# Date 2008-01-16 Time 05:23:38 PST -0800 (1200489818.63 s)
#phil __OFF__

Command line arguments: "../713.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16450
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 713

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.8686, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00072
Completeness in resolution range: 0.949862
Completeness with d_max=infinity: 0.946923

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0007

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00072
Completeness in resolution range: 0.949862
Completeness with d_max=infinity: 0.946923

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2806 [2174/2202]  1954   220  10.1%
  bin  2:  4.2806 -  3.4106 [2068/2087]  1864   204   9.9%
  bin  3:  3.4106 -  2.9833 [2066/2086]  1858   208  10.1%
  bin  4:  2.9833 -  2.7122 [2032/2057]  1830   202   9.9%
  bin  5:  2.7122 -  2.5188 [2013/2032]  1808   205  10.2%
  bin  6:  2.5188 -  2.3709 [2008/2054]  1810   198   9.9%
  bin  7:  2.3709 -  2.2526 [2000/2033]  1803   197   9.8%
  bin  8:  2.2526 -  2.1548 [2002/2038]  1796   206  10.3%
  bin  9:  2.1548 -  2.0721 [1988/2017]  1793   195   9.8%
  bin 10:  2.0721 -  2.0007 [1238/2017]  1114   124  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/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:
        1.64 -     2.29: 11
        2.29 -     2.94: 1576
        2.94 -     3.59: 4398
        3.59 -     4.25: 9003
        4.25 -     4.90: 12812
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.637 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.904 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.904 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.005 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27795 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_713/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/model_refine_001.geo

CPU time processing inputs: 9.46


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.8686 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4476   r_free= 0.4400   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259371                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1406  157 0.3509 0.3467      6.5104      6.4748|
|  2:  4.7741 -  3.8095 0.99   1353  152 0.3837 0.4204      6.7915       6.853|
|  3:  3.8095 -  3.3339 0.99   1331  149 0.4233 0.3824      6.6597      6.5751|
|  4:  3.3339 -  3.0318 0.99   1320  137 0.4346 0.4459      6.4925      6.4537|
|  5:  3.0318 -  2.8160 0.99   1308  150 0.4683 0.4014      6.3476      6.3374|
|  6:  2.8160 -  2.6509 0.98   1302  145 0.4781 0.4947       6.249      6.1603|
|  7:  2.6509 -  2.5188 0.99   1294  149 0.4691 0.4383      6.2172      6.1247|
|  8:  2.5188 -  2.4096 0.98   1305  139 0.4895 0.4824      6.1655       6.156|
|  9:  2.4096 -  2.3172 0.98   1293  147 0.4959 0.4640      6.0944      6.1677|
| 10:  2.3172 -  2.2375 0.98   1273  140 0.5112 0.4655      6.0992      6.0519|
| 11:  2.2375 -  2.1677 0.99   1290  145 0.5011 0.4849      6.0211      6.0353|
| 12:  2.1677 -  2.1059 0.98   1279  138 0.4938 0.5628      5.9519      6.0125|
| 13:  2.1059 -  2.0506 0.97   1259  139 0.5245 0.4804      5.8872        5.82|
| 14:  2.0506 -  2.0007 0.48    617   72 0.4691 0.5405      5.8509      5.7975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1406   157  0.73  31.66   0.83     0.76      61603.53|
|  2:  4.7741 -  3.8095  1353   152  0.73  32.25   0.91     0.81      91588.46|
|  3:  3.8095 -  3.3339  1331   149  0.65  39.63   0.89     0.80      95380.64|
|  4:  3.3339 -  3.0318  1320   137  0.58  45.57   0.90     0.73      84198.89|
|  5:  3.0318 -  2.8160  1308   150  0.52  50.40   0.89     0.67      65046.46|
|  6:  2.8160 -  2.6509  1302   145  0.47  54.37   0.88     0.62      58538.59|
|  7:  2.6509 -  2.5188  1294   149  0.47  54.18   0.92     0.61      53275.66|
|  8:  2.5188 -  2.4096  1305   139  0.45  55.69   0.90     0.61      50356.00|
|  9:  2.4096 -  2.3172  1293   147  0.44  56.79   0.90     0.63      47076.89|
| 10:  2.3172 -  2.2375  1273   140  0.44  56.80   0.92     0.63      43240.48|
| 11:  2.2375 -  2.1677  1290   145  0.40  59.87   0.91     0.59      43051.88|
| 12:  2.1677 -  2.1059  1279   138  0.34  64.54   0.92     0.50      42639.12|
| 13:  2.1059 -  2.0506  1259   139  0.27  70.15   0.89     0.40      39432.76|
| 14:  2.0506 -  2.0007   617    72  0.25  71.34   0.98     0.32      31516.01|
|alpha:            min =        0.32 max =            0.81 mean =         0.63|
|beta:             min =    31516.01 max =        95380.64 mean =     58970.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.09|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.58|
|-----------------------------------------------------------------------------|

