# Date 2008-01-16 Time 05:43:25 PST -0800 (1200491005.43 s)
#phil __OFF__

Command line arguments: "../858.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13380
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 858

-------------------------------------------------------------------------------
  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: (70.9525, 45.9914, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== 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: (70.9525, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95104
Completeness in resolution range: 0.948115
Completeness with d_max=infinity: 0.945324

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9510

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: (70.9525, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95104
Completeness in resolution range: 0.948115
Completeness with d_max=infinity: 0.945324

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1760 [2164/2190]  1951   213   9.8%
  bin  2:  4.1760 -  3.3265 [2091/2111]  1880   211  10.1%
  bin  3:  3.3265 -  2.9095 [2042/2061]  1834   208  10.2%
  bin  4:  2.9095 -  2.6451 [2036/2066]  1841   195   9.6%
  bin  5:  2.6451 -  2.4563 [2037/2056]  1830   207  10.2%
  bin  6:  2.4563 -  2.3121 [2012/2037]  1802   210  10.4%
  bin  7:  2.3121 -  2.1967 [2012/2040]  1816   196   9.7%
  bin  8:  2.1967 -  2.1013 [1987/2023]  1792   195   9.8%
  bin  9:  2.1013 -  2.0206 [1997/2039]  1798   199  10.0%
  bin 10:  2.0206 -  1.9510 [1211/2038]  1086   125  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/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:
        1.44 -     2.13: 21
        2.13 -     2.82: 954
        2.82 -     3.52: 4546
        3.52 -     4.21: 9485
        4.21 -     4.90: 13833
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.439 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.621 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.702 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.809 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28834 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_858/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 70.9525 45.9914 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4813   r_free= 0.4876   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.288413                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6582 0.99   1406  158 0.3877 0.3971      6.5756      6.6124|
|  2:  4.6582 -  3.7159 0.99   1359  146 0.4236 0.4148      6.8366      6.8042|
|  3:  3.7159 -  3.2516 0.99   1316  148 0.4598 0.4648      6.6972      6.7673|
|  4:  3.2516 -  2.9568 0.99   1331  153 0.4688 0.4592      6.5468      6.5083|
|  5:  2.9568 -  2.7463 0.99   1317  140 0.5103 0.4886      6.3783      6.3603|
|  6:  2.7463 -  2.5852 0.99   1298  155 0.5170 0.5531      6.2917      6.3004|
|  7:  2.5852 -  2.4563 0.99   1309  134 0.5136 0.5020      6.2566      6.1794|
|  8:  2.4563 -  2.3498 0.98   1281  150 0.5200 0.5200       6.167      6.2016|
|  9:  2.3498 -  2.2597 0.98   1301  146 0.5178 0.5244      6.1331      6.1293|
| 10:  2.2597 -  2.1820 0.99   1285  141 0.5149 0.5490      6.0939       6.124|
| 11:  2.1820 -  2.1139 0.98   1282  136 0.5178 0.6043      6.0468      6.0563|
| 12:  2.1139 -  2.0537 0.97   1268  148 0.5376 0.5848      5.9654        6.01|
| 13:  2.0537 -  1.9997 0.96   1249  140 0.5299 0.4970      5.8798      5.8231|
| 14:  1.9997 -  1.9510 0.47    628   64 0.5566 0.4549      5.8514      5.7883|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6582  1406   158  0.68  35.92   0.82     0.74      76930.36|
|  2:  4.6582 -  3.7159  1359   146  0.67  37.46   0.90     0.80     119940.30|
|  3:  3.7159 -  3.2516  1316   148  0.56  46.94   0.91     0.76     128380.49|
|  4:  3.2516 -  2.9568  1331   153  0.44  56.35   0.93     0.64     119675.63|
|  5:  2.9568 -  2.7463  1317   140  0.33  64.78   0.87     0.48      93414.62|
|  6:  2.7463 -  2.5852  1298   155  0.28  68.63   0.88     0.42      84757.85|
|  7:  2.5852 -  2.4563  1309   134  0.29  68.32   0.92     0.40      71279.13|
|  8:  2.4563 -  2.3498  1281   150  0.31  66.97   0.88     0.46      63990.36|
|  9:  2.3498 -  2.2597  1301   146  0.31  66.81   0.92     0.46      57521.57|
| 10:  2.2597 -  2.1820  1285   141  0.27  69.77   0.95     0.41      54925.63|
| 11:  2.1820 -  2.1139  1282   136  0.20  74.85   0.96     0.31      54243.58|
| 12:  2.1139 -  2.0537  1268   148  0.21  74.80   0.96     0.34      48180.85|
| 13:  2.0537 -  1.9997  1249   140  0.26  70.46   0.94     0.43      39463.44|
| 14:  1.9997 -  1.9510   628    64  0.38  61.45   0.93     0.58      28804.11|
|alpha:            min =        0.31 max =            0.80 mean =         0.52|
|beta:             min =    28804.11 max =       128380.49 mean =     76639.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.36|
|phase err.(test): min =        0.00 max =           89.99 mean =        61.79|
|-----------------------------------------------------------------------------|

============================== 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 = 15.279141             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.557   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.645453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.070   (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 |  1.439 -  1.785:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.785 -  2.131:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.131 -  2.477:       50 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.477 -  2.823:      904 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.823 -  3.169:     2082 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.169 -  3.515:     2464 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.515 -  3.862:     4682 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.862 -  4.208:     4803 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.208 -  4.554:     6271 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.554 -  4.900:     7562 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.439 |       0.594 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4813   r_free= 0.4876   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.288413                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4728   r_free= 0.4797   ksol= 0.30   Bsol= 20.00   scale= 0.922   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,1.20,1.54,0.00,0.00,0.00); trace/3= 0.19                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.286542                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.365581             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.654   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.560405              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.865   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4728      final r-factor (work) = 0.3807          |
| start r-factor (free) = 0.4797      final r-factor (free) = 0.4132          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.8819 = 11.37 * 0.50 * 6.2811 + 1.00 * 0.1880                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.3255 = 11.37 * 0.50 * 6.1924 + 1.00 * 0.1352                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3807      final r-factor (work) = 0.3459          |
| start r-factor (free) = 0.4132      final r-factor (free) = 0.4238          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6687 = 1.56 * 1.00 * 6.1924 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5351 = 1.56 * 1.00 * 6.0964 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.87  19.61    None  None   None       |
|    all(noH): 2823   0      0.00    102.87  19.61    None  None   None       |
|    Sol.    : 438    0      0.00    102.87  36.96    None  None   None       |
|    Mac.    : 2385   0      0.00    94.29   16.42    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 -  10.287:  880   |   5:    51.436 -  61.723:   68        |
|      1:    10.287 -  20.574:  879   |   6:    61.723 -  72.010:   35        |
|      2:    20.574 -  30.862:  529   |   7:    72.010 -  82.298:   15        |
|      3:    30.862 -  41.149:  266   |   8:    82.298 -  92.585:    6        |
