# Date 2008-01-16 Time 05:38:24 PST -0800 (1200490704.32 s)
#phil __OFF__

Command line arguments: "../820.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10718
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 820

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01046
Completeness in resolution range: 0.97691
Completeness with d_max=infinity: 0.973802

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0105

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01046
Completeness in resolution range: 0.97691
Completeness with d_max=infinity: 0.973802

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.3010 [2103/2130]  1893   210  10.0%
  bin  2:  4.3010 -  3.4270 [2027/2043]  1824   203  10.0%
  bin  3:  3.4270 -  2.9977 [1993/2012]  1792   201  10.1%
  bin  4:  2.9977 -  2.7254 [1975/2005]  1782   193   9.8%
  bin  5:  2.7254 -  2.5310 [1963/1982]  1764   199  10.1%
  bin  6:  2.5310 -  2.3824 [1954/1979]  1756   198  10.1%
  bin  7:  2.3824 -  2.2635 [1953/1987]  1765   188   9.6%
  bin  8:  2.2635 -  2.1653 [1938/1968]  1741   197  10.2%
  bin  9:  2.1653 -  2.0821 [1923/1965]  1728   195  10.1%
  bin 10:  2.0821 -  2.0105 [1760/1981]  1585   175   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2160
        3.04 -     3.66: 4627
        3.66 -     4.28: 8872
        4.28 -     4.90: 12275
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.842 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.195 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.234 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27941 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_820/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 86.82195 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: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3430   r_free= 0.3324   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.101985                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1373  153 0.2917 0.3002      6.3633      6.3251|
|  2:  4.7966 -  3.8278 0.99   1308  146 0.2703 0.2727      6.5116      6.5274|
|  3:  3.8278 -  3.3500 0.99   1294  143 0.2938 0.2856      6.4114       6.396|
|  4:  3.3500 -  3.0465 0.99   1286  139 0.3307 0.2938      6.3353      6.2088|
|  5:  3.0465 -  2.8296 0.99   1262  142 0.3481 0.3069       6.176      6.0914|
|  6:  2.8296 -  2.6638 0.99   1273  144 0.3621 0.3630      6.1118      6.0812|
|  7:  2.6638 -  2.5310 0.99   1259  139 0.3637 0.3385      6.0557      5.9561|
|  8:  2.5310 -  2.4213 0.98   1258  142 0.3743 0.3555       6.036      6.0225|
|  9:  2.4213 -  2.3284 0.98   1252  136 0.3790 0.3763      5.9817      5.9975|
| 10:  2.3284 -  2.2484 0.99   1246  138 0.4035 0.3868      6.0156      5.9378|
| 11:  2.2484 -  2.1783 0.99   1262  144 0.3825 0.3604      5.9015       5.917|
| 12:  2.1783 -  2.1162 0.97   1242  131 0.3988 0.3659      5.8779       5.904|
| 13:  2.1162 -  2.0606 0.99   1234  137 0.4083 0.4172      5.8083      5.8007|
| 14:  2.0606 -  2.0105 0.85   1081  125 0.3894 0.4348      5.7251      5.7183|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1373   153  0.78  27.32   0.86     0.80      46293.32|
|  2:  4.7966 -  3.8278  1308   146  0.83  23.50   0.96     0.89      51007.49|
|  3:  3.8278 -  3.3500  1294   143  0.80  26.46   0.97     0.92      48881.27|
|  4:  3.3500 -  3.0465  1286   139  0.77  29.18   0.96     0.90      41587.46|
|  5:  3.0465 -  2.8296  1262   142  0.71  34.44   0.97     0.86      35472.68|
|  6:  2.8296 -  2.6638  1273   144  0.69  36.54   0.96     0.85      32589.55|
|  7:  2.6638 -  2.5310  1259   139  0.67  38.18   0.99     0.83      30798.28|
|  8:  2.5310 -  2.4213  1258   142  0.67  38.50   0.98     0.85      29591.93|
|  9:  2.4213 -  2.3284  1252   136  0.66  39.41   0.99     0.85      27267.35|
| 10:  2.3284 -  2.2484  1246   138  0.66  39.09   0.99     0.87      25130.36|
| 11:  2.2484 -  2.1783  1262   144  0.65  40.37   1.02     0.88      24168.97|
| 12:  2.1783 -  2.1162  1242   131  0.63  41.67   1.00     0.87      23692.00|
| 13:  2.1162 -  2.0606  1234   137  0.59  44.82   0.98     0.81      22904.89|
| 14:  2.0606 -  2.0105  1081   125  0.55  48.38   1.00     0.73      21029.62|
|alpha:            min =        0.73 max =            0.92 mean =         0.85|
|beta:             min =    21029.62 max =        51007.49 mean =     33218.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           90.00 mean =        36.01|
|phase err.(test): min =        0.00 max =           89.96 mean =        36.21|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.350731              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.085   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.767234              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.006   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      177 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1983 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1824 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2803 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4552 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4320 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5594 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6681 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.149 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    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: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3430   r_free= 0.3324   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.101985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3293   r_free= 0.3190   ksol= 0.31   Bsol= 53.16   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,3.49,-1.07,0.00,-0.00,-0.00); trace/3= -0.17                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.078465                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.845274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.071   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426310              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.879   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3293      final r-factor (work) = 0.1873          |
| start r-factor (free) = 0.3190      final r-factor (free) = 0.2070          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.9860 = 6.85 * 0.50 * 6.0842 + 1.00 * 0.1621                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9244 = 6.85 * 0.50 * 5.7871 + 1.00 * 0.1172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1873      final r-factor (work) = 0.1694          |
| start r-factor (free) = 0.2070      final r-factor (free) = 0.2092          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4736 = 0.43 * 1.00 * 5.7871 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3510 = 0.43 * 1.00 * 5.4827 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.87   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    75.87   17.18    None  None   None       |
|    Sol.    : 438    0      6.03    75.87   39.94    None  None   None       |
|    Mac.    : 2385   0      0.00    71.50   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.587:  520   |   5:    37.933 -  45.520:  106        |
|      1:     7.587 -  15.173: 1294   |   6:    45.520 -  53.106:   85        |
|      2:    15.173 -  22.760:  439   |   7:    53.106 -  60.693:   67        |
|      3:    22.760 -  30.346:  152   |   8:    60.693 -  68.279:   36        |
