# Date 2008-01-16 Time 06:10:32 PST -0800 (1200492632.05 s)
#phil __OFF__

Command line arguments: "../1033.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8347
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1033

-------------------------------------------------------------------------------
  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: (71.3037, 46.93, 88.5498, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.00276
Completeness in resolution range: 0.951384
Completeness with d_max=infinity: 0.948482

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   2.0028

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: (71.3037, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.00276
Completeness in resolution range: 0.951384
Completeness with d_max=infinity: 0.948482

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.2859 [2164/2188]  1945   219  10.1%
  bin  2:  4.2859 -  3.4144 [2071/2091]  1865   206   9.9%
  bin  3:  3.4144 -  2.9865 [2061/2080]  1857   204   9.9%
  bin  4:  2.9865 -  2.7151 [2025/2055]  1823   202  10.0%
  bin  5:  2.7151 -  2.5214 [2017/2036]  1816   201  10.0%
  bin  6:  2.5214 -  2.3733 [2010/2035]  1805   205  10.2%
  bin  7:  2.3733 -  2.2549 [2003/2031]  1800   203  10.1%
  bin  8:  2.2549 -  2.1570 [1977/2013]  1781   196   9.9%
  bin  9:  2.1570 -  2.0742 [1987/2029]  1793   194   9.8%
  bin 10:  2.0742 -  2.0028 [1274/2032]  1145   129  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/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: 13
        2.42 -     3.04: 2164
        3.04 -     3.66: 4562
        3.66 -     4.28: 8863
        4.28 -     4.90: 12157
  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  42 " - " O   HOH Z 183 "  1.974 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.004 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.004 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.188 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27754 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_1033/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/model_refine_001.geo