|      4:    41.149 -  51.436:  141   |   9:    92.585 - 102.872:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3459 r_free = 0.4238             target_work(ml) = 6.101         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3453 r_free = 0.4238             target_work(ml) = 6.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3453   r_free= 0.4238   ksol= 0.30   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,1.20,1.54,0.00,0.00,0.00); trace/3= 0.19                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.100541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3448   r_free= 0.4228   ksol= 0.34   Bsol= 54.92   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.12,0.41,-0.00,0.00,0.00); trace/3= -0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.101403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.177210              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.448   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521992              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.846  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3448      final r-factor (work) = 0.2928          |
| start r-factor (free) = 0.4228      final r-factor (free) = 0.3674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9655 = 6.18 * 0.50 * 6.0967 + 1.00 * 0.1352                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7420 = 6.18 * 0.50 * 6.0427 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2928      final r-factor (work) = 0.2815          |
| start r-factor (free) = 0.3674      final r-factor (free) = 0.3548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1762 = 0.52 * 1.00 * 6.0427 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1471 = 0.52 * 1.00 * 5.9627 + 1.00 * 0.0346                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.63  18.93    None  None   None       |
|    all(noH): 2823   0      0.00    101.63  18.93    None  None   None       |
|    Sol.    : 438    0      0.64    101.63  36.89    None  None   None       |
|    Mac.    : 2385   0      0.00    93.87   15.64    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 -  10.163:  875   |   5:    50.815 -  60.977:   65        |
|      1:    10.163 -  20.326:  980   |   6:    60.977 -  71.140:   36        |
|      2:    20.326 -  30.489:  484   |   7:    71.140 -  81.303:   10        |
|      3:    30.489 -  40.652:  250   |   8:    81.303 -  91.466:    5        |
|      4:    40.652 -  50.815:  114   |   9:    91.466 - 101.629:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2815 r_free = 0.3548             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2813 r_free = 0.3553             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2813   r_free= 0.3553   ksol= 0.34   Bsol= 54.92   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.12,0.41,-0.00,0.00,0.00); trace/3= -0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.949916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2816   r_free= 0.3551   ksol= 0.34   Bsol= 54.92   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.79,-0.03,-0.00,-0.00,-0.00); trace/3= -0.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.949377                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.464280              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.565418              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.341   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2816      final r-factor (work) = 0.2192          |
| start r-factor (free) = 0.3551      final r-factor (free) = 0.2900          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3679 = 5.46 * 0.50 * 5.9622 + 1.00 * 0.0784                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0605 = 5.46 * 0.50 * 5.8534 + 1.00 * 0.0681                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2192      final r-factor (work) = 0.1991          |
| start r-factor (free) = 0.2900      final r-factor (free) = 0.2684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3280 = 0.57 * 1.00 * 5.8534 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2338 = 0.57 * 1.00 * 5.6996 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.49   18.39    None  None   None       |
|    all(noH): 2823   0      0.00    97.49   18.39    None  None   None       |
|    Sol.    : 438    0      3.86    97.49   42.28    None  None   None       |
|    Mac.    : 2385   0      0.00    94.65   14.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.749:  942   |   5:    48.743 -  58.492:   98        |
|      1:     9.749 -  19.497: 1063   |   6:    58.492 -  68.241:   61        |
|      2:    19.497 -  29.246:  302   |   7:    68.241 -  77.989:   15        |
|      3:    29.246 -  38.995:  188   |   8:    77.989 -  87.738:    6        |
|      4:    38.995 -  48.743:  143   |   9:    87.738 -  97.487:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1991 r_free = 0.2684             target_work(ml) = 5.660         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1989 r_free = 0.2679             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1989   r_free= 0.2679   ksol= 0.34   Bsol= 54.92   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.79,-0.03,-0.00,-0.00,-0.00); trace/3= -0.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.658609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1987   r_free= 0.2669   ksol= 0.33   Bsol= 54.92   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-2.13,-1.22,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.657432                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.237404              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.815   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222048              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1987      final r-factor (work) = 0.1587          |
| start r-factor (free) = 0.2669      final r-factor (free) = 0.2140          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3005 = 3.24 * 0.50 * 5.7036 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0676 = 3.24 * 0.50 * 5.5679 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1587      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.2140      final r-factor (free) = 0.1999          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2473 = 0.22 * 1.00 * 5.5679 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2134 = 0.22 * 1.00 * 5.4273 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    92.73   17.66    None  None   None       |
|    all(noH): 2823   0      1.17    92.73   17.66    None  None   None       |
|    Sol.    : 438    0      6.32    92.73   41.80    None  None   None       |
|    Mac.    : 2385   0      1.17    91.78   13.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.173 -  10.329: 1067   |   5:    46.954 -  56.110:  100        |
|      1:    10.329 -  19.485: 1056   |   6:    56.110 -  65.266:   66        |
|      2:    19.485 -  28.641:  238   |   7:    65.266 -  74.422:   25        |
|      3:    28.641 -  37.798:  132   |   8:    74.422 -  83.578:    6        |
|      4:    37.798 -  46.954:  128   |   9:    83.578 -  92.734:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1495 r_free = 0.1999             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1493 r_free = 0.1993             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1493   r_free= 0.1993   ksol= 0.33   Bsol= 54.92   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-2.13,-1.22,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.388100                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1492   r_free= 0.1988   ksol= 0.32   Bsol= 42.33   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.64,-1.67,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.386438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.950370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.294  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.864465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.983  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1492      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3475 = 1.95 * 0.50 * 5.4273 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2534 = 1.95 * 0.50 * 5.3357 + 1.00 * 0.0501                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6208 = 0.86 * 1.00 * 5.3357 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5556 = 0.86 * 1.00 * 5.2580 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    102.77  18.07    None  None   None       |
|    all(noH): 2823   0      0.45    102.77  18.07    None  None   None       |
|    Sol.    : 438    0      6.40    93.58   45.04    None  None   None       |