============================== 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 = 8.406951              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.145   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.869358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.458   (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 |  1.637 -  1.963:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.963 -  2.289:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.289 -  2.616:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.616 -  2.942:     1537 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.942 -  3.268:     1866 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.268 -  3.595:     2532 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.595 -  3.921:     4640 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.921 -  4.247:     4363 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.574:     5797 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     7015 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.637 |       0.208 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4476   r_free= 0.4400   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4362   r_free= 0.4284   ksol= 0.30   Bsol= 50.00   scale= 0.934   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.72,3.82,3.15,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.249633                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.098033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.667   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.966656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.123   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4362      final r-factor (work) = 0.3322          |
| start r-factor (free) = 0.4284      final r-factor (free) = 0.3555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3385 = 7.10 * 0.50 * 6.2473 + 1.00 * 0.1668                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7841 = 7.10 * 0.50 * 6.1051 + 1.00 * 0.1171                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3322      final r-factor (work) = 0.3030          |
| start r-factor (free) = 0.3555      final r-factor (free) = 0.3711          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9074 = 0.97 * 1.00 * 6.1051 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8095 = 0.97 * 1.00 * 5.9913 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.08  18.32    None  None   None       |
|    all(noH): 2823   0      0.00    111.08  18.32    None  None   None       |
|    Sol.    : 438    0      0.00    111.08  39.06    None  None   None       |
|    Mac.    : 2385   0      0.00    85.34   14.51    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 -  11.108: 1109   |   5:    55.538 -  66.645:   60        |
|      1:    11.108 -  22.215:  936   |   6:    66.645 -  77.753:   30        |
|      2:    22.215 -  33.323:  381   |   7:    77.753 -  88.860:   10        |
|      3:    33.323 -  44.430:  172   |   8:    88.860 -  99.968:    3        |
|      4:    44.430 -  55.538:  120   |   9:    99.968 - 111.075:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3030 r_free = 0.3711             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3027 r_free = 0.3709             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3027   r_free= 0.3709   ksol= 0.30   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.72,3.82,3.15,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.999845                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3009   r_free= 0.3682   ksol= 0.31   Bsol= 64.86   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,1.86,1.52,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.998867                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.659534              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.757  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3009      final r-factor (work) = 0.2409          |
| start r-factor (free) = 0.3682      final r-factor (free) = 0.2959          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0752 = 4.66 * 0.50 * 5.9912 + 1.00 * 0.1171                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8497 = 4.66 * 0.50 * 5.9138 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2409      final r-factor (work) = 0.2312          |
| start r-factor (free) = 0.2959      final r-factor (free) = 0.2828          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0172 = 0.34 * 1.00 * 5.9138 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9682 = 0.34 * 1.00 * 5.7891 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.54  17.65    None  None   None       |
|    all(noH): 2823   0      0.00    110.54  17.65    None  None   None       |
|    Sol.    : 438    0      1.03    110.54  38.73    None  None   None       |
|    Mac.    : 2385   0      0.00    83.13   13.78    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 -  11.054: 1200   |   5:    55.271 -  66.325:   53        |
|      1:    11.054 -  22.108:  933   |   6:    66.325 -  77.379:   25        |
|      2:    22.108 -  33.162:  316   |   7:    77.379 -  88.433:   12        |
|      3:    33.162 -  44.217:  169   |   8:    88.433 -  99.487:    2        |
|      4:    44.217 -  55.271:  111   |   9:    99.487 - 110.541:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2312 r_free = 0.2828             target_work(ml) = 5.773         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2310 r_free = 0.2829             target_work(ml) = 5.773         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2310   r_free= 0.2829   ksol= 0.31   Bsol= 64.86   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,1.86,1.52,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.773266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2312   r_free= 0.2829   ksol= 0.33   Bsol= 74.75   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,0.92,0.76,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.773530                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.778080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.596   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.061706              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2312      final r-factor (work) = 0.1706          |
| start r-factor (free) = 0.2829      final r-factor (free) = 0.2146          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7981 = 5.78 * 0.50 * 5.7894 + 1.00 * 0.0722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3965 = 5.78 * 0.50 * 5.6477 + 1.00 * 0.0799                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1706      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2146      final r-factor (free) = 0.2040          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6554 = 2.06 * 1.00 * 5.6477 + 1.00 * 0.0114                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2243 = 2.06 * 1.00 * 5.4367 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.86  18.13    None  None   None       |
|    all(noH): 2823   0      0.00    111.86  18.13    None  None   None       |
|    Sol.    : 438    0      3.86    111.86  46.05    None  None   None       |
|    Mac.    : 2385   0      0.00    101.66  13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.186: 1371   |   5:    55.929 -  67.114:   91        |
|      1:    11.186 -  22.371:  840   |   6:    67.114 -  78.300:   62        |
|      2:    22.371 -  33.557:  205   |   7:    78.300 -  89.486:   26        |
|      3:    33.557 -  44.743:  116   |   8:    89.486 - 100.671:    6        |
|      4:    44.743 -  55.929:  100   |   9:   100.671 - 111.857:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1510 r_free = 0.2040             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1509 r_free = 0.2039             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1509   r_free= 0.2039   ksol= 0.33   Bsol= 74.75   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,0.92,0.76,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410325                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1511   r_free= 0.2039   ksol= 0.34   Bsol= 88.09   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-0.11,0.41,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.411533                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.633642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.922  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.843439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.459  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1511      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.2039      final r-factor (free) = 0.1822          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9627 = 3.63 * 0.50 * 5.4396 + 1.00 * 0.0799                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7983 = 3.63 * 0.50 * 5.3515 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1822      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5290 = 0.84 * 1.00 * 5.3515 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4620 = 0.84 * 1.00 * 5.2737 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.20  17.41    None  None   None       |