CPU time processing inputs: 9.75


============================ 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 = 71.30375 46.93 88.54975 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: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4027   r_free= 0.3926   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.202306                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7806 0.99   1404  155 0.3284 0.3042      6.4816       6.365|
|  2:  4.7806 -  3.8140 0.99   1353  153 0.3269 0.3330      6.6758      6.7118|
|  3:  3.8140 -  3.3376 0.99   1322  141 0.3657 0.3039      6.5695      6.4799|
|  4:  3.3376 -  3.0351 0.99   1319  151 0.3742 0.3836      6.4042       6.385|
|  5:  3.0351 -  2.8190 0.99   1307  147 0.4301 0.4058      6.2905      6.3025|
|  6:  2.8190 -  2.6537 0.99   1308  143 0.4101 0.4418      6.1842      6.1408|
|  7:  2.6537 -  2.5214 0.99   1293  142 0.4362 0.4361      6.1586       6.167|
|  8:  2.5214 -  2.4121 0.98   1281  144 0.4570 0.4238      6.1377      6.1143|
|  9:  2.4121 -  2.3196 0.98   1284  143 0.4459 0.4515      6.0501      6.0941|
| 10:  2.3196 -  2.2398 1.00   1286  144 0.4711 0.4365      6.0601      6.0259|
| 11:  2.2398 -  2.1700 0.98   1295  140 0.4665 0.4572      5.9974      6.0194|
| 12:  2.1700 -  2.1081 0.98   1262  145 0.4675 0.4415      5.9209      5.9719|
| 13:  2.1081 -  2.0527 0.99   1284  141 0.4606 0.5008      5.8188      5.7841|
| 14:  2.0527 -  2.0028 0.48    632   70 0.4454 0.4323      5.8141      5.7514|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.7806  1404   155  0.78  27.07   0.84     0.80      47124.28|
|  2:  4.7806 -  3.8140  1353   153  0.80  26.00   0.93     0.88      65312.30|
|  3:  3.8140 -  3.3376  1322   141  0.73  32.77   0.93     0.86      69118.90|
|  4:  3.3376 -  3.0351  1319   151  0.66  39.10   0.93     0.79      65147.89|
|  5:  3.0351 -  2.8190  1307   147  0.56  46.82   0.92     0.72      55487.84|
|  6:  2.8190 -  2.6537  1308   143  0.53  49.36   0.92     0.67      52154.82|
|  7:  2.6537 -  2.5214  1293   142  0.52  50.42   0.94     0.67      47764.54|
|  8:  2.5214 -  2.4121  1281   144  0.52  50.35   0.92     0.69      43324.79|
|  9:  2.4121 -  2.3196  1284   143  0.53  49.66   0.95     0.71      39309.46|
| 10:  2.3196 -  2.2398  1286   144  0.51  51.69   0.97     0.69      36233.51|
| 11:  2.2398 -  2.1700  1295   140  0.49  52.65   0.95     0.69      35899.99|
| 12:  2.1700 -  2.1081  1262   145  0.48  53.54   0.95     0.69      33397.44|
| 13:  2.1081 -  2.0527  1284   141  0.45  55.91   0.94     0.67      29596.20|
| 14:  2.0527 -  2.0028   632    70  0.48  53.95   0.99     0.63      24782.91|
|alpha:            min =        0.63 max =            0.88 mean =         0.73|
|beta:             min =    24782.91 max =        69118.90 mean =     47033.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.12|
|phase err.(test): min =        0.00 max =           89.79 mean =        44.69|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.487532              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.013   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.321888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.245   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      176 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1988 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1804 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2758 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4580 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4283 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5532 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6625 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    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: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4027   r_free= 0.3926   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.202306                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3883   r_free= 0.3836   ksol= 0.31   Bsol= 69.23   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-3.53,5.57,-0.00,0.00,0.00); trace/3= 0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.184594                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.781997              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.720   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.690863              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.790   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3883      final r-factor (work) = 0.2799          |
| start r-factor (free) = 0.3836      final r-factor (free) = 0.3036          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9462 = 4.78 * 0.50 * 6.1827 + 1.00 * 0.1634                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4602 = 4.78 * 0.50 * 6.0078 + 1.00 * 0.0955                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2799      final r-factor (work) = 0.2590          |
| start r-factor (free) = 0.3036      final r-factor (free) = 0.3055          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1577 = 0.69 * 1.00 * 6.0078 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2341 = 0.69 * 1.00 * 5.8622 + 1.00 * 0.1842                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.31  16.62    None  None   None       |
|    all(noH): 2823   0      0.00    113.31  16.62    None  None   None       |
|    Sol.    : 438    0      0.00    63.63   37.58    None  None   None       |
|    Mac.    : 2385   0      0.00    113.31  12.77    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 -  11.331: 1141   |   5:    56.655 -  67.986:   27        |
|      1:    11.331 -  22.662: 1100   |   6:    67.986 -  79.317:    0        |
|      2:    22.662 -  33.993:  271   |   7:    79.317 -  90.647:    0        |
|      3:    33.993 -  45.324:  170   |   8:    90.647 - 101.978:    0        |
|      4:    45.324 -  56.655:  113   |   9:   101.978 - 113.309:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2590 r_free = 0.3055             target_work(ml) = 5.865         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2587 r_free = 0.3055             target_work(ml) = 5.864         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2587   r_free= 0.3055   ksol= 0.31   Bsol= 69.23   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-3.53,5.57,-0.00,0.00,0.00); trace/3= 0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.864192                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2575   r_free= 0.3047   ksol= 0.33   Bsol= 76.50   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.26,2.58,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.863401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.768497              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.705127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.634   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2575      final r-factor (work) = 0.1890          |
| start r-factor (free) = 0.3047      final r-factor (free) = 0.2339          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2116 = 2.77 * 0.50 * 5.8632 + 1.00 * 0.0955                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9984 = 2.77 * 0.50 * 5.7308 + 1.00 * 0.0656                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1890      final r-factor (work) = 0.1715          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.2256          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8258 = 1.71 * 1.00 * 5.7308 + 1.00 * 0.0540                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4553 = 1.71 * 1.00 * 5.5358 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.40  18.24    None  None   None       |
|    all(noH): 2823   0      0.00    111.40  18.24    None  None   None       |
|    Sol.    : 438    0      2.24    111.40  46.29    None  None   None       |
|    Mac.    : 2385   0      0.00    96.17   13.09    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 -  11.140: 1303   |   5:    55.699 -  66.839:   93        |
|      1:    11.140 -  22.280:  892   |   6:    66.839 -  77.979:   58        |
|      2:    22.280 -  33.420:  224   |   7:    77.979 -  89.119:   33        |
|      3:    33.420 -  44.560:  116   |   8:    89.119 - 100.259:    7        |
|      4:    44.560 -  55.699:   93   |   9:   100.259 - 111.399:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1715 r_free = 0.2256             target_work(ml) = 5.523         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1713 r_free = 0.2255             target_work(ml) = 5.522         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1713   r_free= 0.2255   ksol= 0.33   Bsol= 76.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.26,2.58,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.522334                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1709   r_free= 0.2248   ksol= 0.34   Bsol= 89.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-1.62,1.36,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.520073                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.727538              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.332  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265281              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1709      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2248      final r-factor (free) = 0.1901          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1499 = 4.73 * 0.50 * 5.5354 + 1.00 * 0.0656                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8994 = 4.73 * 0.50 * 5.4243 + 1.00 * 0.0775                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1901      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4551 = 0.27 * 1.00 * 5.4243 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4188 = 0.27 * 1.00 * 5.3076 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.70  17.00    None  None   None       |
|    all(noH): 2823   0      0.00    102.70  17.00    None  None   None       |
|    Sol.    : 438    0      4.71    102.70  42.57    None  None   None       |
|    Mac.    : 2385   0      0.00    86.18   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.270: 1248   |   5:    51.349 -  61.619:   96        |
|      1:    10.270 -  20.540:  975   |   6:    61.619 -  71.888:   45        |
|      2:    20.540 -  30.809:  197   |   7:    71.888 -  82.158:   25        |
|      3:    30.809 -  41.079:  137   |   8:    82.158 -  92.428:    9        |
