PHE A 218 " =    1.570
peak=   -3.246 closest distance to " CB  ALA A  51 " =    1.847
peak=   -3.239 closest distance to " O   HOH Z 423 " =    1.131
peak=   -3.238 closest distance to " CG1 VAL A 250 " =    2.626
peak=   -3.232 closest distance to " CB  ASP A 286 " =    2.134
peak=   -3.231 closest distance to " O   HOH Z 210 " =    1.094
peak=   -3.228 closest distance to " O   HOH Z 137 " =    1.482
peak=   -3.227 closest distance to " C   GLN A 205 " =    1.926
peak=   -3.220 closest distance to " CG2 ILE A 263 " =    2.278
peak=   -3.220 closest distance to " O   MET A  40 " =    2.720
peak=   -3.219 closest distance to " CD  LYS A 289 " =    2.400
peak=   -3.212 closest distance to " CB  PHE A 208 " =    2.207
peak=   -3.209 closest distance to " O   HOH Z 213 " =    1.352
peak=   -3.208 closest distance to " CG1 VAL A 197 " =    2.176
peak=   -3.206 closest distance to " N   GLY A  23 " =    2.350
peak=   -3.204 closest distance to " C   ASP A 231 " =    2.475
peak=   -3.204 closest distance to " O   VAL A 189 " =    2.505
peak=   -3.203 closest distance to " C   MET A 188 " =    1.504
peak=   -3.202 closest distance to " OG  SER A  87 " =    1.278
peak=   -3.199 closest distance to " CB  TRP A  85 " =    2.504
peak=   -3.195 closest distance to " C   PRO A  90 " =    1.467
peak=   -3.193 closest distance to " CG  ASN A 301 " =    1.879
peak=   -3.190 closest distance to " NZ  LYS A 119 " =    3.331
peak=   -3.187 closest distance to " CD  GLN A  58 " =    1.237
peak=   -3.179 closest distance to " O   HOH Z 423 " =    2.139
peak=   -3.178 closest distance to " OD1 ASP A 191 " =    1.437
peak=   -3.177 closest distance to " O   HOH Z  90 " =    2.686
peak=   -3.175 closest distance to " O   HOH Z 200 " =    4.593
peak=   -3.174 closest distance to " OG  SER A  62 " =    1.632
peak=   -3.171 closest distance to " O   HOH Z 322 " =    1.630
peak=   -3.170 closest distance to " N   PHE A  59 " =    1.909
peak=   -3.168 closest distance to " O   GLN A 240 " =    1.915
peak=   -3.160 closest distance to " O   HOH Z 438 " =    1.290
peak=   -3.158 closest distance to " O   ASP A 162 " =    2.187
peak=   -3.155 closest distance to " SD  MET A 188 " =    2.276
peak=   -3.154 closest distance to " O   SER A 146 " =    1.093
peak=   -3.151 closest distance to " O   HOH Z 266 " =    4.410
peak=   -3.148 closest distance to " O   HOH Z  60 " =    2.080
peak=   -3.142 closest distance to " O   HOH Z 377 " =    0.921
peak=   -3.134 closest distance to " CG  PRO A 163 " =    2.460
peak=   -3.130 closest distance to " CD1 ILE A 151 " =    2.226
peak=   -3.129 closest distance to " O   HOH Z   9 " =    2.106
peak=   -3.117 closest distance to " O   HOH Z 426 " =    1.575
peak=   -3.116 closest distance to " O   HOH Z 281 " =    2.767
peak=   -3.112 closest distance to " O   HOH Z 359 " =    3.208
peak=   -3.106 closest distance to " O   HOH Z 234 " =    3.910
peak=   -3.106 closest distance to " CG  TRP A 266 " =    1.839
peak=   -3.103 closest distance to " CG  GLU A 277 " =    1.209
peak=   -3.100 closest distance to " O   HOH Z 324 " =    2.042
peak=   -3.075 closest distance to " CD  GLN A  88 " =    0.860
peak=   -3.072 closest distance to " O   HOH Z 283 " =    2.386
peak=   -3.069 closest distance to " O   HOH Z 323 " =    1.298
peak=   -3.067 closest distance to " CG  GLU A 152 " =    0.840
peak=   -3.062 closest distance to " O   HOH Z 281 " =    3.248
peak=   -3.048 closest distance to " O   HOH Z 421 " =    2.959
peak=   -3.045 closest distance to " OD1AASN A 224 " =    1.799
