# Date 2008-01-16 Time 06:42:04 PST -0800 (1200494524.74 s)
#phil __OFF__

Command line arguments: "../1251.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24092
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1251

-------------------------------------------------------------------------------
  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: (72.0062, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 1.98383
Completeness in resolution range: 0.934367
Completeness with d_max=infinity: 0.9317

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3277
                             d_min =   1.9838

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: (72.0062, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 1.98383
Completeness in resolution range: 0.934367
Completeness with d_max=infinity: 0.9317

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3282 -  4.2466 [2201/2228]  1981   220  10.0%
  bin  2:  4.2466 -  3.3826 [2125/2145]  1913   212  10.0%
  bin  3:  3.3826 -  2.9585 [2079/2098]  1872   207  10.0%
  bin  4:  2.9585 -  2.6896 [2064/2094]  1856   208  10.1%
  bin  5:  2.6896 -  2.4977 [2060/2079]  1862   198   9.6%
  bin  6:  2.4977 -  2.3510 [2049/2074]  1833   216  10.5%
  bin  7:  2.3510 -  2.2336 [2047/2075]  1837   210  10.3%
  bin  8:  2.2336 -  2.1366 [2014/2050]  1814   200   9.9%
  bin  9:  2.1366 -  2.0546 [2020/2062]  1824   196   9.7%
  bin 10:  2.0546 -  1.9838 [ 930/2060]   838    92   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2167
        3.04 -     3.66: 4642
        3.66 -     4.28: 8917
        4.28 -     4.90: 12220
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.127 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.202 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.202 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27959 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_1251/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/model_refine_001.geo

CPU time processing inputs: 9.59


============================ 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 = 72.00625 46.4607 87.68585 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: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4364   r_free= 0.4281   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.239013                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.7372 0.99   1424  159 0.3408 0.3179       6.492      6.4132|
|  2:  4.7372 -  3.7786 0.99   1379  154 0.3655 0.3557      6.7522       6.707|
|  3:  3.7786 -  3.3064 0.99   1340  145 0.3936 0.3752      6.5813      6.5595|
|  4:  3.3064 -  3.0066 0.99   1345  154 0.4216 0.4374      6.4523      6.4571|
|  5:  3.0066 -  2.7925 0.99   1346  147 0.4660 0.4510      6.3275       6.331|
|  6:  2.7925 -  2.6287 0.99   1334  151 0.4513 0.4400       6.205      6.1729|
|  7:  2.6287 -  2.4977 0.99   1316  135 0.4849 0.4455      6.2098      6.1568|
|  8:  2.4977 -  2.3894 0.98   1307  155 0.4941 0.4940      6.1463      6.1468|
|  9:  2.3894 -  2.2977 0.98   1308  146 0.4925 0.4966      6.1023      6.1369|
| 10:  2.2977 -  2.2187 1.00   1302  150 0.5049 0.4791      6.0691      6.0267|
| 11:  2.2187 -  2.1495 0.98   1324  135 0.4927 0.5058      6.0232       6.019|
| 12:  2.1495 -  2.0882 0.98   1275  149 0.4963 0.5048      5.9151      5.9667|
| 13:  2.0882 -  2.0333 0.95   1254  135 0.5044 0.4715      5.8587      5.7885|
| 14:  2.0333 -  1.9838 0.28    376   44 0.4870 0.5634      5.8345      5.8566|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.7372  1424   159  0.76  28.51   0.83     0.79      51744.96|
|  2:  4.7372 -  3.7786  1379   154  0.78  28.17   0.92     0.87      73579.12|
|  3:  3.7786 -  3.3064  1340   145  0.68  37.17   0.92     0.85      83235.93|
|  4:  3.3064 -  3.0066  1345   154  0.60  43.53   0.91     0.78      78631.43|
|  5:  3.0066 -  2.7925  1346   147  0.51  50.94   0.90     0.70      66863.60|
|  6:  2.7925 -  2.6287  1334   151  0.49  52.91   0.92     0.67      57528.77|
|  7:  2.6287 -  2.4977  1316   135  0.47  54.43   0.92     0.62      53586.90|
|  8:  2.4977 -  2.3894  1307   155  0.45  55.69   0.89     0.62      49430.78|
|  9:  2.3894 -  2.2977  1308   146  0.44  56.67   0.93     0.62      45984.27|