|      4:    41.079 -  51.349:   87   |   9:    92.428 - 102.698:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1297 r_free = 0.1759             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1757             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1757   ksol= 0.34   Bsol= 89.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-1.62,1.36,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.266254                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1755   ksol= 0.33   Bsol= 80.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-1.60,0.58,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.265569                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.124065              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.598  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.307898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.805  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7146 = 2.12 * 0.50 * 5.3078 + 1.00 * 0.0775                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6362 = 2.12 * 0.50 * 5.2480 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1684      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6265 = 0.31 * 1.00 * 5.2480 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6176 = 0.31 * 1.00 * 5.2200 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.04  16.63    None  None   None       |
|    all(noH): 2823   0      0.00    102.04  16.63    None  None   None       |
|    Sol.    : 438    0      4.54    102.04  41.37    None  None   None       |
|    Mac.    : 2385   0      0.00    83.85   12.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.205: 1279   |   5:    51.023 -  61.227:   92        |
|      1:    10.205 -  20.409:  951   |   6:    61.227 -  71.431:   43        |
|      2:    20.409 -  30.614:  198   |   7:    71.431 -  81.636:   21        |
|      3:    30.614 -  40.818:  140   |   8:    81.636 -  91.840:    8        |
|      4:    40.818 -  51.023:   87   |   9:    91.840 - 102.045:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1222 r_free = 0.1675             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1675             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1675   ksol= 0.33   Bsol= 80.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-1.60,0.58,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.216406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1674   ksol= 0.32   Bsol= 69.71   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-1.40,0.60,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.216362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.631756              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.291  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.626899              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3218 = 1.63 * 0.50 * 5.2202 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3109 = 1.63 * 0.50 * 5.2127 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4909 = 1.63 * 1.00 * 5.2127 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4868 = 1.63 * 1.00 * 5.2091 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.79  16.68    None  None   None       |
|    all(noH): 2823   0      0.00    106.79  16.68    None  None   None       |
|    Sol.    : 438    0      4.21    106.79  41.98    None  None   None       |
|    Mac.    : 2385   0      0.00    87.53   12.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.679: 1396   |   5:    53.394 -  64.073:   89        |
|      1:    10.679 -  21.358:  850   |   6:    64.073 -  74.752:   33        |
|      2:    21.358 -  32.037:  196   |   7:    74.752 -  85.431:   23        |
|      3:    32.037 -  42.716:  131   |   8:    85.431 -  96.110:    5        |
|      4:    42.716 -  53.394:   96   |   9:    96.110 - 106.789:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1694             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1695             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1695   ksol= 0.32   Bsol= 69.71   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-1.40,0.60,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215776                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7806 0.99   1404  155 0.0997 0.1320      5.3941      5.5436|
|  2:  4.7806 -  3.8140 0.99   1353  153 0.0880 0.1154       5.459      5.6513|
|  3:  3.8140 -  3.3376 0.99   1322  141 0.1130 0.1561      5.5334      5.8698|
|  4:  3.3376 -  3.0351 0.99   1319  151 0.1292 0.1781      5.5108      5.6875|
|  5:  3.0351 -  2.8190 0.99   1307  147 0.1479 0.1869      5.4105       5.627|
|  6:  2.8190 -  2.6537 0.99   1308  143 0.1308 0.2161      5.2802      5.5654|
|  7:  2.6537 -  2.5214 0.99   1293  142 0.1387 0.1686      5.2583      5.3868|
|  8:  2.5214 -  2.4121 0.98   1281  144 0.1261 0.1697      5.1512      5.3866|
|  9:  2.4121 -  2.3196 0.98   1284  143 0.1300 0.2033      5.1248      5.4074|
| 10:  2.3196 -  2.2398 1.00   1286  144 0.1230 0.1805      5.0237      5.2685|
| 11:  2.2398 -  2.1700 0.98   1295  140 0.1243 0.1865      5.0155      5.2953|
| 12:  2.1700 -  2.1081 0.98   1262  145 0.1258 0.1972       4.966      5.2983|
| 13:  2.1081 -  2.0527 0.99   1284  141 0.1238 0.1791      4.8651      5.0822|
| 14:  2.0527 -  2.0028 0.48    632   70 0.1023 0.1754      4.7238      4.9874|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.7806  1404   155  0.94   9.17   0.96     0.93       7277.53|
|  2:  4.7806 -  3.8140  1353   153  0.95   8.17   1.00     0.98       9362.22|
|  3:  3.8140 -  3.3376  1322   141  0.93  11.94   1.02     1.01      11360.28|
|  4:  3.3376 -  3.0351  1319   151  0.91  14.75   1.00     0.98      11510.39|
|  5:  3.0351 -  2.8190  1307   147  0.89  17.49   0.99     0.97       9813.45|
|  6:  2.8190 -  2.6537  1308   143  0.89  17.53   0.97     0.95       8195.43|
|  7:  2.6537 -  2.5214  1293   142  0.89  17.06   0.98     0.95       7424.38|
|  8:  2.5214 -  2.4121  1281   144  0.89  16.94   0.98     0.95       6321.87|
|  9:  2.4121 -  2.3196  1284   143  0.90  16.81   0.99     0.94       5957.30|
| 10:  2.3196 -  2.2398  1286   144  0.89  17.07   0.98     0.94       5044.75|
| 11:  2.2398 -  2.1700  1295   140  0.89  17.31   0.97     0.91       4867.54|
| 12:  2.1700 -  2.1081  1262   145  0.90  17.03   0.99     0.99       4713.81|
| 13:  2.1081 -  2.0527  1284   141  0.89  18.01   0.97     0.95       3987.81|
| 14:  2.0527 -  2.0028   632    70  0.91  15.24   0.95     0.91       2958.16|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2958.16 max =        11510.39 mean =      7243.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.25|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.68|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1694   ksol= 0.32   Bsol= 69.72   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-1.26,0.63,-0.00,0.00,0.00); trace/3= -0.59                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1694   ksol= 0.32   Bsol= 69.72   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-1.26,0.63,-0.00,0.00,0.00); trace/3= -0.59                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215843                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7806 0.99   1404  155 0.0997 0.1320      5.3943      5.5439|
|  2:  4.7806 -  3.8140 0.99   1353  153 0.0880 0.1154      5.4592      5.6513|
|  3:  3.8140 -  3.3376 0.99   1322  141 0.1130 0.1561      5.5333      5.8701|
|  4:  3.3376 -  3.0351 0.99   1319  151 0.1292 0.1781      5.5108      5.6875|
|  5:  3.0351 -  2.8190 0.99   1307  147 0.1478 0.1867      5.4104      5.6268|
|  6:  2.8190 -  2.6537 0.99   1308  143 0.1308 0.2163      5.2804       5.566|
|  7:  2.6537 -  2.5214 0.99   1293  142 0.1387 0.1685      5.2584      5.3869|
|  8:  2.5214 -  2.4121 0.98   1281  144 0.1260 0.1696      5.1513      5.3867|
|  9:  2.4121 -  2.3196 0.98   1284  143 0.1299 0.2035      5.1249       5.408|
| 10:  2.3196 -  2.2398 1.00   1286  144 0.1230 0.1801      5.0236       5.267|
| 11:  2.2398 -  2.1700 0.98   1295  140 0.1243 0.1864      5.0152      5.2947|
| 12:  2.1700 -  2.1081 0.98   1262  145 0.1258 0.1970      4.9658      5.2981|
| 13:  2.1081 -  2.0527 0.99   1284  141 0.1238 0.1797      4.8654      5.0832|
| 14:  2.0527 -  2.0028 0.48    632   70 0.1023 0.1755      4.7247      4.9879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.7806  1404   155  0.94   9.17   0.96     0.93       7281.45|
|  2:  4.7806 -  3.8140  1353   153  0.95   8.17   1.00     0.98       9364.95|
|  3:  3.8140 -  3.3376  1322   141  0.93  11.94   1.02     1.02      11359.86|
|  4:  3.3376 -  3.0351  1319   151  0.91  14.75   1.00     0.98      11510.14|
|  5:  3.0351 -  2.8190  1307   147  0.89  17.50   1.00     0.97       9818.31|
|  6:  2.8190 -  2.6537  1308   143  0.89  17.53   0.98     0.95       8196.39|
|  7:  2.6537 -  2.5214  1293   142  0.89  17.07   0.99     0.95       7426.77|
|  8:  2.5214 -  2.4121  1281   144  0.89  16.95   0.99     0.96       6325.49|
|  9:  2.4121 -  2.3196  1284   143  0.90  16.81   0.99     0.94       5960.42|
| 10:  2.3196 -  2.2398  1286   144  0.89  17.07   0.99     0.95       5039.84|
| 11:  2.2398 -  2.1700  1295   140  0.89  17.29   0.97     0.92       4858.50|
| 12:  2.1700 -  2.1081  1262   145  0.90  17.01   1.00     0.99       4708.05|
| 13:  2.1081 -  2.0527  1284   141  0.89  18.02   0.98     0.95       3991.08|
| 14:  2.0527 -  2.0028   632    70  0.91  15.28   0.95     0.92       2966.49|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2966.49 max =        11510.14 mean =      7244.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.25|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.340)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.79  16.68    None  None   None       |
|    all(noH): 2823   0      0.00    106.79  16.68    None  None   None       |
|    Sol.    : 438    0      4.21    106.79  41.99    None  None   None       |
|    Mac.    : 2385   0      0.00    87.53   12.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.682: 1396   |   5:    53.397 -  64.076:   89        |
|      1:    10.682 -  21.361:  850   |   6:    64.076 -  74.755:   33        |
|      2:    21.361 -  32.040:  196   |   7:    74.755 -  85.434:   23        |
|      3:    32.040 -  42.719:  131   |   8:    85.434 -  96.113:    5        |
|      4:    42.719 -  53.397:   96   |   9:    96.113 - 106.792:    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)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 4.739
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 299
   mapped sites are within: 0.740 - 4.739