peak=   -3.012 closest distance to " CD1 ILE A 199 " =    2.501

================= 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    :  0.3506 0.3469   6.100980e+00   6.090816e+00
   1_bss:  0.3359 0.3306   6.086621e+00   6.058912e+00
   1_xyz:  0.1847 0.2085   5.537355e+00   5.643823e+00
   1_adp:  0.1694 0.2154   5.490166e+00   5.684259e+00
   1_occ:  0.1691 0.2154   5.488725e+00   5.683151e+00
   2_bss:  0.1669 0.2123   5.478553e+00   5.671768e+00
   2_xyz:  0.1312 0.1718   5.261100e+00   5.474407e+00
   2_adp:  0.1259 0.1641   5.219679e+00   5.428048e+00
   2_occ:  0.1257 0.1642   5.219225e+00   5.427993e+00
   3_bss:  0.1259 0.1645   5.219531e+00   5.429052e+00
   3_xyz:  0.1126 0.1528   5.127713e+00   5.359468e+00
   3_adp:  0.1102 0.1523   5.115461e+00   5.353975e+00
   3_occ:  0.1101 0.1524   5.115487e+00   5.354301e+00
   4_bss:  0.1101 0.1524   5.115243e+00   5.354235e+00
   4_xyz:  0.1062 0.1523   5.099054e+00   5.353863e+00
   4_adp:  0.1054 0.1535   5.100246e+00   5.360467e+00
   4_occ:  0.1054 0.1535   5.100313e+00   5.360704e+00
   5_bss:  0.1053 0.1534   5.099975e+00   5.360220e+00
   5_xyz:  0.1058 0.1544   5.105079e+00   5.366317e+00
   5_adp:  0.1059 0.1539   5.103620e+00   5.363830e+00
   5_occ:  0.1059 0.1539   5.103808e+00   5.364223e+00
   5_bss:  0.1061 0.1538   5.105041e+00   5.362996e+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:  0.327  32.479  -3.181  -0.133   0.919  -0.000   0.000   0.000
   1_xyz:  0.327  32.479  -3.181  -0.133   0.919  -0.000   0.000   0.000
   1_adp:  0.327  32.479  -3.181  -0.133   0.919  -0.000   0.000   0.000
   1_occ:  0.327  32.479  -3.181  -0.133   0.919  -0.000   0.000   0.000
   2_bss:  0.311  38.735  -3.022  -2.215  -1.320  -0.000  -0.000  -0.000
   2_xyz:  0.311  38.735  -3.022  -2.215  -1.320  -0.000  -0.000  -0.000
   2_adp:  0.311  38.735  -3.022  -2.215  -1.320  -0.000  -0.000  -0.000
   2_occ:  0.311  38.735  -3.022  -2.215  -1.320  -0.000  -0.000  -0.000
   3_bss:  0.318  38.735  -2.748  -2.441  -1.549  -0.000  -0.000  -0.000
   3_xyz:  0.318  38.735  -2.748  -2.441  -1.549  -0.000  -0.000  -0.000
   3_adp:  0.318  38.735  -2.748  -2.441  -1.549  -0.000  -0.000  -0.000
   3_occ:  0.318  38.735  -2.748  -2.441  -1.549  -0.000  -0.000  -0.000
   4_bss:  0.318  38.735  -2.601  -2.465  -1.619  -0.000  -0.000  -0.000
   4_xyz:  0.318  38.735  -2.601  -2.465  -1.619  -0.000  -0.000  -0.000
   4_adp:  0.318  38.735  -2.601  -2.465  -1.619  -0.000  -0.000  -0.000
   4_occ:  0.318  38.735  -2.601  -2.465  -1.619  -0.000  -0.000  -0.000
   5_bss:  0.321  42.031  -2.380  -2.305  -1.451  -0.000  -0.000  -0.000
   5_xyz:  0.321  42.031  -2.380  -2.305  -1.451  -0.000  -0.000  -0.000
   5_adp:  0.321  42.031  -2.380  -2.305  -1.451  -0.000  -0.000  -0.000
   5_occ:  0.321  42.031  -2.380  -2.305  -1.451  -0.000  -0.000  -0.000
   5_bss:  0.322  44.350  -2.187  -2.136  -1.274  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.376 0.6887  0.8864    35239.995
   1_bss:  34.737 0.7052  0.8808    31001.582
   1_xyz:  19.506 0.8681  1.0138    11069.365
   1_adp:  20.641 0.8565  1.0065    11910.324
   1_occ:  20.624 0.8566  1.0063    11864.615
   2_bss:  20.211 0.8603  0.9617    11485.082
   2_xyz:  15.743 0.9002  0.9852     7445.227
   2_adp:  14.712 0.9092  0.9877     6861.422
   2_occ:  14.714 0.9092  0.9875     6855.099
   3_bss:  14.722 0.9092  0.9852     6896.049
   3_xyz:  13.364 0.9197  0.9889     5891.226
   3_adp:  13.233 0.9209  0.9846     5833.713
