# Date 2008-01-16 Time 04:53:42 PST -0800 (1200488022.32 s)
#phil __OFF__

Command line arguments: "../504.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14111
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 504

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 88.1178, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96297
Completeness in resolution range: 0.937632
Completeness with d_max=infinity: 0.934857

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9630

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96297
Completeness in resolution range: 0.937632
Completeness with d_max=infinity: 0.934857

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2011 [2192/2217]  1971   221  10.1%
  bin  2:  4.2011 -  3.3467 [2111/2131]  1903   208   9.9%
  bin  3:  3.3467 -  2.9272 [2088/2107]  1879   209  10.0%
  bin  4:  2.9272 -  2.6612 [2056/2086]  1843   213  10.4%
  bin  5:  2.6612 -  2.4713 [2052/2071]  1853   199   9.7%
  bin  6:  2.4713 -  2.3262 [2043/2068]  1838   205  10.0%
  bin  7:  2.3262 -  2.2101 [2014/2042]  1810   204  10.1%
  bin  8:  2.2101 -  2.1141 [2024/2060]  1822   202  10.0%
  bin  9:  2.1141 -  2.0330 [2013/2062]  1818   195   9.7%
  bin 10:  2.0330 -  1.9630 [ 996/2048]   893   103  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 18
        2.11 -     2.80: 776
        2.80 -     3.50: 4497
        3.50 -     4.20: 9373
        4.20 -     4.90: 13742
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.407 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.703 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.728 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.822 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28401 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_504/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/model_refine_001.geo

CPU time processing inputs: 8.74


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.9914 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4509   r_free= 0.4557   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.265565                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6861 0.99   1426  156 0.3602 0.3448      6.5524      6.4919|
|  2:  4.6861 -  3.7384 0.99   1374  156 0.3802 0.4019      6.7676      6.7421|
|  3:  3.7384 -  3.2714 0.99   1343  147 0.4134 0.3919      6.6481      6.6451|
|  4:  3.2714 -  2.9748 0.99   1337  153 0.4468 0.4734      6.5108      6.5325|
|  5:  2.9748 -  2.7630 0.99   1319  145 0.4851 0.4465      6.3402      6.3465|
|  6:  2.7630 -  2.6010 0.99   1331  143 0.4754 0.5151      6.2491      6.1764|
|  7:  2.6010 -  2.4713 0.99   1319  150 0.4884 0.4915      6.2158      6.1713|
|  8:  2.4713 -  2.3642 0.98   1307  147 0.5065 0.5369      6.1709      6.1643|
|  9:  2.3642 -  2.2735 0.98   1295  140 0.4934 0.5179      6.1088      6.1559|
| 10:  2.2735 -  2.1953 1.00   1312  148 0.5086 0.5169      6.0737      6.0936|
| 11:  2.1953 -  2.1268 0.98   1304  144 0.5027 0.4799        6.02      6.0178|
| 12:  2.1268 -  2.0662 0.98   1293  142 0.5052 0.4721      5.9472      5.9555|
| 13:  2.0662 -  2.0119 0.93   1218  136 0.4903 0.4933      5.8776      5.8072|
| 14:  2.0119 -  1.9630 0.34    452   52 0.5341 0.5210      5.8931       5.839|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6861  1426   156  0.74  30.87   0.83     0.80      61897.99|
|  2:  4.6861 -  3.7384  1374   156  0.73  32.93   0.91     0.84      97122.92|
|  3:  3.7384 -  3.2714  1343   147  0.62  42.33   0.93     0.80     106404.82|
|  4:  3.2714 -  2.9748  1337   153  0.52  50.17   0.91     0.71      99606.19|
|  5:  2.9748 -  2.7630  1319   145  0.45  55.79   0.90     0.64      75139.30|
|  6:  2.7630 -  2.6010  1331   143  0.44  57.00   0.90     0.59      65371.36|
|  7:  2.6010 -  2.4713  1319   150  0.41  58.95   0.92     0.57      59993.20|
|  8:  2.4713 -  2.3642  1307   147  0.38  61.57   0.92     0.54      56373.55|
|  9:  2.3642 -  2.2735  1295   140  0.37  61.86   0.94     0.54      52983.23|
| 10:  2.2735 -  2.1953  1312   148  0.37  61.97   0.93     0.55      46909.30|
| 11:  2.1953 -  2.1268  1304   144  0.37  62.64   0.94     0.56      47003.93|
| 12:  2.1268 -  2.0662  1293   142  0.36  63.30   0.96     0.57      41609.69|
| 13:  2.0662 -  2.0119  1218   136  0.36  63.07   0.94     0.58      36047.94|
| 14:  2.0119 -  1.9630   452    52  0.42  58.40   0.99     0.60      26514.85|
|alpha:            min =        0.54 max =            0.84 mean =         0.64|
|beta:             min =    26514.85 max =       106404.82 mean =     64541.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.98 mean =        53.83|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.43|
|-----------------------------------------------------------------------------|