peak=   11.475 closest distance to " O  BHOH Z  74 " =    1.094
peak=    5.392 closest distance to " CB  GLN A 223 " =    1.427
peak=    5.265 closest distance to " CZ  PHE A 218 " =    1.097
peak=    5.095 closest distance to " CG  PRO A  54 " =    1.366
peak=    4.824 closest distance to " CB  ARG A 190 " =    1.655
peak=    4.724 closest distance to " NE2 GLN A  11 " =    1.065
peak=    4.692 closest distance to " CB  PRO A  54 " =    1.045
peak=    4.652 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.591 closest distance to " CZ3 TRP A 266 " =    1.142
peak=    4.574 closest distance to " CB  LEU A 228 " =    1.132
peak=    4.555 closest distance to " O   HOH Z 298 " =    2.070
peak=    4.544 closest distance to " O   HOH Z 369 " =    2.151
peak=    4.531 closest distance to " CG  PRO A 198 " =    1.248
peak=    4.521 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.502 closest distance to " CB  ASN A 148 " =    1.498
peak=    4.478 closest distance to " O   HOH Z 188 " =    2.814
peak=    4.441 closest distance to " CG  PRO A  90 " =    1.214
peak=    4.406 closest distance to " O   HOH Z 142 " =    1.888
peak=    4.398 closest distance to " CD  ARG A 159 " =    0.812
peak=    4.397 closest distance to " O   HOH Z 232 " =    2.255
peak=    4.396 closest distance to " O   HOH Z 111 " =    2.072
peak=    4.322 closest distance to " O   HOH Z 287 " =    1.962
peak=    4.259 closest distance to " CB  ASP A 124 " =    0.857
peak=    4.230 closest distance to " CB  SER A  63 " =    1.276
peak=    4.205 closest distance to " O   HOH Z  53 " =    2.508
peak=    4.200 closest distance to " CA  TYR A  30 " =    1.044
peak=    4.196 closest distance to " ND2 ASN A 187 " =    1.484
peak=    4.137 closest distance to " CE  LYS A  76 " =    0.885
peak=    4.134 closest distance to " CB  TRP A 266 " =    1.048
peak=    4.132 closest distance to " CB  TYR A 169 " =    0.740
peak=    4.129 closest distance to " NH1AARG A 145 " =    1.313
peak=    4.128 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.094 closest distance to " ND2 ASN A 249 " =    0.855
peak=    4.087 closest distance to " CB  ASN A  39 " =    0.952
peak=    4.083 closest distance to " CB  GLU A 277 " =    3.830
peak=    4.076 closest distance to " CB  VAL A 265 " =    1.280
peak=    4.075 closest distance to " CA  ARG A 195 " =    1.267
peak=    4.056 closest distance to " CZ  PHE A  38 " =    1.246
peak=    4.045 closest distance to " O   HOH Z 126 " =    2.016
peak=    4.036 closest distance to " O   HOH Z   9 " =    2.045
peak=    4.026 closest distance to " CB  GLU A 128 " =    0.935
peak=    4.021 closest distance to " CD2 TRP A 179 " =    1.294
peak=    4.014 closest distance to " CD  ARG A 269 " =    0.935
peak=    3.996 closest distance to " O   HOH Z 427 " =    3.146
peak=    3.989 closest distance to " O   THR A 220 " =    1.252
peak=    3.988 closest distance to " CG2 VAL A 257 " =    0.858
peak=    3.978 closest distance to " CB  SER A 210 " =    0.872
peak=    3.960 closest distance to " CG  PRO A 243 " =    1.058
peak=    3.959 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.957 closest distance to " CB  ASN A 142 " =    1.003
peak=    3.954 closest distance to " O   HOH Z 214 " =    2.343
peak=    3.928 closest distance to " CB  ARG A  79 " =    1.414
peak=    3.925 closest distance to " O   PRO A 198 " =    1.541
peak=    3.902 closest distance to " O   HOH Z  78 " =    1.620
peak=    3.896 closest distance to " CB  ASP A 140 " =    0.986
peak=    3.895 closest distance to " CA  THR A 264 " =    0.909
peak=    3.894 closest distance to " O   HOH Z  21 " =    1.815
peak=    3.886 closest distance to " O   HOH Z  69 " =    0.806
peak=    3.886 closest distance to " CA  SER A  87 " =    0.989
peak=    3.884 closest distance to " O   HOH Z 406 " =    1.739
peak=    3.881 closest distance to " CB  SER A 212 " =    1.234
peak=    3.853 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.840 closest distance to " O   HOH Z 316 " =    3.176
peak=    3.840 closest distance to " CG  LEU A 167 " =    1.222
peak=    3.825 closest distance to " NE2 HIS A 207 " =    1.168
peak=    3.823 closest distance to " CD1 LEU A 300 " =    1.133
peak=    3.822 closest distance to " O   HOH Z 411 " =    3.868
peak=    3.802 closest distance to " CA  ALA A 160 " =    0.970
peak=    3.802 closest distance to " CB  LYS A 117 " =    1.178
peak=    3.796 closest distance to " CB  MET A  40 " =    0.744
peak=    3.790 closest distance to " CD  ARG A  66 " =    2.284
peak=    3.787 closest distance to " CA  VAL A 125 " =    1.241
peak=    3.782 closest distance to " O  BHOH Z 338 " =    2.340
peak=    3.782 closest distance to " O   HOH Z 303 " =    2.254
peak=    3.775 closest distance to " CA  ASN A 127 " =    1.171
peak=    3.773 closest distance to " O   HOH Z 265 " =    2.135
peak=    3.758 closest distance to " O   HOH Z 290 " =    1.110
peak=    3.748 closest distance to " O   HOH Z 285 " =    2.161
peak=    3.745 closest distance to " O   HOH Z 353 " =    2.658
peak=    3.745 closest distance to " O   HOH Z 180 " =    2.128
peak=    3.728 closest distance to " CD ALYS A 290 " =    0.963
peak=    3.721 closest distance to " CG2 THR A 221 " =    0.997
peak=    3.716 closest distance to " O   HOH Z 133 " =    2.737
peak=    3.711 closest distance to " CG  ARG A 138 " =    1.246
peak=    3.710 closest distance to " O   HOH Z 368 " =    2.027
peak=    3.707 closest distance to " O   HOH Z  90 " =    2.363
peak=    3.707 closest distance to " CB  ALA A 104 " =    0.764
peak=    3.698 closest distance to " CB  PRO A  90 " =    1.061
peak=    3.697 closest distance to " O   THR A 251 " =    1.194
peak=    3.669 closest distance to " O   SER A  87 " =    2.289
peak=    3.666 closest distance to " O   HOH Z 313 " =    1.956
peak=    3.656 closest distance to " CG  GLU A  37 " =    0.956
peak=    3.649 closest distance to " CB  TYR A 116 " =    0.824
peak=    3.637 closest distance to " CG2AVAL A 121 " =    2.399
peak=    3.635 closest distance to " O   ASN A  74 " =    1.449
peak=    3.635 closest distance to " O   HOH Z  78 " =    2.142
peak=    3.635 closest distance to " CA  ALA A 154 " =    1.081
peak=    3.627 closest distance to " CB  SER A 216 " =    0.974
peak=    3.624 closest distance to " CA  ARG A  36 " =    1.177
peak=    3.618 closest distance to " O   HOH Z 158 " =    3.069
peak=    3.615 closest distance to " O   HOH Z  88 " =    3.667
peak=    3.604 closest distance to " O   HOH Z 368 " =    3.681
peak=    3.598 closest distance to " O   HOH Z  63 " =    1.926
peak=    3.593 closest distance to " CB  LEU A  83 " =    0.758
peak=    3.593 closest distance to " O   THR A 182 " =    1.409
peak=    3.584 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.570 closest distance to " NZ  LYS A 117 " =    3.137
peak=    3.566 closest distance to " O   HOH Z 365 " =    2.995
peak=    3.564 closest distance to " O   HOH Z 172 " =    3.507
peak=    3.558 closest distance to " CB  ASN A 187 " =    1.129
peak=    3.555 closest distance to " O   HOH Z 126 " =    1.547
peak=    3.552 closest distance to " O   HOH Z  80 " =    1.735
peak=    3.550 closest distance to " O   ALA A 165 " =    1.605
peak=    3.549 closest distance to " CG2 VAL A 197 " =    1.167
peak=    3.547 closest distance to " O   HOH Z 183 " =    1.417
peak=    3.544 closest distance to " CB  GLN A  89 " =    1.304
peak=    3.542 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.532 closest distance to " CG AARG A 275 " =    1.275
peak=    3.529 closest distance to " O   HOH Z 394 " =    3.974
peak=    3.527 closest distance to " O   HOH Z 425 " =    1.321
peak=    3.526 closest distance to " CA  MET A 105 " =    1.059
peak=    3.521 closest distance to " CA  ASN A 215 " =    1.107
peak=    3.520 closest distance to " O   TYR A 116 " =    1.284
peak=    3.519 closest distance to " NE  ARG A  79 " =    1.020
peak=    3.508 closest distance to " OG1 THR A  82 " =    0.877
peak=    3.501 closest distance to " CD1 LEU A  96 " =    0.778
peak=    3.496 closest distance to " CA  ILE A 234 " =    1.046
peak=    3.490 closest distance to " CA  TYR A 116 " =    1.357
peak=    3.480 closest distance to " O   HOH Z 261 " =    1.737
peak=    3.475 closest distance to " O   HOH Z 359 " =    1.498
peak=    3.473 closest distance to " ND2 ASN A 127 " =    1.141
peak=    3.473 closest distance to " CD  LYS A  76 " =    2.104
peak=    3.473 closest distance to " N   PHE A 130 " =    1.251
peak=    3.470 closest distance to " O   HOH Z 250 " =    1.498
peak=    3.470 closest distance to " N   ASN A  39 " =    1.347
peak=    3.463 closest distance to " O   HOH Z  61 " =    1.708
peak=    3.459 closest distance to " O   PHE A 192 " =    1.367
peak=    3.453 closest distance to " CA  GLN A  94 " =    0.776
peak=    3.450 closest distance to " OE2 GLU A  53 " =    1.306
peak=    3.446 closest distance to " CB  ALA A 114 " =    0.772
peak=    3.444 closest distance to " O   HOH Z 248 " =    1.586
peak=    3.441 closest distance to " ND2BASN A 224 " =    0.882
peak=    3.437 closest distance to " OG1 THR A 279 " =    1.451
peak=    3.436 closest distance to " CA  ARG A 156 " =    1.133
peak=    3.434 closest distance to " CA  ALA A 158 " =    1.247
peak=    3.434 closest distance to " O   HOH Z 185 " =    1.937
