# Date 2008-01-16 Time 05:31:32 PST -0800 (1200490292.64 s)
#phil __OFF__

Command line arguments: "../770.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6189
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 770

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 84.2302, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95124
Completeness in resolution range: 0.939926
Completeness with d_max=infinity: 0.937093

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95124
Completeness in resolution range: 0.939926
Completeness with d_max=infinity: 0.937093

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1761 [2189/2218]  1973   216   9.9%
  bin  2:  4.1761 -  3.3267 [2098/2117]  1887   211  10.1%
  bin  3:  3.3267 -  2.9097 [2074/2094]  1863   211  10.2%
  bin  4:  2.9097 -  2.6453 [2062/2087]  1865   197   9.6%
  bin  5:  2.6453 -  2.4566 [2044/2064]  1830   214  10.5%
  bin  6:  2.4566 -  2.3123 [2037/2083]  1839   198   9.7%
  bin  7:  2.3123 -  2.1969 [2013/2045]  1811   202  10.0%
  bin  8:  2.1969 -  2.1015 [2009/2045]  1808   201  10.0%
  bin  9:  2.1015 -  2.0208 [2009/2039]  1806   203  10.1%
  bin 10:  2.0208 -  1.9512 [1054/2049]   948   106  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 24
        2.26 -     2.92: 1522
        2.92 -     3.58: 4547
        3.58 -     4.24: 9318
        4.24 -     4.90: 13253
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.598 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.652 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  22 " - " O   HOH Z 320 "  1.890 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28659 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_770/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/model_refine_001.geo

CPU time processing inputs: 9.31


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 84.23025 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: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3815   r_free= 0.3816   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.172597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6582 0.99   1417  159 0.3182 0.3166      6.4459      6.4448|
|  2:  4.6582 -  3.7161 0.99   1371  145 0.3148 0.2866      6.6191      6.5497|
|  3:  3.7161 -  3.2519 0.99   1341  157 0.3467 0.3594      6.5101      6.6693|
|  4:  3.2519 -  2.9571 0.99   1341  148 0.3501 0.3597      6.3714      6.3709|
|  5:  2.9571 -  2.7465 0.99   1312  148 0.3933 0.3704      6.2496       6.251|
|  6:  2.7465 -  2.5855 0.98   1321  145 0.4135 0.4148      6.1667      6.1278|
|  7:  2.5855 -  2.4566 0.99   1315  147 0.3978 0.3773      6.1379      6.0891|
|  8:  2.4566 -  2.3501 0.98   1297  140 0.4211 0.4175      6.0719      6.1068|
|  9:  2.3501 -  2.2599 0.98   1316  151 0.4104 0.4159      6.0299      5.9793|
| 10:  2.2599 -  2.1822 0.98   1285  141 0.4289 0.4629      6.0095       6.067|
| 11:  2.1822 -  2.1141 0.99   1303  143 0.4348 0.4945      5.9647      6.0445|
| 12:  2.1141 -  2.0539 0.98   1284  144 0.4316 0.4420      5.8871      5.9119|
| 13:  2.0539 -  1.9999 0.95   1260  140 0.4490 0.4380      5.8214      5.7802|
| 14:  1.9999 -  1.9512 0.36    467   51 0.5144 0.4999      5.8339      5.7442|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6582  1417   159  0.76  28.75   0.86     0.78      50572.62|
|  2:  4.6582 -  3.7161  1371   145  0.78  27.61   0.95     0.89      68922.73|
|  3:  3.7161 -  3.2519  1341   157  0.72  33.85   0.97     0.91      73156.65|
|  4:  3.2519 -  2.9571  1341   148  0.66  39.01   0.99     0.87      66390.81|
|  5:  2.9571 -  2.7465  1312   148  0.60  44.01   0.95     0.81      54204.52|
|  6:  2.7465 -  2.5855  1321   145  0.58  45.37   0.95     0.79      46816.89|
|  7:  2.5855 -  2.4566  1315   147  0.60  43.96   0.99     0.79      41504.11|
|  8:  2.4566 -  2.3501  1297   140  0.58  45.85   0.96     0.81      37755.04|
|  9:  2.3501 -  2.2599  1316   151  0.57  46.37   1.01     0.80      35454.33|
| 10:  2.2599 -  2.1822  1285   141  0.53  49.34   1.02     0.77      35930.50|
| 11:  2.1822 -  2.1141  1303   143  0.51  51.40   1.02     0.74      34701.00|
| 12:  2.1141 -  2.0539  1284   144  0.50  52.66   1.03     0.76      32634.39|
| 13:  2.0539 -  1.9999  1260   140  0.48  53.63   1.00     0.72      28013.57|
| 14:  1.9999 -  1.9512   467    51  0.44  57.35   0.96     0.61      25385.87|
|alpha:            min =        0.61 max =            0.91 mean =         0.80|
|beta:             min =    25385.87 max =        73156.65 mean =     46335.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.97 mean =        43.37|
|phase err.(test): min =        0.00 max =           89.87 mean =        43.48|
|-----------------------------------------------------------------------------|