============================== 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 = 13.733952             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.768   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.339145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.682   (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 |  1.407 -  1.757:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.757 -  2.106:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.106 -  2.455:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.455 -  2.804:      744 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.804 -  3.154:     2093 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.154 -  3.503:     2404 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.503 -  3.852:     4586 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.852 -  4.201:     4787 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.201 -  4.551:     6203 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7539 |
|-----------------------------------------------------------------------------|
|-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 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.407 |       0.463 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4509   r_free= 0.4557   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.265565                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4390   r_free= 0.4456   ksol= 0.33   Bsol= 36.04   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,2.09,3.13,0.00,0.00,0.00); trace/3= 0.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256814                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.794316             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.739   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.102120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.458   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4390      final r-factor (work) = 0.3171          |
| start r-factor (free) = 0.4456      final r-factor (free) = 0.3576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.9205 = 10.79 * 0.50 * 6.2513 + 1.00 * 0.1814                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1108 = 10.79 * 0.50 * 6.1099 + 1.00 * 0.1348                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3171      final r-factor (work) = 0.2868          |
| start r-factor (free) = 0.3576      final r-factor (free) = 0.3728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7402 = 1.10 * 1.00 * 6.1099 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5933 = 1.10 * 1.00 * 5.9624 + 1.00 * 0.0219                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.16  18.47    None  None   None       |
|    all(noH): 2823   0      0.00    106.16  18.47    None  None   None       |
|    Sol.    : 438    0      0.81    106.16  40.33    None  None   None       |
|    Mac.    : 2385   0      0.00    78.15   14.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.616:  999   |   5:    53.082 -  63.698:   67        |
|      1:    10.616 -  21.233:  992   |   6:    63.698 -  74.314:   33        |
|      2:    21.233 -  31.849:  401   |   7:    74.314 -  84.931:   15        |
|      3:    31.849 -  42.465:  207   |   8:    84.931 -  95.547:    5        |
|      4:    42.465 -  53.082:  101   |   9:    95.547 - 106.163:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2868 r_free = 0.3728             target_work(ml) = 5.977         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2866 r_free = 0.3741             target_work(ml) = 5.977         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2866   r_free= 0.3741   ksol= 0.33   Bsol= 36.04   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,2.09,3.13,0.00,0.00,0.00); trace/3= 0.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.977421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2846   r_free= 0.3709   ksol= 0.34   Bsol= 61.94   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-0.17,1.13,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.975212                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.225123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.838  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.623785              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.498   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2846      final r-factor (work) = 0.2352          |
| start r-factor (free) = 0.3709      final r-factor (free) = 0.3028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7299 = 4.23 * 0.50 * 5.9621 + 1.00 * 0.1347                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5439 = 4.23 * 0.50 * 5.9084 + 1.00 * 0.0621                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2352      final r-factor (work) = 0.2231          |
| start r-factor (free) = 0.3028      final r-factor (free) = 0.2895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7054 = 0.62 * 1.00 * 5.9084 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6232 = 0.62 * 1.00 * 5.7803 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.86  18.42    None  None   None       |
|    all(noH): 2823   0      0.00    105.86  18.42    None  None   None       |
|    Sol.    : 438    0      1.75    105.86  41.94    None  None   None       |
|    Mac.    : 2385   0      0.00    81.34   14.10    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 -  10.586: 1071   |   5:    52.932 -  63.518:   73        |
|      1:    10.586 -  21.173:  964   |   6:    63.518 -  74.105:   36        |
|      2:    21.173 -  31.759:  332   |   7:    74.105 -  84.691:   13        |
|      3:    31.759 -  42.346:  195   |   8:    84.691 -  95.277:    7        |
|      4:    42.346 -  52.932:  131   |   9:    95.277 - 105.864:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2231 r_free = 0.2895             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2229 r_free = 0.2891             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2229   r_free= 0.2891   ksol= 0.34   Bsol= 61.94   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-0.17,1.13,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.762911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2230   r_free= 0.2891   ksol= 0.33   Bsol= 62.77   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-0.76,0.67,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.762395                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.887142              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.755  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.788050              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.378  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2230      final r-factor (work) = 0.1699          |
| start r-factor (free) = 0.2891      final r-factor (free) = 0.2241          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2960 = 3.89 * 0.50 * 5.7801 + 1.00 * 0.0621                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0424 = 3.89 * 0.50 * 5.6488 + 1.00 * 0.0636                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1699      final r-factor (work) = 0.1533          |
| start r-factor (free) = 0.2241      final r-factor (free) = 0.2069          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4661 = 0.79 * 1.00 * 5.6488 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3148 = 0.79 * 1.00 * 5.4592 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.79  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    104.79  18.07    None  None   None       |
|    Sol.    : 438    0      5.66    104.79  45.49    None  None   None       |
|    Mac.    : 2385   0      0.00    85.48   13.03    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 -  10.479: 1200   |   5:    52.396 -  62.875:  101        |
|      1:    10.479 -  20.958:  948   |   6:    62.875 -  73.354:   66        |
|      2:    20.958 -  31.438:  240   |   7:    73.354 -  83.834:   21        |
|      3:    31.438 -  41.917:  126   |   8:    83.834 -  94.313:    9        |
|      4:    41.917 -  52.396:  111   |   9:    94.313 - 104.792:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1533 r_free = 0.2069             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1531 r_free = 0.2067             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1531   r_free= 0.2067   ksol= 0.33   Bsol= 62.77   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-0.76,0.67,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.419857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.2063   ksol= 0.32   Bsol= 62.77   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.73,0.09,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.418380                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.646162              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.760  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.215426              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.902  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1533      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.2063      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0217 = 3.65 * 0.50 * 5.4622 + 1.00 * 0.0636                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8216 = 3.65 * 0.50 * 5.3517 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1654 = 0.22 * 1.00 * 5.3517 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1432 = 0.22 * 1.00 * 5.2641 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.71    97.44   17.07    None  None   None       |