|      4:    30.346 -  37.933:  112   |   9:    68.279 -  75.866:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1694 r_free = 0.2092             target_work(ml) = 5.488         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1691 r_free = 0.2089             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1691   r_free= 0.2089   ksol= 0.31   Bsol= 53.16   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,3.49,-1.07,0.00,-0.00,-0.00); trace/3= -0.17                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.486761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1658   r_free= 0.2048   ksol= 0.33   Bsol= 66.17   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-0.32,-1.24,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.472325                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.295577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.216   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.354   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1658      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4138 = 2.30 * 0.50 * 5.4858 + 1.00 * 0.1172                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2282 = 2.30 * 0.50 * 5.3756 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3400 = 0.25 * 1.00 * 5.3756 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3011 = 0.25 * 1.00 * 5.2511 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.64    78.32   16.89    None  None   None       |
|    all(noH): 2823   0      1.64    78.32   16.89    None  None   None       |
|    Sol.    : 438    0      5.65    77.86   39.51    None  None   None       |
|    Mac.    : 2385   0      1.64    78.32   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.641 -   9.309:  895   |   5:    39.981 -  47.649:  106        |
|      1:     9.309 -  16.977: 1136   |   6:    47.649 -  55.317:   79        |
|      2:    16.977 -  24.645:  287   |   7:    55.317 -  62.985:   56        |
|      3:    24.645 -  32.313:  125   |   8:    62.985 -  70.653:   27        |
|      4:    32.313 -  39.981:  105   |   9:    70.653 -  78.321:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1648             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1649             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1649   ksol= 0.33   Bsol= 66.17   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-0.32,-1.24,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.238064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1645   ksol= 0.33   Bsol= 66.17   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.18,-1.02,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.236146                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.189137              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.080  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.291922              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8047 = 2.19 * 0.50 * 5.2500 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7473 = 2.19 * 0.50 * 5.1918 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5243 = 0.29 * 1.00 * 5.1918 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5159 = 0.29 * 1.00 * 5.1629 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    81.22   16.63    None  None   None       |
|    all(noH): 2823   0      0.73    81.22   16.63    None  None   None       |
|    Sol.    : 438    0      5.44    77.51   39.09    None  None   None       |
|    Mac.    : 2385   0      0.73    81.22   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:     0.731 -   8.780:  816   |   5:    40.974 -  49.022:  106        |
|      1:     8.780 -  16.828: 1219   |   6:    49.022 -  57.071:   84        |
|      2:    16.828 -  24.877:  295   |   7:    57.071 -  65.119:   50        |
|      3:    24.877 -  32.925:  129   |   8:    65.119 -  73.168:   14        |
|      4:    32.925 -  40.974:  104   |   9:    73.168 -  81.217:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1579             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1578             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1578   ksol= 0.33   Bsol= 66.17   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.18,-1.02,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.160809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1577   ksol= 0.32   Bsol= 60.62   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.35,-0.79,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.160193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.179851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.938  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.986635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.415  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6917 = 2.18 * 0.50 * 5.1629 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6788 = 2.18 * 0.50 * 5.1515 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2428 = 1.99 * 1.00 * 5.1515 + 1.00 * 0.0087                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2287 = 1.99 * 1.00 * 5.1435 + 1.00 * 0.0106                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.94   16.75    None  None   None       |
|    all(noH): 2823   0      0.00    89.94   16.75    None  None   None       |
|    Sol.    : 438    0      5.45    78.80   40.27    None  None   None       |
|    Mac.    : 2385   0      0.00    89.94   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.994:  926   |   5:    44.971 -  53.966:   98        |
|      1:     8.994 -  17.989: 1183   |   6:    53.966 -  62.960:   77        |
|      2:    17.989 -  26.983:  248   |   7:    62.960 -  71.954:   32        |
|      3:    26.983 -  35.977:  134   |   8:    71.954 -  80.948:   12        |
|      4:    35.977 -  44.971:  109   |   9:    80.948 -  89.943:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1591             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1591             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1591   ksol= 0.32   Bsol= 60.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.35,-0.79,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150652                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1589   ksol= 0.32   Bsol= 61.68   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.16,-0.50,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.150606                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.289299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.971  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.554232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.452  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9530 = 2.29 * 0.50 * 5.1447 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9564 = 2.29 * 0.50 * 5.1472 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.4520 = 4.55 * 1.00 * 5.1472 + 1.00 * 0.0105                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.4572 = 4.55 * 1.00 * 5.1482 + 1.00 * 0.0111                              |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   16.53    None  None   None       |
|    Sol.    : 438    0      5.21    78.87   40.24    None  None   None       |
|    Mac.    : 2385   0      0.00    90.51   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.051: 1013   |   5:    45.254 -  54.305:   95        |
|      1:     9.051 -  18.102: 1113   |   6:    54.305 -  63.356:   75        |
|      2:    18.102 -  27.153:  234   |   7:    63.356 -  72.407:   33        |
|      3:    27.153 -  36.204:  132   |   8:    72.407 -  81.458:   11        |
|      4:    36.204 -  45.254:  113   |   9:    81.458 -  90.509:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1609             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1609             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1609   ksol= 0.32   Bsol= 61.68   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.16,-0.50,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.151181                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1373  153 0.0992 0.1333      5.3968      5.5323|
|  2:  4.7966 -  3.8278 0.99   1308  146 0.0828 0.1074      5.4199      5.6173|
|  3:  3.8278 -  3.3500 0.99   1294  143 0.1016 0.1471      5.4575      5.8546|
|  4:  3.3500 -  3.0465 0.99   1286  139 0.1187 0.1548      5.4521      5.6017|
|  5:  3.0465 -  2.8296 0.99   1262  142 0.1327 0.1845      5.3456       5.569|
|  6:  2.8296 -  2.6638 0.99   1273  144 0.1248 0.1789      5.2476      5.4649|
|  7:  2.6638 -  2.5310 0.99   1259  139 0.1247 0.1757      5.1703      5.4127|