|    Mac.    : 2385   0      0.45    102.77  13.11    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:     0.449 -  10.680: 1190   |   5:    51.607 -  61.839:   84        |
|      1:    10.680 -  20.912: 1000   |   6:    61.839 -  72.070:   73        |
|      2:    20.912 -  31.144:  211   |   7:    72.070 -  82.302:   31        |
|      3:    31.144 -  41.375:  114   |   8:    82.302 -  92.534:    9        |
|      4:    41.375 -  51.607:  108   |   9:    92.534 - 102.766:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1748             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1269 r_free = 0.1747             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1747   ksol= 0.32   Bsol= 42.33   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.64,-1.67,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248602                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6582 0.99   1406  158 0.1048 0.1349      5.4243      5.5931|
|  2:  4.6582 -  3.7159 0.99   1359  146 0.0939 0.1224       5.521      5.7761|
|  3:  3.7159 -  3.2516 0.99   1316  148 0.1229 0.1690       5.599      5.9201|
|  4:  3.2516 -  2.9568 0.99   1331  153 0.1425 0.1837      5.5946      5.7465|
|  5:  2.9568 -  2.7463 0.99   1317  140 0.1511 0.1911      5.4187       5.577|
|  6:  2.7463 -  2.5852 0.99   1298  155 0.1386 0.1827      5.2965      5.4759|
|  7:  2.5852 -  2.4563 0.99   1309  134 0.1402 0.1912      5.2505      5.4754|
|  8:  2.4563 -  2.3498 0.98   1281  150 0.1342 0.1926      5.1641      5.4488|
|  9:  2.3498 -  2.2597 0.98   1301  146 0.1344 0.2051      5.1408      5.3913|
| 10:  2.2597 -  2.1820 0.99   1285  141 0.1252 0.1988      5.0578        5.32|
| 11:  2.1820 -  2.1139 0.98   1282  136 0.1302 0.2030      5.0586      5.3933|
| 12:  2.1139 -  2.0537 0.97   1268  148 0.1239 0.1735      4.9667      5.1545|
| 13:  2.0537 -  1.9997 0.96   1249  140 0.1326 0.1963      4.8946      5.1327|
| 14:  1.9997 -  1.9510 0.47    628   64 0.1265 0.1705      4.7859      5.0561|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6582  1406   158  0.93   9.78   0.98     0.96       7728.28|
|  2:  4.6582 -  3.7159  1359   146  0.95   9.08   1.03     1.01      10506.68|
|  3:  3.7159 -  3.2516  1316   148  0.92  13.10   1.05     1.05      12846.43|
|  4:  3.2516 -  2.9568  1331   153  0.90  16.17   1.02     1.00      13286.57|
|  5:  2.9568 -  2.7463  1317   140  0.89  17.11   1.00     0.98       9440.46|
|  6:  2.7463 -  2.5852  1298   155  0.89  17.33   1.00     0.98       8153.16|
|  7:  2.5852 -  2.4563  1309   134  0.89  17.00   1.00     0.98       7320.51|
|  8:  2.4563 -  2.3498  1281   150  0.89  17.59   1.00     0.96       6327.06|
|  9:  2.3498 -  2.2597  1301   146  0.89  17.56   1.01     0.99       6285.49|
| 10:  2.2597 -  2.1820  1285   141  0.89  17.68   1.01     0.97       5523.99|
| 11:  2.1820 -  2.1139  1282   136  0.88  18.98   1.01     0.96       5602.42|
| 12:  2.1139 -  2.0537  1268   148  0.89  17.40   1.02     1.00       4807.98|
| 13:  2.0537 -  1.9997  1249   140  0.89  18.14   1.01     1.00       4045.56|
| 14:  1.9997 -  1.9510   628    64  0.89  16.99   1.00     0.97       3208.77|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     3208.77 max =        13286.57 mean =      7717.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.88|
|phase err.(test): min =        0.00 max =           88.04 mean =        15.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1747   ksol= 0.31   Bsol= 43.63   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.62,-1.66,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248304                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1747   ksol= 0.31   Bsol= 43.63   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.62,-1.66,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248304                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6582 0.99   1406  158 0.1046 0.1347      5.4216      5.5934|
|  2:  4.6582 -  3.7159 0.99   1359  146 0.0941 0.1225      5.5222      5.7787|
|  3:  3.7159 -  3.2516 0.99   1316  148 0.1230 0.1692         5.6      5.9218|
|  4:  3.2516 -  2.9568 0.99   1331  153 0.1425 0.1837      5.5948      5.7463|
|  5:  2.9568 -  2.7463 0.99   1317  140 0.1511 0.1909      5.4184      5.5761|
|  6:  2.7463 -  2.5852 0.99   1298  155 0.1385 0.1825      5.2961      5.4755|
|  7:  2.5852 -  2.4563 0.99   1309  134 0.1401 0.1912      5.2499      5.4751|
|  8:  2.4563 -  2.3498 0.98   1281  150 0.1342 0.1924      5.1636      5.4476|
|  9:  2.3498 -  2.2597 0.98   1301  146 0.1344 0.2051      5.1403      5.3914|
| 10:  2.2597 -  2.1820 0.99   1285  141 0.1251 0.1986      5.0572      5.3192|
| 11:  2.1820 -  2.1139 0.98   1282  136 0.1301 0.2030      5.0582      5.3932|
| 12:  2.1139 -  2.0537 0.97   1268  148 0.1238 0.1735      4.9665      5.1544|
| 13:  2.0537 -  1.9997 0.96   1249  140 0.1326 0.1963      4.8945      5.1327|
| 14:  1.9997 -  1.9510 0.47    628   64 0.1265 0.1706      4.7856      5.0558|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6582  1406   158  0.93   9.77   0.98     0.96       7709.77|
|  2:  4.6582 -  3.7159  1359   146  0.94   9.09   1.03     1.01      10523.02|
|  3:  3.7159 -  3.2516  1316   148  0.92  13.12   1.05     1.05      12889.01|
|  4:  3.2516 -  2.9568  1331   153  0.90  16.18   1.02     1.00      13302.52|
|  5:  2.9568 -  2.7463  1317   140  0.89  17.09   1.00     0.98       9428.89|
|  6:  2.7463 -  2.5852  1298   155  0.89  17.32   1.00     0.98       8144.16|
|  7:  2.5852 -  2.4563  1309   134  0.89  16.99   1.00     0.98       7309.03|
|  8:  2.4563 -  2.3498  1281   150  0.89  17.58   1.00     0.96       6319.43|
|  9:  2.3498 -  2.2597  1301   146  0.89  17.54   1.01     0.99       6276.39|
| 10:  2.2597 -  2.1820  1285   141  0.89  17.67   1.01     0.97       5517.23|
| 11:  2.1820 -  2.1139  1282   136  0.88  18.97   1.01     0.96       5597.21|
| 12:  2.1139 -  2.0537  1268   148  0.89  17.39   1.02     1.00       4806.23|
| 13:  2.0537 -  1.9997  1249   140  0.89  18.14   1.01     1.00       4044.55|
| 14:  1.9997 -  1.9510   628    64  0.89  16.99   1.00     0.97       3206.95|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     3206.95 max =        13302.52 mean =      7717.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.87|
|phase err.(test): min =        0.00 max =           88.05 mean =        15.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.480)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    102.75  18.05    None  None   None       |
|    all(noH): 2823   0      0.43    102.75  18.05    None  None   None       |
|    Sol.    : 438    0      6.38    93.57   45.03    None  None   None       |
|    Mac.    : 2385   0      0.43    102.75  13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.435 -  10.666: 1190   |   5:    51.593 -  61.825:   84        |
|      1:    10.666 -  20.898: 1000   |   6:    61.825 -  72.057:   73        |
|      2:    20.898 -  31.130:  211   |   7:    72.057 -  82.288:   31        |
|      3:    31.130 -  41.361:  114   |   8:    82.288 -  92.520:    9        |
|      4:    41.361 -  51.593:  108   |   9:    92.520 - 102.752:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.546
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 317
   mapped sites are within: 0.732 - 5.546

peak=    6.172 closest distance to " O   HOH Z 390 " =    1.114
peak=    6.109 closest distance to " NE2 GLN A  11 " =    1.404
peak=    6.066 closest distance to " O   HOH Z 385 " =    1.120
peak=    5.886 closest distance to " O   HOH Z 278 " =    1.562
peak=    5.753 closest distance to " O   HOH Z   7 " =    1.845
peak=    5.747 closest distance to " O   HOH Z 205 " =    1.088
peak=    5.723 closest distance to " O   HOH Z  65 " =    1.201
peak=    5.631 closest distance to " O   HOH Z 103 " =    0.964
peak=    5.592 closest distance to " O   HOH Z  97 " =    1.531
peak=    5.502 closest distance to " O   HOH Z 214 " =    1.832
peak=    5.474 closest distance to " O   HOH Z 144 " =    1.927
peak=    5.407 closest distance to " O   HOH Z 222 " =    1.219
peak=    5.231 closest distance to " O   HOH Z 126 " =    2.018
peak=    5.101 closest distance to " NH2 ARG A  56 " =    2.042
peak=    5.011 closest distance to " O   HOH Z 130 " =    0.929
peak=    4.960 closest distance to " CG  PRO A  54 " =    1.291
peak=    4.955 closest distance to " CG  PRO A 213 " =    1.316
peak=    4.939 closest distance to " O   HOH Z 134 " =    1.773
peak=    4.904 closest distance to " O   HOH Z 403 " =    1.451
peak=    4.903 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.863 closest distance to " O   HOH Z  78 " =    1.694