|    all(noH): 2823   0      0.71    97.44   17.07    None  None   None       |
|    Sol.    : 438    0      4.74    97.44   41.94    None  None   None       |
|    Mac.    : 2385   0      0.71    87.57   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.715 -  10.387: 1228   |   5:    49.078 -  58.750:   94        |
|      1:    10.387 -  20.060:  967   |   6:    58.750 -  68.423:   59        |
|      2:    20.060 -  29.732:  216   |   7:    68.423 -  78.095:   22        |
|      3:    29.732 -  39.405:  116   |   8:    78.095 -  87.768:    9        |
|      4:    39.405 -  49.078:  110   |   9:    87.768 -  97.440:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1256 r_free = 0.1729             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1255 r_free = 0.1728             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1728   ksol= 0.32   Bsol= 62.77   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.73,0.09,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1729   ksol= 0.32   Bsol= 57.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.05,-0.06,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.238009                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.811469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.189  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521150              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.784  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8336 = 1.81 * 0.50 * 5.2647 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7832 = 1.81 * 0.50 * 5.2234 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7312 = 0.52 * 1.00 * 5.2234 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7174 = 0.52 * 1.00 * 5.1955 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    96.41   16.98    None  None   None       |
|    all(noH): 2823   0      0.23    96.41   16.98    None  None   None       |
|    Sol.    : 438    0      4.62    96.41   41.93    None  None   None       |
|    Mac.    : 2385   0      0.23    90.13   12.40    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:     0.232 -   9.850: 1132   |   5:    48.319 -  57.936:   93        |
|      1:     9.850 -  19.467: 1046   |   6:    57.936 -  67.554:   65        |
|      2:    19.467 -  29.084:  216   |   7:    67.554 -  77.171:   29        |
|      3:    29.084 -  38.702:  132   |   8:    77.171 -  86.788:    7        |
|      4:    38.702 -  48.319:   99   |   9:    86.788 -  96.406:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1658             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1658             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1658   ksol= 0.32   Bsol= 57.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.05,-0.06,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196670                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6861 0.99   1426  156 0.1009 0.1298      5.4028      5.5702|
|  2:  4.6861 -  3.7384 0.99   1374  156 0.0880 0.1159      5.4613      5.6589|
|  3:  3.7384 -  3.2714 0.99   1343  147 0.1145 0.1539      5.5281      5.8414|
|  4:  3.2714 -  2.9748 0.99   1337  153 0.1338 0.1810      5.5122      5.6736|
|  5:  2.9748 -  2.7630 0.99   1319  145 0.1441 0.1818      5.3883      5.5864|
|  6:  2.7630 -  2.6010 0.99   1331  143 0.1312 0.2109      5.2635       5.526|
|  7:  2.6010 -  2.4713 0.99   1319  150 0.1383 0.1666      5.2369      5.3726|
|  8:  2.4713 -  2.3642 0.98   1307  147 0.1289 0.1772      5.1434      5.3801|
|  9:  2.3642 -  2.2735 0.98   1295  140 0.1259 0.1950      5.0836      5.3957|
| 10:  2.2735 -  2.1953 1.00   1312  148 0.1188 0.1768      4.9755      5.2177|
| 11:  2.1953 -  2.1268 0.98   1304  144 0.1175 0.1920      4.9657      5.3354|
| 12:  2.1268 -  2.0662 0.98   1293  142 0.1260 0.1859      4.9405      5.2032|
| 13:  2.0662 -  2.0119 0.93   1218  136 0.1081 0.1664      4.7812      4.9986|
| 14:  2.0119 -  1.9630 0.34    452   52 0.0898 0.1428      4.5898      4.8242|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6861  1426   156  0.94   9.51   0.97     0.95       7502.25|
|  2:  4.6861 -  3.7384  1374   156  0.95   8.09   1.02     1.00       9370.74|
|  3:  3.7384 -  3.2714  1343   147  0.93  11.93   1.03     1.03      11215.63|
|  4:  3.2714 -  2.9748  1337   153  0.91  15.04   1.01     0.99      11378.08|
|  5:  2.9748 -  2.7630  1319   145  0.90  16.65   1.00     0.98       9135.49|
|  6:  2.7630 -  2.6010  1331   143  0.89  17.21   0.98     0.95       7693.06|
|  7:  2.6010 -  2.4713  1319   150  0.89  16.87   1.00     0.96       7064.95|
|  8:  2.4713 -  2.3642  1307   147  0.89  17.11   0.99     0.97       6222.53|
|  9:  2.3642 -  2.2735  1295   140  0.90  16.33   0.99     0.95       5406.38|
| 10:  2.2735 -  2.1953  1312   148  0.90  16.15   1.01     0.98       4570.26|
| 11:  2.1953 -  2.1268  1304   144  0.90  16.53   0.99     0.94       4563.75|
| 12:  2.1268 -  2.0662  1293   142  0.89  17.13   1.00     1.01       4440.15|
| 13:  2.0662 -  2.0119  1218   136  0.90  16.46   1.00     0.98       3427.50|
| 14:  2.0119 -  1.9630   452    52  0.94  12.06   0.99     0.96       2221.81|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2221.81 max =        11378.08 mean =      7002.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.85|
|phase err.(test): min =        0.00 max =           89.37 mean =        14.41|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1657   ksol= 0.32   Bsol= 57.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.08,-0.01,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1657   ksol= 0.32   Bsol= 57.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.08,-0.01,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196525                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6861 0.99   1426  156 0.1009 0.1298       5.403      5.5707|
|  2:  4.6861 -  3.7384 0.99   1374  156 0.0880 0.1159      5.4616      5.6589|
|  3:  3.7384 -  3.2714 0.99   1343  147 0.1145 0.1539      5.5283      5.8416|
|  4:  3.2714 -  2.9748 0.99   1337  153 0.1338 0.1810      5.5122      5.6735|
|  5:  2.9748 -  2.7630 0.99   1319  145 0.1440 0.1817       5.388      5.5861|
|  6:  2.7630 -  2.6010 0.99   1331  143 0.1311 0.2108      5.2631      5.5257|
|  7:  2.6010 -  2.4713 0.99   1319  150 0.1383 0.1667      5.2368      5.3728|
|  8:  2.4713 -  2.3642 0.98   1307  147 0.1290 0.1772      5.1434      5.3796|
|  9:  2.3642 -  2.2735 0.98   1295  140 0.1259 0.1948      5.0835      5.3954|
| 10:  2.2735 -  2.1953 1.00   1312  148 0.1188 0.1769      4.9753      5.2186|
| 11:  2.1953 -  2.1268 0.98   1304  144 0.1175 0.1919      4.9656      5.3356|
| 12:  2.1268 -  2.0662 0.98   1293  142 0.1260 0.1858      4.9404      5.2028|
| 13:  2.0662 -  2.0119 0.93   1218  136 0.1080 0.1661        4.78      4.9968|
| 14:  2.0119 -  1.9630 0.34    452   52 0.0898 0.1424      4.5882      4.8216|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6861  1426   156  0.94   9.52   0.97     0.95       7506.22|
|  2:  4.6861 -  3.7384  1374   156  0.95   8.10   1.02     1.00       9376.80|
|  3:  3.7384 -  3.2714  1343   147  0.93  11.94   1.03     1.03      11224.94|
|  4:  3.2714 -  2.9748  1337   153  0.91  15.04   1.02     0.99      11377.48|
|  5:  2.9748 -  2.7630  1319   145  0.90  16.65   1.00     0.98       9128.88|
|  6:  2.7630 -  2.6010  1331   143  0.89  17.20   0.98     0.95       7685.57|
|  7:  2.6010 -  2.4713  1319   150  0.89  16.87   1.00     0.96       7062.50|
|  8:  2.4713 -  2.3642  1307   147  0.89  17.12   1.00     0.97       6221.29|
|  9:  2.3642 -  2.2735  1295   140  0.90  16.33   0.99     0.95       5408.06|
| 10:  2.2735 -  2.1953  1312   148  0.90  16.15   1.01     0.98       4571.57|
| 11:  2.1953 -  2.1268  1304   144  0.90  16.54   0.99     0.94       4566.61|
| 12:  2.1268 -  2.0662  1293   142  0.89  17.13   1.01     1.01       4439.26|
| 13:  2.0662 -  2.0119  1218   136  0.90  16.44   1.00     0.98       3417.20|
| 14:  2.0119 -  1.9630   452    52  0.94  11.97   0.99     0.96       2209.83|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2209.83 max =        11377.48 mean =      7002.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.85|
|phase err.(test): min =        0.00 max =           89.37 mean =        14.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.742)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    96.40   16.97    None  None   None       |
|    all(noH): 2823   0      0.23    96.40   16.97    None  None   None       |
|    Sol.    : 438    0      4.61    96.40   41.92    None  None   None       |
|    Mac.    : 2385   0      0.23    90.12   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.226 -   9.844: 1132   |   5:    48.313 -  57.931:   93        |
|      1:     9.844 -  19.461: 1046   |   6:    57.931 -  67.548:   65        |
|      2:    19.461 -  29.079:  216   |   7:    67.548 -  77.165:   29        |
|      3:    29.079 -  38.696:  132   |   8:    77.165 -  86.783:    7        |
|      4:    38.696 -  48.313:   99   |   9:    86.783 -  96.400:    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)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.659 - 4.622
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 296
   mapped sites are within: 0.728 - 4.622