|    all(noH): 2823   0      0.00    110.20  17.41    None  None   None       |
|    Sol.    : 438    0      4.51    110.20  45.03    None  None   None       |
|    Mac.    : 2385   0      0.00    106.00  12.34    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 -  11.020: 1408   |   5:    55.100 -  66.120:   79        |
|      1:    11.020 -  22.040:  846   |   6:    66.120 -  77.140:   56        |
|      2:    22.040 -  33.060:  180   |   7:    77.140 -  88.160:   30        |
|      3:    33.060 -  44.080:  119   |   8:    88.160 -  99.180:    9        |
|      4:    44.080 -  55.100:   90   |   9:    99.180 - 110.200:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1761             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1761             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1761   ksol= 0.34   Bsol= 88.09   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-0.11,0.41,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.253546                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1758   ksol= 0.33   Bsol= 81.24   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-0.33,0.62,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.254150                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.011590              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.745  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332371              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0173 = 3.01 * 0.50 * 5.2742 + 1.00 * 0.0755                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9561 = 3.01 * 0.50 * 5.2341 + 1.00 * 0.0746                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7534 = 0.33 * 1.00 * 5.2341 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7439 = 0.33 * 1.00 * 5.2131 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.74  16.58    None  None   None       |
|    all(noH): 2823   0      0.00    106.74  16.58    None  None   None       |
|    Sol.    : 438    0      1.97    106.74  41.99    None  None   None       |
|    Mac.    : 2385   0      0.00    101.11  11.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.675: 1402   |   5:    53.372 -  64.047:   71        |
|      1:    10.675 -  21.349:  861   |   6:    64.047 -  74.721:   47        |
|      2:    21.349 -  32.023:  193   |   7:    74.721 -  85.396:   18        |
|      3:    32.023 -  42.698:  118   |   8:    85.396 -  96.070:    8        |
|      4:    42.698 -  53.372:   99   |   9:    96.070 - 106.744:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1660             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1660             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1660   ksol= 0.33   Bsol= 81.24   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-0.33,0.62,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.203810                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1406  157 0.1012 0.1343      5.4138      5.5992|
|  2:  4.7741 -  3.8095 0.99   1353  152 0.0852 0.1056      5.4419      5.6316|
|  3:  3.8095 -  3.3339 0.99   1331  149 0.1078 0.1537      5.4942      5.8631|
|  4:  3.3339 -  3.0318 0.99   1320  137 0.1280 0.1720      5.4976      5.6534|
|  5:  3.0318 -  2.8160 0.99   1308  150 0.1446 0.1805      5.4021       5.586|
|  6:  2.8160 -  2.6509 0.98   1302  145 0.1361 0.2195        5.29      5.5642|
|  7:  2.6509 -  2.5188 0.99   1294  149 0.1377 0.1748       5.239      5.3876|
|  8:  2.5188 -  2.4096 0.98   1305  139 0.1262 0.1779      5.1528      5.3903|
|  9:  2.4096 -  2.3172 0.98   1293  147 0.1290 0.1948      5.1029      5.4109|
| 10:  2.3172 -  2.2375 0.98   1273  140 0.1255 0.1752       5.047      5.1938|
| 11:  2.2375 -  2.1677 0.99   1290  145 0.1239 0.1889      4.9845      5.3121|
| 12:  2.1677 -  2.1059 0.98   1279  138 0.1195 0.1900      4.9198      5.2448|
| 13:  2.1059 -  2.0506 0.97   1259  139 0.1195 0.1724      4.8304      5.0278|
| 14:  2.0506 -  2.0007 0.48    617   72 0.1073 0.1870      4.7244      5.0192|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1406   157  0.94   9.70   0.96     0.93       7797.78|
|  2:  4.7741 -  3.8095  1353   152  0.95   8.34   1.00     0.98       9404.64|
|  3:  3.8095 -  3.3339  1331   149  0.93  11.59   1.02     1.02      10860.25|
|  4:  3.3339 -  3.0318  1320   137  0.91  14.57   1.01     0.98      11329.46|
|  5:  3.0318 -  2.8160  1308   150  0.89  17.43   1.00     0.97       9608.03|
|  6:  2.8160 -  2.6509  1302   145  0.88  17.92   0.98     0.96       8264.19|
|  7:  2.6509 -  2.5188  1294   149  0.90  16.65   0.99     0.96       6949.76|
|  8:  2.5188 -  2.4096  1305   139  0.90  16.55   0.99     0.96       6346.61|
|  9:  2.4096 -  2.3172  1293   147  0.89  17.25   0.99     0.93       5641.81|
| 10:  2.3172 -  2.2375  1273   140  0.89  17.52   0.99     0.95       5242.64|
| 11:  2.2375 -  2.1677  1290   145  0.89  17.00   0.98     0.94       4730.66|
| 12:  2.1677 -  2.1059  1279   138  0.90  16.42   1.00     0.99       4317.50|
| 13:  2.1059 -  2.0506  1259   139  0.89  17.15   0.98     0.97       3647.18|
| 14:  2.0506 -  2.0007   617    72  0.91  15.41   0.96     0.92       2891.59|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2891.59 max =        11329.46 mean =      7128.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.51 mean =        14.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1660   ksol= 0.32   Bsol= 71.20   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.38,0.72,-0.00,0.00,0.00); trace/3= -0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.203597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1660   ksol= 0.32   Bsol= 71.20   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.38,0.72,-0.00,0.00,0.00); trace/3= -0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.203597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1406  157 0.1008 0.1340      5.4102      5.5948|
|  2:  4.7741 -  3.8095 0.99   1353  152 0.0848 0.1049      5.4376      5.6258|
|  3:  3.8095 -  3.3339 0.99   1331  149 0.1078 0.1538       5.492      5.8649|
|  4:  3.3339 -  3.0318 0.99   1320  137 0.1283 0.1722      5.4993      5.6536|
|  5:  3.0318 -  2.8160 0.99   1308  150 0.1449 0.1809      5.4042      5.5884|
|  6:  2.8160 -  2.6509 0.98   1302  145 0.1361 0.2197       5.291      5.5651|
|  7:  2.6509 -  2.5188 0.99   1294  149 0.1379 0.1752      5.2401       5.389|
|  8:  2.5188 -  2.4096 0.98   1305  139 0.1262 0.1779      5.1536      5.3906|
|  9:  2.4096 -  2.3172 0.98   1293  147 0.1290 0.1947      5.1033      5.4112|
| 10:  2.3172 -  2.2375 0.98   1273  140 0.1255 0.1757      5.0475      5.1957|
| 11:  2.2375 -  2.1677 0.99   1290  145 0.1239 0.1889      4.9846      5.3114|
| 12:  2.1677 -  2.1059 0.98   1279  138 0.1195 0.1901      4.9198      5.2456|
| 13:  2.1059 -  2.0506 0.97   1259  139 0.1196 0.1722      4.8304       5.027|
| 14:  2.0506 -  2.0007 0.48    617   72 0.1073 0.1867      4.7241      5.0182|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1406   157  0.94   9.68   0.96     0.93       7757.94|
|  2:  4.7741 -  3.8095  1353   152  0.95   8.31   1.00     0.99       9313.41|
|  3:  3.8095 -  3.3339  1331   149  0.93  11.51   1.02     1.02      10770.35|
|  4:  3.3339 -  3.0318  1320   137  0.91  14.58   1.01     0.98      11352.58|
|  5:  3.0318 -  2.8160  1308   150  0.89  17.45   1.00     0.97       9638.69|
|  6:  2.8160 -  2.6509  1302   145  0.88  17.95   0.98     0.96       8287.83|
|  7:  2.6509 -  2.5188  1294   149  0.90  16.67   0.99     0.96       6965.50|
|  8:  2.5188 -  2.4096  1305   139  0.90  16.56   0.99     0.96       6358.59|
|  9:  2.4096 -  2.3172  1293   147  0.89  17.27   0.99     0.93       5651.79|
| 10:  2.3172 -  2.2375  1273   140  0.89  17.54   0.99     0.95       5249.89|
| 11:  2.2375 -  2.1677  1290   145  0.89  17.01   0.98     0.94       4735.36|
| 12:  2.1677 -  2.1059  1279   138  0.90  16.42   1.00     1.00       4319.14|
| 13:  2.1059 -  2.0506  1259   139  0.89  17.14   0.98     0.97       3643.42|
| 14:  2.0506 -  2.0007   617    72  0.91  15.39   0.96     0.92       2885.13|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2885.13 max =        11352.58 mean =      7120.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.76 mean =        14.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.75  16.58    None  None   None       |
|    all(noH): 2823   0      0.00    106.75  16.58    None  None   None       |
|    Sol.    : 438    0      1.98    106.75  41.99    None  None   None       |
|    Mac.    : 2385   0      0.00    101.12  11.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.677: 1402   |   5:    53.375 -  64.050:   71        |
|      1:    10.677 -  21.352:  861   |   6:    64.050 -  74.724:   47        |
|      2:    21.352 -  32.026:  193   |   7:    74.724 -  85.399:   18        |
|      3:    32.026 -  42.701:  118   |   8:    85.399 -  96.073:    8        |
|      4:    42.701 -  53.375:   99   |   9:    96.073 - 106.747:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.525 - 5.704
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 319
   mapped sites are within: 0.726 - 5.704