   3_occ:  13.238 0.9208  0.9845     5836.353
   4_bss:  13.234 0.9209  0.9853     5837.653
   4_xyz:  13.179 0.9215  0.9850     5833.324
   4_adp:  13.305 0.9206  0.9783     5900.897
   4_occ:  13.309 0.9206  0.9782     5903.853
   5_bss:  13.301 0.9206  0.9851     5900.764
   5_xyz:  13.414 0.9198  0.9843     5985.229
   5_adp:  13.358 0.9202  0.9785     5956.383
   5_occ:  13.366 0.9201  0.9784     5960.002
   5_bss:  13.365 0.9201  0.9840     5956.858
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6362e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6362e-01
   1_xyz:   1.073  0.008  0.073 14.957  0.005  4.107   6.8536e-02
   1_adp:   1.073  0.008  0.073 14.957  0.005  4.107   6.8536e-02
   1_occ:   1.073  0.008  0.073 14.957  0.005  4.107   6.8536e-02
   2_bss:   1.073  0.008  0.073 14.957  0.005  4.107   6.8536e-02
   2_xyz:   0.895  0.004  0.065 14.156  0.004  4.112   4.7127e-02
   2_adp:   0.895  0.004  0.065 14.156  0.004  4.112   4.7127e-02
   2_occ:   0.895  0.004  0.065 14.156  0.004  4.112   4.7127e-02
   3_bss:   0.895  0.004  0.065 14.156  0.004  4.112   4.7127e-02
   3_xyz:   0.970  0.006  0.072 14.610  0.004  4.112   5.6047e-02
   3_adp:   0.970  0.006  0.072 14.610  0.004  4.112   5.6047e-02
   3_occ:   0.970  0.006  0.072 14.610  0.004  4.112   5.6047e-02
   4_bss:   0.970  0.006  0.072 14.610  0.004  4.112   5.6047e-02
   4_xyz:   1.012  0.007  0.074 14.710  0.004  4.113   6.0731e-02
   4_adp:   1.012  0.007  0.074 14.710  0.004  4.113   6.0731e-02
   4_occ:   1.012  0.007  0.074 14.710  0.004  4.113   6.0731e-02
   5_bss:   1.012  0.007  0.074 14.710  0.004  4.113   6.0731e-02
   5_xyz:   0.962  0.006  0.072 14.468  0.004  4.109   5.5315e-02
   5_adp:   0.962  0.006  0.072 14.468  0.004  4.109   5.5315e-02
   5_occ:   0.962  0.006  0.072 14.468  0.004  4.109   5.5315e-02
   5_bss:   0.962  0.006  0.072 14.468  0.004  4.109   5.5315e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3863e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3863e-01
   1_xyz:   7.917  0.055  0.376 86.513  0.032  2.216   7.2003e-02
   1_adp:   7.917  0.055  0.376 86.513  0.032  2.216   7.2003e-02
   1_occ:   7.917  0.055  0.376 86.513  0.032  2.216   7.2003e-02
   2_bss:   7.917  0.055  0.376 86.513  0.032  2.216   7.2003e-02
   2_xyz:   7.021  0.030  0.209 83.211  0.042  2.397   3.2306e-02
   2_adp:   7.021  0.030  0.209 83.211  0.042  2.397   3.2306e-02
   2_occ:   7.021  0.030  0.209 83.211  0.042  2.397   3.2306e-02
   3_bss:   7.021  0.030  0.209 83.211  0.042  2.397   3.2306e-02
   3_xyz:   7.047  0.039  0.223 85.195  0.036  2.308   4.7313e-02
   3_adp:   7.047  0.039  0.223 85.195  0.036  2.308   4.7313e-02
   3_occ:   7.047  0.039  0.223 85.195  0.036  2.308   4.7313e-02
   4_bss:   7.047  0.039  0.223 85.195  0.036  2.308   4.7313e-02
   4_xyz:   6.416  0.039  0.232 83.447  0.043  2.276   4.7045e-02
   4_adp:   6.416  0.039  0.232 83.447  0.043  2.276   4.7045e-02
   4_occ:   6.416  0.039  0.232 83.447  0.043  2.276   4.7045e-02
   5_bss:   6.416  0.039  0.232 83.447  0.043  2.276   4.7045e-02
   5_xyz:   6.438  0.034  0.229 83.426  0.038  2.326   4.0380e-02
   5_adp:   6.438  0.034  0.229 83.426  0.038  2.326   4.0380e-02
   5_occ:   6.438  0.034  0.229 83.426  0.038  2.326   4.0380e-02
   5_bss:   6.438  0.034  0.229 83.426  0.038  2.326   4.0380e-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:  71.65   0.00  17.20  66.58   0.00  13.11  71.65   7.39  39.50
   1_occ:  71.65   0.00  17.20  66.58   0.00  13.11  71.65   7.39  39.50