peak=    5.725 closest distance to " NE2 GLN A  11 " =    1.237
peak=    5.670 closest distance to " CG  PRO A  54 " =    1.425
peak=    5.608 closest distance to " O   HOH Z 142 " =    2.035
peak=    5.532 closest distance to " O   HOH Z 287 " =    2.098
peak=    5.342 closest distance to " O   HOH Z 423 " =    1.931
peak=    5.288 closest distance to " O   HOH Z  63 " =    1.711
peak=    5.262 closest distance to " O   HOH Z 417 " =    2.285
peak=    5.123 closest distance to " O   HOH Z 375 " =    1.232
peak=    5.029 closest distance to " O   HOH Z  49 " =    1.321
peak=    5.003 closest distance to " O   HOH Z  65 " =    1.180
peak=    4.892 closest distance to " O   HOH Z 126 " =    2.068
peak=    4.855 closest distance to " O   HOH Z 419 " =    2.462
peak=    4.778 closest distance to " O   HOH Z   7 " =    1.488
peak=    4.755 closest distance to " NH2 ARG A  56 " =    2.065
peak=    4.740 closest distance to " O   HOH Z 403 " =    1.687
peak=    4.731 closest distance to " O   HOH Z 371 " =    2.126
peak=    4.726 closest distance to " CB  PRO A  54 " =    1.116
peak=    4.711 closest distance to " O   HOH Z   9 " =    1.978
peak=    4.672 closest distance to " CB  GLN A 223 " =    1.526
peak=    4.646 closest distance to " O   HOH Z 427 " =    2.366
peak=    4.625 closest distance to " O   HOH Z 380 " =    1.859
peak=    4.621 closest distance to " O   HOH Z 232 " =    2.223
peak=    4.606 closest distance to " CG2 VAL A 257 " =    0.911
peak=    4.598 closest distance to " O   HOH Z  78 " =    1.583
peak=    4.550 closest distance to " CG  PRO A 198 " =    1.276
peak=    4.496 closest distance to " O   HOH Z 422 " =    0.934
peak=    4.465 closest distance to " O   HOH Z 425 " =    1.451
peak=    4.455 closest distance to " O   HOH Z 222 " =    1.141
peak=    4.384 closest distance to " CB  ARG A 275 " =    0.967
peak=    4.372 closest distance to " CB  SER A  63 " =    1.258
peak=    4.346 closest distance to " CG  PRO A  90 " =    1.351
peak=    4.316 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.303 closest distance to " O   HOH Z   1 " =    1.871
peak=    4.302 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.271 closest distance to " O   HOH Z  69 " =    1.217
peak=    4.268 closest distance to " CA  TYR A  30 " =    1.043
peak=    4.266 closest distance to " O   HOH Z 278 " =    1.166
peak=    4.259 closest distance to " O   HOH Z 298 " =    1.907
peak=    4.259 closest distance to " CE  LYS A 119 " =    1.258
peak=    4.220 closest distance to " CA  ARG A 195 " =    1.291
peak=    4.195 closest distance to " CB  ARG A  79 " =    1.249
peak=    4.186 closest distance to " NH1AARG A 145 " =    1.224
peak=    4.164 closest distance to " CB  GLU A 277 " =    3.605
peak=    4.160 closest distance to " CB  ARG A 190 " =    1.586
peak=    4.159 closest distance to " O   HOH Z  39 " =    1.009
peak=    4.151 closest distance to " CB  VAL A 265 " =    1.320
peak=    4.116 closest distance to " O   HOH Z 245 " =    1.052
peak=    4.103 closest distance to " O   HOH Z 145 " =    1.226
peak=    4.097 closest distance to " CD  ARG A 159 " =    0.810
peak=    4.097 closest distance to " O   HOH Z 327 " =    1.662
peak=    4.073 closest distance to " CZ3 TRP A 266 " =    1.181
peak=    4.071 closest distance to " NH2AARG A 190 " =    1.863
peak=    4.040 closest distance to " OG ASER A 258 " =    3.101
peak=    4.028 closest distance to " NZ  LYS A 119 " =    2.356
peak=    4.015 closest distance to " CG  TRP A 179 " =    2.199
peak=    4.011 closest distance to " CB  SER A 216 " =    0.979
peak=    3.984 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.959 closest distance to " CA  ASN A 127 " =    1.074
peak=    3.954 closest distance to " CA  VAL A 125 " =    1.139
peak=    3.942 closest distance to " O   HOH Z 437 " =    1.680
peak=    3.925 closest distance to " CB  ASN A 142 " =    0.950
peak=    3.915 closest distance to " CB  SER A   3 " =    1.320
peak=    3.899 closest distance to " CB  ASN A  39 " =    0.957
peak=    3.879 closest distance to " CB  GLN A 183 " =    1.212
peak=    3.878 closest distance to " O   HOH Z 362 " =    2.051
peak=    3.876 closest distance to " O   HOH Z 406 " =    1.610
peak=    3.876 closest distance to " ND2 ASN A 187 " =    1.704
peak=    3.853 closest distance to " O   SER A  87 " =    2.268
peak=    3.853 closest distance to " ND2 ASN A 249 " =    0.864
peak=    3.849 closest distance to " CZ  PHE A 218 " =    1.084
peak=    3.844 closest distance to " O   HOH Z 214 " =    2.458
peak=    3.836 closest distance to " N   GLN A 278 " =    1.357
peak=    3.827 closest distance to " CA  ALA A 160 " =    1.463
peak=    3.823 closest distance to " O   HOH Z 272 " =    1.782
peak=    3.807 closest distance to " O   HOH Z 218 " =    1.746
peak=    3.802 closest distance to " CB  SER A 212 " =    1.272
peak=    3.800 closest distance to " CD2 TRP A 179 " =    1.262
peak=    3.795 closest distance to " CE3 TRP A 150 " =    1.102
peak=    3.795 closest distance to " CB  SER A 210 " =    0.807
peak=    3.781 closest distance to " CB  GLU A  46 " =    1.077
peak=    3.776 closest distance to " O   HOH Z  40 " =    1.755
peak=    3.768 closest distance to " CG  GLN A  58 " =    0.943
peak=    3.765 closest distance to " CG  LEU A 167 " =    1.254
peak=    3.764 closest distance to " O   ASN A  74 " =    1.437
peak=    3.763 closest distance to " O   HOH Z 225 " =    1.527
peak=    3.759 closest distance to " CG  LYS A  76 " =    1.842
peak=    3.754 closest distance to " O   HOH Z 286 " =    2.144
peak=    3.750 closest distance to " CB  ALA A 114 " =    0.835
peak=    3.747 closest distance to " O   HOH Z 215 " =    1.530
peak=    3.742 closest distance to " CB  LYS A 117 " =    1.234
peak=    3.737 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.731 closest distance to " CB  ASP A 191 " =    1.263
peak=    3.730 closest distance to " O   HOH Z  24 " =    1.884
peak=    3.730 closest distance to " O   HOH Z 365 " =    2.743
peak=    3.730 closest distance to " O   HOH Z  61 " =    1.707
peak=    3.723 closest distance to " O   HOH Z 414 " =    1.302
peak=    3.720 closest distance to " OG  SER A  62 " =    2.981
peak=    3.715 closest distance to " O   HOH Z 357 " =    2.032
peak=    3.702 closest distance to " O   HOH Z 188 " =    2.779
peak=    3.702 closest distance to " O   HOH Z 236 " =    1.475
peak=    3.698 closest distance to " O   HOH Z   2 " =    1.662
peak=    3.695 closest distance to " CA  SER A  87 " =    1.025
peak=    3.689 closest distance to " N   CYS A 260 " =    0.874
peak=    3.686 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.682 closest distance to " NZ  LYS A 117 " =    2.787
peak=    3.681 closest distance to " CD  ARG A  66 " =    2.385
peak=    3.679 closest distance to " OD1 ASN A  69 " =    2.605
peak=    3.651 closest distance to " CB  TYR A 169 " =    0.792
peak=    3.651 closest distance to " O  BHOH Z  74 " =    1.304
peak=    3.636 closest distance to " CB  ALA A 114 " =    1.105
peak=    3.634 closest distance to " CB  VAL A 202 " =    1.682
peak=    3.633 closest distance to " O   TYR A 116 " =    1.298
peak=    3.627 closest distance to " O   HOH Z 368 " =    3.597
peak=    3.626 closest distance to " CB  GLU A 128 " =    0.946
peak=    3.621 closest distance to " O   HOH Z 345 " =    1.866
peak=    3.621 closest distance to " O   HOH Z 258 " =    2.155
peak=    3.612 closest distance to " O   HOH Z   1 " =    1.772
peak=    3.610 closest distance to " O   HOH Z 203 " =    1.734
peak=    3.608 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.607 closest distance to " O   HOH Z  26 " =    1.391
peak=    3.605 closest distance to " O   HOH Z 359 " =    1.437
peak=    3.603 closest distance to " O   HOH Z 112 " =    1.093
peak=    3.591 closest distance to " O   HOH Z 394 " =    1.779
peak=    3.591 closest distance to " ND1 HIS A  86 " =    1.756
peak=    3.582 closest distance to " CB  ASN A 110 " =    1.008
peak=    3.576 closest distance to " OG BSER A 164 " =    2.268
peak=    3.574 closest distance to " CB  GLU A 152 " =    1.308
peak=    3.572 closest distance to " O   HOH Z 158 " =    3.065
peak=    3.562 closest distance to " CB  SER A 276 " =    1.194
peak=    3.560 closest distance to " CB  TRP A 179 " =    1.383
peak=    3.560 closest distance to " O   HOH Z 422 " =    2.408
peak=    3.550 closest distance to " O   HOH Z  68 " =    2.094
peak=    3.547 closest distance to " CG2 THR A 221 " =    1.090
peak=    3.547 closest distance to " O   HOH Z 290 " =    1.059
peak=    3.541 closest distance to " O   HOH Z 405 " =    1.477
peak=    3.540 closest distance to " O   HOH Z 346 " =    1.648
peak=    3.537 closest distance to " CB  TYR A  30 " =    1.381
peak=    3.518 closest distance to " O   HOH Z 172 " =    2.317
peak=    3.516 closest distance to " CD  ARG A 259 " =    1.778
peak=    3.516 closest distance to " NE2 HIS A 207 " =    1.101
peak=    3.515 closest distance to " O   HOH Z 116 " =    2.972
peak=    3.514 closest distance to " O   HOH Z 201 " =    1.402
peak=    3.509 closest distance to " CB  THR A  31 " =    1.627
peak=    3.506 closest distance to " O   HOH Z 261 " =    2.085
peak=    3.504 closest distance to " OE1 GLN A  77 " =    1.255
peak=    3.498 closest distance to " CB  PRO A  90 " =    1.055
peak=    3.497 closest distance to " O   HOH Z 421 " =    2.163