peak=    4.807 closest distance to " O   HOH Z 117 " =    1.394
peak=    4.726 closest distance to " O   HOH Z 183 " =    1.470
peak=    4.703 closest distance to " O   HOH Z  61 " =    1.371
peak=    4.699 closest distance to " O   HOH Z 427 " =    2.222
peak=    4.694 closest distance to " O   HOH Z 245 " =    1.361
peak=    4.685 closest distance to " O   HOH Z  11 " =    1.372
peak=    4.675 closest distance to " NH2BARG A 102 " =    1.033
peak=    4.657 closest distance to " CB  GLU A 128 " =    0.985
peak=    4.656 closest distance to " CG  PRO A 198 " =    1.372
peak=    4.633 closest distance to " O   HOH Z  63 " =    1.650
peak=    4.619 closest distance to " CB  ASN A 148 " =    1.427
peak=    4.609 closest distance to " O   HOH Z 414 " =    1.413
peak=    4.570 closest distance to " O   HOH Z 236 " =    1.598
peak=    4.565 closest distance to " O   HOH Z 375 " =    1.069
peak=    4.545 closest distance to " O   HOH Z 358 " =    1.371
peak=    4.519 closest distance to " O   HOH Z 260 " =    1.308
peak=    4.510 closest distance to " O   HOH Z 132 " =    1.281
peak=    4.470 closest distance to " O   HOH Z 344 " =    1.240
peak=    4.469 closest distance to " CB  GLN A 223 " =    1.369
peak=    4.461 closest distance to " O   HOH Z 193 " =    1.704
peak=    4.418 closest distance to " CB  SER A   3 " =    1.380
peak=    4.415 closest distance to " O   HOH Z 124 " =    1.524
peak=    4.391 closest distance to " CG  PRO A  90 " =    1.098
peak=    4.372 closest distance to " CG2 VAL A 257 " =    0.939
peak=    4.366 closest distance to " O   HOH Z 261 " =    2.044
peak=    4.347 closest distance to " O   HOH Z  49 " =    1.530
peak=    4.341 closest distance to " O   HOH Z 247 " =    1.200
peak=    4.341 closest distance to " O   HOH Z 316 " =    2.916
peak=    4.338 closest distance to " CA  GLY A 241 " =    3.544
peak=    4.336 closest distance to " O   HOH Z 202 " =    1.510
peak=    4.335 closest distance to " O   HOH Z 272 " =    1.812
peak=    4.325 closest distance to " O   HOH Z 425 " =    1.629
peak=    4.302 closest distance to " O   HOH Z 221 " =    1.850
peak=    4.286 closest distance to " O   HOH Z 199 " =    1.056
peak=    4.278 closest distance to " O   HOH Z 232 " =    2.208
peak=    4.260 closest distance to " OG BSER A 258 " =    0.969
peak=    4.256 closest distance to " O   HOH Z 234 " =    3.750
peak=    4.236 closest distance to " O   HOH Z 105 " =    1.249
peak=    4.235 closest distance to " N   GLN A 278 " =    0.966
peak=    4.225 closest distance to " O   HOH Z   1 " =    1.834
peak=    4.225 closest distance to " O   HOH Z 133 " =    1.488
peak=    4.225 closest distance to " O   HOH Z 350 " =    1.206
peak=    4.201 closest distance to " O   SER A  87 " =    2.173
peak=    4.194 closest distance to " O   HOH Z 427 " =    1.233
peak=    4.174 closest distance to " O   HOH Z 171 " =    2.574
peak=    4.166 closest distance to " O   HOH Z 287 " =    1.755
peak=    4.151 closest distance to " O   HOH Z 389 " =    1.803
peak=    4.142 closest distance to " O   HOH Z 145 " =    1.528
peak=    4.120 closest distance to " CB  ARG A 275 " =    0.975
peak=    4.108 closest distance to " O   HOH Z 298 " =    2.062
peak=    4.108 closest distance to " O   HOH Z  97 " =    1.784
peak=    4.100 closest distance to " O   HOH Z 276 " =    1.516
peak=    4.094 closest distance to " O   HOH Z  59 " =    1.411
peak=    4.088 closest distance to " O   HOH Z 227 " =    1.821
peak=    4.086 closest distance to " CB  TRP A 179 " =    1.422
peak=    4.085 closest distance to " O   HOH Z 211 " =    1.332
peak=    4.070 closest distance to " CB  GLN A 183 " =    1.081
peak=    4.050 closest distance to " O   HOH Z 302 " =    1.448
peak=    4.047 closest distance to " O   HOH Z 139 " =    1.556
peak=    4.043 closest distance to " O   HOH Z 109 " =    1.459
peak=    4.029 closest distance to " CB  GLU A 152 " =    1.318
peak=    4.027 closest distance to " O   HOH Z   5 " =    1.362
peak=    4.012 closest distance to " O   HOH Z 138 " =    0.995
peak=    4.004 closest distance to " CB  TYR A 169 " =    0.852
peak=    3.977 closest distance to " O   HOH Z  48 " =    1.648
peak=    3.971 closest distance to " O   HOH Z  28 " =    1.342
peak=    3.966 closest distance to " CA  SER A  62 " =    1.188
peak=    3.962 closest distance to " O   HOH Z  68 " =    1.753
peak=    3.953 closest distance to " O   HOH Z 155 " =    1.991
peak=    3.953 closest distance to " NZ  LYS A 117 " =    1.031
peak=    3.944 closest distance to " CA  TYR A  30 " =    1.044
peak=    3.935 closest distance to " O   HOH Z 423 " =    1.899
peak=    3.924 closest distance to " O   HOH Z 371 " =    2.088
peak=    3.923 closest distance to " CA  LEU A 282 " =    1.081
peak=    3.917 closest distance to " CG  LEU A 167 " =    1.208
peak=    3.915 closest distance to " O   HOH Z 133 " =    2.261
peak=    3.911 closest distance to " O   HOH Z 371 " =    1.927
peak=    3.865 closest distance to " O   HOH Z 334 " =    2.769
peak=    3.864 closest distance to " CB  SER A  63 " =    1.306
peak=    3.856 closest distance to " CB  ARG A 102 " =    0.891
peak=    3.854 closest distance to " CG  GLN A  88 " =    1.027
peak=    3.847 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.832 closest distance to " CB  VAL A 202 " =    1.650
peak=    3.829 closest distance to " O   HOH Z  11 " =    2.196
peak=    3.829 closest distance to " NE1 TRP A 274 " =    0.990
peak=    3.828 closest distance to " O   HOH Z 269 " =    1.292
peak=    3.824 closest distance to " O   HOH Z 352 " =    1.507
peak=    3.820 closest distance to " O   HOH Z 220 " =    1.292
peak=    3.819 closest distance to " O   HOH Z  39 " =    1.242
peak=    3.819 closest distance to " O   HOH Z  10 " =    1.904
peak=    3.813 closest distance to " CG  GLN A  11 " =    2.077
peak=    3.787 closest distance to " ND2 ASN A  60 " =    3.246
peak=    3.784 closest distance to " O   HOH Z 147 " =    1.375
peak=    3.779 closest distance to " O   HOH Z 263 " =    2.375
peak=    3.778 closest distance to " CB  SER A 216 " =    1.037
peak=    3.756 closest distance to " NZ BLYS A 290 " =    1.031
peak=    3.754 closest distance to " N   GLU A   2 " =    1.392
peak=    3.728 closest distance to " OD2 ASP A 286 " =    2.548
peak=    3.725 closest distance to " O   HOH Z 380 " =    1.624
peak=    3.723 closest distance to " CG2 THR A 221 " =    1.389
peak=    3.705 closest distance to " O   HOH Z 303 " =    1.653
peak=    3.702 closest distance to " O   HOH Z 426 " =    3.498
peak=    3.696 closest distance to " CD  LYS A 166 " =    1.451
peak=    3.693 closest distance to " O   HOH Z 417 " =    1.325
peak=    3.692 closest distance to " NE AARG A 275 " =    1.447
peak=    3.680 closest distance to " O   HOH Z 215 " =    1.474
peak=    3.676 closest distance to " O   HOH Z 409 " =    1.826
peak=    3.669 closest distance to " O   HOH Z 112 " =    1.003
peak=    3.666 closest distance to " CA  ALA A 299 " =    0.966
peak=    3.665 closest distance to " O   HOH Z 108 " =    1.948
peak=    3.664 closest distance to " O   HOH Z 400 " =    0.732
peak=    3.661 closest distance to " O   HOH Z 225 " =    1.549
peak=    3.655 closest distance to " O   HOH Z 250 " =    1.341
peak=    3.652 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.652 closest distance to " O   HOH Z 392 " =    1.259
peak=    3.637 closest distance to " O   HOH Z 258 " =    2.089
peak=    3.627 closest distance to " CB  VAL A 265 " =    1.321
peak=    3.622 closest distance to " O   HOH Z 258 " =    1.149
peak=    3.615 closest distance to " O   HOH Z 286 " =    2.453
peak=    3.613 closest distance to " O   HOH Z 371 " =    3.102
peak=    3.608 closest distance to " O   HOH Z 378 " =    1.093
peak=    3.596 closest distance to " CA  THR A 264 " =    0.738
peak=    3.591 closest distance to " O   HOH Z 116 " =    2.715
peak=    3.589 closest distance to " O   HOH Z 166 " =    1.413
peak=    3.589 closest distance to " O   HOH Z 394 " =    1.577
peak=    3.584 closest distance to " O   HOH Z 217 " =    1.612
peak=    3.577 closest distance to " O   HOH Z 279 " =    0.943
peak=    3.577 closest distance to " O   HOH Z 363 " =    1.137
peak=    3.576 closest distance to " CG  GLN A  77 " =    2.152
peak=    3.573 closest distance to " CB  ASN A  60 " =    0.837
peak=    3.572 closest distance to " NH2 ARG A 219 " =    1.694
peak=    3.570 closest distance to " CG  GLN A  55 " =    1.830
peak=    3.567 closest distance to " CA  ARG A  36 " =    1.296
peak=    3.565 closest distance to " NH1 ARG A  14 " =    1.059