|  8:  2.5310 -  2.4213 0.98   1258  142 0.1165 0.1768      5.0995      5.3695|
|  9:  2.4213 -  2.3284 0.98   1252  136 0.1154 0.1754      5.0344      5.2963|
| 10:  2.3284 -  2.2484 0.99   1246  138 0.1116 0.1929      4.9978       5.285|
| 11:  2.2484 -  2.1783 0.99   1262  144 0.1161 0.1811       4.958      5.2779|
| 12:  2.1783 -  2.1162 0.97   1242  131 0.1128 0.1706      4.9189      5.2345|
| 13:  2.1162 -  2.0606 0.99   1234  137 0.1115 0.1786      4.8151      5.0966|
| 14:  2.0606 -  2.0105 0.85   1081  125 0.1034 0.1815      4.6748      4.9889|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1373   153  0.94   9.55   0.96     0.94       7692.20|
|  2:  4.7966 -  3.8278  1308   146  0.95   7.94   1.00     0.98       8939.11|
|  3:  3.8278 -  3.3500  1294   143  0.94  10.90   1.02     1.01      10098.45|
|  4:  3.3500 -  3.0465  1286   139  0.92  13.38   1.00     0.98      10337.64|
|  5:  3.0465 -  2.8296  1262   142  0.90  15.94   0.99     0.97       8727.44|
|  6:  2.8296 -  2.6638  1273   144  0.90  16.48   0.98     0.94       7515.57|
|  7:  2.6638 -  2.5310  1259   139  0.90  15.84   0.98     0.96       6406.34|
|  8:  2.5310 -  2.4213  1258   142  0.91  15.35   0.98     0.95       5719.36|
|  9:  2.4213 -  2.3284  1252   136  0.91  15.59   0.98     0.94       5078.04|
| 10:  2.3284 -  2.2484  1246   138  0.90  16.21   0.98     0.93       4825.84|
| 11:  2.2484 -  2.1783  1262   144  0.90  16.55   0.98     0.94       4527.65|
| 12:  2.1783 -  2.1162  1242   131  0.91  15.71   0.98     0.97       4339.47|
| 13:  2.1162 -  2.0606  1234   137  0.90  15.87   0.97     0.95       3555.45|
| 14:  2.0606 -  2.0105  1081   125  0.91  15.01   0.95     0.91       2632.80|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2632.80 max =        10337.64 mean =      6532.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.24|
|phase err.(test): min =        0.00 max =           88.98 mean =        13.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1607   ksol= 0.32   Bsol= 61.51   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-0.90,-0.19,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.151290                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1607   ksol= 0.32   Bsol= 61.51   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-0.90,-0.19,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.151290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1373  153 0.0992 0.1335      5.3978       5.534|
|  2:  4.7966 -  3.8278 0.99   1308  146 0.0828 0.1074      5.4206      5.6171|
|  3:  3.8278 -  3.3500 0.99   1294  143 0.1016 0.1472      5.4577      5.8552|
|  4:  3.3500 -  3.0465 0.99   1286  139 0.1187 0.1548      5.4522       5.602|
|  5:  3.0465 -  2.8296 0.99   1262  142 0.1327 0.1845      5.3454      5.5685|
|  6:  2.8296 -  2.6638 0.99   1273  144 0.1248 0.1788      5.2475      5.4645|
|  7:  2.6638 -  2.5310 0.99   1259  139 0.1247 0.1759      5.1703       5.413|
|  8:  2.5310 -  2.4213 0.98   1258  142 0.1165 0.1767      5.0997      5.3694|
|  9:  2.4213 -  2.3284 0.98   1252  136 0.1153 0.1753      5.0345      5.2964|
| 10:  2.3284 -  2.2484 0.99   1246  138 0.1116 0.1930      4.9979      5.2853|
| 11:  2.2484 -  2.1783 0.99   1262  144 0.1161 0.1811       4.958      5.2779|
| 12:  2.1783 -  2.1162 0.97   1242  131 0.1128 0.1705      4.9188      5.2343|
| 13:  2.1162 -  2.0606 0.99   1234  137 0.1115 0.1786      4.8149      5.0965|
| 14:  2.0606 -  2.0105 0.85   1081  125 0.1033 0.1814      4.6745      4.9886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1373   153  0.94   9.57   0.97     0.94       7716.58|
|  2:  4.7966 -  3.8278  1308   146  0.95   7.94   1.00     0.99       8953.83|
|  3:  3.8278 -  3.3500  1294   143  0.94  10.90   1.02     1.02      10104.33|
|  4:  3.3500 -  3.0465  1286   139  0.92  13.38   1.01     0.99      10338.68|
|  5:  3.0465 -  2.8296  1262   142  0.90  15.94   1.00     0.97       8723.73|
|  6:  2.8296 -  2.6638  1273   144  0.90  16.47   0.99     0.95       7511.44|
|  7:  2.6638 -  2.5310  1259   139  0.90  15.84   0.99     0.97       6404.42|
|  8:  2.5310 -  2.4213  1258   142  0.91  15.35   0.99     0.96       5719.28|
|  9:  2.4213 -  2.3284  1252   136  0.91  15.59   0.99     0.95       5079.68|
| 10:  2.3284 -  2.2484  1246   138  0.90  16.21   0.99     0.94       4825.70|
| 11:  2.2484 -  2.1783  1262   144  0.90  16.55   0.99     0.95       4526.91|
| 12:  2.1783 -  2.1162  1242   131  0.91  15.71   1.00     0.98       4338.42|
| 13:  2.1162 -  2.0606  1234   137  0.90  15.86   0.99     0.97       3553.01|
| 14:  2.0606 -  2.0105  1081   125  0.91  15.01   0.96     0.92       2630.27|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2630.27 max =        10338.68 mean =      6534.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.24|
|phase err.(test): min =        0.00 max =           88.98 mean =        13.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.193)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   16.54    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   16.54    None  None   None       |
|    Sol.    : 438    0      5.21    78.87   40.25    None  None   None       |
|    Mac.    : 2385   0      0.00    90.51   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.054: 1013   |   5:    45.257 -  54.308:   95        |
|      1:     9.054 -  18.105: 1113   |   6:    54.308 -  63.359:   75        |
|      2:    18.105 -  27.156:  234   |   7:    63.359 -  72.410:   33        |
|      3:    27.156 -  36.206:  132   |   8:    72.410 -  81.461:   11        |
|      4:    36.206 -  45.257:  113   |   9:    81.461 -  90.512:    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)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 4.854
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.716 - 4.854

peak=    5.819 closest distance to " NH2 ARG A  56 " =    2.358
peak=    5.525 closest distance to " CB  GLN A 223 " =    1.382
peak=    5.353 closest distance to " CG  PRO A  54 " =    1.315
peak=    4.946 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.878 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.839 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.785 closest distance to " CB  SER A  63 " =    1.215
peak=    4.750 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.620 closest distance to " CB  ARG A 190 " =    1.707
peak=    4.611 closest distance to " O   HOH Z 298 " =    1.912
peak=    4.565 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.528 closest distance to " CB  TYR A 169 " =    0.776
peak=    4.510 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.399 closest distance to " CG  PRO A  90 " =    1.180
peak=    4.394 closest distance to " O   HOH Z 369 " =    2.214
peak=    4.389 closest distance to " CB  PRO A  54 " =    0.889
peak=    4.378 closest distance to " C   PRO A 198 " =    1.502
peak=    4.360 closest distance to " O   HOH Z 234 " =    3.843
peak=    4.345 closest distance to " CB  ARG A  79 " =    1.357
peak=    4.325 closest distance to " CB  GLU A 152 " =    1.114
peak=    4.307 closest distance to " O   HOH Z 403 " =    1.684
peak=    4.269 closest distance to " O   HOH Z 126 " =    1.850
peak=    4.242 closest distance to " O   HOH Z  15 " =    2.194
peak=    4.241 closest distance to " CB  GLU A 128 " =    1.108
peak=    4.219 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.216 closest distance to " CD  ARG A 269 " =    0.946
peak=    4.187 closest distance to " O   HOH Z 158 " =    3.087
peak=    4.151 closest distance to " CB  GLU A 277 " =    3.717
peak=    4.119 closest distance to " CB  ASN A 148 " =    1.415
peak=    4.114 closest distance to " CB  ASP A 140 " =    1.000
peak=    4.077 closest distance to " OD1 ASN A  69 " =    2.532
peak=    4.049 closest distance to " CB  LEU A 228 " =    1.099
peak=    4.048 closest distance to " CD2 LEU A 297 " =    0.891
peak=    4.046 closest distance to " CA  ALA A  51 " =    0.941
peak=    4.046 closest distance to " NZ  LYS A 117 " =    3.241
peak=    4.030 closest distance to " C   ILE A 106 " =    1.878