peak=    3.495 closest distance to " O   HOH Z   3 " =    1.920
peak=    3.495 closest distance to " CB  LEU A 228 " =    1.101
peak=    3.493 closest distance to " CZ  PHE A  38 " =    1.242
peak=    3.491 closest distance to " O   PRO A 198 " =    1.280
peak=    3.490 closest distance to " CB  PHE A 130 " =    0.895
peak=    3.484 closest distance to " CB  ASN A 187 " =    1.029
peak=    3.484 closest distance to " O   HOH Z 344 " =    3.051
peak=    3.479 closest distance to " CA  TYR A 116 " =    1.393
peak=    3.478 closest distance to " N   SER A  97 " =    0.811
peak=    3.477 closest distance to " O   HOH Z  88 " =    3.764
peak=    3.477 closest distance to " O   HOH Z 391 " =    2.908
peak=    3.473 closest distance to " O   HOH Z  44 " =    1.780
peak=    3.470 closest distance to " CG  PRO A 243 " =    1.051
peak=    3.468 closest distance to " CB  LEU A 300 " =    0.919
peak=    3.467 closest distance to " O   HOH Z 153 " =    3.711
peak=    3.466 closest distance to " O   HOH Z 130 " =    2.121
peak=    3.465 closest distance to " ND2BASN A 224 " =    0.832
peak=    3.464 closest distance to " NZ  LYS A 119 " =    1.435
peak=    3.463 closest distance to " CB  ASP A 124 " =    0.820
peak=    3.460 closest distance to " O   HOH Z 132 " =    2.369
peak=    3.449 closest distance to " N   TYR A 116 " =    1.294
peak=    3.448 closest distance to " O   HOH Z 394 " =    3.837
peak=    3.444 closest distance to " CB  ALA A 291 " =    1.068
peak=    3.440 closest distance to " O   HOH Z 392 " =    1.245
peak=    3.434 closest distance to " CG2 VAL A 197 " =    1.012
peak=    3.430 closest distance to " O   HOH Z  40 " =    2.094
peak=    3.428 closest distance to " CB  SER A  62 " =    0.863
peak=    3.419 closest distance to " O   HOH Z  59 " =    1.746
peak=    3.417 closest distance to " CA  ASN A 217 " =    1.203
peak=    3.416 closest distance to " O   HOH Z 156 " =    2.611
peak=    3.410 closest distance to " CG2 ILE A 239 " =    0.816
peak=    3.407 closest distance to " O   HOH Z  28 " =    1.865
peak=    3.402 closest distance to " N   GLU A   2 " =    1.376
peak=    3.398 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.397 closest distance to " O   HOH Z 285 " =    2.571
peak=    3.396 closest distance to " CB  THR A 157 " =    1.167
peak=    3.396 closest distance to " OE2 GLU A  53 " =    1.916
peak=    3.395 closest distance to " CG2 ILE A 120 " =    1.350
peak=    3.395 closest distance to " N   ARG A 156 " =    1.284
peak=    3.393 closest distance to " O   HOH Z  10 " =    1.695
peak=    3.391 closest distance to " CG2 ILE A  20 " =    1.600
peak=    3.385 closest distance to " OG BSER A 134 " =    2.898
peak=    3.385 closest distance to " O   HOH Z 213 " =    2.322
peak=    3.379 closest distance to " O   HOH Z 193 " =    1.642
peak=    3.379 closest distance to " O   HOH Z 402 " =    1.485
peak=    3.374 closest distance to " O   HOH Z  42 " =    1.542
peak=    3.368 closest distance to " CG AARG A 275 " =    1.135
peak=    3.349 closest distance to " CA  ASN A 215 " =    1.027
peak=    3.348 closest distance to " CB  ALA A  43 " =    0.822
peak=    3.347 closest distance to " CG1 ILE A 120 " =    1.445
peak=    3.346 closest distance to " CD  ARG A 269 " =    0.957
peak=    3.345 closest distance to " O   HOH Z 234 " =    3.615
peak=    3.342 closest distance to " NH1 ARG A  14 " =    1.111
peak=    3.338 closest distance to " O   HOH Z 128 " =    2.141
peak=    3.332 closest distance to " CG1BVAL A  72 " =    1.308
peak=    3.329 closest distance to " O   HOH Z 368 " =    1.764
peak=    3.329 closest distance to " O   HOH Z 368 " =    4.297
peak=    3.326 closest distance to " CD1AILE A 234 " =    0.907
peak=    3.326 closest distance to " NZ  LYS A 117 " =    1.296
peak=    3.324 closest distance to " CB  ASN A 215 " =    1.093
peak=    3.323 closest distance to " CD1 LEU A 300 " =    1.046
peak=    3.321 closest distance to " O   HOH Z 143 " =    1.302
peak=    3.315 closest distance to " O   HOH Z 434 " =    1.530
peak=    3.314 closest distance to " O   HOH Z 128 " =    1.938
peak=    3.313 closest distance to " O   PRO A 198 " =    1.531
peak=    3.311 closest distance to " CA  MET A 105 " =    0.920
peak=    3.308 closest distance to " O   HOH Z 248 " =    1.556
peak=    3.308 closest distance to " NH1BARG A 145 " =    1.325
peak=    3.305 closest distance to " O   HOH Z  90 " =    2.116
peak=    3.304 closest distance to " CA  ARG A 156 " =    1.078
peak=    3.302 closest distance to " N   TYR A  15 " =    1.128
peak=    3.302 closest distance to " O   HOH Z 425 " =    1.899
peak=    3.301 closest distance to " O   HOH Z  88 " =    2.719
peak=    3.299 closest distance to " CB  SER A 273 " =    0.904
peak=    3.292 closest distance to " O   HOH Z 411 " =    3.888
peak=    3.286 closest distance to " OG BSER A  99 " =    2.409
peak=    3.284 closest distance to " NZ  LYS A 166 " =    1.041
peak=    3.279 closest distance to " O   HOH Z 216 " =    4.108
peak=    3.274 closest distance to " O   HOH Z 180 " =    2.245
peak=    3.272 closest distance to " O   THR A 220 " =    1.371
peak=    3.271 closest distance to " CB  ARG A 138 " =    0.916
peak=    3.270 closest distance to " CE AMET A  47 " =    1.310
peak=    3.266 closest distance to " O   HOH Z  88 " =    2.962
peak=    3.263 closest distance to " CB  ARG A 219 " =    1.047
peak=    3.261 closest distance to " O   HOH Z 175 " =    2.127
peak=    3.257 closest distance to " O   HOH Z 250 " =    1.425
peak=    3.255 closest distance to " O   HOH Z 305 " =    3.623
peak=    3.255 closest distance to " CG1 ILE A 151 " =    1.041
peak=    3.250 closest distance to " O   PHE A 192 " =    1.412
peak=    3.249 closest distance to " O   HOH Z 194 " =    2.439
peak=    3.249 closest distance to " O   HOH Z 219 " =    2.131
peak=    3.245 closest distance to " O   HOH Z 124 " =    2.080
peak=    3.244 closest distance to " O   GLY A 302 " =    2.203
peak=    3.243 closest distance to " CA  ALA A 129 " =    1.212
peak=    3.242 closest distance to " CA  ASP A 124 " =    0.841
peak=    3.241 closest distance to " CB  ARG A  79 " =    0.872
peak=    3.232 closest distance to " O   HOH Z 383 " =    1.971
peak=    3.227 closest distance to " O   HOH Z 427 " =    1.201
peak=    3.223 closest distance to " O   HOH Z  49 " =    3.376
peak=    3.216 closest distance to " O   HOH Z 325 " =    2.207
peak=    3.211 closest distance to " N   ASN A 127 " =    1.406
peak=    3.207 closest distance to " CD2 LEU A   5 " =    1.355
peak=    3.206 closest distance to " O   HOH Z 126 " =    1.462
peak=    3.203 closest distance to " CG  ARG A 159 " =    0.728
peak=    3.203 closest distance to " CB  SER A  99 " =    0.835
peak=    3.192 closest distance to " CA  ARG A  36 " =    0.982
peak=    3.186 closest distance to " CE3 TRP A  85 " =    0.981
peak=    3.184 closest distance to " O   HOH Z 352 " =    1.410
peak=    3.183 closest distance to " NH2BARG A 190 " =    1.366
peak=    3.179 closest distance to " NH2BARG A 145 " =    1.801
peak=    3.175 closest distance to " CA  ILE A 234 " =    1.005
peak=    3.172 closest distance to " CA  ARG A 102 " =    1.204
peak=    3.171 closest distance to " CA  ALA A 299 " =    0.888
peak=    3.162 closest distance to " O   HOH Z 148 " =    2.097
peak=    3.153 closest distance to " CB  ASP A 140 " =    0.975
peak=    3.150 closest distance to " O   HOH Z 244 " =    1.667
peak=    3.150 closest distance to " CA  THR A 264 " =    0.820
peak=    3.148 closest distance to " CG2 VAL A 232 " =    0.866
peak=    3.145 closest distance to " CA  THR A 221 " =    1.000
peak=    3.144 closest distance to " O   HOH Z  58 " =    1.804
peak=    3.143 closest distance to " CB  ALA A   1 " =    4.622
peak=    3.137 closest distance to " O   HOH Z 371 " =    3.089
peak=    3.130 closest distance to " O   HOH Z  17 " =    1.720
peak=    3.127 closest distance to " NE1 TRP A  85 " =    0.998
peak=    3.125 closest distance to " O   HOH Z 298 " =    2.629
peak=    3.125 closest distance to " CB  PHE A 204 " =    0.751
peak=    3.123 closest distance to " NH1 ARG A 138 " =    1.025
peak=    3.114 closest distance to " O   HOH Z 285 " =    2.139
peak=    3.112 closest distance to " CA  ALA A 233 " =    0.998
peak=    3.109 closest distance to " N   VAL A 296 " =    1.736
peak=    3.097 closest distance to " CA  ASP A 162 " =    1.088
peak=    3.090 closest distance to " O   HOH Z 106 " =    4.027
peak=    3.090 closest distance to " O   HOH Z 198 " =    1.605
peak=    3.090 closest distance to " O   HOH Z 371 " =    2.109
peak=    3.083 closest distance to " O   TRP A  70 " =    1.590
peak=    3.080 closest distance to " O   HOH Z 371 " =    3.215
peak=    3.079 closest distance to " CZ3 TRP A 274 " =    1.358
peak=    3.078 closest distance to " CB  HIS A 108 " =    0.827
peak=    3.075 closest distance to " O   HOH Z 154 " =    1.979
peak=    3.068 closest distance to " O   HOH Z 272 " =    2.025
peak=    3.058 closest distance to " O   HOH Z 124 " =    1.325
peak=    3.058 closest distance to " O   THR A 294 " =    0.960
peak=    3.047 closest distance to " O  BHOH Z 338 " =    2.370
peak=    3.029 closest distance to " O   HOH Z 385 " =    2.718
peak=    3.021 closest distance to " O   HOH Z 288 " =    1.855
peak=    2.936 closest distance to " O   HOH Z 222 " =    2.188