peak=    3.432 closest distance to " CB  ILE A 120 " =    1.276
peak=    3.431 closest distance to " NH1 ARG A 138 " =    1.031
peak=    3.431 closest distance to " O   HOH Z 166 " =    3.968
peak=    3.431 closest distance to " O   HOH Z  43 " =    1.906
peak=    3.429 closest distance to " O   HOH Z  57 " =    1.955
peak=    3.428 closest distance to " CD  ARG A  66 " =    2.208
peak=    3.422 closest distance to " CA  ARG A 102 " =    1.186
peak=    3.419 closest distance to " CA  ASP A 124 " =    0.784
peak=    3.417 closest distance to " O   HOH Z 234 " =    3.773
peak=    3.417 closest distance to " N   ASN A 127 " =    1.304
peak=    3.415 closest distance to " CB  ALA A 291 " =    1.185
peak=    3.415 closest distance to " OD1 ASP A 171 " =    1.223
peak=    3.408 closest distance to " O   HOH Z 145 " =    1.278
peak=    3.406 closest distance to " O   HOH Z 422 " =    2.702
peak=    3.404 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.402 closest distance to " C   ILE A 106 " =    1.916
peak=    3.402 closest distance to " O   HOH Z 272 " =    1.731
peak=    3.401 closest distance to " CA  MET A  40 " =    1.289
peak=    3.398 closest distance to " OE2 GLU A  53 " =    1.908
peak=    3.398 closest distance to " O   HOH Z 106 " =    4.187
peak=    3.397 closest distance to " O   HOH Z 167 " =    1.659
peak=    3.397 closest distance to " CB  ASN A 173 " =    1.132
peak=    3.396 closest distance to " O   HOH Z 193 " =    1.832
peak=    3.394 closest distance to " CG2 ILE A 151 " =    0.936
peak=    3.392 closest distance to " CA  ALA A 100 " =    1.004
peak=    3.392 closest distance to " CB  GLU A  37 " =    0.997
peak=    3.382 closest distance to " CG  PHE A 204 " =    0.856
peak=    3.382 closest distance to " O   HOH Z  10 " =    1.943
peak=    3.380 closest distance to " CD  ARG A 219 " =    1.120
peak=    3.373 closest distance to " CG1 ILE A 151 " =    1.097
peak=    3.370 closest distance to " O   HOH Z 302 " =    2.087
peak=    3.369 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.359 closest distance to " OE1 GLN A  55 " =    1.495
peak=    3.344 closest distance to " CB  HIS A  86 " =    1.016
peak=    3.342 closest distance to " CB  MET A  47 " =    0.918
peak=    3.341 closest distance to " O   HOH Z 291 " =    1.468
peak=    3.339 closest distance to " O   HOH Z 148 " =    3.543
peak=    3.337 closest distance to " O   ALA A 158 " =    1.230
peak=    3.328 closest distance to " O   HOH Z 392 " =    2.944
peak=    3.328 closest distance to " OD1 ASN A  69 " =    2.642
peak=    3.324 closest distance to " N   SER A 271 " =    0.977
peak=    3.323 closest distance to " CA  ALA A 295 " =    1.158
peak=    3.322 closest distance to " O   HOH Z   1 " =    1.997
peak=    3.319 closest distance to " CB  LEU A  96 " =    1.432
peak=    3.318 closest distance to " CB  THR A  31 " =    1.582
peak=    3.315 closest distance to " ND2 ASN A 249 " =    1.866
peak=    3.310 closest distance to " N   TYR A  15 " =    0.758
peak=    3.307 closest distance to " CB  ASN A 215 " =    1.268
peak=    3.305 closest distance to " O   HOH Z  59 " =    1.860
peak=    3.304 closest distance to " CB  SER A  97 " =    0.975
peak=    3.301 closest distance to " CG  GLN A  11 " =    1.619
peak=    3.297 closest distance to " O   HOH Z 294 " =    1.595
peak=    3.297 closest distance to " N   ARG A 156 " =    1.373
peak=    3.297 closest distance to " O   HOH Z 193 " =    2.094
peak=    3.296 closest distance to " N   SER A 146 " =    1.636
peak=    3.292 closest distance to " CB  TRP A 179 " =    1.442
peak=    3.291 closest distance to " CG2 THR A  29 " =    1.405
peak=    3.288 closest distance to " O   ASP A 191 " =    1.486
peak=    3.286 closest distance to " CA  ALA A 233 " =    1.650
peak=    3.284 closest distance to " O   HOH Z 325 " =    2.311
peak=    3.284 closest distance to " O   HOH Z 368 " =    4.216
peak=    3.281 closest distance to " CB  GLU A 152 " =    1.393
peak=    3.280 closest distance to " O   HOH Z 298 " =    2.598
peak=    3.276 closest distance to " CB  ALA A  43 " =    0.826
peak=    3.275 closest distance to " CA  ARG A 139 " =    1.059
peak=    3.274 closest distance to " CG  GLN A 144 " =    0.872
peak=    3.271 closest distance to " OG BSER A 134 " =    2.829
peak=    3.270 closest distance to " O   HOH Z 280 " =    3.044
peak=    3.269 closest distance to " CB  ALA A 227 " =    1.168
peak=    3.265 closest distance to " CB  ILE A 199 " =    1.153
peak=    3.257 closest distance to " CG2 ILE A 239 " =    0.788
peak=    3.254 closest distance to " CG2 ILE A 120 " =    1.098
peak=    3.253 closest distance to " CD2 LEU A 297 " =    0.911
peak=    3.253 closest distance to " O   HOH Z 371 " =    2.906
peak=    3.249 closest distance to " O   HOH Z  49 " =    0.958
peak=    3.245 closest distance to " O   HOH Z 346 " =    1.713
peak=    3.244 closest distance to " CG1 ILE A  20 " =    1.353
peak=    3.243 closest distance to " NH2BARG A 145 " =    2.184
peak=    3.243 closest distance to " CB  SER A   3 " =    1.398
peak=    3.239 closest distance to " O   HOH Z 213 " =    2.281
peak=    3.234 closest distance to " CB  PRO A 243 " =    1.120
peak=    3.233 closest distance to " O   HOH Z 423 " =    1.523
peak=    3.232 closest distance to " O   HOH Z 218 " =    4.725
peak=    3.226 closest distance to " N   GLU A 152 " =    1.468
peak=    3.225 closest distance to " O   PRO A 213 " =    1.483
peak=    3.224 closest distance to " CD1 ILE A 199 " =    1.092
peak=    3.223 closest distance to " CB  SER A  62 " =    0.844
peak=    3.221 closest distance to " CG2AVAL A  72 " =    1.824
peak=    3.220 closest distance to " CB  ALA A 137 " =    1.066
peak=    3.218 closest distance to " CA  ASP A 162 " =    1.024
peak=    3.216 closest distance to " OG  SER A  28 " =    1.691
peak=    3.215 closest distance to " CG BARG A 275 " =    1.476
peak=    3.214 closest distance to " O   HOH Z 352 " =    1.864
peak=    3.212 closest distance to " OG BSER A  99 " =    2.303
peak=    3.211 closest distance to " O   HOH Z 116 " =    3.233
peak=    3.209 closest distance to " OG  SER A 245 " =    1.778
peak=    3.192 closest distance to " O   HOH Z  32 " =    1.650
peak=    3.190 closest distance to " CB  ASN A 110 " =    1.171
peak=    3.190 closest distance to " O   HOH Z 199 " =    1.526
peak=    3.189 closest distance to " CG  MET A 185 " =    1.221
peak=    3.186 closest distance to " CG1 ILE A 234 " =    1.088
peak=    3.182 closest distance to " O   HOH Z 327 " =    1.905
peak=    3.182 closest distance to " O   HOH Z 116 " =    1.830
peak=    3.181 closest distance to " CA  GLU A 152 " =    0.876
peak=    3.176 closest distance to " CB  ASN A 285 " =    0.948
peak=    3.175 closest distance to " CA  THR A 221 " =    1.102
peak=    3.174 closest distance to " CA  GLY A 241 " =    0.859
peak=    3.169 closest distance to " O   SER A 164 " =    1.600
peak=    3.166 closest distance to " OG  SER A  22 " =    2.848
peak=    3.162 closest distance to " CB  ALA A   1 " =    4.739
peak=    3.159 closest distance to " CE3 TRP A  85 " =    1.061
peak=    3.157 closest distance to " O   HOH Z 227 " =    1.886
peak=    3.153 closest distance to " O   HOH Z 152 " =    2.261
peak=    3.152 closest distance to " N   ALA A 256 " =    1.234
peak=    3.151 closest distance to " O   HOH Z 426 " =    1.885
peak=    3.151 closest distance to " O   HOH Z  88 " =    3.729
peak=    3.147 closest distance to " CB  ALA A  34 " =    1.059
peak=    3.145 closest distance to " O   HOH Z 305 " =    3.771
peak=    3.145 closest distance to " CD1 ILE A 106 " =    0.819
peak=    3.144 closest distance to " CB  PHE A 204 " =    0.755
peak=    3.142 closest distance to " CA  ALA A  21 " =    1.196
peak=    3.140 closest distance to " CD  ARG A 195 " =    3.465
peak=    3.140 closest distance to " OG  SER A  62 " =    2.915
peak=    3.137 closest distance to " OG  SER A  62 " =    2.969
peak=    3.132 closest distance to " O   HOH Z 367 " =    2.860
peak=    3.128 closest distance to " O   HOH Z 273 " =    2.786
peak=    3.127 closest distance to " CB  ALA A 299 " =    0.933
peak=    3.124 closest distance to " CB  VAL A 268 " =    0.892
peak=    3.122 closest distance to " CE1 HIS A 115 " =    0.987
peak=    3.122 closest distance to " O   HOH Z 271 " =    2.690
peak=    3.119 closest distance to " O   HOH Z 153 " =    3.934
peak=    3.114 closest distance to " O   THR A 294 " =    1.158
peak=    3.099 closest distance to " CB  ARG A 138 " =    1.016
peak=    3.097 closest distance to " CB  LYS A 193 " =    0.935
peak=    3.097 closest distance to " CB  SER A  62 " =    1.054
peak=    3.087 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.085 closest distance to " CB  ARG A 102 " =    0.743
peak=    3.070 closest distance to " CG  MET A 185 " =    1.003
peak=    3.067 closest distance to " CB  ARG A 156 " =    1.078
peak=    3.059 closest distance to " O   TRP A  70 " =    1.499
peak=    3.058 closest distance to " CG2 ILE A  20 " =    1.275
peak=    3.058 closest distance to " O   HOH Z 211 " =    1.094
peak=    3.056 closest distance to " C   ALA A 299 " =    0.959
peak=    3.041 closest distance to " O   HOH Z 120 " =    3.271
peak=    3.035 closest distance to " O   HOH Z 124 " =    1.938
peak=    3.012 closest distance to " O   HOH Z 213 " =    2.040