peak=    4.029 closest distance to " O   HOH Z 236 " =    2.074
peak=    4.028 closest distance to " CD1 LEU A 300 " =    1.175
peak=    4.010 closest distance to " O   HOH Z 203 " =    1.826
peak=    3.997 closest distance to " O   HOH Z 303 " =    2.217
peak=    3.994 closest distance to " NE2 GLN A  11 " =    0.986
peak=    3.992 closest distance to " O   HOH Z  40 " =    1.837
peak=    3.983 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.982 closest distance to " O   HOH Z 142 " =    1.518
peak=    3.969 closest distance to " O   HOH Z 189 " =    2.484
peak=    3.969 closest distance to " O   HOH Z  78 " =    1.676
peak=    3.960 closest distance to " O   HOH Z  43 " =    1.964
peak=    3.955 closest distance to " O   HOH Z 427 " =    3.074
peak=    3.955 closest distance to " O   HOH Z 402 " =    1.443
peak=    3.946 closest distance to " CA  ARG A  36 " =    1.142
peak=    3.939 closest distance to " CB  TRP A 266 " =    1.009
peak=    3.932 closest distance to " O   HOH Z 423 " =    1.979
peak=    3.913 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.912 closest distance to " CG  ARG A  66 " =    2.505
peak=    3.907 closest distance to " CG  PRO A 243 " =    1.076
peak=    3.900 closest distance to " O   HOH Z 280 " =    2.999
peak=    3.895 closest distance to " O   HOH Z 272 " =    1.892
peak=    3.881 closest distance to " O   HOH Z 209 " =    2.273
peak=    3.876 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.873 closest distance to " O   HOH Z  19 " =    1.924
peak=    3.871 closest distance to " O   HOH Z 271 " =    2.800
peak=    3.858 closest distance to " ND2 ASN A 187 " =    1.471
peak=    3.857 closest distance to " CA  ALA A  21 " =    1.276
peak=    3.856 closest distance to " CG2 ILE A 120 " =    1.052
peak=    3.849 closest distance to " NH2 ARG A 156 " =    1.194
peak=    3.844 closest distance to " O   HOH Z 346 " =    1.590
peak=    3.842 closest distance to " O   HOH Z 193 " =    1.904
peak=    3.840 closest distance to " O   HOH Z 371 " =    3.159
peak=    3.837 closest distance to " CA  THR A 221 " =    0.938
peak=    3.823 closest distance to " CB  VAL A 202 " =    1.568
peak=    3.805 closest distance to " O   HOH Z 214 " =    2.204
peak=    3.802 closest distance to " CB  VAL A 265 " =    1.216
peak=    3.785 closest distance to " CB  ASN A  39 " =    0.833
peak=    3.784 closest distance to " O   HOH Z 316 " =    3.122
peak=    3.779 closest distance to " O   HOH Z 128 " =    2.060
peak=    3.779 closest distance to " O   HOH Z 361 " =    3.513
peak=    3.778 closest distance to " O   HOH Z 147 " =    1.826
peak=    3.773 closest distance to " O   HOH Z  63 " =    2.012
peak=    3.767 closest distance to " O   HOH Z  97 " =    1.949
peak=    3.756 closest distance to " CA  ASN A 176 " =    1.807
peak=    3.750 closest distance to " O   HOH Z 250 " =    1.477
peak=    3.742 closest distance to " CG1 ILE A  33 " =    1.197
peak=    3.738 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.737 closest distance to " O   HOH Z 412 " =    3.744
peak=    3.737 closest distance to " O   HOH Z  68 " =    1.821
peak=    3.733 closest distance to " O   HOH Z 133 " =    2.511
peak=    3.708 closest distance to " NH1AARG A 145 " =    1.261
peak=    3.707 closest distance to " O   SER A  87 " =    2.236
peak=    3.700 closest distance to " CD  LYS A 166 " =    1.326
peak=    3.700 closest distance to " CA  PRO A  54 " =    1.358
peak=    3.697 closest distance to " O   HOH Z 265 " =    2.173
peak=    3.697 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.696 closest distance to " O   HOH Z  80 " =    1.693
peak=    3.691 closest distance to " O   HOH Z  21 " =    1.805
peak=    3.691 closest distance to " CG2 VAL A 257 " =    0.873
peak=    3.688 closest distance to " CA  ASN A 215 " =    1.129
peak=    3.671 closest distance to " O   HOH Z 285 " =    2.879
peak=    3.665 closest distance to " O   HOH Z 368 " =    2.142
peak=    3.660 closest distance to " CD2 TRP A 179 " =    1.355
peak=    3.656 closest distance to " O   HOH Z 426 " =    1.585
peak=    3.653 closest distance to " CB  SER A   3 " =    1.300
peak=    3.647 closest distance to " O   HOH Z 279 " =    2.233
peak=    3.642 closest distance to " OG BSER A 164 " =    2.410
peak=    3.641 closest distance to " O   HOH Z 261 " =    1.845
peak=    3.631 closest distance to " O   HOH Z 383 " =    2.190
peak=    3.629 closest distance to " O   HOH Z 389 " =    1.970
peak=    3.628 closest distance to " CA  ALA A 160 " =    0.921
peak=    3.626 closest distance to " NH2BARG A 145 " =    2.196
peak=    3.620 closest distance to " CD BLYS A 290 " =    0.972
peak=    3.614 closest distance to " O   HOH Z 245 " =    1.281
peak=    3.610 closest distance to " O   HOH Z 391 " =    2.948
peak=    3.599 closest distance to " CG1BVAL A  72 " =    1.846
peak=    3.592 closest distance to " CD  ARG A 159 " =    0.820
peak=    3.589 closest distance to " N   ASN A  39 " =    1.291
peak=    3.583 closest distance to " OD2 ASP A 298 " =    3.913
peak=    3.569 closest distance to " CB  TRP A 179 " =    1.367
peak=    3.569 closest distance to " O   HOH Z  20 " =    1.523
peak=    3.562 closest distance to " CD1 ILE A 106 " =    0.837
peak=    3.560 closest distance to " O   HOH Z 134 " =    1.344
peak=    3.559 closest distance to " CG1 VAL A 153 " =    1.004
peak=    3.555 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.543 closest distance to " O   HOH Z 359 " =    1.477
peak=    3.541 closest distance to " O   HOH Z 291 " =    1.510
peak=    3.538 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.538 closest distance to " O   THR A 251 " =    1.137
peak=    3.538 closest distance to " ND1 HIS A  81 " =    1.659
peak=    3.536 closest distance to " O   HOH Z 406 " =    1.584
peak=    3.532 closest distance to " O   THR A 220 " =    1.190
peak=    3.530 closest distance to " CG2 ILE A  20 " =    1.328
peak=    3.527 closest distance to " O   HOH Z 163 " =    1.559
peak=    3.514 closest distance to " CB  TYR A 169 " =    0.723
peak=    3.512 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.503 closest distance to " O   ALA A 165 " =    1.449
peak=    3.503 closest distance to " O   HOH Z   1 " =    2.289
peak=    3.500 closest distance to " O   HOH Z 258 " =    2.024
peak=    3.492 closest distance to " O   HOH Z 421 " =    1.666
peak=    3.487 closest distance to " O   HOH Z 357 " =    2.088
peak=    3.486 closest distance to " CA  ASP A 124 " =    0.716
peak=    3.478 closest distance to " OD2 ASP A 286 " =    2.893
peak=    3.474 closest distance to " CA  MET A 105 " =    1.077
peak=    3.473 closest distance to " O   HOH Z 305 " =    3.747
peak=    3.473 closest distance to " CB  GLN A  89 " =    1.313
peak=    3.468 closest distance to " CB  ILE A 120 " =    1.258
peak=    3.465 closest distance to " CB  ASN A 142 " =    1.165
peak=    3.464 closest distance to " O   HOH Z 197 " =    2.823
peak=    3.457 closest distance to " NE2 GLN A  77 " =    3.355
peak=    3.455 closest distance to " CA  SER A  87 " =    1.111
peak=    3.443 closest distance to " CG  GLN A  58 " =    2.706
peak=    3.440 closest distance to " CB  TYR A 116 " =    0.806
peak=    3.439 closest distance to " N   CYS A 260 " =    0.811
peak=    3.438 closest distance to " O   HOH Z 294 " =    1.533
peak=    3.437 closest distance to " O   ASN A  74 " =    1.514
peak=    3.437 closest distance to " OG1 THR A 294 " =    2.407
peak=    3.435 closest distance to " CB  ARG A 139 " =    0.914
peak=    3.434 closest distance to " O   HOH Z 132 " =    2.626
peak=    3.429 closest distance to " O   HOH Z  59 " =    2.320
peak=    3.428 closest distance to " CG2 THR A 221 " =    1.156
peak=    3.427 closest distance to " O   HOH Z  62 " =    2.260
peak=    3.427 closest distance to " CZ3 TRP A 266 " =    1.094
peak=    3.427 closest distance to " CA  ASP A 191 " =    0.863
peak=    3.427 closest distance to " CG2BVAL A  41 " =    0.826
peak=    3.420 closest distance to " CB  ASN A 215 " =    1.189
peak=    3.412 closest distance to " CB  MET A  47 " =    0.964