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.646 - 5.244
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.754 - 5.244

peak=   -4.517 closest distance to " CD  ARG A  14 " =    3.329
peak=   -4.412 closest distance to " O   PRO A 198 " =    1.188
peak=   -4.393 closest distance to " CB  ALA A  43 " =    2.427
peak=   -4.268 closest distance to " CB  PRO A 243 " =    2.611
peak=   -4.217 closest distance to " OG BSER A 134 " =    1.396
peak=   -4.214 closest distance to " O   HOH Z  60 " =    1.540
peak=   -4.212 closest distance to " CD  ARG A 156 " =    2.059
peak=   -4.193 closest distance to " O   HOH Z 131 " =    3.992
peak=   -4.093 closest distance to " O   HOH Z 351 " =    1.583
peak=   -4.064 closest distance to " O   HOH Z 377 " =    1.887
peak=   -4.061 closest distance to " O   HOH Z  69 " =    1.618
peak=   -3.988 closest distance to " O   HOH Z 231 " =    2.045
peak=   -3.975 closest distance to " CZ2 TRP A  92 " =    2.846
peak=   -3.974 closest distance to " O   HOH Z 290 " =    0.981
peak=   -3.964 closest distance to " O   HOH Z 211 " =    1.130
peak=   -3.946 closest distance to " O   HOH Z 185 " =    2.098
peak=   -3.926 closest distance to " CA  GLY A  98 " =    1.768
peak=   -3.906 closest distance to " CD2 TYR A 293 " =    1.808
peak=   -3.901 closest distance to " N   THR A 157 " =    1.535
peak=   -3.878 closest distance to " CD1 LEU A 101 " =    2.223
peak=   -3.869 closest distance to " CA  GLY A 241 " =    2.224
peak=   -3.863 closest distance to " O   ALA A  10 " =    1.633
peak=   -3.862 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.860 closest distance to " O   SER A  22 " =    2.617
peak=   -3.850 closest distance to " O   HOH Z 298 " =    2.558
peak=   -3.840 closest distance to " CE BMET A  47 " =    1.165
peak=   -3.834 closest distance to " O   PRO A 243 " =    2.578
peak=   -3.833 closest distance to " C   HIS A 108 " =    1.188
peak=   -3.822 closest distance to " O   GLU A 152 " =    1.367
peak=   -3.796 closest distance to " CZ2 TRP A 274 " =    0.907
peak=   -3.768 closest distance to " ND2 ASN A 249 " =    2.186
peak=   -3.737 closest distance to " CG  GLN A  58 " =    1.014
peak=   -3.735 closest distance to " O   HOH Z  24 " =    1.080
peak=   -3.733 closest distance to " CD1 LEU A 255 " =    2.887
peak=   -3.719 closest distance to " CG2 THR A  18 " =    2.841
peak=   -3.706 closest distance to " O   HOH Z  39 " =    1.113
peak=   -3.706 closest distance to " O   SER A 135 " =    1.436
peak=   -3.701 closest distance to " O   HOH Z 231 " =    0.998
peak=   -3.692 closest distance to " CA  GLY A 133 " =    1.916
peak=   -3.672 closest distance to " CB  GLN A  55 " =    1.160
peak=   -3.672 closest distance to " OD1 ASP A 171 " =    1.636
peak=   -3.659 closest distance to " O   HOH Z 385 " =    1.535
peak=   -3.639 closest distance to " CB  ALA A 158 " =    1.736
peak=   -3.619 closest distance to " O   HOH Z 292 " =    1.502
peak=   -3.610 closest distance to " O   HOH Z 276 " =    1.418
peak=   -3.590 closest distance to " O   VAL A  67 " =    2.585
peak=   -3.584 closest distance to " O   HOH Z 266 " =    5.244
peak=   -3.583 closest distance to " OD2 ASP A 191 " =    1.338
peak=   -3.579 closest distance to " O   PRO A 198 " =    1.405
peak=   -3.562 closest distance to " NE2 GLN A 278 " =    1.522
peak=   -3.556 closest distance to " N   ALA A  43 " =    2.581
peak=   -3.555 closest distance to " O   HOH Z 429 " =    1.947
peak=   -3.553 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.549 closest distance to " CD2 PHE A  61 " =    2.029
peak=   -3.538 closest distance to " O   PRO A 163 " =    1.403
peak=   -3.537 closest distance to " CG2 ILE A  20 " =    2.989
peak=   -3.524 closest distance to " O   HOH Z 313 " =    1.661
peak=   -3.523 closest distance to " O   GLN A 240 " =    1.969
peak=   -3.518 closest distance to " O   HOH Z 198 " =    1.226
peak=   -3.516 closest distance to " CE2 PHE A 218 " =    2.435
peak=   -3.503 closest distance to " CB  ASN A  45 " =    2.086
peak=   -3.502 closest distance to " O   HOH Z 219 " =    4.609
peak=   -3.498 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.497 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.496 closest distance to " CD2 LEU A 237 " =    2.889
peak=   -3.492 closest distance to " ND2 ASN A 187 " =    1.475
peak=   -3.487 closest distance to " CG  LEU A  83 " =    2.116
peak=   -3.487 closest distance to " O   HOH Z  28 " =    1.585
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.477 closest distance to " O   HOH Z  52 " =    1.343
peak=   -3.466 closest distance to " CA  ASP A 298 " =    1.121
peak=   -3.464 closest distance to " ND2 ASN A 285 " =    2.093
peak=   -3.457 closest distance to " CG2 ILE A 151 " =    2.551
peak=   -3.450 closest distance to " CG  GLN A 223 " =    2.096
peak=   -3.449 closest distance to " O   HOH Z  65 " =    1.315
peak=   -3.447 closest distance to " O   HOH Z 389 " =    2.183
peak=   -3.440 closest distance to " O   HOH Z 372 " =    2.442
peak=   -3.435 closest distance to " CB  PHE A 192 " =    1.952
peak=   -3.433 closest distance to " CB  ASP A 200 " =    2.560
peak=   -3.432 closest distance to " OG  SER A  97 " =    2.137
peak=   -3.428 closest distance to " O   HOH Z  11 " =    1.632
peak=   -3.427 closest distance to " O   ARG A 145 " =    1.236
peak=   -3.426 closest distance to " O   HOH Z 412 " =    3.955
peak=   -3.419 closest distance to " O   HOH Z 374 " =    1.836
peak=   -3.418 closest distance to " CE2 TYR A  30 " =    2.610
peak=   -3.418 closest distance to " CZ  PHE A  59 " =    1.392
peak=   -3.407 closest distance to " CD  GLN A  88 " =    0.855
peak=   -3.403 closest distance to " OD1 ASP A 191 " =    1.772
peak=   -3.402 closest distance to " SG BCYS A 201 " =    1.949
peak=   -3.393 closest distance to " CD  GLU A 277 " =    1.122
peak=   -3.390 closest distance to " CG2 THR A 178 " =    2.111
peak=   -3.390 closest distance to " CD  GLN A  77 " =    1.324
peak=   -3.386 closest distance to " O   HOH Z 286 " =    1.528
peak=   -3.385 closest distance to " O   ALA A   1 " =    1.593
peak=   -3.384 closest distance to " OD1 ASN A 148 " =    1.350
peak=   -3.380 closest distance to " O   HOH Z 140 " =    1.152
peak=   -3.377 closest distance to " CB  ASP A 132 " =    2.329
peak=   -3.371 closest distance to " O   HOH Z 174 " =    2.632
peak=   -3.370 closest distance to " O   HOH Z  49 " =    1.056
peak=   -3.370 closest distance to " O   HOH Z 359 " =    3.173
peak=   -3.362 closest distance to " O   PHE A 218 " =    1.455
peak=   -3.361 closest distance to " CB  ALA A 114 " =    2.568
peak=   -3.361 closest distance to " CA  GLY A 203 " =    2.395