peak=    6.383 closest distance to " O   HOH Z 210 " =    1.374
peak=    5.409 closest distance to " O   HOH Z 113 " =    2.010
peak=    5.372 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.178 closest distance to " CB  SER A  63 " =    1.160
peak=    5.115 closest distance to " CG  PRO A  54 " =    1.398
peak=    4.923 closest distance to " O   HOH Z  49 " =    1.234
peak=    4.725 closest distance to " CB  ARG A 190 " =    1.745
peak=    4.700 closest distance to " CB  GLN A 183 " =    1.266
peak=    4.668 closest distance to " CD2 TRP A 179 " =    1.274
peak=    4.606 closest distance to " CG  PRO A  90 " =    1.316
peak=    4.597 closest distance to " O   PRO A 198 " =    1.563
peak=    4.562 closest distance to " CZ  PHE A 218 " =    1.162
peak=    4.535 closest distance to " CA  ALA A  51 " =    0.952
peak=    4.486 closest distance to " O   HOH Z 369 " =    2.141
peak=    4.359 closest distance to " O   HOH Z  43 " =    1.987
peak=    4.337 closest distance to " CD  LYS A 166 " =    1.371
peak=    4.320 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.293 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.266 closest distance to " O   HOH Z 234 " =    3.850
peak=    4.253 closest distance to " CA  TYR A  30 " =    0.907
peak=    4.181 closest distance to " CB  GLU A 152 " =    1.149
peak=    4.171 closest distance to " O   HOH Z 403 " =    1.700
peak=    4.156 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.154 closest distance to " O   HOH Z 298 " =    1.913
peak=    4.116 closest distance to " O   HOH Z 214 " =    1.386
peak=    4.110 closest distance to " O   HOH Z 368 " =    2.222
peak=    4.110 closest distance to " CG  PRO A 198 " =    1.152
peak=    4.102 closest distance to " O   HOH Z 402 " =    1.623
peak=    4.101 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    4.089 closest distance to " O   HOH Z 346 " =    1.527
peak=    4.087 closest distance to " CD  ARG A 269 " =    1.023
peak=    4.071 closest distance to " CB  VAL A 202 " =    1.501
peak=    4.070 closest distance to " CB  PRO A  54 " =    0.912
peak=    4.057 closest distance to " CZ  PHE A  38 " =    1.232
peak=    4.054 closest distance to " O   SER A  87 " =    2.263
peak=    4.035 closest distance to " O   HOH Z 189 " =    2.845
peak=    4.010 closest distance to " O   HOH Z 362 " =    3.369
peak=    4.009 closest distance to " O   HOH Z  44 " =    2.247
peak=    3.999 closest distance to " CB  TRP A 266 " =    1.051
peak=    3.998 closest distance to " O   HOH Z 423 " =    1.852
peak=    3.989 closest distance to " O   HOH Z 412 " =    3.644
peak=    3.989 closest distance to " ND2 ASN A 187 " =    1.546
peak=    3.983 closest distance to " CG  ARG A  66 " =    2.636
peak=    3.976 closest distance to " CA  ARG A  36 " =    1.079
peak=    3.970 closest distance to " O   HOH Z 134 " =    1.501
peak=    3.969 closest distance to " CB  GLU A 128 " =    1.122
peak=    3.965 closest distance to " CB  GLU A 277 " =    3.823
peak=    3.956 closest distance to " CB  TYR A 169 " =    0.819
peak=    3.954 closest distance to " CA  ARG A 195 " =    1.193
peak=    3.952 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.944 closest distance to " O   ALA A 165 " =    1.329
peak=    3.911 closest distance to " NE2 GLN A  77 " =    3.293
peak=    3.909 closest distance to " O   HOH Z 425 " =    1.424
peak=    3.908 closest distance to " O   HOH Z 248 " =    1.551
peak=    3.899 closest distance to " CG  PRO A 243 " =    1.086
peak=    3.892 closest distance to " O   HOH Z  40 " =    1.857
peak=    3.890 closest distance to " O   HOH Z  21 " =    1.786
peak=    3.881 closest distance to " O   HOH Z 285 " =    2.551
peak=    3.865 closest distance to " CA  ALA A 295 " =    1.076
peak=    3.856 closest distance to " CA  ALA A 160 " =    0.942
peak=    3.835 closest distance to " CB  TRP A 179 " =    1.366
peak=    3.833 closest distance to " O   HOH Z 316 " =    3.066
peak=    3.830 closest distance to " O   HOH Z 258 " =    2.073
peak=    3.829 closest distance to " O   HOH Z  15 " =    2.280
peak=    3.820 closest distance to " NE2 GLN A  11 " =    1.156
peak=    3.805 closest distance to " O   HOH Z 406 " =    1.646
peak=    3.803 closest distance to " O   HOH Z 261 " =    2.123
peak=    3.800 closest distance to " O   HOH Z 357 " =    2.180
peak=    3.793 closest distance to " NH1AARG A 145 " =    1.382
peak=    3.776 closest distance to " O   HOH Z 265 " =    2.098
peak=    3.769 closest distance to " CG  GLN A  11 " =    1.264
peak=    3.760 closest distance to " O   HOH Z 336 " =    1.931
peak=    3.760 closest distance to " CA  ILE A 106 " =    0.821
peak=    3.756 closest distance to " O   HOH Z  48 " =    1.851
peak=    3.742 closest distance to " O   HOH Z 251 " =    1.585
peak=    3.735 closest distance to " O   HOH Z 433 " =    1.503
peak=    3.734 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.730 closest distance to " CB  ARG A  79 " =    1.122
peak=    3.730 closest distance to " OG BSER A 164 " =    2.276
peak=    3.727 closest distance to " O   HOH Z  63 " =    1.980
peak=    3.722 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.710 closest distance to " O   ASN A  74 " =    1.625
peak=    3.700 closest distance to " O   HOH Z  97 " =    2.053
peak=    3.699 closest distance to " CB  ASP A 140 " =    0.953
peak=    3.698 closest distance to " O   HOH Z 280 " =    2.997
peak=    3.694 closest distance to " O   HOH Z 287 " =    1.887
peak=    3.681 closest distance to " CD  PRO A  54 " =    0.977
peak=    3.673 closest distance to " N   CYS A 260 " =    0.798
peak=    3.667 closest distance to " O   HOH Z  19 " =    1.731
peak=    3.658 closest distance to " O   HOH Z 427 " =    3.089
peak=    3.657 closest distance to " CB  ASP A 124 " =    0.755
peak=    3.649 closest distance to " O   HOH Z 214 " =    2.194
peak=    3.646 closest distance to " CB  PRO A  90 " =    1.200
peak=    3.642 closest distance to " CG1 VAL A 153 " =    1.068
peak=    3.641 closest distance to " CG1 ILE A  33 " =    1.207
peak=    3.638 closest distance to " CB  ASN A 285 " =    0.950
peak=    3.636 closest distance to " O   HOH Z 176 " =    1.569
peak=    3.634 closest distance to " OH  TYR A 116 " =    1.188
peak=    3.633 closest distance to " OD1 ASN A 217 " =    1.721
peak=    3.628 closest distance to " N   ASN A  39 " =    1.311
peak=    3.625 closest distance to " CA  GLU A  46 " =    0.880
peak=    3.623 closest distance to " O   HOH Z  59 " =    2.379
peak=    3.622 closest distance to " ND2 ASN A 249 " =    0.945
peak=    3.618 closest distance to " CB  SER A  62 " =    0.858
peak=    3.617 closest distance to " O   HOH Z 133 " =    2.859
peak=    3.615 closest distance to " OD1 ASN A  69 " =    2.444
peak=    3.611 closest distance to " CD1 LEU A  96 " =    0.797
peak=    3.611 closest distance to " CB  ASN A 148 " =    1.444
peak=    3.608 closest distance to " CB  ASN A 142 " =    1.111
peak=    3.607 closest distance to " O   HOH Z 142 " =    1.589
peak=    3.605 closest distance to " O   HOH Z  30 " =    1.119
peak=    3.599 closest distance to " CA  SER A  87 " =    1.060
peak=    3.598 closest distance to " CG2BVAL A  41 " =    0.890
peak=    3.591 closest distance to " CB  ASN A 187 " =    1.191
peak=    3.590 closest distance to " O   HOH Z  80 " =    1.943
peak=    3.587 closest distance to " O   HOH Z 389 " =    2.008
peak=    3.586 closest distance to " OE1 GLN A  55 " =    1.551
peak=    3.586 closest distance to " CB  ALA A 291 " =    1.140
peak=    3.585 closest distance to " CB  LEU A  83 " =    0.841
peak=    3.581 closest distance to " CB  THR A  52 " =    0.867
peak=    3.580 closest distance to " O   HOH Z 156 " =    2.690
peak=    3.579 closest distance to " O   HOH Z 294 " =    1.513
peak=    3.578 closest distance to " O   ALA A 158 " =    1.099
peak=    3.576 closest distance to " CG2AVAL A  72 " =    1.903
peak=    3.575 closest distance to " O   HOH Z  78 " =    1.634
peak=    3.571 closest distance to " O   HOH Z 193 " =    1.850
peak=    3.570 closest distance to " O  BHOH Z 338 " =    2.118
peak=    3.566 closest distance to " CA  GLU A 152 " =    0.895
peak=    3.562 closest distance to " O   HOH Z 359 " =    1.603
peak=    3.559 closest distance to " CA  PRO A  54 " =    1.146
peak=    3.557 closest distance to " CG2 VAL A 197 " =    1.158
peak=    3.555 closest distance to " CD2 LEU A 297 " =    0.962
peak=    3.552 closest distance to " O   HOH Z 126 " =    1.550
peak=    3.549 closest distance to " O   HOH Z 203 " =    1.840
peak=    3.548 closest distance to " O   HOH Z 174 " =    2.336
peak=    3.548 closest distance to " NZ  LYS A 117 " =    2.948
peak=    3.547 closest distance to " O   HOH Z 147 " =    1.733
peak=    3.541 closest distance to " O   HOH Z 374 " =    2.992
peak=    3.540 closest distance to " CB  GLN A  88 " =    1.127
peak=    3.540 closest distance to " CA  ASP A 162 " =    1.069
peak=    3.538 closest distance to " O   HOH Z 325 " =    2.214
peak=    3.536 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.532 closest distance to " NZ  LYS A  48 " =    1.383
peak=    3.532 closest distance to " CB  VAL A 265 " =    1.220
peak=    3.531 closest distance to " O   HOH Z 303 " =    2.371
peak=    3.531 closest distance to " O   HOH Z 383 " =    2.177
peak=    3.531 closest distance to " O   HOH Z 130 " =    2.237
peak=    3.530 closest distance to " CD1 LEU A 300 " =    1.126
peak=    3.529 closest distance to " O   PRO A 213 " =    1.548
peak=    3.515 closest distance to " O   HOH Z 250 " =    1.499
peak=    3.515 closest distance to " O   HOH Z 345 " =    1.692
peak=    3.512 closest distance to " O   HOH Z  40 " =    2.137
peak=    3.506 closest distance to " CA  TYR A 116 " =    1.315
peak=    3.502 closest distance to " O   HOH Z  20 " =    1.559
peak=    3.496 closest distance to " CG  ARG A 138 " =    1.207
peak=    3.492 closest distance to " O   HOH Z 126 " =    2.018
peak=    3.490 closest distance to " CB  ALA A   9 " =    1.652