peak=    3.406 closest distance to " O   HOH Z 403 " =    1.375
peak=    3.406 closest distance to " CB  SER A  62 " =    0.797
peak=    3.405 closest distance to " OG BSER A 134 " =    2.902
peak=    3.405 closest distance to " CG2 VAL A 197 " =    1.176
peak=    3.404 closest distance to " CB  GLN A 103 " =    0.851
peak=    3.401 closest distance to " O   HOH Z 365 " =    2.858
peak=    3.397 closest distance to " CA  ALA A 295 " =    1.109
peak=    3.395 closest distance to " N   ASN A 127 " =    1.289
peak=    3.395 closest distance to " O   HOH Z 325 " =    2.300
peak=    3.394 closest distance to " CB  SER A 212 " =    1.041
peak=    3.392 closest distance to " O   HOH Z 345 " =    1.641
peak=    3.391 closest distance to " NH2AARG A 275 " =    3.590
peak=    3.390 closest distance to " CB  ALA A 248 " =    1.280
peak=    3.382 closest distance to " OG  SER A  22 " =    2.710
peak=    3.381 closest distance to " O   HOH Z 353 " =    2.782
peak=    3.380 closest distance to " CA  GLU A 152 " =    0.856
peak=    3.380 closest distance to " NZ  LYS A  48 " =    1.317
peak=    3.378 closest distance to " O   HOH Z 327 " =    1.664
peak=    3.372 closest distance to " O   HOH Z 193 " =    2.178
peak=    3.371 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.369 closest distance to " O   HOH Z 148 " =    3.292
peak=    3.365 closest distance to " CA  MET A  40 " =    1.153
peak=    3.364 closest distance to " CB  MET A  40 " =    0.840
peak=    3.361 closest distance to " CA  ALA A  84 " =    1.284
peak=    3.361 closest distance to " O   HOH Z  44 " =    1.769
peak=    3.359 closest distance to " O   HOH Z 173 " =    2.146
peak=    3.358 closest distance to " O   TYR A 116 " =    1.358
peak=    3.352 closest distance to " O   HOH Z 102 " =    1.307
peak=    3.349 closest distance to " O   HOH Z 425 " =    1.994
peak=    3.348 closest distance to " O   ASN A  74 " =    2.096
peak=    3.347 closest distance to " CB  SER A 273 " =    0.884
peak=    3.345 closest distance to " CZ  PHE A  38 " =    1.292
peak=    3.343 closest distance to " CG  GLU A  37 " =    0.870
peak=    3.338 closest distance to " O   HOH Z 374 " =    2.752
peak=    3.337 closest distance to " O   HOH Z 422 " =    2.671
peak=    3.334 closest distance to " O   HOH Z  54 " =    1.650
peak=    3.331 closest distance to " O   HOH Z 411 " =    1.763
peak=    3.328 closest distance to " CA  VAL A 125 " =    1.224
peak=    3.325 closest distance to " CG1 ILE A 151 " =    0.988
peak=    3.320 closest distance to " CB  SER A  26 " =    1.745
peak=    3.318 closest distance to " O   HOH Z 163 " =    2.005
peak=    3.316 closest distance to " CE1 TYR A 186 " =    1.281
peak=    3.314 closest distance to " O   HOH Z 299 " =    4.528
peak=    3.309 closest distance to " O   HOH Z 109 " =    2.727
peak=    3.306 closest distance to " CB  SER A 141 " =    0.979
peak=    3.295 closest distance to " CA  ASN A 217 " =    1.206
peak=    3.294 closest distance to " N   GLY A  98 " =    1.135
peak=    3.286 closest distance to " O   HOH Z  66 " =    2.109
peak=    3.281 closest distance to " N   ARG A 156 " =    1.444
peak=    3.281 closest distance to " CA  LYS A 117 " =    1.260
peak=    3.281 closest distance to " O   HOH Z 344 " =    3.252
peak=    3.280 closest distance to " CG  ARG A 219 " =    1.150
peak=    3.278 closest distance to " O   ASP A 124 " =    1.242
peak=    3.278 closest distance to " O   HOH Z 183 " =    1.485
peak=    3.262 closest distance to " CG  MET A 185 " =    1.172
peak=    3.250 closest distance to " CA  THR A 264 " =    0.891
peak=    3.249 closest distance to " O   HOH Z 295 " =    1.469
peak=    3.247 closest distance to " CA  ALA A 233 " =    1.646
peak=    3.243 closest distance to " CZ2 TRP A 179 " =    1.725
peak=    3.242 closest distance to " N   ILE A  33 " =    1.052
peak=    3.239 closest distance to " O   TRP A 274 " =    1.891
peak=    3.239 closest distance to " O   HOH Z 135 " =    1.785
peak=    3.237 closest distance to " CD2 HIS A  81 " =    1.072
peak=    3.237 closest distance to " CG  LEU A 167 " =    1.191
peak=    3.233 closest distance to " CA  LEU A  83 " =    1.318
peak=    3.233 closest distance to " ND2 ASN A 249 " =    0.891
peak=    3.232 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.231 closest distance to " CA  ASP A 140 " =    1.201
peak=    3.228 closest distance to " CB  ALA A 227 " =    1.093
peak=    3.226 closest distance to " CB  SER A 216 " =    0.833
peak=    3.225 closest distance to " O   HOH Z 285 " =    1.463
peak=    3.222 closest distance to " CB  ALA A   1 " =    4.854
peak=    3.221 closest distance to " CA  ALA A 248 " =    1.176
peak=    3.220 closest distance to " CG2 ILE A 234 " =    0.805
peak=    3.217 closest distance to " O   HOH Z 128 " =    2.284
peak=    3.213 closest distance to " CG  GLN A  11 " =    1.508
peak=    3.209 closest distance to " O   ALA A 158 " =    1.164
peak=    3.209 closest distance to " CB  ASN A 187 " =    1.082
peak=    3.207 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.203 closest distance to " CD1AILE A 234 " =    0.859
peak=    3.199 closest distance to " CA  ALA A 154 " =    0.998
peak=    3.197 closest distance to " O   HOH Z 393 " =    3.266
peak=    3.196 closest distance to " O   HOH Z 313 " =    1.878
peak=    3.193 closest distance to " OG  SER A 245 " =    1.641
peak=    3.192 closest distance to " CB  THR A 157 " =    1.128
peak=    3.192 closest distance to " CB  ALA A  34 " =    0.958
peak=    3.192 closest distance to " O   HOH Z  48 " =    1.796
peak=    3.192 closest distance to " CB  THR A  31 " =    1.830
peak=    3.188 closest distance to " O   HOH Z 407 " =    2.945
peak=    3.188 closest distance to " CB  ASP A 298 " =    1.263
peak=    3.182 closest distance to " CG BARG A 275 " =    1.403
peak=    3.182 closest distance to " CB  GLN A  88 " =    1.213
peak=    3.180 closest distance to " CB  ALA A 114 " =    0.998
peak=    3.180 closest distance to " O   HOH Z 124 " =    2.196
peak=    3.180 closest distance to " CA  MET A 188 " =    0.986
peak=    3.179 closest distance to " C   TYR A 214 " =    1.486
peak=    3.176 closest distance to " O   HOH Z 417 " =    3.066
peak=    3.173 closest distance to " CA  ASN A  74 " =    1.334
peak=    3.170 closest distance to " CB  ALA A 248 " =    0.954
peak=    3.169 closest distance to " ND2 ASN A 301 " =    1.685
peak=    3.168 closest distance to " CA  ALA A 158 " =    1.209
peak=    3.167 closest distance to " CD  ARG A  66 " =    2.410
peak=    3.166 closest distance to " O   HOH Z 156 " =    2.604
peak=    3.164 closest distance to " CB  HIS A 108 " =    0.791
peak=    3.164 closest distance to " CA  ALA A 291 " =    0.819
peak=    3.160 closest distance to " O   HOH Z 425 " =    1.261
peak=    3.158 closest distance to " O   HOH Z 171 " =    3.948
peak=    3.157 closest distance to " CG  LYS A  76 " =    1.041
peak=    3.157 closest distance to " CB  SER A  28 " =    1.056
peak=    3.154 closest distance to " OE1 GLU A   2 " =    2.108
peak=    3.153 closest distance to " CB  GLN A 205 " =    1.063
peak=    3.153 closest distance to " O   HOH Z 329 " =    3.891
peak=    3.152 closest distance to " CZ  PHE A 192 " =    0.968
peak=    3.151 closest distance to " CZ3 TRP A  85 " =    0.876
peak=    3.146 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.145 closest distance to " ND2 ASN A 110 " =    1.580
peak=    3.145 closest distance to " O   ALA A 100 " =    1.524
peak=    3.142 closest distance to " O   HOH Z 387 " =    2.964
peak=    3.142 closest distance to " O   HOH Z 193 " =    1.658
peak=    3.138 closest distance to " O   HOH Z 130 " =    2.288
peak=    3.136 closest distance to " O   HOH Z 298 " =    2.548
peak=    3.136 closest distance to " CB  TYR A 247 " =    0.949
peak=    3.132 closest distance to " O   HOH Z 250 " =    1.499
peak=    3.129 closest distance to " O   HOH Z  89 " =    2.154
peak=    3.123 closest distance to " O   HOH Z  97 " =    2.449
peak=    3.122 closest distance to " CE  LYS A  48 " =    1.047
peak=    3.121 closest distance to " O   HOH Z  88 " =    3.408