peak=   -3.361 closest distance to " CB  TYR A  15 " =    2.246
peak=   -3.359 closest distance to " O   HOH Z 348 " =    1.881
peak=   -3.357 closest distance to " O   HOH Z 407 " =    2.974
peak=   -3.356 closest distance to " CA  ASP A  27 " =    2.344
peak=   -3.347 closest distance to " CG1 VAL A 112 " =    3.121
peak=   -3.344 closest distance to " CE1 PHE A  59 " =    2.119
peak=   -3.338 closest distance to " O   HOH Z 427 " =    1.749
peak=   -3.338 closest distance to " OE1 GLN A 183 " =    1.632
peak=   -3.337 closest distance to " O   HOH Z 275 " =    1.651
peak=   -3.322 closest distance to " OXT GLY A 302 " =    3.227
peak=   -3.321 closest distance to " O   HOH Z 389 " =    1.287
peak=   -3.318 closest distance to " O   HOH Z 318 " =    1.797
peak=   -3.315 closest distance to " O   HOH Z 111 " =    2.118
peak=   -3.315 closest distance to " CZ  PHE A 155 " =    1.154
peak=   -3.313 closest distance to " O   HOH Z 414 " =    1.324
peak=   -3.307 closest distance to " O   HOH Z 295 " =    1.924
peak=   -3.306 closest distance to " CE  MET A 105 " =    2.418
peak=   -3.305 closest distance to " CG1 VAL A 265 " =    2.792
peak=   -3.303 closest distance to " CG  ASN A  39 " =    1.675
peak=   -3.302 closest distance to " O   HOH Z 348 " =    2.118
peak=   -3.297 closest distance to " OE2 GLU A 152 " =    1.160
peak=   -3.297 closest distance to " OG  SER A  87 " =    1.395
peak=   -3.295 closest distance to " O   ILE A  49 " =    1.681
peak=   -3.294 closest distance to " O   GLY A  17 " =    1.178
peak=   -3.287 closest distance to " O   HOH Z 134 " =    3.907
peak=   -3.286 closest distance to " O   ASN A 249 " =    1.610
peak=   -3.284 closest distance to " CB  ALA A   9 " =    2.337
peak=   -3.273 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.269 closest distance to " CG2BVAL A  72 " =    1.958
peak=   -3.266 closest distance to " O   HOH Z 201 " =    1.888
peak=   -3.266 closest distance to " CB  ASP A 171 " =    2.253
peak=   -3.262 closest distance to " O   HOH Z 278 " =    1.445
peak=   -3.260 closest distance to " CA  GLY A  57 " =    2.089
peak=   -3.260 closest distance to " O   HOH Z  73 " =    2.294
peak=   -3.249 closest distance to " N   ASN A 127 " =    1.456
peak=   -3.249 closest distance to " CG2 VAL A 232 " =    2.130
peak=   -3.248 closest distance to " CG2 ILE A 263 " =    2.339
peak=   -3.247 closest distance to " CB  ASN A  39 " =    2.317
peak=   -3.246 closest distance to " NH2 ARG A 219 " =    1.778
peak=   -3.246 closest distance to " O   VAL A 189 " =    2.579
peak=   -3.243 closest distance to " O   HOH Z  71 " =    1.152
peak=   -3.242 closest distance to " O   HOH Z 102 " =    1.441
peak=   -3.238 closest distance to " O   HOH Z 253 " =    3.793
peak=   -3.238 closest distance to " CD  PRO A 213 " =    2.025
peak=   -3.225 closest distance to " N   VAL A 232 " =    2.050
peak=   -3.215 closest distance to " O   HOH Z 100 " =    1.317
peak=   -3.215 closest distance to " N   GLN A  58 " =    1.336
peak=   -3.210 closest distance to " O   HOH Z 281 " =    2.687
peak=   -3.209 closest distance to " O   HOH Z 357 " =    1.817
peak=   -3.209 closest distance to " O   HOH Z 368 " =    1.503
peak=   -3.205 closest distance to " O   HOH Z  64 " =    1.356
peak=   -3.196 closest distance to " CB  ALA A  10 " =    2.302
peak=   -3.194 closest distance to " ND2 ASN A  45 " =    2.165
peak=   -3.194 closest distance to " OG BSER A 134 " =    1.799
peak=   -3.194 closest distance to " O   HOH Z 364 " =    1.709
peak=   -3.193 closest distance to " CE3 TRP A 274 " =    2.329
peak=   -3.191 closest distance to " O   HOH Z 438 " =    1.299
peak=   -3.188 closest distance to " O   HOH Z  26 " =    0.944
peak=   -3.184 closest distance to " CG  PHE A 283 " =    2.633
peak=   -3.179 closest distance to " O   HOH Z 340 " =    2.004
peak=   -3.179 closest distance to " CB  GLN A  11 " =    1.746
peak=   -3.177 closest distance to " NE2 GLN A  55 " =    1.279
peak=   -3.177 closest distance to " CB  SER A 245 " =    2.158
peak=   -3.176 closest distance to " CG2 THR A  42 " =    1.777
peak=   -3.176 closest distance to " ND2BASN A 224 " =    1.749
peak=   -3.175 closest distance to " O   TRP A  70 " =    1.385
peak=   -3.174 closest distance to " CG  MET A 105 " =    0.999
peak=   -3.172 closest distance to " CG  ARG A 269 " =    2.318
peak=   -3.166 closest distance to " CE  LYS A  76 " =    2.807
peak=   -3.165 closest distance to " OG BSER A 210 " =    2.304
peak=   -3.160 closest distance to " NE2 GLN A 223 " =    1.730
peak=   -3.157 closest distance to " CD2 PHE A  61 " =    2.409
peak=   -3.157 closest distance to " CB  TRP A  85 " =    2.334
peak=   -3.156 closest distance to " O   HOH Z 171 " =    1.535
peak=   -3.152 closest distance to " O   ILE A 106 " =    2.031
peak=   -3.151 closest distance to " O   ALA A 161 " =    1.609
peak=   -3.148 closest distance to " O   HOH Z  60 " =    2.381
peak=   -3.146 closest distance to " O   HOH Z  60 " =    1.495
peak=   -3.145 closest distance to " CA  ILE A 263 " =    0.923
peak=   -3.144 closest distance to " O   HOH Z 394 " =    1.655
peak=   -3.142 closest distance to " CD  ARG A  79 " =    1.121
peak=   -3.140 closest distance to " O   HOH Z  51 " =    0.754
peak=   -3.138 closest distance to " O   HOH Z 126 " =    1.541
peak=   -3.137 closest distance to " CB  SER A 210 " =    1.075
peak=   -3.136 closest distance to " O   HOH Z 216 " =    1.407
peak=   -3.136 closest distance to " O   HOH Z 428 " =    2.534
peak=   -3.133 closest distance to " CG1 VAL A  78 " =    2.660
peak=   -3.130 closest distance to " CB  PRO A  54 " =    2.416
peak=   -3.130 closest distance to " O   HOH Z 108 " =    1.311
peak=   -3.119 closest distance to " O   HOH Z 128 " =    2.610
peak=   -3.117 closest distance to " O   HOH Z 384 " =    3.085
peak=   -3.112 closest distance to " ND2 ASN A  45 " =    1.196
peak=   -3.108 closest distance to " CZ  TYR A 169 " =    1.831
peak=   -3.099 closest distance to " CZ  PHE A  38 " =    2.536
peak=   -3.097 closest distance to " O   ALA A 180 " =    1.191
peak=   -3.088 closest distance to " O   HOH Z 346 " =    1.714
peak=   -3.083 closest distance to " O   HOH Z 265 " =    2.644
peak=   -3.083 closest distance to " O   HOH Z 383 " =    1.369
peak=   -3.079 closest distance to " OG  SER A 245 " =    1.498
peak=   -3.074 closest distance to " O   HOH Z 390 " =    2.512
peak=   -3.055 closest distance to " CD2 LEU A 237 " =    2.259
peak=   -3.054 closest distance to " N   SER A 212 " =    1.972
peak=   -3.041 closest distance to " CG  GLU A 128 " =    1.541
peak=   -3.023 closest distance to " C   GLN A  58 " =    1.970