============================== 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 = 7.747070              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.959   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.195843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.662   (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 |  1.598 -  1.929:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.929 -  2.259:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.259 -  2.589:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.589 -  2.919:     1485 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.919 -  3.249:     1929 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.249 -  3.579:     2618 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.579 -  3.910:     4760 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.910 -  4.240:     4558 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.240 -  4.570:     6037 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.570 -  4.900:     7216 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.598 |       0.394 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    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: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3815   r_free= 0.3816   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.172597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3664   r_free= 0.3665   ksol= 0.32   Bsol= 27.40   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.46,3.48,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.161376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.086108              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.114   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561547              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.592   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3664      final r-factor (work) = 0.2394          |
| start r-factor (free) = 0.3665      final r-factor (free) = 0.2670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9109 = 6.09 * 0.50 * 6.1568 + 1.00 * 0.1754                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1596 = 6.09 * 0.50 * 5.9349 + 1.00 * 0.0994                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2394      final r-factor (work) = 0.2194          |
| start r-factor (free) = 0.2670      final r-factor (free) = 0.2759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3387 = 0.56 * 1.00 * 5.9349 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2244 = 0.56 * 1.00 * 5.7224 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.98   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    73.98   17.53    None  None   None       |
|    Sol.    : 438    0      2.69    73.98   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    73.06   13.37    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 -   7.398:  521   |   5:    36.989 -  44.386:  134        |
|      1:     7.398 -  14.795: 1171   |   6:    44.386 -  51.784:   90        |
|      2:    14.795 -  22.193:  501   |   7:    51.784 -  59.182:   58        |
|      3:    22.193 -  29.591:  175   |   8:    59.182 -  66.579:   39        |
|      4:    29.591 -  36.989:  115   |   9:    66.579 -  73.977:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2194 r_free = 0.2759             target_work(ml) = 5.734         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2191 r_free = 0.2761             target_work(ml) = 5.733         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2191   r_free= 0.2761   ksol= 0.32   Bsol= 27.40   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.46,3.48,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.733387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2160   r_free= 0.2720   ksol= 0.33   Bsol= 43.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.56,-0.23,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.720481                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.864536              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.559   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.258229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.124  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2160      final r-factor (work) = 0.1541          |
| start r-factor (free) = 0.2720      final r-factor (free) = 0.2029          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1529 = 3.86 * 0.50 * 5.7205 + 1.00 * 0.0994                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8738 = 3.86 * 0.50 * 5.5969 + 1.00 * 0.0590                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1541      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.2029      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4563 = 0.26 * 1.00 * 5.5969 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3982 = 0.26 * 1.00 * 5.3841 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    74.99   17.22    None  None   None       |
|    all(noH): 2823   0      1.34    74.99   17.22    None  None   None       |
|    Sol.    : 438    0      6.85    73.35   39.85    None  None   None       |
|    Mac.    : 2385   0      1.34    74.99   13.07    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:     1.339 -   8.704:  670   |   5:    38.165 -  45.530:  107        |
|      1:     8.704 -  16.070: 1243   |   6:    45.530 -  52.895:  105        |
|      2:    16.070 -  23.435:  359   |   7:    52.895 -  60.261:   46        |
|      3:    23.435 -  30.800:  127   |   8:    60.261 -  67.626:   29        |
|      4:    30.800 -  38.165:  119   |   9:    67.626 -  74.991:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1423 r_free = 0.1886             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1421 r_free = 0.1884             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1421   r_free= 0.1884   ksol= 0.33   Bsol= 43.78   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.56,-0.23,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.345395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1418   r_free= 0.1872   ksol= 0.33   Bsol= 43.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.43,-1.42,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.340721                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.210586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214318              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.735  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0085 = 2.21 * 0.50 * 5.3827 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8873 = 2.21 * 0.50 * 5.2768 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1387 = 0.21 * 1.00 * 5.2768 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1184 = 0.21 * 1.00 * 5.1840 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.00    79.08   17.02    None  None   None       |
|    all(noH): 2823   0      2.00    79.08   17.02    None  None   None       |
|    Sol.    : 438    0      5.54    75.38   39.25    None  None   None       |
|    Mac.    : 2385   0      2.00    79.08   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.998 -   9.707:  912   |   5:    40.541 -  48.249:  107        |
|      1:     9.707 -  17.415: 1139   |   6:    48.249 -  55.958:   84        |
|      2:    17.415 -  25.124:  283   |   7:    55.958 -  63.666:   33        |
|      3:    25.124 -  32.832:  115   |   8:    63.666 -  71.374:   27        |
|      4:    32.832 -  40.541:  117   |   9:    71.374 -  79.083:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1586             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1585             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1585   ksol= 0.33   Bsol= 43.78   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.43,-1.42,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168658                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1583   ksol= 0.33   Bsol= 43.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.51,-1.91,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168031                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.413562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.688  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.328  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7189 = 1.41 * 0.50 * 5.1840 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6929 = 1.41 * 0.50 * 5.1554 + 1.00 * 0.0491                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7013 = 0.33 * 1.00 * 5.1554 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6976 = 0.33 * 1.00 * 5.1428 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    83.50   17.00    None  None   None       |