peak=    3.487 closest distance to " O   HOH Z 403 " =    2.202
peak=    3.477 closest distance to " O   HOH Z 291 " =    1.419
peak=    3.475 closest distance to " CB  PHE A 204 " =    0.829
peak=    3.467 closest distance to " CG  GLU A  37 " =    0.959
peak=    3.465 closest distance to " O   HOH Z 299 " =    4.465
peak=    3.463 closest distance to " CG  MET A 185 " =    1.117
peak=    3.460 closest distance to " N   HIS A 108 " =    1.906
peak=    3.458 closest distance to " CA  ALA A  21 " =    1.319
peak=    3.457 closest distance to " CA  ALA A 100 " =    0.867
peak=    3.455 closest distance to " OG BSER A 134 " =    2.892
peak=    3.455 closest distance to " O   HOH Z 298 " =    2.374
peak=    3.454 closest distance to " O   HOH Z 422 " =    2.608
peak=    3.450 closest distance to " NH2AARG A 275 " =    3.341
peak=    3.447 closest distance to " O   HOH Z 285 " =    1.844
peak=    3.445 closest distance to " O   HOH Z 271 " =    2.635
peak=    3.445 closest distance to " CE  LYS A  76 " =    0.812
peak=    3.440 closest distance to " O   HOH Z 435 " =    2.889
peak=    3.437 closest distance to " OG  SER A 245 " =    1.646
peak=    3.437 closest distance to " O   HOH Z 180 " =    2.198
peak=    3.436 closest distance to " CG  GLN A  58 " =    0.959
peak=    3.434 closest distance to " O   HOH Z 394 " =    1.609
peak=    3.424 closest distance to " O   HOH Z 418 " =    1.385
peak=    3.424 closest distance to " O   HOH Z 393 " =    3.257
peak=    3.414 closest distance to " NH2BARG A 145 " =    2.117
peak=    3.412 closest distance to " O   HOH Z 196 " =    1.198
peak=    3.409 closest distance to " O   HOH Z 417 " =    3.152
peak=    3.406 closest distance to " O   HOH Z 411 " =    1.652
peak=    3.404 closest distance to " O   HOH Z 185 " =    1.733
peak=    3.402 closest distance to " O   HOH Z 353 " =    2.761
peak=    3.401 closest distance to " CG  LEU A 167 " =    1.091
peak=    3.395 closest distance to " CG2 ILE A 120 " =    1.178
peak=    3.394 closest distance to " O   TYR A 116 " =    1.383
peak=    3.391 closest distance to " CG2 ILE A  20 " =    1.391
peak=    3.391 closest distance to " CG2 THR A 221 " =    1.072
peak=    3.389 closest distance to " OD2 ASP A 298 " =    3.918
peak=    3.386 closest distance to " CB  SER A 141 " =    1.056
peak=    3.386 closest distance to " O   HOH Z 365 " =    2.722
peak=    3.379 closest distance to " CA  ALA A 154 " =    1.001
peak=    3.376 closest distance to " O   HOH Z 244 " =    1.717
peak=    3.367 closest distance to " CB  GLU A  37 " =    0.879
peak=    3.358 closest distance to " OE1 GLN A  11 " =    2.144
peak=    3.358 closest distance to " N   ARG A 156 " =    1.557
peak=    3.355 closest distance to " O   HOH Z 286 " =    2.205
peak=    3.354 closest distance to " CA  ASN A 217 " =    1.365
peak=    3.354 closest distance to " CB  LEU A 228 " =    1.072
peak=    3.345 closest distance to " CB  TRP A 150 " =    1.486
peak=    3.344 closest distance to " O   HOH Z  65 " =    1.038
peak=    3.342 closest distance to " OG  SER A  22 " =    2.771
peak=    3.336 closest distance to " OG  SER A 276 " =    1.487
peak=    3.336 closest distance to " CA  SER A  32 " =    1.639
peak=    3.335 closest distance to " OG  SER A  28 " =    1.543
peak=    3.332 closest distance to " CB  PRO A 198 " =    1.068
peak=    3.331 closest distance to " CB  TYR A 116 " =    1.145
peak=    3.330 closest distance to " O   ASP A 124 " =    1.336
peak=    3.326 closest distance to " CB  ALA A   1 " =    5.046
peak=    3.324 closest distance to " O   THR A 220 " =    1.147
peak=    3.315 closest distance to " CA  ASP A 124 " =    0.844
peak=    3.312 closest distance to " O   HOH Z 132 " =    2.828
peak=    3.310 closest distance to " CB  MET A  40 " =    0.969
peak=    3.308 closest distance to " O   HOH Z 150 " =    1.480
peak=    3.303 closest distance to " O   HOH Z 162 " =    1.643
peak=    3.297 closest distance to " O   HOH Z 327 " =    1.706
peak=    3.295 closest distance to " O   HOH Z 193 " =    2.161
peak=    3.293 closest distance to " O   HOH Z 361 " =    2.673
peak=    3.287 closest distance to " N   ILE A  33 " =    0.996
peak=    3.280 closest distance to " O   HOH Z  47 " =    2.573
peak=    3.278 closest distance to " CD2 TYR A 186 " =    1.015
peak=    3.276 closest distance to " O   HOH Z 394 " =    3.906
peak=    3.276 closest distance to " CB  SER A   3 " =    1.554
peak=    3.275 closest distance to " CD1 ILE A 199 " =    1.196
peak=    3.268 closest distance to " O   HOH Z  44 " =    1.757
peak=    3.268 closest distance to " CA  MET A 105 " =    1.046
peak=    3.266 closest distance to " OG  SER A 135 " =    1.298
peak=    3.266 closest distance to " O   HOH Z  88 " =    1.607
peak=    3.265 closest distance to " CB  ALA A 248 " =    1.244
peak=    3.263 closest distance to " O   THR A 251 " =    1.107
peak=    3.263 closest distance to " N   TYR A 116 " =    1.568
peak=    3.262 closest distance to " O   HOH Z 355 " =    1.736
peak=    3.261 closest distance to " CA  GLY A 267 " =    0.925
peak=    3.259 closest distance to " CE3 TRP A 150 " =    1.113
peak=    3.254 closest distance to " O   HOH Z 146 " =    2.145
peak=    3.247 closest distance to " CG1 ILE A  20 " =    1.273
peak=    3.247 closest distance to " CA  THR A 264 " =    0.838
peak=    3.239 closest distance to " CA  ALA A 233 " =    1.797
peak=    3.238 closest distance to " O   HOH Z 371 " =    2.778
peak=    3.238 closest distance to " O   HOH Z 158 " =    3.079
peak=    3.237 closest distance to " O   ASP A 200 " =    1.696
peak=    3.237 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.236 closest distance to " O   HOH Z 313 " =    1.834
peak=    3.233 closest distance to " O   HOH Z 125 " =    3.844
peak=    3.231 closest distance to " CB  ASP A 298 " =    1.149
peak=    3.228 closest distance to " O   ASN A 209 " =    1.187
peak=    3.226 closest distance to " O   HOH Z  88 " =    3.291
peak=    3.217 closest distance to " CD  ARG A 159 " =    0.850
peak=    3.216 closest distance to " CA  SER A  12 " =    1.554
peak=    3.214 closest distance to " CA  VAL A 125 " =    1.267
peak=    3.213 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.212 closest distance to " CA  GLY A 196 " =    1.026
peak=    3.206 closest distance to " O   LEU A 228 " =    1.843
peak=    3.202 closest distance to " O   HOH Z 380 " =    1.824
peak=    3.202 closest distance to " CG  LYS A  76 " =    1.091
peak=    3.200 closest distance to " CG2 ILE A 234 " =    1.139
peak=    3.196 closest distance to " CB  ASN A 215 " =    1.201
peak=    3.192 closest distance to " CZ3 TRP A  85 " =    0.920
peak=    3.191 closest distance to " O   HOH Z 141 " =    1.681
peak=    3.191 closest distance to " O   ALA A 242 " =    1.413
peak=    3.182 closest distance to " NE2 GLN A  58 " =    4.705
peak=    3.180 closest distance to " CB  MET A  47 " =    0.923
peak=    3.179 closest distance to " CB  PRO A 243 " =    1.555
peak=    3.177 closest distance to " O   HOH Z 199 " =    1.693
peak=    3.176 closest distance to " CA  ASN A 249 " =    1.458
peak=    3.176 closest distance to " CG  ARG A 219 " =    1.174
peak=    3.170 closest distance to " CG  MET A 185 " =    1.073
peak=    3.170 closest distance to " O   HOH Z  54 " =    1.246
peak=    3.167 closest distance to " CG2BVAL A 121 " =    0.831
peak=    3.166 closest distance to " O   HOH Z  78 " =    1.960
peak=    3.159 closest distance to " CE1 HIS A 108 " =    1.120
peak=    3.157 closest distance to " CD2 LEU A 297 " =    0.920
peak=    3.157 closest distance to " NE2 HIS A 207 " =    1.067
peak=    3.156 closest distance to " CB  TYR A 247 " =    0.988
peak=    3.150 closest distance to " O   HOH Z 381 " =    1.890
peak=    3.146 closest distance to " O   HOH Z   1 " =    2.687
peak=    3.145 closest distance to " CA  ARG A 156 " =    1.107
peak=    3.139 closest distance to " CE1 PHE A 218 " =    1.215
peak=    3.137 closest distance to " O   HOH Z 109 " =    2.658
peak=    3.136 closest distance to " CA  GLY A  98 " =    1.113
peak=    3.135 closest distance to " CB  ALA A 248 " =    0.981
peak=    3.134 closest distance to " O   HOH Z 305 " =    3.716
peak=    3.134 closest distance to " CD  PRO A 213 " =    1.393
peak=    3.131 closest distance to " O   HOH Z 102 " =    1.257
peak=    3.130 closest distance to " O   HOH Z 116 " =    2.896
peak=    3.122 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.122 closest distance to " O   HOH Z 183 " =    1.567
peak=    3.121 closest distance to " N   SER A 164 " =    1.047
peak=    3.120 closest distance to " CB  ALA A 242 " =    0.899
peak=    3.118 closest distance to " CB  ALA A 100 " =    1.327
peak=    3.116 closest distance to " CB  LYS A 117 " =    1.151
peak=    3.112 closest distance to " CB  SER A  97 " =    1.296
peak=    3.110 closest distance to " O   HOH Z  90 " =    2.209
peak=    3.109 closest distance to " O   HOH Z 173 " =    2.195
peak=    3.107 closest distance to " O   HOH Z 420 " =    5.704
peak=    3.106 closest distance to " NE2 GLN A  58 " =    3.617
peak=    3.105 closest distance to " CA  ASP A 191 " =    0.967
peak=    3.105 closest distance to " CA  GLN A 223 " =    0.846
peak=    3.104 closest distance to " N   GLU A  44 " =    2.293
peak=    3.104 closest distance to " CB  ASN A 127 " =    0.895
peak=    3.104 closest distance to " O   THR A 182 " =    1.478
peak=    3.095 closest distance to " NE AARG A 275 " =    1.275
peak=    3.088 closest distance to " CA  VAL A  41 " =    0.879
peak=    3.075 closest distance to " O   HOH Z 327 " =    2.138
peak=    3.073 closest distance to " O   HOH Z 357 " =    2.560
peak=    3.068 closest distance to " O   HOH Z 213 " =    1.973
peak=    3.067 closest distance to " NH1 ARG A 269 " =    0.726
peak=    3.050 closest distance to " O   HOH Z  53 " =    1.642
peak=    3.046 closest distance to " O   HOH Z  90 " =    1.897
peak=    3.038 closest distance to " CB  SER A  62 " =    0.825
peak=    3.031 closest distance to " CB  ASP A 253 " =    1.000