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.763
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.737 - 5.763

peak=   -4.429 closest distance to " CG1 VAL A 112 " =    2.645
peak=   -4.425 closest distance to " CD  ARG A  14 " =    3.548
peak=   -4.395 closest distance to " O   PRO A 198 " =    1.258
peak=   -4.366 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.358 closest distance to " O   HOH Z 377 " =    2.014
peak=   -4.356 closest distance to " CD  GLN A  58 " =    0.938
peak=   -4.216 closest distance to " O   HOH Z  73 " =    2.255
peak=   -4.208 closest distance to " CG2 ILE A  49 " =    2.783
peak=   -4.113 closest distance to " CD  ARG A 156 " =    2.090
peak=   -4.094 closest distance to " CD2 TYR A 293 " =    1.891
peak=   -4.039 closest distance to " CG1 VAL A 250 " =    2.656
peak=   -4.009 closest distance to " O   HOH Z 196 " =    2.231
peak=   -3.988 closest distance to " CB  HIS A  86 " =    1.136
peak=   -3.940 closest distance to " CG  GLN A 223 " =    2.178
peak=   -3.939 closest distance to " N   ALA A  43 " =    2.638
peak=   -3.935 closest distance to " OG BSER A 134 " =    1.366
peak=   -3.902 closest distance to " CA  GLY A 241 " =    2.372
peak=   -3.893 closest distance to " O   HOH Z 394 " =    1.626
peak=   -3.891 closest distance to " CE2 TYR A  30 " =    2.717
peak=   -3.886 closest distance to " CE2 PHE A  61 " =    2.690
peak=   -3.867 closest distance to " OE1 GLN A  88 " =    1.078
peak=   -3.864 closest distance to " O   HOH Z 411 " =    5.571
peak=   -3.860 closest distance to " O   HOH Z 231 " =    2.335
peak=   -3.834 closest distance to " CB  ALA A  43 " =    2.745
peak=   -3.831 closest distance to " O   HOH Z 211 " =    0.737
peak=   -3.820 closest distance to " ND2 ASN A  45 " =    2.051
peak=   -3.807 closest distance to " CG  PRO A 198 " =    1.994
peak=   -3.800 closest distance to " O   HOH Z 290 " =    1.155
peak=   -3.787 closest distance to " CZ3 TRP A 179 " =    1.176
peak=   -3.779 closest distance to " O   HOH Z 407 " =    3.248
peak=   -3.776 closest distance to " O   HOH Z  38 " =    1.417
peak=   -3.765 closest distance to " OD1 ASN A 148 " =    1.414
peak=   -3.763 closest distance to " O   HOH Z 295 " =    1.727
peak=   -3.756 closest distance to " C   HIS A 108 " =    1.118
peak=   -3.746 closest distance to " OD1 ASP A 171 " =    1.591
peak=   -3.717 closest distance to " O   GLY A  17 " =    1.220
peak=   -3.711 closest distance to " CG  MET A 105 " =    1.009
peak=   -3.708 closest distance to " CA  GLY A 241 " =    3.431
peak=   -3.700 closest distance to " O   HOH Z  51 " =    1.614
peak=   -3.691 closest distance to " CB  ASP A 286 " =    2.067
peak=   -3.689 closest distance to " O   HOH Z  10 " =    1.510
peak=   -3.687 closest distance to " O   HOH Z 114 " =    1.124
peak=   -3.673 closest distance to " O   HOH Z 133 " =    1.180
peak=   -3.649 closest distance to " CE BMET A  47 " =    1.635
peak=   -3.648 closest distance to " CD2 LEU A 237 " =    2.956
peak=   -3.646 closest distance to " O   HOH Z  11 " =    2.312
peak=   -3.645 closest distance to " CA  VAL A  67 " =    3.009
peak=   -3.639 closest distance to " O   ALA A  10 " =    1.721
peak=   -3.637 closest distance to " CD1 PHE A  59 " =    2.016
peak=   -3.636 closest distance to " O   VAL A  67 " =    2.770
peak=   -3.612 closest distance to " CE  MET A 105 " =    2.339
peak=   -3.603 closest distance to " CD  ARG A  79 " =    1.148
peak=   -3.592 closest distance to " O   HOH Z 128 " =    2.627
peak=   -3.590 closest distance to " O   HOH Z  60 " =    1.236
peak=   -3.590 closest distance to " O   HOH Z  52 " =    1.486
peak=   -3.588 closest distance to " N   THR A  52 " =    1.621
peak=   -3.585 closest distance to " CB  ALA A 100 " =    2.189
peak=   -3.585 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.584 closest distance to " O   HOH Z 102 " =    1.628
peak=   -3.583 closest distance to " CG  GLU A  53 " =    1.329
peak=   -3.583 closest distance to " O   HOH Z 216 " =    1.009
peak=   -3.573 closest distance to " ND2 ASN A 249 " =    2.454
peak=   -3.560 closest distance to " CB  GLN A  11 " =    1.576
peak=   -3.560 closest distance to " CB  ALA A 129 " =    2.493
peak=   -3.559 closest distance to " CB  ASP A  27 " =    2.467
peak=   -3.549 closest distance to " O   HOH Z 232 " =    1.744
peak=   -3.529 closest distance to " O   HOH Z 166 " =    1.790
peak=   -3.527 closest distance to " C   ASN A 285 " =    2.493
peak=   -3.523 closest distance to " CB  TRP A  85 " =    2.542
peak=   -3.508 closest distance to " NH2AARG A 275 " =    5.596
peak=   -3.497 closest distance to " ND2 ASN A  60 " =    1.487
peak=   -3.493 closest distance to " O   VAL A 189 " =    2.585
peak=   -3.492 closest distance to " O   HOH Z  64 " =    1.465
peak=   -3.489 closest distance to " O   HOH Z 359 " =    3.045
peak=   -3.488 closest distance to " O   HOH Z 185 " =    2.440
peak=   -3.486 closest distance to " O   HOH Z 103 " =    1.774
peak=   -3.485 closest distance to " CG1 VAL A 125 " =    1.813
peak=   -3.481 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.476 closest distance to " O   HOH Z 281 " =    2.568
peak=   -3.464 closest distance to " O   HOH Z  69 " =    1.927
peak=   -3.446 closest distance to " NH2 ARG A  79 " =    1.506
peak=   -3.440 closest distance to " O   HOH Z 193 " =    1.290
peak=   -3.440 closest distance to " CG1 VAL A 112 " =    3.058
peak=   -3.439 closest distance to " O   HOH Z 368 " =    1.768
peak=   -3.435 closest distance to " CG  ARG A 269 " =    2.385
peak=   -3.429 closest distance to " CB  ASP A 132 " =    2.264
peak=   -3.424 closest distance to " CD2 LEU A 143 " =    2.585
peak=   -3.424 closest distance to " O   GLY A 211 " =    1.318
peak=   -3.423 closest distance to " CE3 TRP A 150 " =    2.239
peak=   -3.418 closest distance to " O   HOH Z 252 " =    3.982
peak=   -3.405 closest distance to " O   HOH Z 198 " =    1.820
peak=   -3.402 closest distance to " O   HOH Z 275 " =    1.581
peak=   -3.400 closest distance to " CG  PRO A 243 " =    1.802
peak=   -3.390 closest distance to " CA  GLY A 203 " =    2.518
peak=   -3.386 closest distance to " CD  GLN A 223 " =    1.425
peak=   -3.385 closest distance to " O   HOH Z 191 " =    5.763
peak=   -3.384 closest distance to " OD1 ASP A 191 " =    1.670
peak=   -3.382 closest distance to " O   ILE A 109 " =    2.686
peak=   -3.373 closest distance to " C   LEU A 143 " =    1.268
peak=   -3.366 closest distance to " O   HOH Z 351 " =    1.454
peak=   -3.364 closest distance to " O   HOH Z 278 " =    1.271