|    all(noH): 2823   0      1.70    83.50   17.00    None  None   None       |
|    Sol.    : 438    0      6.34    77.72   39.37    None  None   None       |
|    Mac.    : 2385   0      1.70    83.50   12.90    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:     1.703 -   9.882:  980   |   5:    42.599 -  50.778:  109        |
|      1:     9.882 -  18.061: 1113   |   6:    50.778 -  58.958:   62        |
|      2:    18.061 -  26.240:  257   |   7:    58.958 -  67.137:   28        |
|      3:    26.240 -  34.420:  130   |   8:    67.137 -  75.316:   21        |
|      4:    34.420 -  42.599:  118   |   9:    75.316 -  83.495:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1560             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1560             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1560   ksol= 0.33   Bsol= 43.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.51,-1.91,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1561   ksol= 0.33   Bsol= 43.78   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.41,-1.93,-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: 5.144536                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.283620              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.673324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.405  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3497 = 1.28 * 0.50 * 5.1426 + 1.00 * 0.0491                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3455 = 1.28 * 0.50 * 5.1385 + 1.00 * 0.0476                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6062 = 1.67 * 1.00 * 5.1385 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5993 = 1.67 * 1.00 * 5.1335 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.85   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    93.85   17.20    None  None   None       |
|    Sol.    : 438    0      6.39    84.15   40.55    None  None   None       |
|    Mac.    : 2385   0      0.00    93.85   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.385:  898   |   5:    46.927 -  56.312:  110        |
|      1:     9.385 -  18.771: 1231   |   6:    56.312 -  65.697:   44        |
|      2:    18.771 -  28.156:  245   |   7:    65.697 -  75.082:   31        |
|      3:    28.156 -  37.541:  134   |   8:    75.082 -  84.468:   10        |
|      4:    37.541 -  46.927:  116   |   9:    84.468 -  93.853:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1569             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1569             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1569   ksol= 0.33   Bsol= 43.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.41,-1.93,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140665                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6582 0.99   1417  159 0.0993 0.1257      5.3857        5.54|
|  2:  4.6582 -  3.7161 0.99   1371  145 0.0859 0.1086      5.4287      5.6029|
|  3:  3.7161 -  3.2519 0.99   1341  157 0.1064 0.1554      5.4628        5.85|
|  4:  3.2519 -  2.9571 0.99   1341  148 0.1225 0.1575      5.4532       5.587|
|  5:  2.9571 -  2.7465 0.99   1312  148 0.1269 0.1663       5.294      5.4718|
|  6:  2.7465 -  2.5855 0.98   1321  145 0.1210 0.1759      5.1885      5.4165|
|  7:  2.5855 -  2.4566 0.99   1315  147 0.1207 0.1617      5.1384      5.3571|
|  8:  2.4566 -  2.3501 0.98   1297  140 0.1110 0.1707      5.0224      5.2768|
|  9:  2.3501 -  2.2599 0.98   1316  151 0.1153 0.1848      5.0086      5.3007|
| 10:  2.2599 -  2.1822 0.98   1285  141 0.1110 0.1717      4.9531      5.2098|
| 11:  2.1822 -  2.1141 0.99   1303  143 0.1129 0.1814      4.9425      5.3019|
| 12:  2.1141 -  2.0539 0.98   1284  144 0.1078 0.1689      4.8663      5.0896|
| 13:  2.0539 -  1.9999 0.95   1260  140 0.1161 0.1735      4.7905      5.0395|
| 14:  1.9999 -  1.9512 0.36    467   51 0.1021 0.1663      4.6384      4.9081|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6582  1417   159  0.94   8.59   0.98     0.95       6724.15|
|  2:  4.6582 -  3.7161  1371   145  0.95   7.75   1.02     1.01       8667.82|
|  3:  3.7161 -  3.2519  1341   157  0.93  11.31   1.03     1.03      10066.98|
|  4:  3.2519 -  2.9571  1341   148  0.92  13.61   1.01     1.00      10207.10|
|  5:  2.9571 -  2.7465  1312   148  0.90  15.47   0.99     0.97       7816.63|
|  6:  2.7465 -  2.5855  1321   145  0.90  15.83   0.99     0.96       6754.09|
|  7:  2.5855 -  2.4566  1315   147  0.91  14.71   0.99     0.96       5853.61|
|  8:  2.4566 -  2.3501  1297   140  0.91  15.12   0.99     0.96       4960.67|
|  9:  2.3501 -  2.2599  1316   151  0.91  15.26   1.01     0.98       4803.53|
| 10:  2.2599 -  2.1822  1285   141  0.91  15.22   0.99     0.96       4350.15|
| 11:  2.1822 -  2.1141  1303   143  0.90  16.76   1.00     0.96       4519.96|
| 12:  2.1141 -  2.0539  1284   144  0.91  15.62   1.00     0.98       4006.10|
| 13:  2.0539 -  1.9999  1260   140  0.90  16.00   1.00     0.99       3324.42|
| 14:  1.9999 -  1.9512   467    51  0.90  15.47   0.99     0.95       2482.47|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2482.47 max =        10207.10 mean =      6250.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1570   ksol= 0.32   Bsol= 42.43   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.21,-1.79,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1570   ksol= 0.32   Bsol= 42.43   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.21,-1.79,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6582 0.99   1417  159 0.0993 0.1255      5.3843      5.5395|
|  2:  4.6582 -  3.7161 0.99   1371  145 0.0859 0.1085      5.4282      5.6023|
|  3:  3.7161 -  3.2519 0.99   1341  157 0.1064 0.1554      5.4625      5.8499|
|  4:  3.2519 -  2.9571 0.99   1341  148 0.1225 0.1576      5.4532      5.5872|
|  5:  2.9571 -  2.7465 0.99   1312  148 0.1269 0.1664      5.2942      5.4719|
|  6:  2.7465 -  2.5855 0.98   1321  145 0.1210 0.1762       5.189      5.4175|
|  7:  2.5855 -  2.4566 0.99   1315  147 0.1207 0.1617      5.1391      5.3578|
|  8:  2.4566 -  2.3501 0.98   1297  140 0.1110 0.1707       5.023      5.2777|
|  9:  2.3501 -  2.2599 0.98   1316  151 0.1153 0.1846      5.0088      5.3005|
| 10:  2.2599 -  2.1822 0.98   1285  141 0.1110 0.1717      4.9532      5.2097|
| 11:  2.1822 -  2.1141 0.99   1303  143 0.1129 0.1813      4.9426       5.302|
| 12:  2.1141 -  2.0539 0.98   1284  144 0.1078 0.1689       4.866      5.0895|
| 13:  2.0539 -  1.9999 0.95   1260  140 0.1161 0.1733      4.7904      5.0387|
| 14:  1.9999 -  1.9512 0.36    467   51 0.1021 0.1666      4.6385      4.9098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6582  1417   159  0.94   8.58   0.98     0.95       6687.32|
|  2:  4.6582 -  3.7161  1371   145  0.95   7.74   1.03     1.02       8648.68|
|  3:  3.7161 -  3.2519  1341   157  0.93  11.31   1.03     1.03      10064.23|
|  4:  3.2519 -  2.9571  1341   148  0.92  13.61   1.02     1.00      10204.72|
|  5:  2.9571 -  2.7465  1312   148  0.90  15.48   1.00     0.97       7821.68|
|  6:  2.7465 -  2.5855  1321   145  0.90  15.84   0.99     0.97       6760.89|
|  7:  2.5855 -  2.4566  1315   147  0.91  14.73   1.00     0.97       5863.61|
|  8:  2.4566 -  2.3501  1297   140  0.91  15.13   1.00     0.97       4966.48|
|  9:  2.3501 -  2.2599  1316   151  0.91  15.27   1.01     0.99       4806.49|
| 10:  2.2599 -  2.1822  1285   141  0.91  15.22   1.00     0.96       4350.37|
| 11:  2.1822 -  2.1141  1303   143  0.90  16.76   1.01     0.97       4519.33|
| 12:  2.1141 -  2.0539  1284   144  0.91  15.61   1.01     0.99       4003.84|
| 13:  2.0539 -  1.9999  1260   140  0.90  16.00   1.01     1.00       3324.62|
| 14:  1.9999 -  1.9512   467    51  0.90  15.47   1.00     0.96       2483.56|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2483.56 max =        10204.72 mean =      6248.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.86   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    93.86   17.20    None  None   None       |
|    Sol.    : 438    0      6.40    84.15   40.55    None  None   None       |
|    Mac.    : 2385   0      0.00    93.86   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.388:  898   |   5:    46.929 -  56.315:  110        |
|      1:     9.388 -  18.774: 1231   |   6:    56.315 -  65.700:   44        |
|      2:    18.774 -  28.159:  245   |   7:    65.700 -  75.085:   31        |
|      3:    28.159 -  37.544:  134   |   8:    75.085 -  84.471:   10        |
|      4:    37.544 -  46.929:  116   |   9:    84.471 -  93.856:    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)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 4.459
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 300
   mapped sites are within: 0.728 - 4.459