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.727 - 5.894
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 218
   mapped sites are within: 0.727 - 5.894

peak=   -4.601 closest distance to " O   HOH Z 266 " =    5.538
peak=   -4.578 closest distance to " O   HOH Z   5 " =    1.646
peak=   -4.550 closest distance to " CB  PRO A 243 " =    2.738
peak=   -4.524 closest distance to " CG1 VAL A 250 " =    2.733
peak=   -4.511 closest distance to " CD  GLN A  58 " =    0.923
peak=   -4.347 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -4.276 closest distance to " CD  GLN A 223 " =    1.344
peak=   -4.245 closest distance to " CG2 ILE A  49 " =    2.820
peak=   -4.209 closest distance to " CD  ARG A  14 " =    3.421
peak=   -4.144 closest distance to " O   PRO A 198 " =    1.352
peak=   -4.111 closest distance to " O   HOH Z 166 " =    1.612
peak=   -4.103 closest distance to " CE2 PHE A  61 " =    2.659
peak=   -4.086 closest distance to " OXT GLY A 302 " =    2.998
peak=   -4.080 closest distance to " OE1 GLN A  88 " =    1.007
peak=   -4.065 closest distance to " CD  ARG A 156 " =    2.181
peak=   -4.061 closest distance to " CG  ARG A 269 " =    2.311
peak=   -4.044 closest distance to " O   VAL A  67 " =    2.752
peak=   -4.041 closest distance to " CD1 LEU A 101 " =    2.405
peak=   -4.016 closest distance to " CD1 PHE A  59 " =    2.093
peak=   -3.950 closest distance to " CG2 ILE A  20 " =    3.016
peak=   -3.944 closest distance to " O   HOH Z 283 " =    2.202
peak=   -3.939 closest distance to " O   HOH Z 211 " =    1.315
peak=   -3.936 closest distance to " CH2 TRP A 179 " =    1.227
peak=   -3.933 closest distance to " CD  GLN A  88 " =    0.920
peak=   -3.910 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.896 closest distance to " O   SER A 210 " =    1.892
peak=   -3.884 closest distance to " CD2 TYR A 293 " =    1.935
peak=   -3.851 closest distance to " O   HOH Z 196 " =    2.317
peak=   -3.832 closest distance to " CB  ALA A  10 " =    2.218
peak=   -3.822 closest distance to " C   HIS A 108 " =    1.071
peak=   -3.816 closest distance to " N   ALA A  43 " =    2.780
peak=   -3.811 closest distance to " O   HOH Z 185 " =    2.495
peak=   -3.803 closest distance to " O   HOH Z 128 " =    2.754
peak=   -3.785 closest distance to " O   HOH Z 210 " =    0.818
peak=   -3.780 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.771 closest distance to " O   HOH Z 377 " =    2.019
peak=   -3.768 closest distance to " O   HOH Z 348 " =    2.337
peak=   -3.768 closest distance to " O   HOH Z 290 " =    1.068
peak=   -3.752 closest distance to " OG  SER A  97 " =    2.269
peak=   -3.738 closest distance to " O   HOH Z 231 " =    2.419
peak=   -3.735 closest distance to " O   HOH Z 234 " =    4.408
peak=   -3.735 closest distance to " ND2 ASN A  45 " =    2.008
peak=   -3.729 closest distance to " O   HOH Z 150 " =    1.012
peak=   -3.722 closest distance to " NE2 GLN A 223 " =    1.150
peak=   -3.697 closest distance to " O   ALA A  34 " =    2.519
peak=   -3.691 closest distance to " CG  GLN A  11 " =    1.489
peak=   -3.672 closest distance to " O   HOH Z 394 " =    1.598
peak=   -3.672 closest distance to " O   HOH Z 374 " =    1.990
peak=   -3.669 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.663 closest distance to " CG  GLN A 103 " =    2.490
peak=   -3.662 closest distance to " O   HOH Z 149 " =    2.063
peak=   -3.648 closest distance to " O   HOH Z 171 " =    2.319
peak=   -3.647 closest distance to " OD1 ASN A 148 " =    1.451
peak=   -3.641 closest distance to " ND2BASN A 224 " =    1.864
peak=   -3.624 closest distance to " CZ  TYR A 169 " =    1.851
peak=   -3.614 closest distance to " CB  ALA A 291 " =    2.410
peak=   -3.608 closest distance to " O   ALA A  10 " =    1.730
peak=   -3.596 closest distance to " C   ASN A 285 " =    2.394
peak=   -3.593 closest distance to " O   HOH Z 366 " =    1.687
peak=   -3.578 closest distance to " CG  GLU A  53 " =    1.563
peak=   -3.576 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.569 closest distance to " O   HOH Z  37 " =    1.918
peak=   -3.566 closest distance to " CG  ASP A 132 " =    2.395
peak=   -3.563 closest distance to " O   HOH Z 351 " =    1.636
peak=   -3.551 closest distance to " O   SER A 276 " =    1.753
peak=   -3.544 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.539 closest distance to " CB  PHE A  16 " =    2.471
peak=   -3.535 closest distance to " O   ILE A 109 " =    2.646
peak=   -3.532 closest distance to " C   SER A 206 " =    1.479
peak=   -3.530 closest distance to " O   HOH Z 240 " =    3.970
peak=   -3.528 closest distance to " CE3 TRP A 150 " =    2.298
peak=   -3.522 closest distance to " CG1 VAL A  78 " =    2.664
peak=   -3.517 closest distance to " CG  GLN A  58 " =    1.256
peak=   -3.513 closest distance to " O   HOH Z  71 " =    2.372
peak=   -3.512 closest distance to " O   HOH Z  13 " =    1.939
peak=   -3.503 closest distance to " CG2AVAL A  41 " =    2.868
peak=   -3.499 closest distance to " O   HOH Z 252 " =    3.682
peak=   -3.498 closest distance to " O   HOH Z 418 " =    1.202
peak=   -3.491 closest distance to " CA  GLY A 241 " =    2.383
peak=   -3.484 closest distance to " O   HOH Z 264 " =    1.714
peak=   -3.482 closest distance to " O   HOH Z 407 " =    1.182
peak=   -3.476 closest distance to " CA  GLY A 241 " =    3.245
peak=   -3.467 closest distance to " N   THR A  52 " =    1.721
peak=   -3.465 closest distance to " O   HOH Z 106 " =    1.983
peak=   -3.465 closest distance to " CG  PRO A 243 " =    1.698
peak=   -3.464 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.460 closest distance to " O   PRO A 163 " =    2.028
peak=   -3.448 closest distance to " CB  TRP A  85 " =    2.513
peak=   -3.447 closest distance to " O   HOH Z 197 " =    1.957
peak=   -3.438 closest distance to " CG  MET A 105 " =    1.022
peak=   -3.429 closest distance to " CB  ALA A  43 " =    2.591
peak=   -3.421 closest distance to " O   HOH Z  52 " =    1.645
peak=   -3.419 closest distance to " O   HOH Z 193 " =    1.411
peak=   -3.415 closest distance to " O   HOH Z 200 " =    1.289
peak=   -3.413 closest distance to " O   HOH Z 216 " =    1.087
peak=   -3.408 closest distance to " O   HOH Z 154 " =    1.406
peak=   -3.406 closest distance to " CD  LYS A 289 " =    2.360
peak=   -3.403 closest distance to " NE  ARG A  66 " =    4.388
peak=   -3.403 closest distance to " NH2 ARG A  79 " =    2.117
peak=   -3.402 closest distance to " OH  TYR A 247 " =    2.195
peak=   -3.402 closest distance to " O   HOH Z 407 " =    3.542
peak=   -3.398 closest distance to " O   HOH Z 150 " =    1.955
peak=   -3.398 closest distance to " ND2 ASN A 249 " =    2.190
peak=   -3.397 closest distance to " CZ  PHE A  38 " =    2.460
peak=   -3.393 closest distance to " CD2 PHE A  61 " =    2.103
peak=   -3.389 closest distance to " OD1 ASP A 171 " =    1.639
peak=   -3.386 closest distance to " CG2BVAL A  41 " =    1.611