peak=   -3.363 closest distance to " CB  ASN A  39 " =    2.288
peak=   -3.355 closest distance to " CG  GLN A  88 " =    0.899
peak=   -3.351 closest distance to " O   HOH Z 357 " =    2.208
peak=   -3.347 closest distance to " O   PRO A 163 " =    2.064
peak=   -3.347 closest distance to " N   ASP A 191 " =    1.178
peak=   -3.345 closest distance to " CB  ALA A 291 " =    2.376
peak=   -3.342 closest distance to " CG1BVAL A  41 " =    2.748
peak=   -3.340 closest distance to " O   HOH Z 292 " =    1.699
peak=   -3.339 closest distance to " O   HOH Z 357 " =    2.227
peak=   -3.337 closest distance to " O   VAL A 189 " =    1.665
peak=   -3.336 closest distance to " CD2 PHE A  61 " =    2.134
peak=   -3.334 closest distance to " O   HOH Z 393 " =    1.293
peak=   -3.333 closest distance to " CG  GLU A 277 " =    1.165
peak=   -3.333 closest distance to " O   GLN A 240 " =    2.586
peak=   -3.326 closest distance to " O   HOH Z 111 " =    1.828
peak=   -3.318 closest distance to " O   GLY A 203 " =    2.407
peak=   -3.317 closest distance to " O   ALA A  34 " =    2.427
peak=   -3.308 closest distance to " O   HOH Z   9 " =    1.935
peak=   -3.307 closest distance to " O   HOH Z 174 " =    2.472
peak=   -3.304 closest distance to " O   HOH Z 326 " =    4.956
peak=   -3.297 closest distance to " CA  ASP A 298 " =    1.093
peak=   -3.293 closest distance to " CD1 LEU A   5 " =    2.571
peak=   -3.292 closest distance to " CG2 THR A 178 " =    2.350
peak=   -3.290 closest distance to " N   THR A 264 " =    1.298
peak=   -3.289 closest distance to " CD1 LEU A 101 " =    2.381
peak=   -3.289 closest distance to " O   HOH Z 421 " =    3.149
peak=   -3.288 closest distance to " NH2BARG A 275 " =    1.951
peak=   -3.287 closest distance to " CG  PRO A 163 " =    2.260
peak=   -3.282 closest distance to " O   HOH Z 183 " =    1.360
peak=   -3.280 closest distance to " CB  ALA A 158 " =    1.725
peak=   -3.279 closest distance to " SG BCYS A 201 " =    1.032
peak=   -3.278 closest distance to " CB  PRO A  54 " =    2.615
peak=   -3.275 closest distance to " O   HOH Z 365 " =    1.478
peak=   -3.274 closest distance to " O   HOH Z 389 " =    2.213
peak=   -3.271 closest distance to " O   HOH Z 298 " =    2.524
peak=   -3.267 closest distance to " O   HOH Z 351 " =    1.533
peak=   -3.264 closest distance to " O   HOH Z 247 " =    2.035
peak=   -3.263 closest distance to " OXT GLY A 302 " =    3.236
peak=   -3.263 closest distance to " CD2 HIS A 207 " =    2.245
peak=   -3.261 closest distance to " CA  ASN A 127 " =    1.104
peak=   -3.261 closest distance to " O   HOH Z 189 " =    2.183
peak=   -3.258 closest distance to " O   HOH Z   9 " =    2.471
peak=   -3.252 closest distance to " CD  GLU A 236 " =    1.144
peak=   -3.249 closest distance to " O   HOH Z 134 " =    3.016
peak=   -3.249 closest distance to " CE2 TRP A  70 " =    2.254
peak=   -3.245 closest distance to " C   LEU A 222 " =    0.854
peak=   -3.240 closest distance to " O   HOH Z 177 " =    1.784
peak=   -3.235 closest distance to " O   HOH Z   6 " =    1.388
peak=   -3.234 closest distance to " ND2 ASN A  60 " =    4.121
peak=   -3.231 closest distance to " NE2 GLN A 240 " =    1.635
peak=   -3.229 closest distance to " O   HOH Z 313 " =    1.841
peak=   -3.222 closest distance to " O   GLU A 152 " =    1.393
peak=   -3.222 closest distance to " O   HOH Z 372 " =    2.403
peak=   -3.221 closest distance to " ND2 ASN A  45 " =    1.188
peak=   -3.214 closest distance to " O   HOH Z 426 " =    1.574
peak=   -3.212 closest distance to " CA  SER A 135 " =    1.195
peak=   -3.209 closest distance to " OD2 ASP A 191 " =    1.514
peak=   -3.206 closest distance to " O   HOH Z  71 " =    1.829
peak=   -3.205 closest distance to " OH  TYR A 247 " =    2.223
peak=   -3.202 closest distance to " CA  GLY A 287 " =    1.377
peak=   -3.201 closest distance to " CG  GLN A 103 " =    2.438
peak=   -3.199 closest distance to " O   HOH Z 191 " =    3.226
peak=   -3.196 closest distance to " CA  GLY A  98 " =    2.029
peak=   -3.195 closest distance to " CG2 ILE A 263 " =    2.374
peak=   -3.194 closest distance to " C   ALA A 165 " =    1.985
peak=   -3.193 closest distance to " CB  PHE A  16 " =    2.384
peak=   -3.191 closest distance to " CA  GLY A 133 " =    2.234
peak=   -3.187 closest distance to " CG  LEU A 282 " =    2.478
peak=   -3.186 closest distance to " O   HOH Z 353 " =    2.153
peak=   -3.182 closest distance to " O   HOH Z 219 " =    4.426
peak=   -3.182 closest distance to " O   HOH Z 350 " =    2.219
peak=   -3.171 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.169 closest distance to " O   VAL A 125 " =    2.254
peak=   -3.159 closest distance to " ND2 ASN A 249 " =    2.266
peak=   -3.158 closest distance to " CZ  PHE A 155 " =    1.251
peak=   -3.157 closest distance to " O   HOH Z 317 " =    2.253
peak=   -3.154 closest distance to " CZ  PHE A  38 " =    2.123
peak=   -3.148 closest distance to " CB  TYR A  15 " =    2.392
peak=   -3.147 closest distance to " O   HOH Z 251 " =    4.948
peak=   -3.143 closest distance to " OD2 ASP A 171 " =    1.892
peak=   -3.142 closest distance to " O   SER A 210 " =    1.899
peak=   -3.134 closest distance to " CD1 TRP A  70 " =    1.093
peak=   -3.127 closest distance to " CA  GLY A 241 " =    2.904
peak=   -3.125 closest distance to " O   HOH Z 156 " =    3.463
peak=   -3.119 closest distance to " CB  PRO A 163 " =    2.548
peak=   -3.114 closest distance to " CG2 ILE A 151 " =    2.602
peak=   -3.110 closest distance to " O   HOH Z 323 " =    1.515
peak=   -3.109 closest distance to " CB  ALA A 248 " =    2.412
peak=   -3.108 closest distance to " CE1 PHE A 225 " =    2.088
peak=   -3.105 closest distance to " O   SER A  62 " =    2.264
peak=   -3.104 closest distance to " C   PHE A  59 " =    1.281
peak=   -3.101 closest distance to " CD  GLN A  88 " =    1.281
peak=   -3.095 closest distance to " O   TYR A 186 " =    1.775
peak=   -3.094 closest distance to " CG2BVAL A  41 " =    2.360
peak=   -3.087 closest distance to " CB  ALA A  10 " =    2.208
peak=   -3.083 closest distance to " O   GLY A  80 " =    2.646
peak=   -3.082 closest distance to " CD  PRO A 213 " =    2.162
peak=   -3.072 closest distance to " CE  LYS A  76 " =    2.516
peak=   -3.058 closest distance to " O   HOH Z 251 " =    2.024
peak=   -3.048 closest distance to " O   HOH Z 348 " =    2.138
peak=   -3.047 closest distance to " CG2 VAL A 189 " =    2.139
peak=   -3.016 closest distance to " CB  ASP A 286 " =    1.689