| 10:  2.2977 -  2.2187  1302   150  0.44  57.15   0.93     0.62      42061.37|
| 11:  2.2187 -  2.1495  1324   135  0.42  58.46   0.94     0.61      41739.38|
| 12:  2.1495 -  2.0882  1275   149  0.38  61.65   0.94     0.57      38790.84|
| 13:  2.0882 -  2.0333  1254   135  0.36  63.40   0.92     0.56      34887.89|
| 14:  2.0333 -  1.9838   376    44  0.41  59.49   0.95     0.56      28147.13|
|alpha:            min =        0.56 max =            0.87 mean =         0.68|
|beta:             min =    28147.13 max =        83235.93 mean =     54922.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.79|
|phase err.(test): min =        0.00 max =           89.88 mean =        49.43|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.232039             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.852   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.803447              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.172   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1979 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1837 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4583 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4334 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5571 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6649 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.159 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    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: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4364   r_free= 0.4281   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.239013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4281   r_free= 0.4219   ksol= 0.33   Bsol= 71.89   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,-1.40,1.51,-0.00,0.00,0.00); trace/3= 0.81                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.229944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.652995             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.892140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.779   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4281      final r-factor (work) = 0.2565          |
| start r-factor (free) = 0.4219      final r-factor (free) = 0.2866          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3345 = 10.65 * 0.50 * 6.2277 + 1.00 * 0.1627                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.2150 = 10.65 * 0.50 * 6.0261 + 1.00 * 0.1170                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2565      final r-factor (work) = 0.2345          |
| start r-factor (free) = 0.2866      final r-factor (free) = 0.2951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3827 = 0.89 * 1.00 * 6.0261 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1939 = 0.89 * 1.00 * 5.7693 + 1.00 * 0.0468                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.86   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    80.86   17.38    None  None   None       |
|    Sol.    : 438    0      3.39    67.46   39.68    None  None   None       |
|    Mac.    : 2385   0      0.00    80.86   13.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.086:  678   |   5:    40.432 -  48.518:  127        |
|      1:     8.086 -  16.173: 1066   |   6:    48.518 -  56.604:   92        |
|      2:    16.173 -  24.259:  494   |   7:    56.604 -  64.690:   36        |
|      3:    24.259 -  32.345:  190   |   8:    64.690 -  72.777:    4        |
|      4:    32.345 -  40.432:  135   |   9:    72.777 -  80.863:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2345 r_free = 0.2951             target_work(ml) = 5.782         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2341 r_free = 0.2947             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2341   r_free= 0.2947   ksol= 0.33   Bsol= 71.89   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,-1.40,1.51,-0.00,0.00,0.00); trace/3= 0.81                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.780809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2318   r_free= 0.2946   ksol= 0.34   Bsol= 76.13   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-2.58,-0.42,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.781772                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.031790              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.445   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.034   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2318      final r-factor (work) = 0.1653          |