peak=    3.120 closest distance to " C   GLY A  80 " =    1.050
peak=    3.111 closest distance to " CD1 ILE A 199 " =    1.024
peak=    3.106 closest distance to " O   HOH Z 234 " =    1.795
peak=    3.105 closest distance to " CB  MET A 105 " =    0.870
peak=    3.105 closest distance to " CB  PHE A 204 " =    0.915
peak=    3.086 closest distance to " CB  ALA A 100 " =    1.279
peak=    3.082 closest distance to " O   HOH Z 271 " =    2.152
peak=    3.075 closest distance to " O   HOH Z 345 " =    3.108
peak=    3.073 closest distance to " NE2 HIS A 115 " =    0.983
peak=    3.065 closest distance to " O   HOH Z  68 " =    1.885
peak=    3.063 closest distance to " CA  ILE A 106 " =    0.838
peak=    3.056 closest distance to " CB  ARG A 138 " =    0.968
peak=    3.041 closest distance to " O   THR A 251 " =    1.782
peak=    3.027 closest distance to " O   HOH Z  49 " =    2.518
peak=    3.018 closest distance to " O   HOH Z 374 " =    3.053
peak=    3.000 closest distance to " O   ASP A 124 " =    1.776

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.831 - 5.348
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.831 - 5.348

peak=   -4.857 closest distance to " O   HOH Z 266 " =    5.037
peak=   -4.472 closest distance to " O   HOH Z  10 " =    1.578
peak=   -4.387 closest distance to " CD  GLN A  58 " =    0.985
peak=   -4.385 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.320 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.288 closest distance to " CG1 VAL A 112 " =    2.589
peak=   -4.251 closest distance to " CB  PRO A 243 " =    2.678
peak=   -4.164 closest distance to " OXT GLY A 302 " =    2.925
peak=   -4.132 closest distance to " O   VAL A  67 " =    2.692
peak=   -4.121 closest distance to " CD  ARG A  14 " =    3.473
peak=   -4.113 closest distance to " CB  ALA A 161 " =    2.619
peak=   -4.105 closest distance to " O   HOH Z 231 " =    2.329
peak=   -4.103 closest distance to " O   HOH Z 196 " =    1.997
peak=   -4.072 closest distance to " O   HOH Z 283 " =    2.252
peak=   -4.045 closest distance to " O   HOH Z 292 " =    4.654
peak=   -4.044 closest distance to " OG  SER A  97 " =    2.278
peak=   -4.036 closest distance to " CD  GLN A 223 " =    1.344
peak=   -4.034 closest distance to " CA  ASP A 298 " =    1.055
peak=   -4.031 closest distance to " CG  ASP A 132 " =    2.378
peak=   -4.017 closest distance to " CG1 VAL A 250 " =    2.657
peak=   -3.970 closest distance to " O   HOH Z 377 " =    1.976
peak=   -3.954 closest distance to " OE1 GLN A 223 " =    1.887
peak=   -3.941 closest distance to " CD1 LEU A 101 " =    2.435
peak=   -3.915 closest distance to " CZ3 TRP A 179 " =    1.205
peak=   -3.891 closest distance to " CE2 PHE A  61 " =    2.565
peak=   -3.859 closest distance to " O   HOH Z 372 " =    2.407
peak=   -3.847 closest distance to " N   ALA A  43 " =    2.758
peak=   -3.827 closest distance to " OG BSER A 134 " =    1.355
peak=   -3.825 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.794 closest distance to " CE2 TYR A  30 " =    2.705
peak=   -3.760 closest distance to " CG2 ILE A 263 " =    2.367
peak=   -3.756 closest distance to " CD1 PHE A  59 " =    1.947
peak=   -3.755 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.736 closest distance to " O   HOH Z 166 " =    1.759
peak=   -3.711 closest distance to " NE2 GLN A  88 " =    1.840
peak=   -3.689 closest distance to " O   HOH Z  52 " =    1.495
peak=   -3.686 closest distance to " CB  PHE A 192 " =    1.973
peak=   -3.673 closest distance to " OD1 ASN A 148 " =    1.467
peak=   -3.672 closest distance to " CD1 LEU A  25 " =    2.469
peak=   -3.668 closest distance to " O   HOH Z  13 " =    1.729
peak=   -3.665 closest distance to " CB  PHE A 208 " =    2.262
peak=   -3.647 closest distance to " CD1 ILE A 151 " =    2.400
peak=   -3.642 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.640 closest distance to " ND2 ASN A  45 " =    1.845
peak=   -3.639 closest distance to " CB  ASN A  39 " =    2.378
peak=   -3.630 closest distance to " O   HOH Z 165 " =    1.865
peak=   -3.627 closest distance to " O   HOH Z 353 " =    2.213
peak=   -3.624 closest distance to " O   SER A 210 " =    1.941
peak=   -3.605 closest distance to " CD2 TYR A 293 " =    2.029
peak=   -3.583 closest distance to " O   ALA A  10 " =    1.716
peak=   -3.583 closest distance to " O   HOH Z 290 " =    1.139
peak=   -3.581 closest distance to " O   HOH Z 311 " =    3.789
peak=   -3.578 closest distance to " CB  ALA A 291 " =    2.317
peak=   -3.577 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.564 closest distance to " O   HOH Z 198 " =    2.195
peak=   -3.555 closest distance to " CD  ARG A 139 " =    1.590
peak=   -3.549 closest distance to " O   HOH Z 185 " =    2.427
peak=   -3.542 closest distance to " O   HOH Z 114 " =    3.299
peak=   -3.536 closest distance to " C   ASN A 187 " =    1.934
peak=   -3.535 closest distance to " O   HOH Z  38 " =    1.486
peak=   -3.523 closest distance to " C   SER A 206 " =    1.527
peak=   -3.512 closest distance to " O   HOH Z   6 " =    1.577
peak=   -3.508 closest distance to " CE3 TRP A 150 " =    2.217
peak=   -3.505 closest distance to " NH2AARG A 275 " =    5.348
peak=   -3.505 closest distance to " NH2 ARG A 159 " =    2.367
peak=   -3.503 closest distance to " CA  GLY A 133 " =    2.339
peak=   -3.502 closest distance to " N   ALA A 226 " =    2.088
peak=   -3.501 closest distance to " O   HOH Z 393 " =    1.440
peak=   -3.498 closest distance to " O   HOH Z 128 " =    2.515
peak=   -3.498 closest distance to " O   HOH Z 211 " =    1.611
peak=   -3.492 closest distance to " ND2BASN A 224 " =    1.719
peak=   -3.490 closest distance to " O   HOH Z 166 " =    1.682
peak=   -3.490 closest distance to " O   ALA A  34 " =    2.389
peak=   -3.490 closest distance to " CB  ALA A 291 " =    2.216
peak=   -3.489 closest distance to " O   HOH Z 243 " =    2.044
peak=   -3.487 closest distance to " O   HOH Z 171 " =    2.051
peak=   -3.485 closest distance to " O   HOH Z   6 " =    2.171
peak=   -3.478 closest distance to " OG BSER A 134 " =    1.924
peak=   -3.477 closest distance to " O   HOH Z  37 " =    1.813
peak=   -3.474 closest distance to " CA  GLY A 241 " =    3.181
peak=   -3.471 closest distance to " O   HOH Z 389 " =    1.862
peak=   -3.468 closest distance to " O   PRO A 163 " =    2.100
peak=   -3.467 closest distance to " NH2 ARG A  79 " =    1.555
peak=   -3.456 closest distance to " N   THR A  52 " =    1.663
peak=   -3.451 closest distance to " NE2 GLN A 103 " =    1.785
peak=   -3.448 closest distance to " CA  VAL A  67 " =    3.001
peak=   -3.448 closest distance to " C   LEU A 143 " =    1.117
peak=   -3.446 closest distance to " O   HOH Z 177 " =    1.801
peak=   -3.446 closest distance to " O   HOH Z 377 " =    1.613
peak=   -3.445 closest distance to " OD1 ASP A 171 " =    1.572
peak=   -3.442 closest distance to " CB  ALA A  43 " =    2.633
peak=   -3.437 closest distance to " O   HOH Z  60 " =    2.271
peak=   -3.436 closest distance to " CD  ARG A 195 " =    5.095
peak=   -3.436 closest distance to " CG  GLU A 277 " =    1.100
peak=   -3.435 closest distance to " CD2 LEU A 300 " =    2.958
peak=   -3.426 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.426 closest distance to " CZ  TYR A 169 " =    1.841
peak=   -3.410 closest distance to " CE  MET A 105 " =    2.307
peak=   -3.405 closest distance to " ND2 ASN A 249 " =    2.438
peak=   -3.403 closest distance to " O   HOH Z 252 " =    4.067
peak=   -3.402 closest distance to " NH2 ARG A  79 " =    2.083
peak=   -3.399 closest distance to " O   HOH Z 123 " =    2.388
peak=   -3.389 closest distance to " NE2 GLN A 194 " =    1.861
peak=   -3.388 closest distance to " CD  ARG A  79 " =    1.184
peak=   -3.384 closest distance to " CB  ASP A 286 " =    1.874
peak=   -3.378 closest distance to " CD  PRO A 213 " =    2.221
peak=   -3.376 closest distance to " O   HOH Z 234 " =    4.360
peak=   -3.374 closest distance to " CB  PHE A  16 " =    2.587
peak=   -3.365 closest distance to " CB  TRP A  85 " =    2.403