================= 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    :  0.4027 0.3926   6.202306e+00   6.185823e+00
   1_bss:  0.3883 0.3836   6.184594e+00   6.168198e+00
   1_xyz:  0.2799 0.3036   5.911570e+00   5.978577e+00
   1_adp:  0.2590 0.3055   5.864563e+00   5.986296e+00
   1_occ:  0.2587 0.3055   5.864192e+00   5.987767e+00
   2_bss:  0.2575 0.3047   5.863401e+00   5.988717e+00
   2_xyz:  0.1890 0.2339   5.586911e+00   5.751176e+00
   2_adp:  0.1715 0.2256   5.523099e+00   5.725324e+00
   2_occ:  0.1713 0.2255   5.522334e+00   5.724790e+00
   3_bss:  0.1709 0.2248   5.520073e+00   5.722016e+00
   3_xyz:  0.1362 0.1901   5.325894e+00   5.562481e+00
   3_adp:  0.1297 0.1759   5.267006e+00   5.490336e+00
   3_occ:  0.1296 0.1757   5.266254e+00   5.489804e+00
   4_bss:  0.1296 0.1755   5.265569e+00   5.488680e+00
   4_xyz:  0.1237 0.1684   5.226191e+00   5.447580e+00
   4_adp:  0.1222 0.1675   5.216884e+00   5.441131e+00
   4_occ:  0.1221 0.1675   5.216406e+00   5.440622e+00
   5_bss:  0.1221 0.1674   5.216362e+00   5.440759e+00
   5_xyz:  0.1211 0.1674   5.214278e+00   5.442549e+00
   5_adp:  0.1201 0.1694   5.215629e+00   5.452025e+00
   5_occ:  0.1201 0.1695   5.215776e+00   5.452384e+00
   5_bss:  0.1200 0.1694   5.215843e+00   5.452433e+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:  0.314  69.233  -0.894  -3.527   5.572  -0.000   0.000   0.000
   1_xyz:  0.314  69.233  -0.894  -3.527   5.572  -0.000   0.000   0.000
   1_adp:  0.314  69.233  -0.894  -3.527   5.572  -0.000   0.000   0.000
   1_occ:  0.314  69.233  -0.894  -3.527   5.572  -0.000   0.000   0.000
   2_bss:  0.334  76.502  -1.338  -2.265   2.579  -0.000   0.000   0.000
   2_xyz:  0.334  76.502  -1.338  -2.265   2.579  -0.000   0.000   0.000
   2_adp:  0.334  76.502  -1.338  -2.265   2.579  -0.000   0.000   0.000
   2_occ:  0.334  76.502  -1.338  -2.265   2.579  -0.000   0.000   0.000
   3_bss:  0.343  89.777  -1.253  -1.624   1.357  -0.000   0.000   0.000
   3_xyz:  0.343  89.777  -1.253  -1.624   1.357  -0.000   0.000   0.000
   3_adp:  0.343  89.777  -1.253  -1.624   1.357  -0.000   0.000   0.000
   3_occ:  0.343  89.777  -1.253  -1.624   1.357  -0.000   0.000   0.000
   4_bss:  0.335  80.001  -1.449  -1.605   0.578  -0.000   0.000   0.000
   4_xyz:  0.335  80.001  -1.449  -1.605   0.578  -0.000   0.000   0.000
   4_adp:  0.335  80.001  -1.449  -1.605   0.578  -0.000   0.000   0.000
   4_occ:  0.335  80.001  -1.449  -1.605   0.578  -0.000   0.000   0.000
   5_bss:  0.325  69.714  -1.230  -1.401   0.604  -0.000   0.000   0.000
   5_xyz:  0.325  69.714  -1.230  -1.401   0.604  -0.000   0.000   0.000
   5_adp:  0.325  69.714  -1.230  -1.401   0.604  -0.000   0.000   0.000
   5_occ:  0.325  69.714  -1.230  -1.401   0.604  -0.000   0.000   0.000
   5_bss:  0.325  69.717  -1.143  -1.261   0.629  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.074 0.5824  0.7307    47033.473
   1_bss:  44.021 0.5944  0.7615    44701.375
   1_xyz:  31.366 0.7438  0.9255    24990.200
   1_adp:  31.902 0.7371  0.9048    25634.654
   1_occ:  32.003 0.7359  0.9032    25723.448
   2_bss:  31.743 0.7392  0.8865    25689.757
   2_xyz:  22.947 0.8325  0.9562    13988.582
   2_adp:  22.010 0.8420  0.9505    13162.574
   2_occ:  21.991 0.8422  0.9505    13140.168
   3_bss:  21.837 0.8437  0.9460    13006.033
   3_xyz:  17.979 0.8798  0.9719     9087.534
   3_adp:  16.222 0.8961  0.9734     7924.249
   3_occ:  16.213 0.8962  0.9734     7911.655
   4_bss:  16.188 0.8964  0.9630     7894.040
   4_xyz:  15.166 0.9057  0.9654     7180.001
   4_adp:  14.976 0.9075  0.9590     7092.164
   4_occ:  14.966 0.9076  0.9590     7084.066
   5_bss:  14.973 0.9075  0.9640     7085.091
   5_xyz:  14.998 0.9074  0.9652     7120.086
   5_adp:  15.190 0.9058  0.9574     7241.593
   5_occ:  15.196 0.9058  0.9573     7243.867
   5_bss:  15.197 0.9057  0.9602     7244.536
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6339e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6339e-01
   1_xyz:   1.353  0.010  0.088 15.569  0.006  4.114   9.5472e-02
   1_adp:   1.353  0.010  0.088 15.569  0.006  4.114   9.5472e-02
   1_occ:   1.353  0.010  0.088 15.569  0.006  4.114   9.5472e-02
   2_bss:   1.353  0.010  0.088 15.569  0.006  4.114   9.5472e-02
   2_xyz:   1.093  0.008  0.080 14.461  0.004  4.133   6.5587e-02
   2_adp:   1.093  0.008  0.080 14.461  0.004  4.133   6.5587e-02
   2_occ:   1.093  0.008  0.080 14.461  0.004  4.133   6.5587e-02
   3_bss:   1.093  0.008  0.080 14.461  0.004  4.133   6.5587e-02
   3_xyz:   1.151  0.011  0.084 14.748  0.004  4.120   7.7530e-02
   3_adp:   1.151  0.011  0.084 14.748  0.004  4.120   7.7530e-02
   3_occ:   1.151  0.011  0.084 14.748  0.004  4.120   7.7530e-02
   4_bss:   1.151  0.011  0.084 14.748  0.004  4.120   7.7530e-02
   4_xyz:   1.030  0.009  0.077 14.383  0.004  4.128   6.2696e-02
   4_adp:   1.030  0.009  0.077 14.383  0.004  4.128   6.2696e-02
   4_occ:   1.030  0.009  0.077 14.383  0.004  4.128   6.2696e-02
   5_bss:   1.030  0.009  0.077 14.383  0.004  4.128   6.2696e-02
   5_xyz:   0.989  0.008  0.075 14.288  0.003  4.130   5.7986e-02
   5_adp:   0.989  0.008  0.075 14.288  0.003  4.130   5.7986e-02
   5_occ:   0.989  0.008  0.075 14.288  0.003  4.130   5.7986e-02
   5_bss:   0.989  0.008  0.075 14.288  0.003  4.130   5.7986e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4459e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4459e-01
   1_xyz:   9.489  0.046  0.304 83.692  0.058  2.176   9.2230e-02
   1_adp:   9.489  0.046  0.304 83.692  0.058  2.176   9.2230e-02
   1_occ:   9.489  0.046  0.304 83.692  0.058  2.176   9.2230e-02
   2_bss:   9.489  0.046  0.304 83.692  0.058  2.176   9.2230e-02
   2_xyz:   6.763  0.054  0.311 82.035  0.037  2.338   8.0375e-02
   2_adp:   6.763  0.054  0.311 82.035  0.037  2.338   8.0375e-02
   2_occ:   6.763  0.054  0.311 82.035  0.037  2.338   8.0375e-02
   3_bss:   6.763  0.054  0.311 82.035  0.037  2.338   8.0375e-02
   3_xyz:   7.300  0.054  0.287 87.600  0.033  2.296   5.9180e-02
   3_adp:   7.300  0.054  0.287 87.600  0.033  2.296   5.9180e-02
   3_occ:   7.300  0.054  0.287 87.600  0.033  2.296   5.9180e-02
   4_bss:   7.300  0.054  0.287 87.600  0.033  2.296   5.9180e-02
   4_xyz:   7.563  0.045  0.243 82.990  0.035  2.386   5.0612e-02
   4_adp:   7.563  0.045  0.243 82.990  0.035  2.386   5.0612e-02
   4_occ:   7.563  0.045  0.243 82.990  0.035  2.386   5.0612e-02
   5_bss:   7.563  0.045  0.243 82.990  0.035  2.386   5.0612e-02
   5_xyz:   8.064  0.042  0.229 82.081  0.034  2.429   3.5346e-02
   5_adp:   8.064  0.042  0.229 82.081  0.034  2.429   3.5346e-02
   5_occ:   8.064  0.042  0.229 82.081  0.034  2.429   3.5346e-02
   5_bss:   8.064  0.042  0.229 82.081  0.034  2.429   3.5346e-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: 113.31   0.00  16.62 113.31   0.00  12.77  63.63   0.00  37.58
   1_occ: 113.31   0.00  16.62 113.31   0.00  12.77  63.63   0.00  37.58
   2_bss: 113.31   0.00  16.62 113.31   0.00  12.77  63.63   0.00  37.58
   2_xyz: 113.31   0.00  16.62 113.31   0.00  12.77  63.63   0.00  37.58
   2_adp: 111.40   0.00  18.24  96.17   0.00  13.09 111.40   2.24  46.29
   2_occ: 111.40   0.00  18.24  96.17   0.00  13.09 111.40   2.24  46.29
   3_bss: 111.40   0.00  18.24  96.17   0.00  13.09 111.40   2.24  46.29
   3_xyz: 111.40   0.00  18.24  96.17   0.00  13.09 111.40   2.24  46.29
   3_adp: 102.70   0.00  17.00  86.18   0.00  12.30 102.70   4.71  42.57
   3_occ: 102.70   0.00  17.00  86.18   0.00  12.30 102.70   4.71  42.57
   4_bss: 102.70   0.00  17.00  86.18   0.00  12.30 102.70   4.71  42.57
   4_xyz: 102.70   0.00  17.00  86.18   0.00  12.30 102.70   4.71  42.57
   4_adp: 102.04   0.00  16.63  83.85   0.00  12.08 102.04   4.54  41.37
   4_occ: 102.04   0.00  16.63  83.85   0.00  12.08 102.04   4.54  41.37
   5_bss: 102.04   0.00  16.63  83.85   0.00  12.08 102.04   4.54  41.37
   5_xyz: 102.04   0.00  16.63  83.85   0.00  12.08 102.04   4.54  41.37
   5_adp: 106.79   0.00  16.68  87.53   0.00  12.03 106.79   4.21  41.98
   5_occ: 106.79   0.00  16.68  87.53   0.00  12.03 106.79   4.21  41.98
   5_bss: 106.79   0.00  16.68  87.53   0.00  12.03 106.79   4.21  41.99
------------------------------------------------------------------------
 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:    1.588    0.014    0.316
   1_adp:    1.588    0.014    0.316
   1_occ:    1.588    0.014    0.316
   2_bss:    1.588    0.014    0.316
   2_xyz:    1.301    0.016    0.432
   2_adp:    1.301    0.016    0.432
   2_occ:    1.301    0.016    0.432
   3_bss:    1.301    0.016    0.432
   3_xyz:    1.258    0.016    0.525
   3_adp:    1.258    0.016    0.525
   3_occ:    1.258    0.016    0.525
   4_bss:    1.258    0.016    0.525
   4_xyz:    1.206    0.031    0.548
   4_adp:    1.206    0.031    0.548
   4_occ:    1.206    0.031    0.548
   5_bss:    1.206    0.031    0.548
   5_xyz:    1.253    0.031    0.560
   5_adp:    1.253    0.031    0.560
   5_occ:    1.253    0.031    0.560
   5_bss:    1.253    0.031    0.560
------------------------------------------------------------------------

CPU time actual refinement: 340.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/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_1033/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1033/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.05 
  Macro-tasks:
    bulk solvent and scale       = 56.25  
    individual site refinement   = 132.90 
    weights calculation          = 29.52  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 225.43 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 101.29 
    alpha_beta                      = 8.47   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.75 
    fmodel                         = 8.83   
    r_factors                      = 0.33   
    phase_errors                   = 10.57  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 243.58 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.827 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    621 calls, 101.09 s
gradients_fft:          566 calls,  97.61 s

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

# Date 2008-01-16 Time 06:16:24 PST -0800 (1200492984.64 s)
Start R-work = 0.4027, R-free = 0.3926 (no bulk solvent and anisotropic scale)
Final R-work = 0.1377, R-free = 0.1839 (no bulk solvent and anisotropic scale)

Start R-work = 0.3883, R-free = 0.3836
Final R-work = 0.1200, R-free = 0.1694