   2_bss:  71.65   0.00  17.20  66.58   0.00  13.11  71.65   7.39  39.50
   2_xyz:  71.65   0.00  17.20  66.58   0.00  13.11  71.65   7.39  39.50
   2_adp:  71.94   1.72  16.99  71.94   1.72  12.99  70.81   6.59  38.78
   2_occ:  71.94   1.72  16.99  71.94   1.72  12.99  70.81   6.59  38.78
   3_bss:  71.94   1.72  16.99  71.94   1.72  12.99  70.81   6.59  38.78
   3_xyz:  71.94   1.72  16.99  71.94   1.72  12.99  70.81   6.59  38.78
   3_adp:  78.48   1.17  17.02  78.48   1.17  12.92  75.40   5.57  39.35
   3_occ:  78.48   1.17  17.02  78.48   1.17  12.92  75.40   5.57  39.35
   4_bss:  78.48   1.17  17.02  78.48   1.17  12.92  75.40   5.57  39.35
   4_xyz:  78.48   1.17  17.02  78.48   1.17  12.92  75.40   5.57  39.35
   4_adp:  91.48   0.84  17.04  91.48   0.84  12.87  83.24   6.22  39.72
   4_occ:  91.48   0.84  17.04  91.48   0.84  12.87  83.24   6.22  39.72
   5_bss:  91.48   0.84  17.04  91.48   0.84  12.87  83.24   6.22  39.72
   5_xyz:  91.48   0.84  17.04  91.48   0.84  12.87  83.24   6.22  39.72
   5_adp:  92.89   0.82  16.70  92.89   0.82  12.66  85.34   6.08  38.71
   5_occ:  92.89   0.82  16.70  92.89   0.82  12.66  85.34   6.08  38.71
   5_bss:  92.86   0.79  16.68  92.86   0.79  12.63  85.31   6.06  38.68
------------------------------------------------------------------------
 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:    1.263    0.034    0.350
   1_adp:    1.263    0.034    0.350
   1_occ:    1.263    0.034    0.350
   2_bss:    1.263    0.034    0.350
   2_xyz:    0.849    0.029    0.388
   2_adp:    0.849    0.029    0.388
   2_occ:    0.849    0.029    0.388
   3_bss:    0.849    0.029    0.388
   3_xyz:    0.929    0.045    0.431
   3_adp:    0.929    0.045    0.431
   3_occ:    0.929    0.045    0.431
   4_bss:    0.929    0.045    0.431
   4_xyz:    0.968    0.046    0.447
   4_adp:    0.968    0.046    0.447
   4_occ:    0.968    0.046    0.447
   5_bss:    0.968    0.046    0.447
   5_xyz:    1.101    0.034    0.455
   5_adp:    1.101    0.034    0.455
   5_occ:    1.101    0.034    0.455
   5_bss:    1.101    0.034    0.455
------------------------------------------------------------------------

CPU time actual refinement: 330.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/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_640/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_640/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.94 
  Macro-tasks:
    bulk solvent and scale       = 38.33  
    individual site refinement   = 143.05 
    weights calculation          = 28.92  
    collect and process          = 6.58   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 217.00 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 104.28 
    alpha_beta                      = 8.24   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 115.40 
    fmodel                         = 6.48   
    r_factors                      = 0.20   
    phase_errors                   = 11.21  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 248.96 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.586 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    653 calls, 103.99 s
gradients_fft:          598 calls, 100.87 s

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

# Date 2008-01-16 Time 05:18:35 PST -0800 (1200489515.97 s)
Start R-work = 0.3506, R-free = 0.3469 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.3359, R-free = 0.3306
Final R-work = 0.1061, R-free = 0.1538