peak=    5.770 closest distance to " NH2 ARG A  56 " =    2.118
peak=    5.668 closest distance to " CG  PRO A  54 " =    1.204
peak=    5.651 closest distance to " CG  PRO A 213 " =    1.255
peak=    5.447 closest distance to " CB  GLN A 223 " =    1.431
peak=    5.335 closest distance to " CG  PRO A  90 " =    1.098
peak=    5.284 closest distance to " NE2 GLN A  11 " =    1.126
peak=    5.148 closest distance to " O   HOH Z 126 " =    1.970
peak=    5.100 closest distance to " CB  ARG A 275 " =    0.913
peak=    5.066 closest distance to " O   HOH Z 144 " =    1.701
peak=    5.061 closest distance to " CB  SER A  63 " =    1.280
peak=    4.942 closest distance to " CG  PRO A 198 " =    1.287
peak=    4.908 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.781 closest distance to " O   HOH Z 193 " =    1.809
peak=    4.677 closest distance to " O   HOH Z 232 " =    2.250
peak=    4.660 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.642 closest distance to " O   HOH Z  78 " =    1.777
peak=    4.614 closest distance to " OD1 ASN A  69 " =    2.612
peak=    4.555 closest distance to " CB  ASN A 148 " =    1.439
peak=    4.546 closest distance to " CB  GLU A 128 " =    1.071
peak=    4.525 closest distance to " CB  SER A   3 " =    1.376
peak=    4.522 closest distance to " CB  LEU A 228 " =    1.133
peak=    4.502 closest distance to " O   HOH Z 278 " =    1.003
peak=    4.497 closest distance to " OD2 ASP A 286 " =    2.762
peak=    4.490 closest distance to " CB  TYR A 169 " =    0.825
peak=    4.486 closest distance to " O   HOH Z 427 " =    2.764
peak=    4.457 closest distance to " O   HOH Z 108 " =    1.551
peak=    4.454 closest distance to " C   PRO A 198 " =    1.550
peak=    4.418 closest distance to " CA  TYR A  30 " =    0.968
peak=    4.330 closest distance to " O   HOH Z 298 " =    1.875
peak=    4.276 closest distance to " O   HOH Z 134 " =    1.377
peak=    4.268 closest distance to " CB  GLU A 152 " =    1.226
peak=    4.248 closest distance to " O   HOH Z 368 " =    1.879
peak=    4.241 closest distance to " O   HOH Z 344 " =    2.950
peak=    4.204 closest distance to " CG  PRO A 243 " =    1.115
peak=    4.187 closest distance to " O   HOH Z 287 " =    2.010
peak=    4.179 closest distance to " O   HOH Z 316 " =    3.037
peak=    4.179 closest distance to " O   HOH Z  15 " =    2.244
peak=    4.170 closest distance to " O   HOH Z 203 " =    1.840
peak=    4.152 closest distance to " CG2 VAL A 257 " =    0.906
peak=    4.126 closest distance to " O   HOH Z 207 " =    1.801
peak=    4.116 closest distance to " O   HOH Z  97 " =    1.914
peak=    4.104 closest distance to " O   HOH Z 369 " =    2.015
peak=    4.103 closest distance to " O   HOH Z 260 " =    1.128
peak=    4.092 closest distance to " CB  VAL A 265 " =    1.208
peak=    4.078 closest distance to " CB  TRP A 179 " =    1.298
peak=    4.077 closest distance to " O   HOH Z 234 " =    3.662
peak=    4.068 closest distance to " CA  ALA A  21 " =    1.133
peak=    4.036 closest distance to " O   HOH Z  59 " =    1.881
peak=    4.029 closest distance to " NZ  LYS A 117 " =    3.262
peak=    4.023 closest distance to " O   HOH Z 156 " =    3.272
peak=    4.011 closest distance to " O   HOH Z 247 " =    1.239
peak=    4.001 closest distance to " OE1 GLU A   2 " =    2.172
peak=    3.976 closest distance to " O   HOH Z  88 " =    3.181
peak=    3.966 closest distance to " CA  GLY A 241 " =    3.715
peak=    3.955 closest distance to " O   HOH Z 209 " =    2.245
peak=    3.951 closest distance to " O   HOH Z  93 " =    2.346
peak=    3.942 closest distance to " O   HOH Z 303 " =    2.032
peak=    3.933 closest distance to " CA  THR A 221 " =    0.946
peak=    3.931 closest distance to " CB  ARG A  79 " =    1.488
peak=    3.930 closest distance to " O   HOH Z  10 " =    1.890
peak=    3.920 closest distance to " CD BLYS A 290 " =    1.211
peak=    3.917 closest distance to " CA  ASN A 215 " =    1.185
peak=    3.917 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.914 closest distance to " O   HOH Z 272 " =    1.827
peak=    3.885 closest distance to " O   HOH Z 132 " =    2.269
peak=    3.880 closest distance to " O   HOH Z 135 " =    1.688
peak=    3.878 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.870 closest distance to " O   MET A 105 " =    1.772
peak=    3.869 closest distance to " CD  LYS A 119 " =    1.094
peak=    3.862 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.860 closest distance to " CA  THR A 264 " =    0.843
peak=    3.855 closest distance to " O   HOH Z 189 " =    1.805
peak=    3.852 closest distance to " CG  PRO A 280 " =    0.728
peak=    3.839 closest distance to " O   HOH Z 346 " =    1.663
peak=    3.837 closest distance to " O   HOH Z  21 " =    1.620
peak=    3.834 closest distance to " OG BSER A 164 " =    2.397
peak=    3.830 closest distance to " CB  TRP A 266 " =    1.003
peak=    3.824 closest distance to " CG1 ILE A  33 " =    1.289
peak=    3.818 closest distance to " O   HOH Z 124 " =    1.389
peak=    3.807 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.803 closest distance to " CB  ARG A 139 " =    0.928
peak=    3.791 closest distance to " CG  ARG A  66 " =    2.418
peak=    3.775 closest distance to " O   HOH Z 132 " =    1.003
peak=    3.768 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.766 closest distance to " CD  ARG A 159 " =    0.805
peak=    3.761 closest distance to " O   HOH Z 128 " =    2.133
peak=    3.759 closest distance to " O   HOH Z  43 " =    2.026
peak=    3.750 closest distance to " O   HOH Z 141 " =    1.682
peak=    3.750 closest distance to " CB  VAL A 202 " =    1.670
peak=    3.747 closest distance to " O   SER A  87 " =    2.257
peak=    3.736 closest distance to " O   HOH Z  48 " =    1.410
peak=    3.732 closest distance to " O   HOH Z 133 " =    1.544
peak=    3.723 closest distance to " CB  PRO A 198 " =    0.983
peak=    3.723 closest distance to " NH1BARG A 145 " =    1.331
peak=    3.714 closest distance to " CB  SER A 216 " =    0.780
peak=    3.711 closest distance to " O   HOH Z 227 " =    1.644
peak=    3.694 closest distance to " O   HOH Z 144 " =    2.299
peak=    3.693 closest distance to " CA  MET A  40 " =    1.044
peak=    3.681 closest distance to " O   HOH Z 282 " =    1.530
peak=    3.675 closest distance to " NH1AARG A 145 " =    1.035
peak=    3.667 closest distance to " O   HOH Z 368 " =    3.669
peak=    3.662 closest distance to " O   HOH Z  44 " =    1.880
peak=    3.655 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.653 closest distance to " O   HOH Z  73 " =    1.586
peak=    3.647 closest distance to " O   HOH Z 281 " =    4.459
peak=    3.642 closest distance to " O   HOH Z 284 " =    2.973
peak=    3.632 closest distance to " O   HOH Z 108 " =    1.842
peak=    3.622 closest distance to " O   HOH Z 236 " =    1.482
peak=    3.621 closest distance to " CB  ARG A 190 " =    1.726
peak=    3.618 closest distance to " CB  GLU A 152 " =    1.453
peak=    3.612 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.603 closest distance to " O   HOH Z 409 " =    2.792
peak=    3.598 closest distance to " NH2BARG A 145 " =    1.981
peak=    3.595 closest distance to " O   HOH Z 389 " =    1.786
peak=    3.593 closest distance to " O   HOH Z   1 " =    1.791
peak=    3.586 closest distance to " CD  ARG A 269 " =    1.002
peak=    3.585 closest distance to " CG2 THR A 221 " =    1.099
peak=    3.585 closest distance to " O   HOH Z  61 " =    1.640
peak=    3.563 closest distance to " N   ASN A  39 " =    1.244
peak=    3.558 closest distance to " CB  MET A  47 " =    1.039
peak=    3.549 closest distance to " O   HOH Z 263 " =    2.243
peak=    3.546 closest distance to " CA  VAL A 126 " =    1.125
peak=    3.544 closest distance to " O   HOH Z 172 " =    3.506
peak=    3.538 closest distance to " O   HOH Z 271 " =    2.228
peak=    3.535 closest distance to " CG1BVAL A  72 " =    1.488
peak=    3.530 closest distance to " CE  LYS A  76 " =    0.880
peak=    3.528 closest distance to " O   HOH Z 426 " =    1.599
peak=    3.526 closest distance to " O   HOH Z 163 " =    1.967
peak=    3.522 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.521 closest distance to " O   HOH Z  68 " =    1.527
peak=    3.521 closest distance to " O   HOH Z 214 " =    2.015
peak=    3.510 closest distance to " O   HOH Z   3 " =    1.785
peak=    3.510 closest distance to " CB  SER A 141 " =    1.084
peak=    3.507 closest distance to " CG  GLU A 277 " =    2.006
peak=    3.505 closest distance to " O   HOH Z 295 " =    1.498
peak=    3.503 closest distance to " O   HOH Z 374 " =    2.506
peak=    3.502 closest distance to " O   HOH Z 411 " =    1.796
peak=    3.497 closest distance to " NZ  LYS A  76 " =    1.256
peak=    3.496 closest distance to " O   HOH Z 234 " =    3.809
peak=    3.492 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.489 closest distance to " O   HOH Z  40 " =    1.639
peak=    3.481 closest distance to " CD2 LEU A 255 " =    1.371
peak=    3.480 closest distance to " O   HOH Z 128 " =    2.196
peak=    3.479 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.478 closest distance to " O   HOH Z  63 " =    2.369
peak=    3.477 closest distance to " O   HOH Z 437 " =    1.671
peak=    3.470 closest distance to " O   HOH Z 193 " =    1.956
peak=    3.468 closest distance to " O   HOH Z 163 " =    1.721