peak=   -3.365 closest distance to " NH2 ARG A  66 " =    1.998
peak=   -3.364 closest distance to " O   HOH Z 111 " =    1.473
peak=   -3.364 closest distance to " CA  GLY A 241 " =    2.322
peak=   -3.360 closest distance to " O   HOH Z 407 " =    3.331
peak=   -3.352 closest distance to " CZ  PHE A  59 " =    1.811
peak=   -3.351 closest distance to " O   PHE A 218 " =    1.560
peak=   -3.351 closest distance to " CG  PRO A 243 " =    1.860
peak=   -3.349 closest distance to " ND2 ASN A 187 " =    1.581
peak=   -3.342 closest distance to " CD  LYS A 289 " =    2.441
peak=   -3.337 closest distance to " C   ASN A 285 " =    2.378
peak=   -3.337 closest distance to " OG BSER A 210 " =    2.123
peak=   -3.330 closest distance to " CG  ASP A 231 " =    0.831
peak=   -3.329 closest distance to " O   HOH Z 106 " =    1.936
peak=   -3.328 closest distance to " O   HOH Z  43 " =    1.577
peak=   -3.324 closest distance to " CE BMET A  47 " =    1.943
peak=   -3.324 closest distance to " CG  ASN A 148 " =    2.444
peak=   -3.318 closest distance to " OG  SER A  62 " =    1.708
peak=   -3.315 closest distance to " OE1 GLN A  88 " =    1.144
peak=   -3.313 closest distance to " OE2 GLU A   2 " =    1.737
peak=   -3.311 closest distance to " O   HOH Z 193 " =    1.745
peak=   -3.309 closest distance to " CG  GLN A  11 " =    1.731
peak=   -3.305 closest distance to " O   HOH Z  19 " =    2.142
peak=   -3.301 closest distance to " OD2 ASP A 171 " =    1.853
peak=   -3.297 closest distance to " CZ  PHE A 155 " =    1.263
peak=   -3.296 closest distance to " CG2 VAL A 189 " =    2.244
peak=   -3.292 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.291 closest distance to " OD1 ASP A 191 " =    1.565
peak=   -3.291 closest distance to " N   TYR A  68 " =    3.046
peak=   -3.283 closest distance to " C   ALA A 158 " =    1.340
peak=   -3.282 closest distance to " O   HOH Z 264 " =    1.806
peak=   -3.281 closest distance to " CG1 VAL A  78 " =    2.708
peak=   -3.281 closest distance to " O   HOH Z 351 " =    1.482
peak=   -3.274 closest distance to " CB  ALA A 248 " =    2.150
peak=   -3.272 closest distance to " CD1 LEU A 228 " =    2.307
peak=   -3.267 closest distance to " CG2 ILE A  49 " =    2.851
peak=   -3.265 closest distance to " C   GLY A  17 " =    1.206
peak=   -3.264 closest distance to " CG  ARG A 269 " =    2.341
peak=   -3.263 closest distance to " NE  ARG A  66 " =    4.231
peak=   -3.259 closest distance to " O   HOH Z 357 " =    2.063
peak=   -3.256 closest distance to " N   ALA A 248 " =    1.730
peak=   -3.255 closest distance to " CG  GLU A  53 " =    1.491
peak=   -3.254 closest distance to " O   HOH Z  71 " =    1.769
peak=   -3.247 closest distance to " N   SER A 276 " =    1.456
peak=   -3.230 closest distance to " O   HOH Z 414 " =    1.638
peak=   -3.229 closest distance to " CD2 TYR A 247 " =    2.378
peak=   -3.220 closest distance to " O   HOH Z 275 " =    1.522
peak=   -3.219 closest distance to " O   SER A 135 " =    1.491
peak=   -3.215 closest distance to " CG1 VAL A 125 " =    2.019
peak=   -3.211 closest distance to " C   GLY A 262 " =    1.957
peak=   -3.204 closest distance to " OH  TYR A 247 " =    1.838
peak=   -3.204 closest distance to " O   HOH Z 322 " =    1.696
peak=   -3.195 closest distance to " CD2 TYR A 293 " =    2.160
peak=   -3.194 closest distance to " CB  ALA A  10 " =    2.172
peak=   -3.193 closest distance to " SG ACYS A 201 " =    2.027
peak=   -3.189 closest distance to " CD2 PHE A 225 " =    1.207
peak=   -3.189 closest distance to " O   HOH Z 149 " =    2.135
peak=   -3.186 closest distance to " CE3 TRP A 274 " =    2.520
peak=   -3.182 closest distance to " O   PRO A 198 " =    1.877
peak=   -3.181 closest distance to " O   HOH Z 102 " =    1.529
peak=   -3.178 closest distance to " OD2 ASP A 191 " =    1.568
peak=   -3.176 closest distance to " CE  MET A  93 " =    1.303
peak=   -3.172 closest distance to " O   HOH Z 350 " =    1.924
peak=   -3.169 closest distance to " CG  TRP A 266 " =    1.863
peak=   -3.168 closest distance to " N   GLN A  58 " =    1.602
peak=   -3.167 closest distance to " NH1 ARG A 195 " =    2.654
peak=   -3.163 closest distance to " OD1 ASN A 187 " =    1.698
peak=   -3.161 closest distance to " CE3 TRP A  70 " =    1.893
peak=   -3.156 closest distance to " O   TYR A 186 " =    1.807
peak=   -3.151 closest distance to " O   SER A 276 " =    1.729
peak=   -3.150 closest distance to " CG  PRO A 163 " =    2.456
peak=   -3.150 closest distance to " O   VAL A 189 " =    2.576
peak=   -3.146 closest distance to " O   MET A  40 " =    2.773
peak=   -3.143 closest distance to " O   HOH Z 351 " =    1.519
peak=   -3.142 closest distance to " O   GLY A 203 " =    2.393
peak=   -3.135 closest distance to " CB  TYR A  15 " =    2.261
peak=   -3.135 closest distance to " CG1AVAL A  41 " =    2.781
peak=   -3.132 closest distance to " O   HOH Z 189 " =    1.764
peak=   -3.129 closest distance to " O   HOH Z 298 " =    2.629
peak=   -3.125 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.123 closest distance to " O   HOH Z 396 " =    1.810
peak=   -3.122 closest distance to " O   HOH Z  90 " =    1.833
peak=   -3.110 closest distance to " C   ARG A  79 " =    2.626
peak=   -3.101 closest distance to " N   SER A   3 " =    2.137
peak=   -3.097 closest distance to " CG2BVAL A  41 " =    1.765
peak=   -3.093 closest distance to " CD2 LEU A 237 " =    2.843
peak=   -3.089 closest distance to " OG1 THR A 157 " =    2.919
peak=   -3.080 closest distance to " C   MET A 188 " =    1.612
peak=   -3.069 closest distance to " O   HOH Z 322 " =    1.454
peak=   -3.060 closest distance to " O   HOH Z 353 " =    2.195
peak=   -3.035 closest distance to " NH1BARG A 275 " =    2.314
peak=   -3.031 closest distance to " O   GLY A  98 " =    2.153

================= 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    :  0.3430 0.3324   6.101985e+00   6.070540e+00
   1_bss:  0.3293 0.3190   6.078465e+00   6.042836e+00
   1_xyz:  0.1873 0.2070   5.551147e+00   5.650999e+00
   1_adp:  0.1694 0.2092   5.487881e+00   5.663789e+00
   1_occ:  0.1691 0.2089   5.486761e+00   5.662945e+00
   2_bss:  0.1658 0.2048   5.472325e+00   5.649509e+00
   2_xyz:  0.1336 0.1687   5.272174e+00   5.466279e+00
   2_adp:  0.1283 0.1648   5.238491e+00   5.437550e+00
   2_occ:  0.1282 0.1649   5.238064e+00   5.437686e+00
   3_bss:  0.1283 0.1645   5.236146e+00   5.434929e+00
   3_xyz:  0.1167 0.1586   5.170333e+00   5.397406e+00
   3_adp:  0.1151 0.1579   5.160971e+00   5.392559e+00
   3_occ:  0.1150 0.1578   5.160809e+00   5.392730e+00
   4_bss:  0.1149 0.1577   5.160193e+00   5.392383e+00
   4_xyz:  0.1129 0.1578   5.149237e+00   5.389525e+00
   4_adp:  0.1122 0.1591   5.150666e+00   5.398170e+00
   4_occ:  0.1121 0.1591   5.150652e+00   5.398466e+00
   5_bss:  0.1120 0.1589   5.150606e+00   5.398504e+00
   5_xyz:  0.1110 0.1604   5.150203e+00   5.404106e+00
   5_adp:  0.1111 0.1609   5.151199e+00   5.406844e+00
   5_occ:  0.1111 0.1609   5.151181e+00   5.406942e+00
   5_bss:  0.1109 0.1607   5.151290e+00   5.407056e+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:  0.309  53.159  -2.919   3.492  -1.070   0.000  -0.000  -0.000
   1_xyz:  0.309  53.159  -2.919   3.492  -1.070   0.000  -0.000  -0.000
   1_adp:  0.309  53.159  -2.919   3.492  -1.070   0.000  -0.000  -0.000
   1_occ:  0.309  53.159  -2.919   3.492  -1.070   0.000  -0.000  -0.000
   2_bss:  0.326  66.165  -2.873  -0.323  -1.237  -0.000  -0.000  -0.000
   2_xyz:  0.326  66.165  -2.873  -0.323  -1.237  -0.000  -0.000  -0.000
   2_adp:  0.326  66.165  -2.873  -0.323  -1.237  -0.000  -0.000  -0.000
   2_occ:  0.326  66.165  -2.873  -0.323  -1.237  -0.000  -0.000  -0.000
   3_bss:  0.328  66.165  -2.547  -1.183  -1.022  -0.000  -0.000  -0.000
   3_xyz:  0.328  66.165  -2.547  -1.183  -1.022  -0.000  -0.000  -0.000
   3_adp:  0.328  66.165  -2.547  -1.183  -1.022  -0.000  -0.000  -0.000
   3_occ:  0.328  66.165  -2.547  -1.183  -1.022  -0.000  -0.000  -0.000
   4_bss:  0.322  60.615  -2.258  -1.347  -0.792  -0.000  -0.000  -0.000