| start r-factor (free) = 0.2946      final r-factor (free) = 0.2180          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6699 = 5.03 * 0.50 * 5.7844 + 1.00 * 0.1170                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3037 = 5.03 * 0.50 * 5.6575 + 1.00 * 0.0700                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1653      final r-factor (work) = 0.1513          |
| start r-factor (free) = 0.2180      final r-factor (free) = 0.2022          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1504 = 0.55 * 1.00 * 5.6575 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6642 = 0.55 * 1.00 * 5.4483 + 1.00 * 0.6450                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.22   17.42    None  None   None       |
|    all(noH): 2823   0      0.00    92.22   17.42    None  None   None       |
|    Sol.    : 438    0      5.56    69.58   40.37    None  None   None       |
|    Mac.    : 2385   0      0.00    92.22   13.21    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 -   9.222:  812   |   5:    46.110 -  55.332:  132        |
|      1:     9.222 -  18.444: 1190   |   6:    55.332 -  64.554:   58        |
|      2:    18.444 -  27.666:  349   |   7:    64.554 -  73.776:    4        |
|      3:    27.666 -  36.888:  132   |   8:    73.776 -  82.998:    0        |
|      4:    36.888 -  46.110:  145   |   9:    82.998 -  92.220:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1513 r_free = 0.2022             target_work(ml) = 5.409         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1511 r_free = 0.2019             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1511   r_free= 0.2019   ksol= 0.34   Bsol= 76.13   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-2.58,-0.42,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.408155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.2019   ksol= 0.34   Bsol= 69.01   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-2.61,-0.70,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.406704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.729958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.211  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.100704              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 87.900   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.2019      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7823 = 1.73 * 0.50 * 5.4479 + 1.00 * 0.0700                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6967 = 1.73 * 0.50 * 5.3721 + 1.00 * 0.0499                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.0554 = 4.10 * 1.00 * 5.3721 + 1.00 * 0.0260                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.7880 = 4.10 * 1.00 * 5.3101 + 1.00 * 0.0130                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.61   18.46    None  None   None       |
|    all(noH): 2823   0      0.00    98.61   18.46    None  None   None       |
|    Sol.    : 438    0      5.42    98.61   45.84    None  None   None       |
|    Mac.    : 2385   0      0.00    87.12   13.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.861:  980   |   5:    49.305 -  59.167:   87        |
|      1:     9.861 -  19.722: 1145   |   6:    59.167 -  69.028:   90        |
|      2:    19.722 -  29.583:  239   |   7:    69.028 -  78.889:   38        |
|      3:    29.583 -  39.444:  123   |   8:    78.889 -  88.750:   20        |