peak=    3.465 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.464 closest distance to " O   HOH Z 265 " =    2.344
peak=    3.463 closest distance to " O   HOH Z 183 " =    1.449
peak=    3.463 closest distance to " O   HOH Z 407 " =    2.361
peak=    3.458 closest distance to " C   GLY A  80 " =    1.106
peak=    3.457 closest distance to " ND1 HIS A  86 " =    1.794
peak=    3.457 closest distance to " NH2 ARG A 156 " =    1.265
peak=    3.451 closest distance to " O   HOH Z 211 " =    2.257
peak=    3.442 closest distance to " NH2AARG A 190 " =    1.349
peak=    3.441 closest distance to " CA  LYS A 290 " =    1.257
peak=    3.438 closest distance to " CB  ALA A 291 " =    1.396
peak=    3.431 closest distance to " OG  SER A  62 " =    3.045
peak=    3.427 closest distance to " O   HOH Z 353 " =    2.678
peak=    3.426 closest distance to " O   HOH Z 158 " =    3.006
peak=    3.426 closest distance to " O   HOH Z 173 " =    1.856
peak=    3.415 closest distance to " CG2 VAL A  78 " =    0.889
peak=    3.401 closest distance to " O   SER A  26 " =    1.637
peak=    3.400 closest distance to " O   HOH Z 425 " =    1.270
peak=    3.396 closest distance to " CD2 LEU A 297 " =    0.955
peak=    3.394 closest distance to " N   ARG A 156 " =    1.295
peak=    3.391 closest distance to " NZ  LYS A 119 " =    1.378
peak=    3.386 closest distance to " O   HOH Z 345 " =    3.397
peak=    3.384 closest distance to " O   HOH Z 327 " =    1.704
peak=    3.384 closest distance to " O   HOH Z 289 " =    1.419
peak=    3.374 closest distance to " O   HOH Z  71 " =    1.188
peak=    3.372 closest distance to " O   HOH Z 193 " =    1.567
peak=    3.369 closest distance to " O   HOH Z 133 " =    2.239
peak=    3.368 closest distance to " NH2 ARG A 219 " =    1.895
peak=    3.367 closest distance to " O   HOH Z 286 " =    2.210
peak=    3.365 closest distance to " CG2BVAL A  41 " =    0.913
peak=    3.360 closest distance to " O   HOH Z 326 " =    1.436
peak=    3.354 closest distance to " CG1 ILE A 151 " =    0.878
peak=    3.353 closest distance to " O   HOH Z 125 " =    2.177
peak=    3.350 closest distance to " O   HOH Z 313 " =    1.635
peak=    3.349 closest distance to " CA  ALA A 154 " =    1.042
peak=    3.348 closest distance to " CB  ALA A  34 " =    1.057
peak=    3.348 closest distance to " CA  ALA A 233 " =    1.320
peak=    3.342 closest distance to " CB  SER A 212 " =    0.940
peak=    3.340 closest distance to " O   HOH Z 276 " =    1.247
peak=    3.338 closest distance to " OG BSER A 258 " =    3.541
peak=    3.338 closest distance to " O   HOH Z 273 " =    2.882
peak=    3.333 closest distance to " O   HOH Z 284 " =    1.501
peak=    3.332 closest distance to " O   ALA A 165 " =    1.360
peak=    3.331 closest distance to " CA  ALA A  51 " =    0.894
peak=    3.329 closest distance to " CA  VAL A  41 " =    0.927
peak=    3.329 closest distance to " O   HOH Z 261 " =    1.487
peak=    3.325 closest distance to " O   HOH Z 329 " =    3.446
peak=    3.318 closest distance to " O   HOH Z 227 " =    2.116
peak=    3.315 closest distance to " O   HOH Z 106 " =    2.278
peak=    3.312 closest distance to " CG AARG A 275 " =    0.942
peak=    3.312 closest distance to " N   ASN A 127 " =    1.198
peak=    3.310 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.297 closest distance to " CB  TYR A 116 " =    0.853
peak=    3.290 closest distance to " N   GLN A 278 " =    0.953
peak=    3.283 closest distance to " O   HOH Z 213 " =    1.857
peak=    3.280 closest distance to " CA  ASP A 140 " =    1.100
peak=    3.278 closest distance to " CE AMET A  47 " =    1.453
peak=    3.277 closest distance to " O   HOH Z 337 " =    3.718
peak=    3.277 closest distance to " CA  ALA A  43 " =    1.204
peak=    3.277 closest distance to " O   HOH Z 106 " =    1.855
peak=    3.275 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.270 closest distance to " O   HOH Z 366 " =    3.212
peak=    3.268 closest distance to " CB  GLU A 277 " =    3.536
peak=    3.265 closest distance to " O   HOH Z 291 " =    1.927
peak=    3.264 closest distance to " O   HOH Z 334 " =    1.409
peak=    3.258 closest distance to " OD1BASN A 224 " =    2.299
peak=    3.258 closest distance to " O   ALA A   1 " =    1.471
peak=    3.258 closest distance to " O   HOH Z 116 " =    1.763
peak=    3.256 closest distance to " CB  SER A  62 " =    1.395
peak=    3.255 closest distance to " CD2 HIS A  81 " =    1.156
peak=    3.254 closest distance to " CZ2 TRP A 179 " =    1.656
peak=    3.252 closest distance to " CE BMET A  47 " =    1.491
peak=    3.249 closest distance to " CA  ALA A 160 " =    0.798
peak=    3.248 closest distance to " O   GLY A 229 " =    1.620
peak=    3.244 closest distance to " CA  LEU A 282 " =    1.167
peak=    3.244 closest distance to " CD1AILE A 234 " =    1.027
peak=    3.241 closest distance to " CA  ARG A  36 " =    1.086
peak=    3.239 closest distance to " O   HOH Z 368 " =    2.589
peak=    3.236 closest distance to " CB  GLN A  88 " =    1.175
peak=    3.232 closest distance to " O   HOH Z  44 " =    3.338
peak=    3.232 closest distance to " CB  TRP A 179 " =    1.675
peak=    3.231 closest distance to " O   HOH Z  50 " =    1.524
peak=    3.225 closest distance to " O   HOH Z 151 " =    1.529
peak=    3.225 closest distance to " O   HOH Z 227 " =    1.575
peak=    3.225 closest distance to " CA  ILE A 234 " =    0.939
peak=    3.225 closest distance to " O   HOH Z 188 " =    1.943
peak=    3.218 closest distance to " O   HOH Z  78 " =    2.126
peak=    3.218 closest distance to " O   HOH Z 391 " =    2.976
peak=    3.216 closest distance to " O   HOH Z 279 " =    2.100
peak=    3.216 closest distance to " O   THR A 220 " =    1.365
peak=    3.206 closest distance to " O   HOH Z 367 " =    3.521
peak=    3.204 closest distance to " NE2 GLN A  73 " =    3.599
peak=    3.203 closest distance to " CG  GLN A  88 " =    1.006
peak=    3.201 closest distance to " CZ  PHE A 218 " =    0.996
peak=    3.199 closest distance to " O   HOH Z 357 " =    1.803
peak=    3.199 closest distance to " CA  ARG A  56 " =    1.982
peak=    3.195 closest distance to " O   HOH Z 148 " =    3.158
peak=    3.192 closest distance to " O   HOH Z 197 " =    3.061
peak=    3.186 closest distance to " O   ALA A   1 " =    1.584
peak=    3.182 closest distance to " OG  SER A  22 " =    2.739
peak=    3.176 closest distance to " O   HOH Z  49 " =    2.097
peak=    3.171 closest distance to " OD1 ASP A 238 " =    1.013
peak=    3.169 closest distance to " CB  LEU A 255 " =    0.773
peak=    3.167 closest distance to " O   HOH Z   1 " =    1.652
peak=    3.165 closest distance to " CG  MET A 113 " =    1.155
peak=    3.161 closest distance to " CB  SER A 276 " =    1.080
peak=    3.158 closest distance to " CA  ALA A 291 " =    0.908
peak=    3.154 closest distance to " O   GLY A  57 " =    2.514
peak=    3.152 closest distance to " O   HOH Z 286 " =    2.393
peak=    3.152 closest distance to " CG2 VAL A 174 " =    1.322
peak=    3.152 closest distance to " O   HOH Z 151 " =    1.954
peak=    3.147 closest distance to " CD  PRO A 243 " =    1.608
peak=    3.145 closest distance to " O   HOH Z 115 " =    2.121
peak=    3.144 closest distance to " C   ALA A 299 " =    0.939
peak=    3.143 closest distance to " N   GLY A 241 " =    1.447
peak=    3.143 closest distance to " O   HOH Z  14 " =    1.994
peak=    3.142 closest distance to " O   HOH Z  40 " =    1.950
peak=    3.142 closest distance to " O   HOH Z 287 " =    2.220
peak=    3.140 closest distance to " CG1 VAL A 202 " =    2.017
peak=    3.137 closest distance to " CB  TYR A 169 " =    1.246
peak=    3.125 closest distance to " NZ ALYS A 290 " =    1.091
peak=    3.125 closest distance to " CB  THR A 157 " =    1.009
peak=    3.123 closest distance to " O   HOH Z 248 " =    1.738
peak=    3.114 closest distance to " ND1 HIS A  81 " =    1.544
peak=    3.109 closest distance to " CB  ARG A 102 " =    0.833
peak=    3.109 closest distance to " O   HOH Z  40 " =    2.775
peak=    3.104 closest distance to " CA  GLY A 267 " =    1.256
peak=    3.101 closest distance to " CA  ASN A 176 " =    1.185
peak=    3.101 closest distance to " O   HOH Z 189 " =    1.313
peak=    3.100 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.094 closest distance to " O   HOH Z 280 " =    2.810
peak=    3.092 closest distance to " O   HOH Z  64 " =    2.152
peak=    3.091 closest distance to " O   TRP A 274 " =    1.789
peak=    3.082 closest distance to " OG  SER A 206 " =    1.196
peak=    3.081 closest distance to " N   ALA A 154 " =    0.954
peak=    3.079 closest distance to " CA  PRO A  90 " =    0.928
peak=    3.076 closest distance to " CB  SER A  26 " =    1.580
peak=    3.073 closest distance to " O   HOH Z 181 " =    2.142
peak=    3.067 closest distance to " CB  LYS A 117 " =    1.141
peak=    3.067 closest distance to " O   HOH Z   9 " =    1.612
peak=    3.066 closest distance to " CB  ALA A 248 " =    1.304
peak=    3.061 closest distance to " O   HOH Z 371 " =    1.566
peak=    3.058 closest distance to " CB  THR A  31 " =    1.770
peak=    3.055 closest distance to " O   HOH Z 234 " =    1.807
peak=    3.054 closest distance to " CA  PHE A 208 " =    0.909
peak=    3.041 closest distance to " O   HOH Z 134 " =    3.159
peak=    3.034 closest distance to " O   HOH Z  20 " =    1.428
peak=    3.010 closest distance to " CA  GLU A 152 " =    1.057