================= 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    :  0.4509 0.4557   6.265565e+00   6.250874e+00
   1_bss:  0.4390 0.4456   6.256814e+00   6.239075e+00
   1_xyz:  0.3171 0.3576   6.019764e+00   6.094524e+00
   1_adp:  0.2868 0.3728   5.976884e+00   6.120114e+00
   1_occ:  0.2866 0.3741   5.977421e+00   6.120988e+00
   2_bss:  0.2846 0.3709   5.975212e+00   6.119105e+00
   2_xyz:  0.2352 0.3028   5.801370e+00   5.977708e+00
   2_adp:  0.2231 0.2895   5.764040e+00   5.943398e+00
   2_occ:  0.2229 0.2891   5.762911e+00   5.942074e+00
   3_bss:  0.2230 0.2891   5.762395e+00   5.941939e+00
   3_xyz:  0.1699 0.2241   5.506937e+00   5.713644e+00
   3_adp:  0.1533 0.2069   5.420434e+00   5.640466e+00
   3_occ:  0.1531 0.2067   5.419857e+00   5.639766e+00
   4_bss:  0.1533 0.2063   5.418380e+00   5.637447e+00
   4_xyz:  0.1296 0.1810   5.274615e+00   5.513020e+00
   4_adp:  0.1256 0.1729   5.238476e+00   5.467834e+00
   4_occ:  0.1255 0.1728   5.237814e+00   5.467092e+00
   5_bss:  0.1258 0.1729   5.238009e+00   5.465526e+00
   5_xyz:  0.1209 0.1652   5.202842e+00   5.430223e+00
   5_adp:  0.1191 0.1658   5.196936e+00   5.432061e+00
   5_occ:  0.1191 0.1658   5.196670e+00   5.431810e+00
   5_bss:  0.1190 0.1657   5.196525e+00   5.431654e+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:  0.328  36.036  -3.203   2.091   3.129   0.000   0.000   0.000
   1_xyz:  0.328  36.036  -3.203   2.091   3.129   0.000   0.000   0.000
   1_adp:  0.328  36.036  -3.203   2.091   3.129   0.000   0.000   0.000
   1_occ:  0.328  36.036  -3.203   2.091   3.129   0.000   0.000   0.000
   2_bss:  0.338  61.944  -2.090  -0.168   1.134  -0.000   0.000   0.000
   2_xyz:  0.338  61.944  -2.090  -0.168   1.134  -0.000   0.000   0.000
   2_adp:  0.338  61.944  -2.090  -0.168   1.134  -0.000   0.000   0.000
   2_occ:  0.338  61.944  -2.090  -0.168   1.134  -0.000   0.000   0.000
   3_bss:  0.333  62.770  -1.854  -0.756   0.669  -0.000   0.000   0.000
   3_xyz:  0.333  62.770  -1.854  -0.756   0.669  -0.000   0.000   0.000
   3_adp:  0.333  62.770  -1.854  -0.756   0.669  -0.000   0.000   0.000
   3_occ:  0.333  62.770  -1.854  -0.756   0.669  -0.000   0.000   0.000
   4_bss:  0.325  62.770  -2.139  -1.730   0.089  -0.000   0.000   0.000
   4_xyz:  0.325  62.770  -2.139  -1.730   0.089  -0.000   0.000   0.000
   4_adp:  0.325  62.770  -2.139  -1.730   0.089  -0.000   0.000   0.000
   4_occ:  0.325  62.770  -2.139  -1.730   0.089  -0.000   0.000   0.000
   5_bss:  0.321  57.746  -2.245  -2.045  -0.060  -0.000  -0.000  -0.000
   5_xyz:  0.321  57.746  -2.245  -2.045  -0.060  -0.000  -0.000  -0.000
   5_adp:  0.321  57.746  -2.245  -2.045  -0.060  -0.000  -0.000  -0.000
   5_occ:  0.321  57.746  -2.245  -2.045  -0.060  -0.000  -0.000  -0.000
   5_bss:  0.321  57.740  -2.156  -2.078  -0.012  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.890 0.4721  0.6389    64546.329
   1_bss:  52.716 0.4856  0.6752    61458.585
   1_xyz:  38.274 0.6636  0.8848    35880.442
   1_adp:  40.264 0.6388  0.8584    39175.348
   1_occ:  40.420 0.6369  0.8549    39326.351
   2_bss:  39.988 0.6421  0.8331    38803.766
   2_xyz:  31.224 0.7432  0.9329    24583.486
   2_adp:  29.515 0.7629  0.9395    22643.096
   2_occ:  29.453 0.7636  0.9398    22550.714
   3_bss:  29.400 0.7641  0.9311    22486.668
   3_xyz:  22.126 0.8398  0.9894    12998.186
   3_adp:  20.023 0.8610  0.9893    11106.757
   3_occ:  20.003 0.8612  0.9892    11084.852
   4_bss:  19.920 0.8619  0.9686    11008.840
   4_xyz:  16.885 0.8899  0.9835     8290.628
   4_adp:  15.757 0.9004  0.9819     7665.409
   4_occ:  15.742 0.9005  0.9819     7648.256
   5_bss:  15.718 0.9007  0.9753     7626.672
   5_xyz:  14.841 0.9082  0.9795     6999.466
   5_adp:  14.812 0.9087  0.9749     7010.557
   5_occ:  14.808 0.9088  0.9749     7002.993
   5_bss:  14.804 0.9088  0.9759     7002.462
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8138e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8138e-01
   1_xyz:   1.553  0.012  0.105 16.243  0.007  4.103   1.3475e-01
   1_adp:   1.553  0.012  0.105 16.243  0.007  4.103   1.3475e-01
   1_occ:   1.553  0.012  0.105 16.243  0.007  4.103   1.3475e-01
   2_bss:   1.553  0.012  0.105 16.243  0.007  4.103   1.3475e-01
   2_xyz:   1.057  0.006  0.080 14.867  0.004  4.118   6.2070e-02
   2_adp:   1.057  0.006  0.080 14.867  0.004  4.118   6.2070e-02
   2_occ:   1.057  0.006  0.080 14.867  0.004  4.118   6.2070e-02
   3_bss:   1.057  0.006  0.080 14.867  0.004  4.118   6.2070e-02
   3_xyz:   1.040  0.007  0.074 14.815  0.004  4.128   6.3568e-02
   3_adp:   1.040  0.007  0.074 14.815  0.004  4.128   6.3568e-02
   3_occ:   1.040  0.007  0.074 14.815  0.004  4.128   6.3568e-02
   4_bss:   1.040  0.007  0.074 14.815  0.004  4.128   6.3568e-02
   4_xyz:   1.047  0.008  0.076 14.871  0.004  4.112   6.5128e-02
   4_adp:   1.047  0.008  0.076 14.871  0.004  4.112   6.5128e-02
   4_occ:   1.047  0.008  0.076 14.871  0.004  4.112   6.5128e-02
   5_bss:   1.047  0.008  0.076 14.871  0.004  4.112   6.5128e-02
   5_xyz:   0.918  0.006  0.070 14.484  0.004  4.115   5.2154e-02
   5_adp:   0.918  0.006  0.070 14.484  0.004  4.115   5.2154e-02
   5_occ:   0.918  0.006  0.070 14.484  0.004  4.115   5.2154e-02
   5_bss:   0.918  0.006  0.070 14.484  0.004  4.115   5.2154e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.407   2.4102e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.407   2.4102e-01
   1_xyz:   8.447  0.076  0.345 83.773  0.051  2.035   1.0145e-01
   1_adp:   8.447  0.076  0.345 83.773  0.051  2.035   1.0145e-01
   1_occ:   8.447  0.076  0.345 83.773  0.051  2.035   1.0145e-01
   2_bss:   8.447  0.076  0.345 83.773  0.051  2.035   1.0145e-01
   2_xyz:   8.200  0.039  0.276 83.817  0.034  2.327   6.4077e-02
   2_adp:   8.200  0.039  0.276 83.817  0.034  2.327   6.4077e-02
   2_occ:   8.200  0.039  0.276 83.817  0.034  2.327   6.4077e-02
   3_bss:   8.200  0.039  0.276 83.817  0.034  2.327   6.4077e-02
   3_xyz:   6.427  0.045  0.256 79.729  0.036  2.360   8.6944e-02
   3_adp:   6.427  0.045  0.256 79.729  0.036  2.360   8.6944e-02
   3_occ:   6.427  0.045  0.256 79.729  0.036  2.360   8.6944e-02
   4_bss:   6.427  0.045  0.256 79.729  0.036  2.360   8.6944e-02
   4_xyz:   6.574  0.056  0.245 82.576  0.040  2.341   8.0649e-02
   4_adp:   6.574  0.056  0.245 82.576  0.040  2.341   8.0649e-02
   4_occ:   6.574  0.056  0.245 82.576  0.040  2.341   8.0649e-02
   5_bss:   6.574  0.056  0.245 82.576  0.040  2.341   8.0649e-02
   5_xyz:   6.378  0.043  0.224 82.751  0.035  2.364   3.9945e-02
   5_adp:   6.378  0.043  0.224 82.751  0.035  2.364   3.9945e-02
   5_occ:   6.378  0.043  0.224 82.751  0.035  2.364   3.9945e-02
   5_bss:   6.378  0.043  0.224 82.751  0.035  2.364   3.9945e-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: 106.16   0.00  18.47  78.15   0.00  14.46 106.16   0.81  40.33
   1_occ: 106.16   0.00  18.47  78.15   0.00  14.46 106.16   0.81  40.33
   2_bss: 106.16   0.00  18.47  78.15   0.00  14.46 106.16   0.81  40.33
   2_xyz: 106.16   0.00  18.47  78.15   0.00  14.46 106.16   0.81  40.33
   2_adp: 105.86   0.00  18.42  81.34   0.00  14.10 105.86   1.75  41.94
   2_occ: 105.86   0.00  18.42  81.34   0.00  14.10 105.86   1.75  41.94
   3_bss: 105.86   0.00  18.42  81.34   0.00  14.10 105.86   1.75  41.94
   3_xyz: 105.86   0.00  18.42  81.34   0.00  14.10 105.86   1.75  41.94
   3_adp: 104.79   0.00  18.07  85.48   0.00  13.03 104.79   5.66  45.49
   3_occ: 104.79   0.00  18.07  85.48   0.00  13.03 104.79   5.66  45.49
   4_bss: 104.79   0.00  18.07  85.48   0.00  13.03 104.79   5.66  45.49
   4_xyz: 104.79   0.00  18.07  85.48   0.00  13.03 104.79   5.66  45.49
   4_adp:  97.44   0.71  17.07  87.57   0.71  12.50  97.44   4.74  41.94
   4_occ:  97.44   0.71  17.07  87.57   0.71  12.50  97.44   4.74  41.94
   5_bss:  97.44   0.71  17.07  87.57   0.71  12.50  97.44   4.74  41.94
   5_xyz:  97.44   0.71  17.07  87.57   0.71  12.50  97.44   4.74  41.94
   5_adp:  96.41   0.23  16.98  90.13   0.23  12.40  96.41   4.62  41.93
   5_occ:  96.41   0.23  16.98  90.13   0.23  12.40  96.41   4.62  41.93
   5_bss:  96.40   0.23  16.97  90.12   0.23  12.39  96.40   4.61  41.92
------------------------------------------------------------------------
 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:    2.373    0.008    0.447
   1_adp:    2.373    0.008    0.447
   1_occ:    2.373    0.008    0.447
   2_bss:    2.373    0.008    0.447
   2_xyz:    2.227    0.023    0.519
   2_adp:    2.227    0.023    0.519
   2_occ:    2.227    0.023    0.519
   3_bss:    2.227    0.023    0.519
   3_xyz:    1.902    0.073    0.674
   3_adp:    1.902    0.073    0.674
   3_occ:    1.902    0.073    0.674
   4_bss:    1.902    0.073    0.674
   4_xyz:    1.593    0.064    0.723
   4_adp:    1.593    0.064    0.723
   4_occ:    1.593    0.064    0.723
   5_bss:    1.593    0.064    0.723
   5_xyz:    1.602    0.033    0.740
   5_adp:    1.602    0.033    0.740
   5_occ:    1.602    0.033    0.740
   5_bss:    1.602    0.033    0.740
------------------------------------------------------------------------

CPU time actual refinement: 329.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/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_504/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_504/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.22 
  Macro-tasks:
    bulk solvent and scale       = 42.09  
    individual site refinement   = 130.91 
    weights calculation          = 29.98  
    collect and process          = 6.66   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 209.74 
  Micro-tasks:
    mask                            = 2.20   
    f_calc                          = 105.32 
    alpha_beta                      = 8.48   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 108.11 
    fmodel                         = 6.54   
    r_factors                      = 0.20   
    phase_errors                   = 11.52  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 243.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.747 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    624 calls, 104.79 s
gradients_fft:          569 calls,  97.30 s

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

# Date 2008-01-16 Time 04:59:26 PST -0800 (1200488366.64 s)
Start R-work = 0.4509, R-free = 0.4557 (no bulk solvent and anisotropic scale)
Final R-work = 0.1404, R-free = 0.1836 (no bulk solvent and anisotropic scale)

Start R-work = 0.4390, R-free = 0.4456
Final R-work = 0.1190, R-free = 0.1657