|      4:    39.444 -  49.305:   95   |   9:    88.750 -  98.611:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1326 r_free = 0.1829             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1325 r_free = 0.1829             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1829   ksol= 0.34   Bsol= 69.01   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-2.61,-0.70,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.298131                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1830   ksol= 0.33   Bsol= 72.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.297719                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.988808              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.452  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.440  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9853 = 2.99 * 0.50 * 5.3101 + 1.00 * 0.0499                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9237 = 2.99 * 0.50 * 5.2554 + 1.00 * 0.0699                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7168 = 0.32 * 1.00 * 5.2554 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7023 = 0.32 * 1.00 * 5.2196 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    94.35   17.66    None  None   None       |
|    all(noH): 2823   0      0.29    94.35   17.66    None  None   None       |
|    Sol.    : 438    0      3.46    94.35   42.54    None  None   None       |
|    Mac.    : 2385   0      0.29    84.27   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.291 -   9.697:  953   |   5:    47.321 -  56.727:   93        |
|      1:     9.697 -  19.103: 1179   |   6:    56.727 -  66.133:   60        |
|      2:    19.103 -  28.509:  241   |   7:    66.133 -  75.539:   37        |
|      3:    28.509 -  37.915:  131   |   8:    75.539 -  84.945:   15        |
|      4:    37.915 -  47.321:  108   |   9:    84.945 -  94.351:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1677             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1677             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1677   ksol= 0.33   Bsol= 72.95   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1667   ksol= 0.32   Bsol= 67.44   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201640                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.445148              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.089  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.369143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4516 = 2.45 * 0.50 * 5.2199 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4154 = 2.45 * 0.50 * 5.1945 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9274 = 0.37 * 1.00 * 5.1945 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9254 = 0.37 * 1.00 * 5.1899 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.15    94.25   17.41    None  None   None       |
|    all(noH): 2823   0      0.15    94.25   17.41    None  None   None       |
|    Sol.    : 438    0      4.02    94.25   41.62    None  None   None       |
|    Mac.    : 2385   0      0.15    85.65   12.96    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:     0.148 -   9.557:  944   |   5:    47.197 -  56.607:   99        |
|      1:     9.557 -  18.967: 1182   |   6:    56.607 -  66.017:   53        |
|      2:    18.967 -  28.377:  250   |   7:    66.017 -  75.427:   32        |
|      3:    28.377 -  37.787:  137   |   8:    75.427 -  84.836:   12        |
|      4:    37.787 -  47.197:  107   |   9:    84.836 -  94.246:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1638             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1638             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1638   ksol= 0.32   Bsol= 67.44   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.7372 0.99   1424  159 0.0969 0.1307      5.3735      5.5668|
|  2:  4.7372 -  3.7786 0.99   1379  154 0.0866 0.1075       5.446      5.6093|
|  3:  3.7786 -  3.3064 0.99   1340  145 0.1077 0.1628      5.4845      5.8586|
|  4:  3.3064 -  3.0066 0.99   1345  154 0.1283 0.1755      5.4915      5.6597|
|  5:  3.0066 -  2.7925 0.99   1346  147 0.1382 0.1797       5.358      5.6132|
|  6:  2.7925 -  2.6287 0.99   1334  151 0.1314 0.1912      5.2459      5.4842|
|  7:  2.6287 -  2.4977 0.99   1316  135 0.1303 0.1723      5.2047      5.3605|
|  8:  2.4977 -  2.3894 0.98   1307  155 0.1253 0.1812      5.1159      5.3703|
|  9:  2.3894 -  2.2977 0.98   1308  146 0.1269 0.1931      5.0983      5.3583|
| 10:  2.2977 -  2.2187 1.00   1302  150 0.1176 0.1651      4.9796      5.2074|
| 11:  2.2187 -  2.1495 0.98   1324  135 0.1162 0.1936      4.9744      5.3696|