peak=    3.565 closest distance to " OD1 ASN A 217 " =    1.651
peak=    3.564 closest distance to " O   HOH Z 193 " =    1.637
peak=    3.556 closest distance to " CB  ALA A  43 " =    1.058
peak=    3.550 closest distance to " O   HOH Z  61 " =    1.759
peak=    3.541 closest distance to " O   HOH Z 269 " =    3.225
peak=    3.536 closest distance to " CB  ASP A 200 " =    0.937
peak=    3.535 closest distance to " O   PRO A 198 " =    1.231
peak=    3.535 closest distance to " N   PHE A 130 " =    1.300
peak=    3.534 closest distance to " O   HOH Z  89 " =    1.401
peak=    3.533 closest distance to " CE AMET A  47 " =    1.151
peak=    3.532 closest distance to " O   HOH Z 135 " =    1.620
peak=    3.516 closest distance to " O   HOH Z 207 " =    1.885
peak=    3.507 closest distance to " O   HOH Z 217 " =    2.942
peak=    3.491 closest distance to " O   HOH Z 128 " =    1.333
peak=    3.488 closest distance to " OG ASER A 134 " =    1.416
peak=    3.487 closest distance to " O   HOH Z 345 " =    3.515
peak=    3.481 closest distance to " O   HOH Z 106 " =    2.138
peak=    3.481 closest distance to " O   HOH Z 195 " =    1.642
peak=    3.479 closest distance to " CB  PHE A  16 " =    0.974
peak=    3.478 closest distance to " O   HOH Z  50 " =    1.508
peak=    3.476 closest distance to " N   ALA A   1 " =    1.255
peak=    3.474 closest distance to " O   HOH Z 267 " =    1.265
peak=    3.474 closest distance to " O   HOH Z 437 " =    2.454
peak=    3.470 closest distance to " O   HOH Z  88 " =    2.614
peak=    3.469 closest distance to " N   GLY A 196 " =    1.016
peak=    3.466 closest distance to " O   HOH Z  73 " =    1.737
peak=    3.464 closest distance to " O   ALA A 165 " =    1.223
peak=    3.462 closest distance to " CD BLYS A 290 " =    1.089
peak=    3.462 closest distance to " CB  LEU A 300 " =    0.963
peak=    3.458 closest distance to " O   HOH Z  44 " =    1.497
peak=    3.457 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.455 closest distance to " CG  TRP A 179 " =    2.141
peak=    3.453 closest distance to " O   HOH Z  88 " =    3.064
peak=    3.442 closest distance to " NH2AARG A 190 " =    1.535
peak=    3.441 closest distance to " OD1 ASN A  69 " =    2.579
peak=    3.433 closest distance to " O   HOH Z 124 " =    2.124
peak=    3.431 closest distance to " CG2 VAL A  78 " =    1.025
peak=    3.424 closest distance to " CA  GLU A 152 " =    1.152
peak=    3.417 closest distance to " O   HOH Z 172 " =    2.992
peak=    3.417 closest distance to " O   HOH Z 405 " =    1.471
peak=    3.411 closest distance to " CB  ALA A 291 " =    1.582
peak=    3.406 closest distance to " NH2BARG A 190 " =    1.627
peak=    3.406 closest distance to " CA  ARG A 195 " =    1.406
peak=    3.404 closest distance to " CD1 LEU A 228 " =    1.721
peak=    3.402 closest distance to " O   HOH Z 393 " =    1.272
peak=    3.398 closest distance to " CA  ASN A 127 " =    0.926
peak=    3.397 closest distance to " O   HOH Z 207 " =    1.769
peak=    3.395 closest distance to " OE1 GLN A  58 " =    5.546
peak=    3.395 closest distance to " CD  LYS A 119 " =    1.072
peak=    3.394 closest distance to " O   HOH Z 151 " =    1.906
peak=    3.388 closest distance to " O   HOH Z 186 " =    1.231
peak=    3.384 closest distance to " CB  ALA A  34 " =    1.141
peak=    3.383 closest distance to " O   PRO A 198 " =    1.534
peak=    3.382 closest distance to " O   HOH Z 289 " =    1.432
peak=    3.377 closest distance to " O   HOH Z 368 " =    1.785
peak=    3.376 closest distance to " CD  ARG A 138 " =    0.811
peak=    3.375 closest distance to " O   HOH Z 271 " =    2.144
peak=    3.374 closest distance to " O   HOH Z 313 " =    1.777
peak=    3.369 closest distance to " O   HOH Z  21 " =    1.614
peak=    3.368 closest distance to " O   HOH Z 402 " =    1.591
peak=    3.364 closest distance to " O   HOH Z  24 " =    1.713
peak=    3.362 closest distance to " N   ALA A 100 " =    0.944
peak=    3.357 closest distance to " O   GLN A 278 " =    1.464
peak=    3.357 closest distance to " CB  PRO A 198 " =    1.164
peak=    3.357 closest distance to " O   HOH Z 148 " =    1.702
peak=    3.355 closest distance to " O   HOH Z 182 " =    1.351
peak=    3.354 closest distance to " O   HOH Z  57 " =    1.048
peak=    3.352 closest distance to " CB  GLU A 277 " =    1.131
peak=    3.349 closest distance to " O   HOH Z 434 " =    1.372
peak=    3.347 closest distance to " CB  SER A 276 " =    1.075
peak=    3.340 closest distance to " O   HOH Z 273 " =    1.006
peak=    3.335 closest distance to " CG2 THR A 279 " =    1.065
peak=    3.334 closest distance to " O   HOH Z 180 " =    2.078
peak=    3.332 closest distance to " CA  ALA A  21 " =    1.123
peak=    3.327 closest distance to " O   ALA A 233 " =    1.626
peak=    3.327 closest distance to " OD1 ASN A  45 " =    1.179
peak=    3.323 closest distance to " CA  LYS A  48 " =    1.438
peak=    3.322 closest distance to " O   HOH Z 419 " =    2.385
peak=    3.318 closest distance to " N   ARG A 156 " =    1.208
peak=    3.315 closest distance to " O   HOH Z  35 " =    2.019
peak=    3.299 closest distance to " O   HOH Z  32 " =    2.109
peak=    3.292 closest distance to " CA  THR A 221 " =    0.878
peak=    3.290 closest distance to " CG1 VAL A 153 " =    0.840
peak=    3.289 closest distance to " O   HOH Z   6 " =    1.862
peak=    3.288 closest distance to " OD1BASN A 224 " =    2.150
peak=    3.283 closest distance to " N   ALA A   1 " =    2.588
peak=    3.282 closest distance to " N   TYR A  15 " =    1.063
peak=    3.280 closest distance to " O   HOH Z 412 " =    1.532
peak=    3.276 closest distance to " O   HOH Z 108 " =    1.424
peak=    3.272 closest distance to " O   HOH Z 116 " =    1.550
peak=    3.269 closest distance to " CA  ARG A 102 " =    1.253
peak=    3.268 closest distance to " CG  GLU A   2 " =    1.118
peak=    3.267 closest distance to " O   HOH Z 284 " =    1.582
peak=    3.264 closest distance to " CA  ALA A 160 " =    0.766
peak=    3.253 closest distance to " CA  VAL A  41 " =    0.991
peak=    3.252 closest distance to " CB  ASP A 132 " =    3.830
peak=    3.249 closest distance to " O   HOH Z  44 " =    3.400
peak=    3.243 closest distance to " O   HOH Z 125 " =    2.115
peak=    3.242 closest distance to " CZ3 TRP A 123 " =    1.205
peak=    3.242 closest distance to " O   HOH Z 259 " =    2.259
peak=    3.241 closest distance to " O   HOH Z 411 " =    2.175
peak=    3.241 closest distance to " O   HOH Z 278 " =    1.150
peak=    3.241 closest distance to " OG ASER A  99 " =    1.138
peak=    3.240 closest distance to " O   HOH Z 152 " =    2.500
peak=    3.234 closest distance to " O   HOH Z 141 " =    1.778
peak=    3.229 closest distance to " O   HOH Z 426 " =    1.116
peak=    3.228 closest distance to " O   HOH Z 325 " =    1.743
peak=    3.224 closest distance to " CB  MET A  47 " =    1.322
peak=    3.223 closest distance to " O   HOH Z 344 " =    3.132
peak=    3.221 closest distance to " CB  ALA A  21 " =    1.738
peak=    3.220 closest distance to " O   HOH Z  40 " =    2.100
peak=    3.218 closest distance to " CG  LYS A 166 " =    1.294
peak=    3.215 closest distance to " O   HOH Z 368 " =    3.665
peak=    3.213 closest distance to " CG  PRO A 243 " =    1.008
peak=    3.211 closest distance to " O   HOH Z 112 " =    2.427
peak=    3.210 closest distance to " CD  ARG A  66 " =    2.477
peak=    3.208 closest distance to " O   HOH Z   9 " =    2.259
peak=    3.205 closest distance to " CB  TRP A 266 " =    1.011
peak=    3.205 closest distance to " CA  GLY A 267 " =    1.304
peak=    3.203 closest distance to " CA  PHE A 208 " =    0.888
peak=    3.203 closest distance to " C   THR A  18 " =    1.032
peak=    3.201 closest distance to " O   HOH Z  15 " =    1.502
peak=    3.197 closest distance to " O   HOH Z  54 " =    1.151
peak=    3.187 closest distance to " CB  GLU A 277 " =    3.496
peak=    3.182 closest distance to " O   HOH Z 435 " =    1.948
peak=    3.179 closest distance to " CG  GLN A 240 " =    3.403
peak=    3.179 closest distance to " CA  SER A  32 " =    1.654
peak=    3.174 closest distance to " CB  ILE A 234 " =    0.960
peak=    3.173 closest distance to " O   HOH Z 130 " =    2.345
peak=    3.173 closest distance to " O   HOH Z 425 " =    2.062
peak=    3.171 closest distance to " O   HOH Z 253 " =    1.683
peak=    3.171 closest distance to " O   HOH Z 132 " =    1.956
peak=    3.168 closest distance to " CB  LEU A 237 " =    0.861
peak=    3.168 closest distance to " O   HOH Z 288 " =    1.790