   4_xyz:  0.322  60.615  -2.258  -1.347  -0.792  -0.000  -0.000  -0.000
   4_adp:  0.322  60.615  -2.258  -1.347  -0.792  -0.000  -0.000  -0.000
   4_occ:  0.322  60.615  -2.258  -1.347  -0.792  -0.000  -0.000  -0.000
   5_bss:  0.320  61.676  -1.915  -1.159  -0.502  -0.000  -0.000  -0.000
   5_xyz:  0.320  61.676  -1.915  -1.159  -0.502  -0.000  -0.000  -0.000
   5_adp:  0.320  61.676  -1.915  -1.159  -0.502  -0.000  -0.000  -0.000
   5_occ:  0.320  61.676  -1.915  -1.159  -0.502  -0.000  -0.000  -0.000
   5_bss:  0.320  61.507  -1.584  -0.896  -0.195  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.030 0.6922  0.8512    33216.767
   1_bss:  35.031 0.7020  0.8563    30131.537
   1_xyz:  20.113 0.8612  0.9975    11090.312
   1_adp:  20.599 0.8555  0.9860    11254.782
   1_occ:  20.595 0.8556  0.9856    11233.796
   2_bss:  20.115 0.8604  0.9492    10877.213
   2_xyz:  15.702 0.9006  0.9706     7283.152
   2_adp:  14.998 0.9069  0.9656     6918.548
   2_occ:  14.996 0.9069  0.9656     6919.752
   3_bss:  14.928 0.9075  0.9631     6894.956
   3_xyz:  14.112 0.9143  0.9674     6415.342
   3_adp:  13.970 0.9156  0.9605     6387.661
   3_occ:  13.971 0.9157  0.9604     6387.954
   4_bss:  13.958 0.9157  0.9649     6383.009
   4_xyz:  13.889 0.9162  0.9651     6342.587
   4_adp:  14.052 0.9151  0.9555     6424.520
   4_occ:  14.053 0.9151  0.9554     6427.330
   5_bss:  14.051 0.9151  0.9650     6429.871
   5_xyz:  14.131 0.9145  0.9647     6508.527
   5_adp:  14.186 0.9140  0.9549     6531.735
   5_occ:  14.187 0.9140  0.9548     6531.490
   5_bss:  14.189 0.9140  0.9653     6533.934
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6206e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6206e-01
   1_xyz:   1.400  0.014  0.083 15.126  0.006  4.115   1.1725e-01
   1_adp:   1.400  0.014  0.083 15.126  0.006  4.115   1.1725e-01
   1_occ:   1.400  0.014  0.083 15.126  0.006  4.115   1.1725e-01
   2_bss:   1.400  0.014  0.083 15.126  0.006  4.115   1.1725e-01
   2_xyz:   0.993  0.007  0.073 14.551  0.004  4.127   5.8128e-02
   2_adp:   0.993  0.007  0.073 14.551  0.004  4.127   5.8128e-02
   2_occ:   0.993  0.007  0.073 14.551  0.004  4.127   5.8128e-02
   3_bss:   0.993  0.007  0.073 14.551  0.004  4.127   5.8128e-02
   3_xyz:   1.032  0.009  0.078 14.651  0.004  4.115   6.4482e-02
   3_adp:   1.032  0.009  0.078 14.651  0.004  4.115   6.4482e-02
   3_occ:   1.032  0.009  0.078 14.651  0.004  4.115   6.4482e-02
   4_bss:   1.032  0.009  0.078 14.651  0.004  4.115   6.4482e-02
   4_xyz:   1.027  0.009  0.078 14.551  0.004  4.117   6.4075e-02
   4_adp:   1.027  0.009  0.078 14.551  0.004  4.117   6.4075e-02
   4_occ:   1.027  0.009  0.078 14.551  0.004  4.117   6.4075e-02
   5_bss:   1.027  0.009  0.078 14.551  0.004  4.117   6.4075e-02
   5_xyz:   1.033  0.009  0.079 14.541  0.004  4.118   6.4661e-02
   5_adp:   1.033  0.009  0.079 14.541  0.004  4.118   6.4661e-02
   5_occ:   1.033  0.009  0.079 14.541  0.004  4.118   6.4661e-02
   5_bss:   1.033  0.009  0.079 14.541  0.004  4.118   6.4661e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4330e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4330e-01
   1_xyz:   9.732  0.110  0.321 84.958  0.028  2.267   2.6400e-01
   1_adp:   9.732  0.110  0.321 84.958  0.028  2.267   2.6400e-01
   1_occ:   9.732  0.110  0.321 84.958  0.028  2.267   2.6400e-01
   2_bss:   9.732  0.110  0.321 84.958  0.028  2.267   2.6400e-01
   2_xyz:   6.937  0.053  0.217 82.249  0.043  2.333   4.5215e-02
   2_adp:   6.937  0.053  0.217 82.249  0.043  2.333   4.5215e-02
   2_occ:   6.937  0.053  0.217 82.249  0.043  2.333   4.5215e-02
   3_bss:   6.937  0.053  0.217 82.249  0.043  2.333   4.5215e-02
   3_xyz:   7.869  0.044  0.251 83.452  0.037  2.354   6.8493e-02
   3_adp:   7.869  0.044  0.251 83.452  0.037  2.354   6.8493e-02
   3_occ:   7.869  0.044  0.251 83.452  0.037  2.354   6.8493e-02
   4_bss:   7.869  0.044  0.251 83.452  0.037  2.354   6.8493e-02
   4_xyz:   7.700  0.046  0.255 81.699  0.035  2.360   5.0945e-02
   4_adp:   7.700  0.046  0.255 81.699  0.035  2.360   5.0945e-02
   4_occ:   7.700  0.046  0.255 81.699  0.035  2.360   5.0945e-02
   5_bss:   7.700  0.046  0.255 81.699  0.035  2.360   5.0945e-02
   5_xyz:   7.619  0.046  0.257 82.164  0.035  2.349   4.4880e-02
   5_adp:   7.619  0.046  0.257 82.164  0.035  2.349   4.4880e-02
   5_occ:   7.619  0.046  0.257 82.164  0.035  2.349   4.4880e-02
   5_bss:   7.619  0.046  0.257 82.164  0.035  2.349   4.4880e-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:  75.87   0.00  17.18  71.50   0.00  13.00  75.87   6.03  39.94
   1_occ:  75.87   0.00  17.18  71.50   0.00  13.00  75.87   6.03  39.94
   2_bss:  75.87   0.00  17.18  71.50   0.00  13.00  75.87   6.03  39.94
   2_xyz:  75.87   0.00  17.18  71.50   0.00  13.00  75.87   6.03  39.94
   2_adp:  78.32   1.64  16.89  78.32   1.64  12.73  77.86   5.65  39.51
   2_occ:  78.32   1.64  16.89  78.32   1.64  12.73  77.86   5.65  39.51
   3_bss:  78.32   1.64  16.89  78.32   1.64  12.73  77.86   5.65  39.51
   3_xyz:  78.32   1.64  16.89  78.32   1.64  12.73  77.86   5.65  39.51
   3_adp:  81.22   0.73  16.63  81.22   0.73  12.50  77.51   5.44  39.09
   3_occ:  81.22   0.73  16.63  81.22   0.73  12.50  77.51   5.44  39.09
   4_bss:  81.22   0.73  16.63  81.22   0.73  12.50  77.51   5.44  39.09
   4_xyz:  81.22   0.73  16.63  81.22   0.73  12.50  77.51   5.44  39.09
   4_adp:  89.94   0.00  16.75  89.94   0.00  12.43  78.80   5.45  40.27
   4_occ:  89.94   0.00  16.75  89.94   0.00  12.43  78.80   5.45  40.27
   5_bss:  89.94   0.00  16.75  89.94   0.00  12.43  78.80   5.45  40.27
   5_xyz:  89.94   0.00  16.75  89.94   0.00  12.43  78.80   5.45  40.27
   5_adp:  90.51   0.00  16.53  90.51   0.00  12.18  78.87   5.21  40.24
   5_occ:  90.51   0.00  16.53  90.51   0.00  12.18  78.87   5.21  40.24
   5_bss:  90.51   0.00  16.54  90.51   0.00  12.18  78.87   5.21  40.25
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.008    0.022    0.397
   1_adp:    1.008    0.022    0.397
   1_occ:    1.008    0.022    0.397
   2_bss:    1.008    0.022    0.397
   2_xyz:    0.931    0.033    0.426
   2_adp:    0.931    0.033    0.426
   2_occ:    0.931    0.033    0.426
   3_bss:    0.931    0.033    0.426
   3_xyz:    0.996    0.049    0.471
   3_adp:    0.996    0.049    0.471
   3_occ:    0.996    0.049    0.471
   4_bss:    0.996    0.049    0.471
   4_xyz:    1.012    0.058    0.480
   4_adp:    1.012    0.058    0.480
   4_occ:    1.012    0.058    0.480
   5_bss:    1.012    0.058    0.480
   5_xyz:    1.051    0.057    0.488
   5_adp:    1.051    0.057    0.488
   5_occ:    1.051    0.057    0.488
   5_bss:    1.051    0.057    0.488
------------------------------------------------------------------------

CPU time actual refinement: 325.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/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_820/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_820/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.70 
  Macro-tasks:
    bulk solvent and scale       = 38.73  
    individual site refinement   = 133.65 
    weights calculation          = 28.68  
    collect and process          = 6.65   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.81 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 103.44 
    alpha_beta                      = 8.20   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 112.46 
    fmodel                         = 6.54   
    r_factors                      = 0.19   
    phase_errors                   = 11.28  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 244.70 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.614 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    652 calls, 103.08 s
gradients_fft:          597 calls,  99.02 s

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

# Date 2008-01-16 Time 05:44:02 PST -0800 (1200491042.72 s)
Start R-work = 0.3430, R-free = 0.3324 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.3293, R-free = 0.3190
Final R-work = 0.1109, R-free = 0.1607