| 12:  2.1495 -  2.0882 0.98   1275  149 0.1186 0.1765      4.8956      5.1346|
| 13:  2.0882 -  2.0333 0.95   1254  135 0.1198 0.1670      4.8259      5.0445|
| 14:  2.0333 -  1.9838 0.28    376   44 0.1085 0.1729      4.7215      5.0021|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.7372  1424   159  0.94   8.99   0.96     0.94       6994.47|
|  2:  4.7372 -  3.7786  1379   154  0.95   7.98   1.00     0.99       9140.56|
|  3:  3.7786 -  3.3064  1340   145  0.93  11.60   1.02     1.01      10643.71|
|  4:  3.3064 -  3.0066  1345   154  0.91  14.96   1.00     0.98      11212.38|
|  5:  3.0066 -  2.7925  1346   147  0.90  16.48   0.99     0.97       8912.53|
|  6:  2.7925 -  2.6287  1334   151  0.89  17.04   0.98     0.96       7566.28|
|  7:  2.6287 -  2.4977  1316   135  0.90  16.03   0.99     0.97       6788.00|
|  8:  2.4977 -  2.3894  1307   155  0.90  16.42   0.98     0.94       5737.57|
|  9:  2.3894 -  2.2977  1308   146  0.90  16.82   0.99     0.95       5663.92|
| 10:  2.2977 -  2.2187  1302   150  0.90  16.44   0.99     0.96       4668.90|
| 11:  2.2187 -  2.1495  1324   135  0.90  16.22   0.97     0.92       4490.43|
| 12:  2.1495 -  2.0882  1275   149  0.90  16.39   1.00     1.00       4147.64|
| 13:  2.0882 -  2.0333  1254   135  0.89  17.59   0.98     0.96       3697.73|
| 14:  2.0333 -  1.9838   376    44  0.91  15.55   0.95     0.92       2972.96|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2972.96 max =        11212.38 mean =      6857.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.78|
|phase err.(test): min =        0.00 max =           88.60 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1638   ksol= 0.32   Bsol= 67.44   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1638   ksol= 0.32   Bsol= 67.44   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.74,-0.92,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.7372 0.99   1424  159 0.0969 0.1307      5.3735      5.5668|
|  2:  4.7372 -  3.7786 0.99   1379  154 0.0866 0.1075       5.446      5.6093|
|  3:  3.7786 -  3.3064 0.99   1340  145 0.1077 0.1628      5.4845      5.8586|
|  4:  3.3064 -  3.0066 0.99   1345  154 0.1283 0.1755      5.4915      5.6597|
|  5:  3.0066 -  2.7925 0.99   1346  147 0.1382 0.1797       5.358      5.6132|
|  6:  2.7925 -  2.6287 0.99   1334  151 0.1314 0.1912      5.2459      5.4842|
|  7:  2.6287 -  2.4977 0.99   1316  135 0.1303 0.1723      5.2047      5.3605|
|  8:  2.4977 -  2.3894 0.98   1307  155 0.1253 0.1812      5.1159      5.3703|
|  9:  2.3894 -  2.2977 0.98   1308  146 0.1269 0.1931      5.0983      5.3583|
| 10:  2.2977 -  2.2187 1.00   1302  150 0.1176 0.1651      4.9796      5.2074|
| 11:  2.2187 -  2.1495 0.98   1324  135 0.1162 0.1936      4.9744      5.3696|
| 12:  2.1495 -  2.0882 0.98   1275  149 0.1186 0.1765      4.8956      5.1346|
| 13:  2.0882 -  2.0333 0.95   1254  135 0.1198 0.1670      4.8259      5.0445|
| 14:  2.0333 -  1.9838 0.28    376   44 0.1085 0.1729      4.7215      5.0021|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.7372  1424   159  0.94   8.99   0.96     0.94       6994.47|
|  2:  4.7372 -  3.7786  1379   154  0.95   7.98   1.00     0.99       9140.56|
|  3:  3.7786 -  3.3064  1340   145  0.93  11.60   1.02     1.01      10643.71|
|  4:  3.3064 -  3.0066  1345   154  0.91  14.96   1.00     0.98      11212.38|
|  5:  3.0066 -  2.7925  1346   147  0.90  16.48   0.99     0.97       8912.53|
|  6:  2.7925 -  2.6287  1334   151  0.89  17.04   0.98     0.96       7566.28|
|  7:  2.6287 -  2.4977  1316   135  0.90  16.03   0.99     0.97       6788.00|
|  8:  2.4977 -  2.3894  1307   155  0.90  16.42   0.98     0.94       5737.57|
|  9:  2.3894 -  2.2977  1308   146  0.90  16.82   0.99     0.95       5663.92|
| 10:  2.2977 -  2.2187  1302   150  0.90  16.44   0.99     0.96       4668.90|
| 11:  2.2187 -  2.1495  1324   135  0.90  16.22   0.97     0.92       4490.43|
| 12:  2.1495 -  2.0882  1275   149  0.90  16.39   1.00     1.00       4147.64|
| 13:  2.0882 -  2.0333  1254   135  0.89  17.59   0.98     0.96       3697.73|
| 14:  2.0333 -  1.9838   376    44  0.91  15.55   0.95     0.92       2972.96|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2972.96 max =        11212.38 mean =      6857.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.78|