peak=   -3.382 closest distance to " O   HOH Z 210 " =    1.319
peak=   -3.381 closest distance to " O   HOH Z 236 " =    1.586
peak=   -3.380 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.379 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.378 closest distance to " NE2 GLN A 103 " =    1.818
peak=   -3.376 closest distance to " CH2 TRP A 150 " =    1.177
peak=   -3.376 closest distance to " O   HOH Z 136 " =    2.237
peak=   -3.376 closest distance to " O   HOH Z 165 " =    1.993
peak=   -3.368 closest distance to " O   HOH Z 123 " =    2.467
peak=   -3.367 closest distance to " OG BSER A 210 " =    1.499
peak=   -3.367 closest distance to " N   SER A 276 " =    1.563
peak=   -3.366 closest distance to " CD1 ILE A 151 " =    2.478
peak=   -3.365 closest distance to " CB  PHE A 192 " =    2.003
peak=   -3.365 closest distance to " O   VAL A 189 " =    1.851
peak=   -3.360 closest distance to " O   HOH Z   6 " =    1.346
peak=   -3.360 closest distance to " C   THR A 279 " =    1.088
peak=   -3.346 closest distance to " O   HOH Z 102 " =    1.593
peak=   -3.336 closest distance to " CD2 LEU A 300 " =    2.740
peak=   -3.336 closest distance to " CZ  TYR A  68 " =    1.145
peak=   -3.328 closest distance to " CG2 THR A 182 " =    2.360
peak=   -3.325 closest distance to " CA  SER A  62 " =    2.537
peak=   -3.317 closest distance to " O   HOH Z  40 " =    3.004
peak=   -3.317 closest distance to " O   HOH Z 198 " =    1.684
peak=   -3.314 closest distance to " CD  PRO A 243 " =    2.021
peak=   -3.311 closest distance to " CZ3 TRP A 274 " =    2.464
peak=   -3.311 closest distance to " O   HOH Z  65 " =    0.727
peak=   -3.311 closest distance to " CD  ARG A  79 " =    1.245
peak=   -3.306 closest distance to " OG  SER A 273 " =    2.245
peak=   -3.304 closest distance to " O   HOH Z 196 " =    1.934
peak=   -3.300 closest distance to " CD1 ILE A 109 " =    2.921
peak=   -3.297 closest distance to " CE BMET A  47 " =    1.897
peak=   -3.294 closest distance to " O   VAL A 189 " =    2.648
peak=   -3.294 closest distance to " O   HOH Z  78 " =    1.862
peak=   -3.292 closest distance to " N   THR A 157 " =    1.668
peak=   -3.290 closest distance to " O   HOH Z 422 " =    1.437
peak=   -3.286 closest distance to " O   HOH Z 287 " =    1.928
peak=   -3.282 closest distance to " O   SER A 271 " =    2.037
peak=   -3.281 closest distance to " O   HOH Z 109 " =    3.739
peak=   -3.280 closest distance to " C   LEU A 143 " =    1.150
peak=   -3.279 closest distance to " O   HOH Z  60 " =    1.843
peak=   -3.277 closest distance to " O   ALA A   1 " =    2.020
peak=   -3.271 closest distance to " O   HOH Z 377 " =    1.194
peak=   -3.267 closest distance to " NH2 ARG A 159 " =    2.402
peak=   -3.266 closest distance to " O   TYR A 186 " =    1.828
peak=   -3.266 closest distance to " ND2 ASN A 187 " =    1.639
peak=   -3.264 closest distance to " CD  ARG A 139 " =    1.542
peak=   -3.262 closest distance to " C   VAL A 265 " =    0.836
peak=   -3.259 closest distance to " O   HOH Z 114 " =    1.377
peak=   -3.258 closest distance to " O   HOH Z  56 " =    1.566
peak=   -3.255 closest distance to " O   HOH Z 111 " =    1.789
peak=   -3.254 closest distance to " O   HOH Z 396 " =    2.103
peak=   -3.253 closest distance to " NH1 ARG A 195 " =    1.027
peak=   -3.253 closest distance to " O   HOH Z 156 " =    3.568
peak=   -3.244 closest distance to " O   GLY A  17 " =    1.205
peak=   -3.244 closest distance to " OG BSER A 134 " =    1.343
peak=   -3.243 closest distance to " O   HOH Z 371 " =    1.518
peak=   -3.242 closest distance to " O   SER A   3 " =    1.155
peak=   -3.241 closest distance to " C   ALA A 158 " =    1.666
peak=   -3.240 closest distance to " OD1 ASP A 191 " =    1.508
peak=   -3.233 closest distance to " OE1 GLN A  88 " =    0.866
peak=   -3.225 closest distance to " O   ALA A  34 " =    2.079
peak=   -3.213 closest distance to " O   HOH Z 174 " =    2.292
peak=   -3.209 closest distance to " O   HOH Z 378 " =    1.172
peak=   -3.202 closest distance to " O   HOH Z 275 " =    1.546
peak=   -3.202 closest distance to " CG  LEU A  83 " =    2.084
peak=   -3.200 closest distance to " O   HOH Z 191 " =    5.894
peak=   -3.200 closest distance to " O   HOH Z 259 " =    2.090
peak=   -3.199 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.188 closest distance to " CB  PRO A 163 " =    2.596
peak=   -3.187 closest distance to " O   HOH Z  40 " =    2.448
peak=   -3.187 closest distance to " CB  HIS A  86 " =    1.151
peak=   -3.184 closest distance to " CD1 ILE A 263 " =    1.965
peak=   -3.183 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.173 closest distance to " CD  GLN A  88 " =    0.911
peak=   -3.172 closest distance to " CG1 VAL A 112 " =    2.777
peak=   -3.171 closest distance to " OD2 ASP A 171 " =    1.907
peak=   -3.167 closest distance to " OD2 ASP A 171 " =    2.472
peak=   -3.166 closest distance to " OD2 ASP A 270 " =    1.150
peak=   -3.163 closest distance to " ND2 ASN A  45 " =    1.170
peak=   -3.161 closest distance to " O   HOH Z 177 " =    1.972
peak=   -3.160 closest distance to " O   HOH Z 372 " =    2.495
peak=   -3.160 closest distance to " O   HOH Z 426 " =    1.612
peak=   -3.153 closest distance to " N   ARG A 275 " =    1.715
peak=   -3.153 closest distance to " O   ASP A 171 " =    1.055
peak=   -3.152 closest distance to " CE  MET A  93 " =    1.643
peak=   -3.150 closest distance to " CD  ARG A 139 " =    1.030
peak=   -3.148 closest distance to " O   HOH Z 150 " =    1.704
peak=   -3.146 closest distance to " OG BSER A 134 " =    2.007
peak=   -3.139 closest distance to " O   HOH Z 340 " =    1.687
peak=   -3.136 closest distance to " N   ALA A 226 " =    2.021
peak=   -3.132 closest distance to " OG BSER A 210 " =    2.243
peak=   -3.131 closest distance to " OG  SER A  26 " =    1.305
peak=   -3.130 closest distance to " O   HOH Z  19 " =    2.222
peak=   -3.129 closest distance to " CE3 TRP A  70 " =    1.836
peak=   -3.127 closest distance to " O   HOH Z 409 " =    4.785
peak=   -3.126 closest distance to " O   HOH Z  19 " =    0.859
peak=   -3.125 closest distance to " OE1 GLN A 183 " =    1.655
peak=   -3.125 closest distance to " O   GLY A  80 " =    2.712
peak=   -3.123 closest distance to " CA  GLY A 241 " =    2.886
peak=   -3.121 closest distance to " CA  VAL A 197 " =    0.943
peak=   -3.115 closest distance to " CG  TRP A 266 " =    1.872
peak=   -3.100 closest distance to " CG1AVAL A  41 " =    2.679
peak=   -3.092 closest distance to " O   TRP A  92 " =    1.974
peak=   -3.091 closest distance to " O   HOH Z 285 " =    1.575
peak=   -3.073 closest distance to " CG  ASP A 231 " =    0.820
peak=   -3.068 closest distance to " O   HOH Z 135 " =    1.712
peak=   -3.061 closest distance to " CZ  PHE A  38 " =    1.988
peak=   -3.042 closest distance to " C   GLY A 262 " =    2.135
peak=   -3.040 closest distance to " CD2 LEU A 237 " =    2.900
peak=   -3.009 closest distance to " O   HOH Z 145 " =    2.957