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.359
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.719 - 5.359

peak=   -4.586 closest distance to " O   HOH Z 266 " =    4.269
peak=   -4.445 closest distance to " O   HOH Z 198 " =    2.080
peak=   -4.432 closest distance to " O   HOH Z 377 " =    1.813
peak=   -4.317 closest distance to " ND2 ASN A  45 " =    0.903
peak=   -4.275 closest distance to " O   PRO A 198 " =    1.269
peak=   -4.183 closest distance to " CD  ARG A 156 " =    1.931
peak=   -4.140 closest distance to " CB  PRO A 243 " =    2.561
peak=   -4.130 closest distance to " O   HOH Z  13 " =    1.366
peak=   -4.096 closest distance to " OXT GLY A 302 " =    2.806
peak=   -4.078 closest distance to " SG  CYS A 254 " =    3.261
peak=   -4.078 closest distance to " CG  LYS A 193 " =    2.291
peak=   -4.049 closest distance to " O   HOH Z  43 " =    1.624
peak=   -4.033 closest distance to " O   HOH Z 102 " =    1.749
peak=   -4.026 closest distance to " CG  GLN A 223 " =    2.084
peak=   -4.024 closest distance to " N   ASP A 286 " =    2.478
peak=   -3.984 closest distance to " CE2 TYR A  30 " =    2.894
peak=   -3.957 closest distance to " C   HIS A 108 " =    1.055
peak=   -3.948 closest distance to " N   GLN A  58 " =    1.788
peak=   -3.929 closest distance to " O   HOH Z  98 " =    1.974
peak=   -3.927 closest distance to " O   VAL A  67 " =    2.820
peak=   -3.901 closest distance to " CZ  PHE A  59 " =    1.543
peak=   -3.898 closest distance to " O   HOH Z 231 " =    1.926
peak=   -3.896 closest distance to " O   ILE A 109 " =    2.575
peak=   -3.887 closest distance to " O   HOH Z 290 " =    1.134
peak=   -3.885 closest distance to " CB  TYR A  15 " =    2.184
peak=   -3.880 closest distance to " CE  MET A 105 " =    2.014
peak=   -3.851 closest distance to " O   HOH Z 407 " =    3.118
peak=   -3.843 closest distance to " O   SER A 135 " =    1.478
peak=   -3.842 closest distance to " O   VAL A 153 " =    2.384
peak=   -3.836 closest distance to " CB  ASN A  39 " =    2.169
peak=   -3.817 closest distance to " O   HOH Z 388 " =    1.851
peak=   -3.800 closest distance to " O   PRO A 163 " =    1.958
peak=   -3.795 closest distance to " OE1 GLN A  88 " =    0.986
peak=   -3.777 closest distance to " N   ALA A 248 " =    1.597
peak=   -3.775 closest distance to " CB  CYS A 201 " =    2.577
peak=   -3.764 closest distance to " O   HOH Z  11 " =    1.870
peak=   -3.762 closest distance to " C   ALA A 158 " =    1.238
peak=   -3.738 closest distance to " N   ALA A  43 " =    2.438
peak=   -3.725 closest distance to " O   HOH Z  24 " =    1.431
peak=   -3.725 closest distance to " O   HOH Z  93 " =    1.918
peak=   -3.717 closest distance to " N   MET A 188 " =    1.898
peak=   -3.714 closest distance to " OG BSER A 134 " =    1.131
peak=   -3.708 closest distance to " O   HOH Z 118 " =    2.722
peak=   -3.706 closest distance to " CD  ARG A 139 " =    1.507
peak=   -3.701 closest distance to " CZ  TYR A 169 " =    1.731
peak=   -3.700 closest distance to " OD1 ASP A 191 " =    1.691
peak=   -3.687 closest distance to " O   HOH Z  11 " =    1.911
peak=   -3.671 closest distance to " CD1 LEU A 101 " =    2.432
peak=   -3.666 closest distance to " CA  SER A 146 " =    2.283
peak=   -3.658 closest distance to " CA  GLY A 203 " =    2.298
peak=   -3.652 closest distance to " O   HOH Z 185 " =    2.139
peak=   -3.633 closest distance to " O   HOH Z 395 " =    5.112
peak=   -3.629 closest distance to " OD1 ASN A 187 " =    1.717
peak=   -3.627 closest distance to " O   VAL A  67 " =    2.814
peak=   -3.610 closest distance to " CZ3 TRP A 179 " =    1.293
peak=   -3.599 closest distance to " CB  ALA A 248 " =    1.935
peak=   -3.590 closest distance to " O   GLY A 211 " =    1.338
peak=   -3.584 closest distance to " O   HOH Z 166 " =    1.402
peak=   -3.575 closest distance to " CG  PHE A 283 " =    2.673
peak=   -3.574 closest distance to " O   HOH Z  10 " =    1.392
peak=   -3.574 closest distance to " O   HOH Z 148 " =    3.243
peak=   -3.569 closest distance to " O   HOH Z 353 " =    2.122
peak=   -3.549 closest distance to " CG  ASP A 231 " =    0.816
peak=   -3.544 closest distance to " CB  ALA A 291 " =    2.398
peak=   -3.537 closest distance to " CD1 LEU A 228 " =    2.248
peak=   -3.532 closest distance to " CD2 LEU A 300 " =    2.824
peak=   -3.532 closest distance to " CB  ALA A 291 " =    2.187
peak=   -3.531 closest distance to " CZ3 TRP A 274 " =    2.406
peak=   -3.528 closest distance to " O   HOH Z 351 " =    1.453
peak=   -3.527 closest distance to " OG  SER A  97 " =    2.037
peak=   -3.519 closest distance to " CG1 VAL A 112 " =    2.864
peak=   -3.517 closest distance to " O   HOH Z 311 " =    3.531
peak=   -3.497 closest distance to " C   LEU A 143 " =    1.278
peak=   -3.489 closest distance to " OD1 ASP A 191 " =    1.435
peak=   -3.488 closest distance to " OG ASER A 134 " =    1.110
peak=   -3.485 closest distance to " CB  ASP A  27 " =    2.460
peak=   -3.461 closest distance to " O   HOH Z 385 " =    1.950
peak=   -3.453 closest distance to " CG  MET A 105 " =    0.917
peak=   -3.447 closest distance to " N   SER A 212 " =    1.865
peak=   -3.439 closest distance to " N   SER A 276 " =    1.170
peak=   -3.436 closest distance to " O   HOH Z  52 " =    1.387
peak=   -3.434 closest distance to " O   ALA A 161 " =    1.501
peak=   -3.433 closest distance to " OD1 ASN A 148 " =    1.684
peak=   -3.427 closest distance to " CG  GLU A 277 " =    1.169
peak=   -3.426 closest distance to " CA  GLY A 133 " =    1.847
peak=   -3.423 closest distance to " NH1AARG A 275 " =    1.782
peak=   -3.421 closest distance to " CD  LYS A 289 " =    2.505
peak=   -3.421 closest distance to " O   HOH Z 143 " =    2.451
peak=   -3.419 closest distance to " O   HOH Z 435 " =    2.711
peak=   -3.410 closest distance to " O   HOH Z   3 " =    1.733
peak=   -3.400 closest distance to " O   VAL A 174 " =    2.048
peak=   -3.397 closest distance to " CD1 PHE A  59 " =    1.813
peak=   -3.391 closest distance to " OD2 ASP A 171 " =    2.165
peak=   -3.381 closest distance to " N   ALA A 226 " =    2.113
peak=   -3.381 closest distance to " CD2 LEU A 237 " =    2.330
peak=   -3.377 closest distance to " O   HOH Z 313 " =    1.964
peak=   -3.377 closest distance to " OXT GLY A 302 " =    3.363