|phase err.(test): min =        0.00 max =           88.60 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.14    94.24   17.40    None  None   None       |
|    all(noH): 2823   0      0.14    94.24   17.40    None  None   None       |
|    Sol.    : 438    0      4.02    94.24   41.62    None  None   None       |
|    Mac.    : 2385   0      0.14    85.65   12.96    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:     0.145 -   9.555:  944   |   5:    47.194 -  56.604:   99        |
|      1:     9.555 -  18.965: 1182   |   6:    56.604 -  66.014:   53        |
|      2:    18.965 -  28.375:  250   |   7:    66.014 -  75.424:   32        |
|      3:    28.375 -  37.784:  137   |   8:    75.424 -  84.834:   12        |
|      4:    37.784 -  47.194:  107   |   9:    84.834 -  94.244:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 4.678
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 313
   mapped sites are within: 0.734 - 4.678

peak=    5.654 closest distance to " CB  GLN A 223 " =    1.514
peak=    5.627 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.230 closest distance to " O   HOH Z 232 " =    2.218
peak=    4.982 closest distance to " CG  PRO A  54 " =    1.343
peak=    4.935 closest distance to " O   HOH Z 111 " =    1.867
peak=    4.889 closest distance to " O   HOH Z 144 " =    1.827
peak=    4.802 closest distance to " CZ  PHE A 218 " =    1.049
peak=    4.746 closest distance to " CB  SER A  63 " =    1.302
peak=    4.705 closest distance to " CG  PRO A 280 " =    0.936
peak=    4.675 closest distance to " O   HOH Z 298 " =    2.274
peak=    4.664 closest distance to " CG  PRO A 213 " =    1.297
peak=    4.622 closest distance to " CB  ASN A 148 " =    1.384
peak=    4.565 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.528 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.526 closest distance to " CD  ARG A 159 " =    0.817
peak=    4.512 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.500 closest distance to " O   HOH Z 423 " =    1.737
peak=    4.498 closest distance to " NH1AARG A 145 " =    1.291
peak=    4.477 closest distance to " CB  PRO A  54 " =    1.002
peak=    4.470 closest distance to " CB  ARG A 190 " =    1.576
peak=    4.468 closest distance to " O   HOH Z 369 " =    2.059
peak=    4.384 closest distance to " O   HOH Z 287 " =    2.177
peak=    4.369 closest distance to " CG  PRO A  90 " =    1.256
peak=    4.368 closest distance to " O   HOH Z 126 " =    1.962
peak=    4.286 closest distance to " O   PRO A 198 " =    1.572
peak=    4.249 closest distance to " O   HOH Z  21 " =    1.769
peak=    4.176 closest distance to " O   HOH Z 126 " =    1.478
peak=    4.171 closest distance to " CG  PRO A 243 " =    1.097
peak=    4.167 closest distance to " CB  TRP A 266 " =    1.013
peak=    4.166 closest distance to " CB  GLU A 128 " =    1.041
peak=    4.164 closest distance to " CE  LYS A  76 " =    0.894
peak=    4.163 closest distance to " CB  ARG A  79 " =    1.284
peak=    4.153 closest distance to " O   HOH Z   7 " =    1.364
peak=    4.115 closest distance to " O   HOH Z 183 " =    1.522
peak=    4.110 closest distance to " CG  LEU A 167 " =    1.262
peak=    4.093 closest distance to " O   HOH Z   9 " =    2.127
peak=    4.084 closest distance to " O   HOH Z  78 " =    1.714
peak=    4.080 closest distance to " CD ALYS A 290 " =    1.018
peak=    4.072 closest distance to " CA  TYR A  30 " =    1.029
peak=    4.058 closest distance to " CG2 VAL A 257 " =    0.951
peak=    4.046 closest distance to " CB  ARG A 275 " =    0.952
peak=    4.038 closest distance to " CB  ASP A 124 " =    0.836
peak=    4.037 closest distance to " CG2 THR A 221 " =    0.978
peak=    4.032 closest distance to " CB  SER A 210 " =    0.814
peak=    4.027 closest distance to " O   HOH Z 425 " =    1.409
peak=    4.016 closest distance to " ND1 HIS A  86 " =    1.768
peak=    3.984 closest distance to " CB  ASN A 187 " =    1.029
peak=    3.978 closest distance to " O   HOH Z 133 " =    2.535
peak=    3.965 closest distance to " CD  ARG A 269 " =    0.940
peak=    3.958 closest distance to " CB  SER A 212 " =    1.171
peak=    3.933 closest distance to " O   HOH Z 158 " =    3.012