peak=    3.164 closest distance to " CG  PRO A 280 " =    0.851
peak=    3.156 closest distance to " O   HOH Z 369 " =    1.605
peak=    3.156 closest distance to " CA  ASN A 215 " =    1.169
peak=    3.147 closest distance to " O   SER A  26 " =    1.595
peak=    3.140 closest distance to " CB  TYR A 116 " =    1.018
peak=    3.134 closest distance to " CB  ALA A 100 " =    1.335
peak=    3.125 closest distance to " N   ASN A  39 " =    1.169
peak=    3.124 closest distance to " O   HOH Z 244 " =    1.511
peak=    3.118 closest distance to " O   SER A 164 " =    0.902
peak=    3.116 closest distance to " O   HOH Z 167 " =    1.922
peak=    3.114 closest distance to " CD2 LEU A  83 " =    1.958
peak=    3.114 closest distance to " O   GLY A 147 " =    1.558
peak=    3.114 closest distance to " CB  VAL A 230 " =    0.832
peak=    3.112 closest distance to " OG1 THR A 264 " =    1.681
peak=    3.110 closest distance to " NE2 GLN A 278 " =    3.927
peak=    3.109 closest distance to " CA  ASP A 191 " =    0.765
peak=    3.109 closest distance to " O   HOH Z 326 " =    1.421
peak=    3.104 closest distance to " CG  ASN A  60 " =    1.187
peak=    3.103 closest distance to " ND2 ASN A 187 " =    1.526
peak=    3.098 closest distance to " O   HOH Z 375 " =    2.190
peak=    3.095 closest distance to " O   HOH Z 438 " =    2.483
peak=    3.091 closest distance to " O   HOH Z 104 " =    1.550
peak=    3.077 closest distance to " NE2 GLN A  58 " =    3.218
peak=    3.072 closest distance to " OG  SER A  22 " =    2.947
peak=    3.066 closest distance to " O   HOH Z  61 " =    1.165
peak=    3.064 closest distance to " CB  MET A  40 " =    0.866
peak=    3.061 closest distance to " CA  SER A  87 " =    1.068

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.626 - 5.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.706 - 5.551

peak=   -4.563 closest distance to " O   HOH Z 198 " =    2.211
peak=   -4.543 closest distance to " CG  GLN A  88 " =    0.864
peak=   -4.490 closest distance to " O   PRO A 198 " =    1.362
peak=   -4.347 closest distance to " CD  ARG A  14 " =    3.199
peak=   -4.273 closest distance to " CG  MET A 105 " =    0.912
peak=   -4.269 closest distance to " O   HOH Z 377 " =    1.539
peak=   -4.219 closest distance to " O   HOH Z  24 " =    1.314
peak=   -4.213 closest distance to " O   HOH Z 409 " =    3.108
peak=   -4.124 closest distance to " O   HOH Z  28 " =    1.769
peak=   -4.103 closest distance to " O   HOH Z 138 " =    0.789
peak=   -4.087 closest distance to " O   HOH Z 166 " =    0.969
peak=   -4.072 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -4.068 closest distance to " O   ALA A  51 " =    1.297
peak=   -4.027 closest distance to " O   HOH Z 266 " =    4.360
peak=   -4.021 closest distance to " O   HOH Z 298 " =    1.071
peak=   -4.020 closest distance to " CB  TYR A  15 " =    2.150
peak=   -4.007 closest distance to " OD1 ASN A 301 " =    1.968
peak=   -3.924 closest distance to " CA  GLY A 133 " =    1.867
peak=   -3.898 closest distance to " CB  CYS A 201 " =    2.314
peak=   -3.893 closest distance to " O   HOH Z  98 " =    1.715
peak=   -3.892 closest distance to " O   HOH Z 185 " =    2.261
peak=   -3.887 closest distance to " O   HOH Z 388 " =    1.894
peak=   -3.883 closest distance to " OG ASER A 134 " =    1.016
peak=   -3.867 closest distance to " OD1 ASP A 191 " =    1.925
peak=   -3.863 closest distance to " O   HOH Z 415 " =    1.352
peak=   -3.854 closest distance to " CB  ASP A  27 " =    2.365
peak=   -3.793 closest distance to " O   HOH Z 290 " =    1.181
peak=   -3.777 closest distance to " CB  ALA A 227 " =    2.230
peak=   -3.773 closest distance to " O   HOH Z 124 " =    1.043
peak=   -3.771 closest distance to " O   HOH Z 372 " =    2.350
peak=   -3.763 closest distance to " N   HIS A 115 " =    1.925
peak=   -3.758 closest distance to " N   LYS A 166 " =    1.817
peak=   -3.737 closest distance to " O   HOH Z  65 " =    0.854
peak=   -3.720 closest distance to " O   HOH Z 117 " =    0.801
peak=   -3.716 closest distance to " O   ALA A 161 " =    1.702
peak=   -3.714 closest distance to " CD  LYS A 289 " =    2.564
peak=   -3.712 closest distance to " O   PRO A 243 " =    2.388
peak=   -3.703 closest distance to " O   ALA A   1 " =    1.059
peak=   -3.703 closest distance to " CB  ALA A 248 " =    1.937
peak=   -3.703 closest distance to " C   ASN A 285 " =    2.241
peak=   -3.701 closest distance to " CG  ARG A 219 " =    2.296
peak=   -3.693 closest distance to " O   TRP A  70 " =    1.307
peak=   -3.685 closest distance to " O   HOH Z  43 " =    1.719
peak=   -3.684 closest distance to " OG  SER A  97 " =    2.103
peak=   -3.680 closest distance to " CB  PRO A 243 " =    2.431
peak=   -3.679 closest distance to " N   GLN A  58 " =    1.274
peak=   -3.674 closest distance to " O   HOH Z 410 " =    2.286
peak=   -3.667 closest distance to " O   HOH Z 438 " =    0.920
peak=   -3.626 closest distance to " OE1 GLN A  88 " =    0.926
peak=   -3.622 closest distance to " O   HOH Z 384 " =    3.251
peak=   -3.622 closest distance to " CZ  PHE A  59 " =    1.398
peak=   -3.605 closest distance to " O   HOH Z 111 " =    0.925
peak=   -3.601 closest distance to " O   HOH Z 220 " =    1.210
peak=   -3.589 closest distance to " CD  LYS A 166 " =    2.492
peak=   -3.587 closest distance to " O   HOH Z 390 " =    2.577
peak=   -3.573 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.571 closest distance to " O   HOH Z  13 " =    1.265
peak=   -3.563 closest distance to " O   VAL A  67 " =    2.707
peak=   -3.559 closest distance to " O   ASN A 301 " =    1.343
peak=   -3.558 closest distance to " O   HOH Z 231 " =    1.717
peak=   -3.551 closest distance to " O   GLY A  98 " =    2.065
peak=   -3.550 closest distance to " O   HOH Z  60 " =    1.880
peak=   -3.550 closest distance to " O   HOH Z 250 " =    1.425
peak=   -3.542 closest distance to " CD  ARG A 156 " =    1.905
peak=   -3.531 closest distance to " O   SER A 146 " =    1.167
peak=   -3.530 closest distance to " O   HOH Z  76 " =    1.190
peak=   -3.530 closest distance to " CB  ALA A  43 " =    2.208
peak=   -3.518 closest distance to " CD1 LEU A 101 " =    2.257
peak=   -3.514 closest distance to " O   HOH Z 102 " =    2.112
peak=   -3.495 closest distance to " O   SER A 135 " =    1.583
peak=   -3.493 closest distance to " OG1 THR A 279 " =    1.302
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.551
peak=   -3.481 closest distance to " O   ILE A  49 " =    1.576
peak=   -3.479 closest distance to " O   HOH Z 275 " =    1.664
peak=   -3.473 closest distance to " N   GLN A  58 " =    1.796
peak=   -3.469 closest distance to " O   HOH Z  93 " =    2.211
peak=   -3.463 closest distance to " N   THR A 157 " =    1.547
peak=   -3.459 closest distance to " OH  TYR A 214 " =    1.146
peak=   -3.458 closest distance to " O   HOH Z  39 " =    1.407
peak=   -3.453 closest distance to " CB  ALA A 291 " =    2.125
peak=   -3.444 closest distance to " N   MET A 188 " =    1.871
peak=   -3.441 closest distance to " O   HOH Z  88 " =    2.416
peak=   -3.425 closest distance to " O   HOH Z 385 " =    1.517
peak=   -3.424 closest distance to " ND2 ASN A 249 " =    2.517
peak=   -3.414 closest distance to " O   HOH Z 140 " =    4.432
peak=   -3.412 closest distance to " O   VAL A 197 " =    1.316
peak=   -3.412 closest distance to " OG  SER A 206 " =    1.872
peak=   -3.405 closest distance to " CZ3 TRP A 123 " =    1.770
peak=   -3.404 closest distance to " CB  ALA A 100 " =    2.082
peak=   -3.397 closest distance to " CD1 LEU A 255 " =    2.919
peak=   -3.396 closest distance to " OE1 GLU A  44 " =    1.597
peak=   -3.393 closest distance to " CB  PHE A 283 " =    2.454
peak=   -3.391 closest distance to " CE3 TRP A 150 " =    2.051
peak=   -3.390 closest distance to " N   ASN A  60 " =    1.227
peak=   -3.388 closest distance to " OE1 GLN A 223 " =    2.836
peak=   -3.387 closest distance to " O   HOH Z 207 " =    1.826
peak=   -3.383 closest distance to " O   HOH Z 143 " =    2.433
peak=   -3.383 closest distance to " O   SER A   3 " =    1.024
peak=   -3.382 closest distance to " N   LEU A 282 " =    2.052
peak=   -3.378 closest distance to " O   VAL A 189 " =    2.416
peak=   -3.376 closest distance to " CG1 ILE A  20 " =    2.436
peak=   -3.372 closest distance to " NE2 GLN A 223 " =    1.441
peak=   -3.370 closest distance to " OE2 GLU A 152 " =    2.224
peak=   -3.366 closest distance to " O   HOH Z 220 " =    2.001
peak=   -3.361 closest distance to " OG  SER A  26 " =    1.027