================= 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    :  0.4476 0.4400   6.259371e+00   6.237550e+00
   1_bss:  0.4362 0.4284   6.249633e+00   6.225361e+00
   1_xyz:  0.3322 0.3555   6.048059e+00   6.098423e+00
   1_adp:  0.3030 0.3711   6.000439e+00   6.119744e+00
   1_occ:  0.3027 0.3709   5.999845e+00   6.119957e+00
   2_bss:  0.3009 0.3682   5.998867e+00   6.119609e+00
   2_xyz:  0.2409 0.2959   5.804575e+00   5.960194e+00
   2_adp:  0.2312 0.2828   5.773398e+00   5.925409e+00
   2_occ:  0.2310 0.2829   5.773266e+00   5.926175e+00
   3_bss:  0.2312 0.2829   5.773530e+00   5.925829e+00
   3_xyz:  0.1706 0.2146   5.496356e+00   5.686352e+00
   3_adp:  0.1510 0.2040   5.410925e+00   5.631066e+00
   3_occ:  0.1509 0.2039   5.410325e+00   5.630156e+00
   4_bss:  0.1511 0.2039   5.411533e+00   5.630073e+00
   4_xyz:  0.1307 0.1822   5.290475e+00   5.525323e+00
   4_adp:  0.1260 0.1761   5.254000e+00   5.488819e+00
   4_occ:  0.1259 0.1761   5.253546e+00   5.488269e+00
   5_bss:  0.1261 0.1758   5.254150e+00   5.487703e+00
   5_xyz:  0.1197 0.1696   5.214617e+00   5.455579e+00
   5_adp:  0.1190 0.1660   5.204325e+00   5.440124e+00
   5_occ:  0.1188 0.1660   5.203810e+00   5.439888e+00
   5_bss:  0.1188 0.1660   5.203597e+00   5.439669e+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:  0.298  50.000  -3.719   3.820   3.153   0.000   0.000   0.000
   1_xyz:  0.298  50.000  -3.719   3.820   3.153   0.000   0.000   0.000
   1_adp:  0.298  50.000  -3.719   3.820   3.153   0.000   0.000   0.000
   1_occ:  0.298  50.000  -3.719   3.820   3.153   0.000   0.000   0.000
   2_bss:  0.314  64.864  -1.956   1.860   1.524   0.000   0.000   0.000
   2_xyz:  0.314  64.864  -1.956   1.860   1.524   0.000   0.000   0.000
   2_adp:  0.314  64.864  -1.956   1.860   1.524   0.000   0.000   0.000
   2_occ:  0.314  64.864  -1.956   1.860   1.524   0.000   0.000   0.000
   3_bss:  0.326  74.747  -1.684   0.915   0.757   0.000   0.000   0.000
   3_xyz:  0.326  74.747  -1.684   0.915   0.757   0.000   0.000   0.000
   3_adp:  0.326  74.747  -1.684   0.915   0.757   0.000   0.000   0.000
   3_occ:  0.326  74.747  -1.684   0.915   0.757   0.000   0.000   0.000
   4_bss:  0.339  88.095  -1.763  -0.111   0.414  -0.000   0.000   0.000
   4_xyz:  0.339  88.095  -1.763  -0.111   0.414  -0.000   0.000   0.000
   4_adp:  0.339  88.095  -1.763  -0.111   0.414  -0.000   0.000   0.000
   4_occ:  0.339  88.095  -1.763  -0.111   0.414  -0.000   0.000   0.000
   5_bss:  0.334  81.245  -1.449  -0.331   0.617  -0.000   0.000   0.000
   5_xyz:  0.334  81.245  -1.449  -0.331   0.617  -0.000   0.000   0.000
   5_adp:  0.334  81.245  -1.449  -0.331   0.617  -0.000   0.000   0.000
   5_occ:  0.334  81.245  -1.449  -0.331   0.617  -0.000   0.000   0.000
   5_bss:  0.325  71.203  -1.325  -0.381   0.715  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.141 0.4940  0.6349    58963.302
   1_bss:  50.769 0.5099  0.6821    55717.073
   1_xyz:  39.485 0.6487  0.8431    36241.281
   1_adp:  40.920 0.6310  0.8184    38757.612
   1_occ:  40.925 0.6309  0.8180    38772.573
   2_bss:  40.463 0.6367  0.8130    38430.217
   2_xyz:  31.190 0.7441  0.9215    23821.479
   2_adp:  29.234 0.7666  0.9243    21758.423
   2_occ:  29.257 0.7664  0.9238    21786.252
   3_bss:  29.158 0.7676  0.9104    21745.767
   3_xyz:  21.124 0.8502  0.9769    11841.531
   3_adp:  19.614 0.8650  0.9723    10533.101
   3_occ:  19.595 0.8651  0.9725    10514.103
   4_bss:  19.553 0.8656  0.9573    10502.816
   4_xyz:  17.115 0.8882  0.9673     8381.772
   4_adp:  16.246 0.8962  0.9593     7885.056
   4_occ:  16.233 0.8963  0.9593     7879.060
   5_bss:  16.236 0.8963  0.9630     7884.513
   5_xyz:  15.468 0.9030  0.9683     7316.881
   5_adp:  15.120 0.9061  0.9627     7134.241
   5_occ:  15.111 0.9061  0.9627     7127.032
   5_bss:  15.109 0.9062  0.9649     7119.066
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6682e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6682e-01
   1_xyz:   1.545  0.011  0.094 15.506  0.006  4.113   1.1708e-01
   1_adp:   1.545  0.011  0.094 15.506  0.006  4.113   1.1708e-01
   1_occ:   1.545  0.011  0.094 15.506  0.006  4.113   1.1708e-01
   2_bss:   1.545  0.011  0.094 15.506  0.006  4.113   1.1708e-01
   2_xyz:   1.162  0.008  0.079 14.491  0.004  4.131   7.1800e-02
   2_adp:   1.162  0.008  0.079 14.491  0.004  4.131   7.1800e-02
   2_occ:   1.162  0.008  0.079 14.491  0.004  4.131   7.1800e-02
   3_bss:   1.162  0.008  0.079 14.491  0.004  4.131   7.1800e-02
   3_xyz:   1.177  0.010  0.080 14.897  0.004  4.133   7.9927e-02
   3_adp:   1.177  0.010  0.080 14.897  0.004  4.133   7.9927e-02
   3_occ:   1.177  0.010  0.080 14.897  0.004  4.133   7.9927e-02
   4_bss:   1.177  0.010  0.080 14.897  0.004  4.133   7.9927e-02
   4_xyz:   1.136  0.010  0.083 14.724  0.004  4.114   7.5524e-02
   4_adp:   1.136  0.010  0.083 14.724  0.004  4.114   7.5524e-02
   4_occ:   1.136  0.010  0.083 14.724  0.004  4.114   7.5524e-02
   5_bss:   1.136  0.010  0.083 14.724  0.004  4.114   7.5524e-02
   5_xyz:   1.121  0.010  0.082 14.657  0.004  4.115   7.4619e-02
   5_adp:   1.121  0.010  0.082 14.657  0.004  4.115   7.4619e-02
   5_occ:   1.121  0.010  0.082 14.657  0.004  4.115   7.4619e-02
   5_bss:   1.121  0.010  0.082 14.657  0.004  4.115   7.4619e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.637   2.4443e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.637   2.4443e-01
   1_xyz:   9.153  0.064  0.395 84.572  0.047  2.018   1.0075e-01
   1_adp:   9.153  0.064  0.395 84.572  0.047  2.018   1.0075e-01
   1_occ:   9.153  0.064  0.395 84.572  0.047  2.018   1.0075e-01
   2_bss:   9.153  0.064  0.395 84.572  0.047  2.018   1.0075e-01
   2_xyz:   7.200  0.047  0.252 82.353  0.030  2.284   8.1053e-02
   2_adp:   7.200  0.047  0.252 82.353  0.030  2.284   8.1053e-02
   2_occ:   7.200  0.047  0.252 82.353  0.030  2.284   8.1053e-02
   3_bss:   7.200  0.047  0.252 82.353  0.030  2.284   8.1053e-02
   3_xyz:   7.463  0.062  0.264 81.829  0.040  2.174   7.8362e-02
   3_adp:   7.463  0.062  0.264 81.829  0.040  2.174   7.8362e-02
   3_occ:   7.463  0.062  0.264 81.829  0.040  2.174   7.8362e-02
   4_bss:   7.463  0.062  0.264 81.829  0.040  2.174   7.8362e-02
   4_xyz:   8.202  0.050  0.273 83.715  0.049  2.336   6.9061e-02
   4_adp:   8.202  0.050  0.273 83.715  0.049  2.336   6.9061e-02
   4_occ:   8.202  0.050  0.273 83.715  0.049  2.336   6.9061e-02
   5_bss:   8.202  0.050  0.273 83.715  0.049  2.336   6.9061e-02
   5_xyz:   8.412  0.051  0.297 81.865  0.041  2.337   4.9578e-02
   5_adp:   8.412  0.051  0.297 81.865  0.041  2.337   4.9578e-02
   5_occ:   8.412  0.051  0.297 81.865  0.041  2.337   4.9578e-02
   5_bss:   8.412  0.051  0.297 81.865  0.041  2.337   4.9578e-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: 111.08   0.00  18.32  85.34   0.00  14.51 111.08   0.00  39.06
   1_occ: 111.08   0.00  18.32  85.34   0.00  14.51 111.08   0.00  39.06
   2_bss: 111.08   0.00  18.32  85.34   0.00  14.51 111.08   0.00  39.06
   2_xyz: 111.08   0.00  18.32  85.34   0.00  14.51 111.08   0.00  39.06
   2_adp: 110.54   0.00  17.65  83.13   0.00  13.78 110.54   1.03  38.73
   2_occ: 110.54   0.00  17.65  83.13   0.00  13.78 110.54   1.03  38.73
   3_bss: 110.54   0.00  17.65  83.13   0.00  13.78 110.54   1.03  38.73
   3_xyz: 110.54   0.00  17.65  83.13   0.00  13.78 110.54   1.03  38.73
   3_adp: 111.86   0.00  18.13 101.66   0.00  13.00 111.86   3.86  46.05
   3_occ: 111.86   0.00  18.13 101.66   0.00  13.00 111.86   3.86  46.05
   4_bss: 111.86   0.00  18.13 101.66   0.00  13.00 111.86   3.86  46.05
   4_xyz: 111.86   0.00  18.13 101.66   0.00  13.00 111.86   3.86  46.05
   4_adp: 110.20   0.00  17.41 106.00   0.00  12.34 110.20   4.51  45.03
   4_occ: 110.20   0.00  17.41 106.00   0.00  12.34 110.20   4.51  45.03
   5_bss: 110.20   0.00  17.41 106.00   0.00  12.34 110.20   4.51  45.03
   5_xyz: 110.20   0.00  17.41 106.00   0.00  12.34 110.20   4.51  45.03
   5_adp: 106.74   0.00  16.58 101.11   0.00  11.91 106.74   1.97  41.99
   5_occ: 106.74   0.00  16.58 101.11   0.00  11.91 106.74   1.97  41.99
   5_bss: 106.75   0.00  16.58 101.12   0.00  11.92 106.75   1.98  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:    1.758    0.012    0.359
   1_adp:    1.758    0.012    0.359
   1_occ:    1.758    0.012    0.359
   2_bss:    1.758    0.012    0.359
   2_xyz:    1.322    0.037    0.480
   2_adp:    1.322    0.037    0.480
   2_occ:    1.322    0.037    0.480
   3_bss:    1.322    0.037    0.480
   3_xyz:    1.348    0.088    0.658
   3_adp:    1.348    0.088    0.658
   3_occ:    1.348    0.088    0.658
   4_bss:    1.348    0.088    0.658
   4_xyz:    1.367    0.056    0.714
   4_adp:    1.367    0.056    0.714
   4_occ:    1.367    0.056    0.714
   5_bss:    1.367    0.056    0.714
   5_xyz:    1.302    0.096    0.739
   5_adp:    1.302    0.096    0.739
   5_occ:    1.302    0.096    0.739
   5_bss:    1.302    0.096    0.739
------------------------------------------------------------------------

CPU time actual refinement: 333.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/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_713/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_713/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.54 
  Macro-tasks:
    bulk solvent and scale       = 49.76  
    individual site refinement   = 128.35 
    weights calculation          = 29.72  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.48 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 101.77 
    alpha_beta                      = 8.53   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 109.73 
    fmodel                         = 8.04   
    r_factors                      = 0.26   
    phase_errors                   = 10.35  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 242.43 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.784 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    630 calls, 101.39 s
gradients_fft:          575 calls,  97.04 s

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

# Date 2008-01-16 Time 05:29:24 PST -0800 (1200490164.62 s)
Start R-work = 0.4476, R-free = 0.4400 (no bulk solvent and anisotropic scale)
Final R-work = 0.1361, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.4362, R-free = 0.4284
Final R-work = 0.1188, R-free = 0.1660