peak=   -3.371 closest distance to " N   THR A 157 " =    1.513
peak=   -3.368 closest distance to " O   TRP A  92 " =    1.667
peak=   -3.357 closest distance to " O   ASN A  45 " =    1.894
peak=   -3.355 closest distance to " NH2 ARG A  79 " =    1.779
peak=   -3.351 closest distance to " OD1 ASP A 200 " =    1.303
peak=   -3.344 closest distance to " CE  MET A  93 " =    1.149
peak=   -3.344 closest distance to " O   HOH Z  47 " =    1.472
peak=   -3.337 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.337 closest distance to " O   ASN A 249 " =    1.542
peak=   -3.332 closest distance to " O   HOH Z 210 " =    1.093
peak=   -3.329 closest distance to " CB  ASP A 132 " =    2.252
peak=   -3.327 closest distance to " O   HOH Z  15 " =    1.657
peak=   -3.320 closest distance to " O   HOH Z 263 " =    2.913
peak=   -3.315 closest distance to " O   HOH Z 298 " =    1.157
peak=   -3.314 closest distance to " CE  LYS A  76 " =    2.654
peak=   -3.310 closest distance to " O   HOH Z 193 " =    1.771
peak=   -3.308 closest distance to " CB  ALA A 131 " =    2.020
peak=   -3.303 closest distance to " OG  SER A  62 " =    1.637
peak=   -3.302 closest distance to " O   HOH Z 213 " =    1.252
peak=   -3.302 closest distance to " NH2AARG A 275 " =    5.359
peak=   -3.301 closest distance to " CE2 PHE A 218 " =    2.534
peak=   -3.298 closest distance to " CB  CYS A 254 " =    2.270
peak=   -3.295 closest distance to " CG  GLU A  53 " =    1.358
peak=   -3.295 closest distance to " CA  TRP A 274 " =    1.597
peak=   -3.293 closest distance to " O   HOH Z 389 " =    1.781
peak=   -3.293 closest distance to " O   HOH Z  63 " =    1.396
peak=   -3.289 closest distance to " O   HOH Z 348 " =    1.708
peak=   -3.286 closest distance to " O   HOH Z 198 " =    1.549
peak=   -3.281 closest distance to " CD2 LEU A 237 " =    2.761
peak=   -3.281 closest distance to " SG ACYS A 201 " =    2.103
peak=   -3.280 closest distance to " O   HOH Z 417 " =    2.466
peak=   -3.275 closest distance to " OD1 ASN A 249 " =    0.963
peak=   -3.273 closest distance to " CG  LEU A  83 " =    1.875
peak=   -3.267 closest distance to " SD BMET A  47 " =    1.014
peak=   -3.261 closest distance to " ND2 ASN A 187 " =    1.570
peak=   -3.258 closest distance to " N   HIS A 115 " =    1.880
peak=   -3.257 closest distance to " O   HOH Z 281 " =    2.823
peak=   -3.256 closest distance to " CB  ALA A  43 " =    2.332
peak=   -3.253 closest distance to " NH1 ARG A 195 " =    2.619
peak=   -3.251 closest distance to " O   HOH Z 207 " =    1.913
peak=   -3.249 closest distance to " CD2 TYR A 293 " =    2.047
peak=   -3.246 closest distance to " C   LEU A 222 " =    0.719
peak=   -3.245 closest distance to " O   HOH Z  97 " =    1.736
peak=   -3.240 closest distance to " CE3 TRP A 123 " =    1.191
peak=   -3.237 closest distance to " O   PHE A 218 " =    1.495
peak=   -3.231 closest distance to " O   ALA A  51 " =    1.407
peak=   -3.231 closest distance to " OG  SER A 245 " =    1.083
peak=   -3.229 closest distance to " O   HOH Z 165 " =    2.008
peak=   -3.226 closest distance to " O   HOH Z  60 " =    1.861
peak=   -3.226 closest distance to " O   HOH Z 266 " =    4.576
peak=   -3.224 closest distance to " O   HOH Z 132 " =    1.104
peak=   -3.223 closest distance to " CD  GLN A  88 " =    0.849
peak=   -3.221 closest distance to " O   HOH Z 292 " =    4.486
peak=   -3.219 closest distance to " O   HOH Z   6 " =    1.618
peak=   -3.216 closest distance to " O   GLY A 196 " =    1.008
peak=   -3.209 closest distance to " CB  ASP A 132 " =    2.175
peak=   -3.206 closest distance to " O   TRP A  70 " =    1.483
peak=   -3.206 closest distance to " CB  PRO A 163 " =    2.530
peak=   -3.203 closest distance to " CG2 ILE A 263 " =    2.298
peak=   -3.201 closest distance to " O   HOH Z  88 " =    2.130
peak=   -3.199 closest distance to " CB  PHE A 192 " =    1.853
peak=   -3.195 closest distance to " CD2 LEU A 143 " =    2.740
peak=   -3.184 closest distance to " ND2 ASN A 215 " =    2.122
peak=   -3.183 closest distance to " OH  TYR A 214 " =    1.246
peak=   -3.176 closest distance to " O   HOH Z 222 " =    1.166
peak=   -3.175 closest distance to " O   SER A 146 " =    0.967
peak=   -3.173 closest distance to " CG  PRO A 163 " =    2.440
peak=   -3.168 closest distance to " O   PRO A 243 " =    2.511
peak=   -3.157 closest distance to " N   ALA A   9 " =    1.526
peak=   -3.157 closest distance to " O   HOH Z 396 " =    1.488
peak=   -3.156 closest distance to " CA  TYR A  30 " =    2.893
peak=   -3.143 closest distance to " O   SER A  62 " =    2.120
peak=   -3.142 closest distance to " CG  GLU A 152 " =    1.522
peak=   -3.142 closest distance to " CB  SER A 245 " =    2.504
peak=   -3.140 closest distance to " C   LEU A   5 " =    1.001
peak=   -3.133 closest distance to " CD  PRO A 198 " =    1.401
peak=   -3.128 closest distance to " NH1 ARG A  56 " =    2.557
peak=   -3.128 closest distance to " ND2 ASN A 249 " =    2.511
peak=   -3.127 closest distance to " O   HOH Z 234 " =    3.992
peak=   -3.126 closest distance to " O   HOH Z 298 " =    2.472
peak=   -3.125 closest distance to " O   HOH Z 244 " =    2.085
peak=   -3.124 closest distance to " ND2 ASN A  60 " =    1.542
peak=   -3.121 closest distance to " ND2 ASN A 252 " =    1.557
peak=   -3.121 closest distance to " O   VAL A 197 " =    1.207
peak=   -3.111 closest distance to " OG BSER A 134 " =    1.692
peak=   -3.108 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.103 closest distance to " O   ASP A 162 " =    2.211
peak=   -3.099 closest distance to " CB  ASP A 149 " =    2.016
peak=   -3.095 closest distance to " O   GLY A  80 " =    2.396
peak=   -3.087 closest distance to " O   HOH Z 278 " =    2.376
peak=   -3.086 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.074 closest distance to " O   HOH Z 252 " =    4.343
peak=   -3.073 closest distance to " O   HOH Z 417 " =    2.529
peak=   -3.073 closest distance to " CG1 VAL A 197 " =    2.234
peak=   -3.069 closest distance to " O   ASP A 231 " =    2.488
peak=   -3.061 closest distance to " O   HOH Z 310 " =    3.487
peak=   -3.042 closest distance to " O   HOH Z 385 " =    1.847
peak=   -3.026 closest distance to " OG  SER A 206 " =    1.812
peak=   -3.009 closest distance to " O   HOH Z 139 " =    2.855