peak=   -3.361 closest distance to " O   HOH Z 139 " =    2.702
peak=   -3.359 closest distance to " CG  GLU A 277 " =    1.238
peak=   -3.356 closest distance to " O   HOH Z 385 " =    2.332
peak=   -3.352 closest distance to " CG2 THR A 294 " =    2.692
peak=   -3.350 closest distance to " CA  GLN A  55 " =    1.220
peak=   -3.349 closest distance to " CD2 LEU A 237 " =    2.616
peak=   -3.335 closest distance to " O   HOH Z 417 " =    2.482
peak=   -3.334 closest distance to " O   ALA A 165 " =    1.069
peak=   -3.334 closest distance to " N   GLN A 122 " =    1.471
peak=   -3.330 closest distance to " CG  GLU A 152 " =    2.428
peak=   -3.329 closest distance to " CG  ASP A 162 " =    1.487
peak=   -3.324 closest distance to " O   HOH Z 234 " =    4.794
peak=   -3.322 closest distance to " O   HOH Z 404 " =    1.092
peak=   -3.318 closest distance to " OE1 GLN A  58 " =    2.575
peak=   -3.317 closest distance to " O   HOH Z  51 " =    1.001
peak=   -3.316 closest distance to " C   ASP A 191 " =    1.758
peak=   -3.315 closest distance to " CA  GLY A 241 " =    2.127
peak=   -3.314 closest distance to " O   ALA A 100 " =    2.325
peak=   -3.313 closest distance to " O   HOH Z 124 " =    3.097
peak=   -3.310 closest distance to " OG BSER A 134 " =    1.261
peak=   -3.308 closest distance to " O   ALA A 180 " =    1.176
peak=   -3.303 closest distance to " CB  PRO A  90 " =    1.434
peak=   -3.299 closest distance to " O   HOH Z   1 " =    3.734
peak=   -3.298 closest distance to " O   HOH Z 389 " =    1.946
peak=   -3.296 closest distance to " N   ARG A  14 " =    1.002
peak=   -3.295 closest distance to " O   HOH Z 143 " =    1.226
peak=   -3.293 closest distance to " O   HOH Z 134 " =    2.010
peak=   -3.284 closest distance to " O   HOH Z 351 " =    1.443
peak=   -3.274 closest distance to " O   LEU A 282 " =    2.208
peak=   -3.273 closest distance to " CG  PRO A 163 " =    2.379
peak=   -3.272 closest distance to " CG1 VAL A 265 " =    2.059
peak=   -3.272 closest distance to " O   HOH Z 179 " =    1.746
peak=   -3.266 closest distance to " O   HOH Z  97 " =    1.236
peak=   -3.266 closest distance to " CA  GLY A 203 " =    2.200
peak=   -3.265 closest distance to " O   VAL A 197 " =    1.050
peak=   -3.263 closest distance to " CE  LYS A 166 " =    1.082
peak=   -3.259 closest distance to " C   ALA A 158 " =    1.325
peak=   -3.254 closest distance to " N   GLN A  88 " =    1.749
peak=   -3.247 closest distance to " O   HOH Z 211 " =    0.918
peak=   -3.243 closest distance to " CB  TRP A  85 " =    2.311
peak=   -3.243 closest distance to " O   GLN A  73 " =    1.447
peak=   -3.243 closest distance to " CZ  PHE A  16 " =    1.521
peak=   -3.241 closest distance to " O   HOH Z  92 " =    1.555
peak=   -3.236 closest distance to " O   HOH Z 205 " =    0.769
peak=   -3.235 closest distance to " O   PRO A 163 " =    1.839
peak=   -3.231 closest distance to " O   HOH Z 137 " =    1.402
peak=   -3.226 closest distance to " N   ALA A   1 " =    0.975
peak=   -3.224 closest distance to " O   HOH Z 132 " =    0.706
peak=   -3.224 closest distance to " O   HOH Z 234 " =    4.237
peak=   -3.222 closest distance to " CD  ARG A 219 " =    2.491
peak=   -3.219 closest distance to " O   HOH Z 274 " =    2.898
peak=   -3.219 closest distance to " O   HOH Z 264 " =    1.367
peak=   -3.217 closest distance to " O   HOH Z  20 " =    2.551
peak=   -3.214 closest distance to " CD2 TYR A 293 " =    2.086
peak=   -3.210 closest distance to " OE1 GLN A 278 " =    1.782
peak=   -3.209 closest distance to " NE2 GLN A  55 " =    0.922
peak=   -3.206 closest distance to " OG  SER A   3 " =    1.667
peak=   -3.204 closest distance to " C   ARG A 190 " =    1.109
peak=   -3.204 closest distance to " NH2 ARG A  79 " =    1.886
peak=   -3.203 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.203 closest distance to " CB  ALA A   7 " =    1.982
peak=   -3.201 closest distance to " O   HOH Z 150 " =    2.849
peak=   -3.200 closest distance to " N   ALA A 248 " =    1.727
peak=   -3.195 closest distance to " CE2 TYR A 116 " =    2.976
peak=   -3.189 closest distance to " OG  SER A  87 " =    1.271
peak=   -3.189 closest distance to " O   HOH Z  40 " =    4.123
peak=   -3.185 closest distance to " ND2 ASN A  60 " =    1.295
peak=   -3.182 closest distance to " C   GLY A  23 " =    1.909
peak=   -3.177 closest distance to " O   ASN A 170 " =    2.087
peak=   -3.176 closest distance to " C   HIS A 108 " =    1.172
peak=   -3.175 closest distance to " O   HOH Z  52 " =    2.038
peak=   -3.175 closest distance to " OD2 ASP A 171 " =    1.799
peak=   -3.171 closest distance to " C   SER A 135 " =    1.308
peak=   -3.167 closest distance to " C   LEU A 143 " =    1.366
peak=   -3.157 closest distance to " O   HOH Z 292 " =    1.744
peak=   -3.155 closest distance to " CD2 LEU A 237 " =    2.544
peak=   -3.155 closest distance to " N   GLY A 302 " =    1.410
peak=   -3.152 closest distance to " OG BSER A 134 " =    1.749
peak=   -3.147 closest distance to " CG2AVAL A  41 " =    2.764
peak=   -3.147 closest distance to " CZ2 TRP A 179 " =    2.405
peak=   -3.145 closest distance to " O   HOH Z 433 " =    1.325
peak=   -3.139 closest distance to " OG  SER A 245 " =    1.216
peak=   -3.136 closest distance to " O   HOH Z  68 " =    1.827
peak=   -3.125 closest distance to " CD1 TRP A 179 " =    1.151
peak=   -3.123 closest distance to " OG1 THR A   4 " =    1.816
peak=   -3.117 closest distance to " O   HOH Z 278 " =    1.540
peak=   -3.117 closest distance to " OD1 ASN A 148 " =    1.829
peak=   -3.109 closest distance to " O   HOH Z 298 " =    2.453
peak=   -3.103 closest distance to " O   HOH Z 109 " =    3.524
peak=   -3.093 closest distance to " O   HOH Z 247 " =    1.591
peak=   -3.092 closest distance to " C   VAL A 265 " =    0.913
peak=   -3.091 closest distance to " O   GLY A  80 " =    2.337
peak=   -3.080 closest distance to " O   SER A 206 " =    1.518
peak=   -3.079 closest distance to " CA  SER A 146 " =    2.270
peak=   -3.078 closest distance to " O   HOH Z 318 " =    1.485
peak=   -3.072 closest distance to " CG2 VAL A 125 " =    1.315
peak=   -3.067 closest distance to " CG1BVAL A  41 " =    2.774
peak=   -3.063 closest distance to " O   SER A 210 " =    1.268
peak=   -3.059 closest distance to " CD  GLN A  58 " =    1.208
peak=   -3.055 closest distance to " O   ASN A 215 " =    1.658
peak=   -3.038 closest distance to " CD1 TRP A 274 " =    1.353
peak=   -3.036 closest distance to " CD1 ILE A 239 " =    2.265
peak=   -3.016 closest distance to " CG  ARG A 269 " =    2.247

================= 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    :  0.4813 0.4876   6.288413e+00   6.287886e+00
   1_bss:  0.4728 0.4797   6.286542e+00   6.278937e+00
   1_xyz:  0.3807 0.4132   6.147003e+00   6.200957e+00
   1_adp:  0.3459 0.4238   6.101402e+00   6.213028e+00
   1_occ:  0.3453 0.4238   6.100541e+00   6.211899e+00
   2_bss:  0.3448 0.4228   6.101403e+00   6.210504e+00
   2_xyz:  0.2928 0.3674   5.974310e+00   6.120335e+00
   2_adp:  0.2815 0.3548   5.950358e+00   6.100161e+00
   2_occ:  0.2813 0.3553   5.949916e+00   6.100003e+00
   3_bss:  0.2816 0.3551   5.949377e+00   6.099888e+00
   3_xyz:  0.2192 0.2900   5.742524e+00   5.932796e+00
   3_adp:  0.1991 0.2684   5.660005e+00   5.869215e+00
   3_occ:  0.1989 0.2679   5.658609e+00   5.867590e+00
   4_bss:  0.1987 0.2669   5.657432e+00   5.865471e+00
   4_xyz:  0.1587 0.2140   5.449348e+00   5.678555e+00
   4_adp:  0.1495 0.1999   5.389728e+00   5.610955e+00
   4_occ:  0.1493 0.1993   5.388100e+00   5.608930e+00
   5_bss:  0.1492 0.1988   5.386438e+00   5.607104e+00
   5_xyz:  0.1319 0.1782   5.275568e+00   5.501407e+00
   5_adp:  0.1269 0.1748   5.248992e+00   5.481854e+00
   5_occ:  0.1269 0.1747   5.248602e+00   5.481765e+00
   5_bss:  0.1268 0.1747   5.248304e+00   5.481786e+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:  0.300  20.000  -2.178   1.200   1.536   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -2.178   1.200   1.536   0.000   0.000   0.000
   1_adp:  0.300  20.000  -2.178   1.200   1.536   0.000   0.000   0.000
   1_occ:  0.300  20.000  -2.178   1.200   1.536   0.000   0.000   0.000
   2_bss:  0.340  54.919  -1.209  -0.123   0.414  -0.000   0.000   0.000
   2_xyz:  0.340  54.919  -1.209  -0.123   0.414  -0.000   0.000   0.000
   2_adp:  0.340  54.919  -1.209  -0.123   0.414  -0.000   0.000   0.000
   2_occ:  0.340  54.919  -1.209  -0.123   0.414  -0.000   0.000   0.000
   3_bss:  0.340  54.919  -1.100  -0.786  -0.032  -0.000  -0.000  -0.000