================= 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    :  0.3815 0.3816   6.172597e+00   6.178834e+00
   1_bss:  0.3664 0.3665   6.161376e+00   6.150053e+00
   1_xyz:  0.2394 0.2670   5.779322e+00   5.882616e+00
   1_adp:  0.2194 0.2759   5.734248e+00   5.910182e+00
   1_occ:  0.2191 0.2761   5.733387e+00   5.909436e+00
   2_bss:  0.2160 0.2720   5.720481e+00   5.898188e+00
   2_xyz:  0.1541 0.2029   5.419093e+00   5.625079e+00
   2_adp:  0.1423 0.1886   5.346446e+00   5.554846e+00
   2_occ:  0.1421 0.1884   5.345395e+00   5.554144e+00
   3_bss:  0.1418 0.1872   5.340721e+00   5.549246e+00
   3_xyz:  0.1218 0.1619   5.199063e+00   5.416335e+00
   3_adp:  0.1179 0.1586   5.169218e+00   5.387755e+00
   3_occ:  0.1178 0.1585   5.168658e+00   5.387578e+00
   4_bss:  0.1177 0.1583   5.168031e+00   5.387061e+00
   4_xyz:  0.1141 0.1555   5.147589e+00   5.369638e+00
   4_adp:  0.1130 0.1560   5.143663e+00   5.370149e+00
   4_occ:  0.1129 0.1560   5.143432e+00   5.370086e+00
   5_bss:  0.1131 0.1561   5.144536e+00   5.371911e+00
   5_xyz:  0.1114 0.1553   5.137673e+00   5.370459e+00
   5_adp:  0.1107 0.1569   5.140577e+00   5.380991e+00
   5_occ:  0.1107 0.1569   5.140665e+00   5.381316e+00
   5_bss:  0.1106 0.1570   5.140646e+00   5.381383e+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:  0.317  27.397  -2.680  -2.463   3.481  -0.000   0.000   0.000
   1_xyz:  0.317  27.397  -2.680  -2.463   3.481  -0.000   0.000   0.000
   1_adp:  0.317  27.397  -2.680  -2.463   3.481  -0.000   0.000   0.000
   1_occ:  0.317  27.397  -2.680  -2.463   3.481  -0.000   0.000   0.000
   2_bss:  0.326  43.785  -2.413  -2.558  -0.234  -0.000  -0.000  -0.000
   2_xyz:  0.326  43.785  -2.413  -2.558  -0.234  -0.000  -0.000  -0.000
   2_adp:  0.326  43.785  -2.413  -2.558  -0.234  -0.000  -0.000  -0.000
   2_occ:  0.326  43.785  -2.413  -2.558  -0.234  -0.000  -0.000  -0.000
   3_bss:  0.326  43.785  -2.389  -2.430  -1.418  -0.000  -0.000  -0.000
   3_xyz:  0.326  43.785  -2.389  -2.430  -1.418  -0.000  -0.000  -0.000
   3_adp:  0.326  43.785  -2.389  -2.430  -1.418  -0.000  -0.000  -0.000
   3_occ:  0.326  43.785  -2.389  -2.430  -1.418  -0.000  -0.000  -0.000
   4_bss:  0.326  43.785  -2.533  -2.512  -1.907  -0.000  -0.000  -0.000
   4_xyz:  0.326  43.785  -2.533  -2.512  -1.907  -0.000  -0.000  -0.000
   4_adp:  0.326  43.785  -2.533  -2.512  -1.907  -0.000  -0.000  -0.000
   4_occ:  0.326  43.785  -2.533  -2.512  -1.907  -0.000  -0.000  -0.000
   5_bss:  0.326  43.785  -2.421  -2.408  -1.926  -0.000  -0.000  -0.000
   5_xyz:  0.326  43.785  -2.421  -2.408  -1.926  -0.000  -0.000  -0.000
   5_adp:  0.326  43.785  -2.421  -2.408  -1.926  -0.000  -0.000  -0.000
   5_occ:  0.326  43.785  -2.421  -2.408  -1.926  -0.000  -0.000  -0.000
   5_bss:  0.322  42.432  -2.226  -2.213  -1.785  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.381 0.6039  0.7985    46339.063
   1_bss:  41.666 0.6224  0.8079    41700.003
   1_xyz:  27.280 0.7885  0.9687    19500.041
   1_adp:  28.552 0.7738  0.9563    20755.463
   1_occ:  28.551 0.7737  0.9561    20729.596
   2_bss:  27.882 0.7810  0.9262    20073.913
   2_xyz:  19.694 0.8641  0.9861    10572.440
   2_adp:  17.790 0.8826  0.9938     9180.832
   2_occ:  17.764 0.8828  0.9937     9158.532
   3_bss:  17.625 0.8840  0.9816     9053.199
   3_xyz:  14.689 0.9089  0.9924     6699.704
   3_adp:  14.051 0.9145  0.9926     6382.003
   3_occ:  14.037 0.9146  0.9924     6375.349
   4_bss:  14.027 0.9147  0.9838     6372.692
   4_xyz:  13.685 0.9176  0.9843     6132.969
   4_adp:  13.668 0.9179  0.9811     6139.810
   4_occ:  13.664 0.9179  0.9810     6140.429
   5_bss:  13.704 0.9176  0.9829     6187.567
   5_xyz:  13.669 0.9178  0.9827     6139.547
   5_adp:  13.875 0.9162  0.9776     6246.071
   5_occ:  13.879 0.9162  0.9775     6251.642
   5_bss:  13.882 0.9162  0.9838     6248.933
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7541e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7541e-01
   1_xyz:   1.260  0.010  0.080 15.812  0.006  4.109   9.9400e-02
   1_adp:   1.260  0.010  0.080 15.812  0.006  4.109   9.9400e-02
   1_occ:   1.260  0.010  0.080 15.812  0.006  4.109   9.9400e-02
   2_bss:   1.260  0.010  0.080 15.812  0.006  4.109   9.9400e-02
   2_xyz:   1.002  0.006  0.070 14.265  0.004  4.115   5.9022e-02
   2_adp:   1.002  0.006  0.070 14.265  0.004  4.115   5.9022e-02
   2_occ:   1.002  0.006  0.070 14.265  0.004  4.115   5.9022e-02
   3_bss:   1.002  0.006  0.070 14.265  0.004  4.115   5.9022e-02
   3_xyz:   0.946  0.006  0.068 14.416  0.004  4.109   5.4963e-02
   3_adp:   0.946  0.006  0.068 14.416  0.004  4.109   5.4963e-02
   3_occ:   0.946  0.006  0.068 14.416  0.004  4.109   5.4963e-02
   4_bss:   0.946  0.006  0.068 14.416  0.004  4.109   5.4963e-02
   4_xyz:   0.900  0.005  0.066 14.264  0.003  4.110   4.9136e-02
   4_adp:   0.900  0.005  0.066 14.264  0.003  4.110   4.9136e-02
   4_occ:   0.900  0.005  0.066 14.264  0.003  4.110   4.9136e-02
   5_bss:   0.900  0.005  0.066 14.264  0.003  4.110   4.9136e-02
   5_xyz:   0.882  0.005  0.065 14.195  0.003  4.110   4.7592e-02
   5_adp:   0.882  0.005  0.065 14.195  0.003  4.110   4.7592e-02
   5_occ:   0.882  0.005  0.065 14.195  0.003  4.110   4.7592e-02
   5_bss:   0.882  0.005  0.065 14.195  0.003  4.110   4.7592e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.598   2.3915e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.598   2.3915e-01
   1_xyz:   8.637  0.056  0.315 85.924  0.046  2.264   1.6050e-01
   1_adp:   8.637  0.056  0.315 85.924  0.046  2.264   1.6050e-01
   1_occ:   8.637  0.056  0.315 85.924  0.046  2.264   1.6050e-01
   2_bss:   8.637  0.056  0.315 85.924  0.046  2.264   1.6050e-01
   2_xyz:   6.913  0.038  0.266 81.278  0.037  2.386   1.0440e-01
   2_adp:   6.913  0.038  0.266 81.278  0.037  2.386   1.0440e-01
   2_occ:   6.913  0.038  0.266 81.278  0.037  2.386   1.0440e-01
   3_bss:   6.913  0.038  0.266 81.278  0.037  2.386   1.0440e-01
   3_xyz:   7.016  0.047  0.239 84.618  0.033  2.335   8.1812e-02
   3_adp:   7.016  0.047  0.239 84.618  0.033  2.335   8.1812e-02
   3_occ:   7.016  0.047  0.239 84.618  0.033  2.335   8.1812e-02
   4_bss:   7.016  0.047  0.239 84.618  0.033  2.335   8.1812e-02
   4_xyz:   6.761  0.036  0.198 83.887  0.033  2.375   3.0933e-02
   4_adp:   6.761  0.036  0.198 83.887  0.033  2.375   3.0933e-02
   4_occ:   6.761  0.036  0.198 83.887  0.033  2.375   3.0933e-02
   5_bss:   6.761  0.036  0.198 83.887  0.033  2.375   3.0933e-02
   5_xyz:   6.749  0.044  0.203 83.784  0.029  2.358   2.9154e-02
   5_adp:   6.749  0.044  0.203 83.784  0.029  2.358   2.9154e-02
   5_occ:   6.749  0.044  0.203 83.784  0.029  2.358   2.9154e-02
   5_bss:   6.749  0.044  0.203 83.784  0.029  2.358   2.9154e-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:  73.98   0.00  17.53  73.06   0.00  13.37  73.98   2.69  40.13
   1_occ:  73.98   0.00  17.53  73.06   0.00  13.37  73.98   2.69  40.13
   2_bss:  73.98   0.00  17.53  73.06   0.00  13.37  73.98   2.69  40.13
   2_xyz:  73.98   0.00  17.53  73.06   0.00  13.37  73.98   2.69  40.13
   2_adp:  74.99   1.34  17.22  74.99   1.34  13.07  73.35   6.85  39.85
   2_occ:  74.99   1.34  17.22  74.99   1.34  13.07  73.35   6.85  39.85
   3_bss:  74.99   1.34  17.22  74.99   1.34  13.07  73.35   6.85  39.85
   3_xyz:  74.99   1.34  17.22  74.99   1.34  13.07  73.35   6.85  39.85
   3_adp:  79.08   2.00  17.02  79.08   2.00  12.93  75.38   5.54  39.25
   3_occ:  79.08   2.00  17.02  79.08   2.00  12.93  75.38   5.54  39.25
   4_bss:  79.08   2.00  17.02  79.08   2.00  12.93  75.38   5.54  39.25
   4_xyz:  79.08   2.00  17.02  79.08   2.00  12.93  75.38   5.54  39.25
   4_adp:  83.50   1.70  17.00  83.50   1.70  12.90  77.72   6.34  39.37
   4_occ:  83.50   1.70  17.00  83.50   1.70  12.90  77.72   6.34  39.37
   5_bss:  83.50   1.70  17.00  83.50   1.70  12.90  77.72   6.34  39.37
   5_xyz:  83.50   1.70  17.00  83.50   1.70  12.90  77.72   6.34  39.37
   5_adp:  93.85   0.00  17.20  93.85   0.00  12.91  84.15   6.39  40.55
   5_occ:  93.85   0.00  17.20  93.85   0.00  12.91  84.15   6.39  40.55
   5_bss:  93.86   0.00  17.20  93.86   0.00  12.91  84.15   6.40  40.55
------------------------------------------------------------------------
 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:    1.846    0.017    0.397
   1_adp:    1.846    0.017    0.397
   1_occ:    1.846    0.017    0.397
   2_bss:    1.846    0.017    0.397
   2_xyz:    1.299    0.028    0.458
   2_adp:    1.299    0.028    0.458
   2_occ:    1.299    0.028    0.458
   3_bss:    1.299    0.028    0.458
   3_xyz:    1.236    0.039    0.510
   3_adp:    1.236    0.039    0.510
   3_occ:    1.236    0.039    0.510
   4_bss:    1.236    0.039    0.510
   4_xyz:    1.308    0.035    0.518
   4_adp:    1.308    0.035    0.518
   4_occ:    1.308    0.035    0.518
   5_bss:    1.308    0.035    0.518
   5_xyz:    1.344    0.046    0.531
   5_adp:    1.344    0.046    0.531
   5_occ:    1.344    0.046    0.531
   5_bss:    1.344    0.046    0.531
------------------------------------------------------------------------

CPU time actual refinement: 344.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/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_770/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_770/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.28 
  Macro-tasks:
    bulk solvent and scale       = 36.34  
    individual site refinement   = 149.52 
    weights calculation          = 29.53  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 222.02 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 113.63 
    alpha_beta                      = 8.10   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 122.96 
    fmodel                         = 6.62   
    r_factors                      = 0.21   
    phase_errors                   = 10.98  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 265.76 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.820 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    653 calls, 113.32 s
gradients_fft:          598 calls, 108.91 s

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

# Date 2008-01-16 Time 05:37:29 PST -0800 (1200490649.95 s)
Start R-work = 0.3815, R-free = 0.3816 (no bulk solvent and anisotropic scale)
Final R-work = 0.1354, R-free = 0.1778 (no bulk solvent and anisotropic scale)

Start R-work = 0.3664, R-free = 0.3665
Final R-work = 0.1106, R-free = 0.1570