   3_xyz:  0.340  54.919  -1.100  -0.786  -0.032  -0.000  -0.000  -0.000
   3_adp:  0.340  54.919  -1.100  -0.786  -0.032  -0.000  -0.000  -0.000
   3_occ:  0.340  54.919  -1.100  -0.786  -0.032  -0.000  -0.000  -0.000
   4_bss:  0.333  54.919  -1.736  -2.126  -1.216  -0.000  -0.000  -0.000
   4_xyz:  0.333  54.919  -1.736  -2.126  -1.216  -0.000  -0.000  -0.000
   4_adp:  0.333  54.919  -1.736  -2.126  -1.216  -0.000  -0.000  -0.000
   4_occ:  0.333  54.919  -1.736  -2.126  -1.216  -0.000  -0.000  -0.000
   5_bss:  0.316  42.334  -2.119  -2.638  -1.671  -0.000  -0.000  -0.000
   5_xyz:  0.316  42.334  -2.119  -2.638  -1.671  -0.000  -0.000  -0.000
   5_adp:  0.316  42.334  -2.119  -2.638  -1.671  -0.000  -0.000  -0.000
   5_occ:  0.316  42.334  -2.119  -2.638  -1.671  -0.000  -0.000  -0.000
   5_bss:  0.311  43.630  -2.105  -2.624  -1.657  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.402 0.3750  0.5178    76650.541
   1_bss:  60.226 0.3885  0.5428    72866.311
   1_xyz:  46.742 0.5606  0.7650    50504.465
   1_adp:  48.115 0.5426  0.7522    52162.938
   1_occ:  48.086 0.5429  0.7519    52039.103
   2_bss:  47.857 0.5458  0.7464    51808.025
   2_xyz:  40.200 0.6388  0.8637    37741.959
   2_adp:  38.144 0.6640  0.8843    35334.918
   2_occ:  38.144 0.6640  0.8835    35329.480
   3_bss:  38.058 0.6649  0.8735    35167.335
   3_xyz:  29.556 0.7622  0.9733    22155.413
   3_adp:  26.518 0.7959  0.9863    18785.825
   3_occ:  26.457 0.7965  0.9864    18684.839
   4_bss:  26.367 0.7973  0.9502    18534.755
   4_xyz:  20.876 0.8527  0.9875    11909.725
   4_adp:  18.919 0.8724  0.9924    10378.630
   4_occ:  18.869 0.8729  0.9924    10321.183
   5_bss:  18.827 0.8731  0.9755    10223.017
   5_xyz:  16.349 0.8952  0.9883     8007.994
   5_adp:  15.848 0.8999  0.9865     7731.620
   5_occ:  15.833 0.9001  0.9864     7718.987
   5_bss:  15.828 0.9001  0.9865     7718.420
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8801e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8801e-01
   1_xyz:   1.576  0.012  0.103 16.124  0.006  4.106   1.3522e-01
   1_adp:   1.576  0.012  0.103 16.124  0.006  4.106   1.3522e-01
   1_occ:   1.576  0.012  0.103 16.124  0.006  4.106   1.3522e-01
   2_bss:   1.576  0.012  0.103 16.124  0.006  4.106   1.3522e-01
   2_xyz:   1.226  0.008  0.079 14.754  0.005  4.107   7.8420e-02
   2_adp:   1.226  0.008  0.079 14.754  0.005  4.107   7.8420e-02
   2_occ:   1.226  0.008  0.079 14.754  0.005  4.107   7.8420e-02
   3_bss:   1.226  0.008  0.079 14.754  0.005  4.107   7.8420e-02
   3_xyz:   1.098  0.008  0.076 14.393  0.004  4.111   6.8060e-02
   3_adp:   1.098  0.008  0.076 14.393  0.004  4.111   6.8060e-02
   3_occ:   1.098  0.008  0.076 14.393  0.004  4.111   6.8060e-02
   4_bss:   1.098  0.008  0.076 14.393  0.004  4.111   6.8060e-02
   4_xyz:   0.972  0.005  0.066 14.097  0.004  4.107   5.4879e-02
   4_adp:   0.972  0.005  0.066 14.097  0.004  4.107   5.4879e-02
   4_occ:   0.972  0.005  0.066 14.097  0.004  4.107   5.4879e-02
   5_bss:   0.972  0.005  0.066 14.097  0.004  4.107   5.4879e-02
   5_xyz:   0.912  0.005  0.064 14.137  0.003  4.109   5.0084e-02
   5_adp:   0.912  0.005  0.064 14.137  0.003  4.109   5.0084e-02
   5_occ:   0.912  0.005  0.064 14.137  0.003  4.109   5.0084e-02
   5_bss:   0.912  0.005  0.064 14.137  0.003  4.109   5.0084e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.439   2.3849e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.439   2.3849e-01
   1_xyz:  10.797  0.088  0.422 89.771  0.029  1.923   1.0705e-01
   1_adp:  10.797  0.088  0.422 89.771  0.029  1.923   1.0705e-01
   1_occ:  10.797  0.088  0.422 89.771  0.029  1.923   1.0705e-01
   2_bss:  10.797  0.088  0.422 89.771  0.029  1.923   1.0705e-01
   2_xyz:   8.050  0.048  0.241 89.000  0.054  2.343   8.1634e-02
   2_adp:   8.050  0.048  0.241 89.000  0.054  2.343   8.1634e-02
   2_occ:   8.050  0.048  0.241 89.000  0.054  2.343   8.1634e-02
   3_bss:   8.050  0.048  0.241 89.000  0.054  2.343   8.1634e-02
   3_xyz:   9.126  0.053  0.288 88.857  0.029  2.245   7.4802e-02
   3_adp:   9.126  0.053  0.288 88.857  0.029  2.245   7.4802e-02
   3_occ:   9.126  0.053  0.288 88.857  0.029  2.245   7.4802e-02
   4_bss:   9.126  0.053  0.288 88.857  0.029  2.245   7.4802e-02
   4_xyz:   6.363  0.038  0.242 79.255  0.033  2.341   5.4384e-02
   4_adp:   6.363  0.038  0.242 79.255  0.033  2.341   5.4384e-02
   4_occ:   6.363  0.038  0.242 79.255  0.033  2.341   5.4384e-02
   5_bss:   6.363  0.038  0.242 79.255  0.033  2.341   5.4384e-02
   5_xyz:   7.528  0.048  0.212 84.997  0.029  2.350   3.5968e-02
   5_adp:   7.528  0.048  0.212 84.997  0.029  2.350   3.5968e-02
   5_occ:   7.528  0.048  0.212 84.997  0.029  2.350   3.5968e-02
   5_bss:   7.528  0.048  0.212 84.997  0.029  2.350   3.5968e-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: 102.87   0.00  19.61  94.29   0.00  16.42 102.87   0.00  36.96
   1_occ: 102.87   0.00  19.61  94.29   0.00  16.42 102.87   0.00  36.96
   2_bss: 102.87   0.00  19.61  94.29   0.00  16.42 102.87   0.00  36.96
   2_xyz: 102.87   0.00  19.61  94.29   0.00  16.42 102.87   0.00  36.96
   2_adp: 101.63   0.00  18.93  93.87   0.00  15.64 101.63   0.64  36.89
   2_occ: 101.63   0.00  18.93  93.87   0.00  15.64 101.63   0.64  36.89
   3_bss: 101.63   0.00  18.93  93.87   0.00  15.64 101.63   0.64  36.89
   3_xyz: 101.63   0.00  18.93  93.87   0.00  15.64 101.63   0.64  36.89
   3_adp:  97.49   0.00  18.39  94.65   0.00  14.01  97.49   3.86  42.28
   3_occ:  97.49   0.00  18.39  94.65   0.00  14.01  97.49   3.86  42.28
   4_bss:  97.49   0.00  18.39  94.65   0.00  14.01  97.49   3.86  42.28
   4_xyz:  97.49   0.00  18.39  94.65   0.00  14.01  97.49   3.86  42.28
   4_adp:  92.73   1.17  17.66  91.78   1.17  13.22  92.73   6.32  41.80
   4_occ:  92.73   1.17  17.66  91.78   1.17  13.22  92.73   6.32  41.80
   5_bss:  92.73   1.17  17.66  91.78   1.17  13.22  92.73   6.32  41.80
   5_xyz:  92.73   1.17  17.66  91.78   1.17  13.22  92.73   6.32  41.80
   5_adp: 102.77   0.45  18.07 102.77   0.45  13.11  93.58   6.40  45.04
   5_occ: 102.77   0.45  18.07 102.77   0.45  13.11  93.58   6.40  45.04
   5_bss: 102.75   0.43  18.05 102.75   0.43  13.10  93.57   6.38  45.03
------------------------------------------------------------------------
 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:    1.952    0.009    0.352
   1_adp:    1.952    0.009    0.352
   1_occ:    1.952    0.009    0.352
   2_bss:    1.952    0.009    0.352
   2_xyz:    1.494    0.032    0.498
   2_adp:    1.494    0.032    0.498
   2_occ:    1.494    0.032    0.498
   3_bss:    1.494    0.032    0.498
   3_xyz:    1.496    0.072    0.664
   3_adp:    1.496    0.072    0.664
   3_occ:    1.496    0.072    0.664
   4_bss:    1.496    0.072    0.664
   4_xyz:    1.588    0.045    0.759
   4_adp:    1.588    0.045    0.759
   4_occ:    1.588    0.045    0.759
   5_bss:    1.588    0.045    0.759
   5_xyz:    1.615    0.068    0.798
   5_adp:    1.615    0.068    0.798
   5_occ:    1.615    0.068    0.798
   5_bss:    1.615    0.068    0.798
------------------------------------------------------------------------

CPU time actual refinement: 364.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/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_858/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_858/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.76 
  Macro-tasks:
    bulk solvent and scale       = 43.94  
    individual site refinement   = 161.83 
    weights calculation          = 29.91  
    collect and process          = 6.39   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 242.19 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 119.26 
    alpha_beta                      = 8.14   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 129.49 
    fmodel                         = 7.14   
    r_factors                      = 0.21   
    phase_errors                   = 10.28  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 278.34 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.074 micro seconds
Total CPU time: 6.31 minutes
from_scatterers_fft:    648 calls, 118.88 s
gradients_fft:          593 calls, 115.28 s

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

# Date 2008-01-16 Time 05:49:43 PST -0800 (1200491383.88 s)
Start R-work = 0.4813, R-free = 0.4876 (no bulk solvent and anisotropic scale)
Final R-work = 0.1496, R-free = 0.1955 (no bulk solvent and anisotropic scale)

Start R-work = 0.4728, R-free = 0.4797
Final R-work = 0.1268, R-free = 0.1747