peak=    3.931 closest distance to " CD  ARG A  66 " =    2.157
peak=    3.930 closest distance to " O   HOH Z 180 " =    2.106
peak=    3.927 closest distance to " O   HOH Z 188 " =    2.814
peak=    3.927 closest distance to " O   HOH Z 214 " =    2.084
peak=    3.926 closest distance to " CA  SER A  87 " =    0.996
peak=    3.919 closest distance to " O   HOH Z 250 " =    1.474
peak=    3.919 closest distance to " CB  ALA A 104 " =    0.768
peak=    3.914 closest distance to " CZ3 TRP A 266 " =    1.146
peak=    3.909 closest distance to " CA  ARG A 195 " =    1.368
peak=    3.894 closest distance to " CD1 LEU A 300 " =    1.208
peak=    3.892 closest distance to " CB  SER A 216 " =    0.979
peak=    3.889 closest distance to " ND2 ASN A 187 " =    1.397
peak=    3.885 closest distance to " O   HOH Z 303 " =    2.277
peak=    3.884 closest distance to " O   HOH Z  78 " =    2.050
peak=    3.883 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.868 closest distance to " O   TYR A 116 " =    1.324
peak=    3.861 closest distance to " CB  TYR A 169 " =    0.734
peak=    3.860 closest distance to " O   HOH Z 427 " =    2.949
peak=    3.855 closest distance to " CB  ASN A 142 " =    0.964
peak=    3.827 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.823 closest distance to " CB  SER A   3 " =    1.524
peak=    3.803 closest distance to " CB  ASP A 132 " =    4.069
peak=    3.802 closest distance to " O   HOH Z 437 " =    1.400
peak=    3.795 closest distance to " CA  MET A  40 " =    1.282
peak=    3.788 closest distance to " CA  THR A 264 " =    0.875
peak=    3.786 closest distance to " O   HOH Z 406 " =    1.736
peak=    3.786 closest distance to " O   HOH Z 365 " =    2.831
peak=    3.772 closest distance to " O   HOH Z 316 " =    3.056
peak=    3.761 closest distance to " O   HOH Z 290 " =    1.131
peak=    3.750 closest distance to " O   HOH Z  10 " =    1.849
peak=    3.742 closest distance to " CA  ALA A 158 " =    1.138
peak=    3.734 closest distance to " O   HOH Z  58 " =    1.801
peak=    3.719 closest distance to " O   HOH Z 380 " =    1.678
peak=    3.715 closest distance to " CA  TYR A 116 " =    1.400
peak=    3.712 closest distance to " CB  ASN A 110 " =    1.139
peak=    3.701 closest distance to " CG BARG A 275 " =    1.499
peak=    3.698 closest distance to " CB  TYR A 116 " =    0.937
peak=    3.694 closest distance to " O   HOH Z 132 " =    2.513
peak=    3.694 closest distance to " O   HOH Z 411 " =    3.459
peak=    3.685 closest distance to " CB  MET A  40 " =    0.770
peak=    3.681 closest distance to " O   HOH Z 135 " =    1.686
peak=    3.678 closest distance to " CB  ASP A 140 " =    0.903
peak=    3.677 closest distance to " O   HOH Z 265 " =    2.056
peak=    3.665 closest distance to " O   HOH Z 353 " =    2.612
peak=    3.664 closest distance to " O   HOH Z 193 " =    1.674
peak=    3.660 closest distance to " O   HOH Z 346 " =    1.687
peak=    3.649 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.646 closest distance to " CB  LEU A 143 " =    1.146
peak=    3.638 closest distance to " O   HOH Z 217 " =    3.036
peak=    3.636 closest distance to " N   PHE A 130 " =    1.222
peak=    3.634 closest distance to " O   HOH Z  61 " =    1.621
peak=    3.633 closest distance to " N   TYR A  15 " =    0.808
peak=    3.631 closest distance to " O   HOH Z   1 " =    1.841
peak=    3.631 closest distance to " OH  TYR A 186 " =    1.094
peak=    3.625 closest distance to " O   HOH Z 391 " =    2.876
peak=    3.623 closest distance to " O   HOH Z 261 " =    1.883
peak=    3.620 closest distance to " CA  ASP A 124 " =    0.770
peak=    3.618 closest distance to " CA  PRO A  54 " =    1.386
peak=    3.618 closest distance to " O   HOH Z  88 " =    3.442
peak=    3.616 closest distance to " O   HOH Z 234 " =    3.889
peak=    3.616 closest distance to " O   ASN A 209 " =    1.406
peak=    3.613 closest distance to " O   HOH Z 332 " =    1.651
peak=    3.611 closest distance to " O   HOH Z 213 " =    2.158
peak=    3.610 closest distance to " O   HOH Z 285 " =    2.378
peak=    3.609 closest distance to " CB  VAL A 202 " =    1.603
peak=    3.598 closest distance to " NH2 ARG A 156 " =    1.169
peak=    3.592 closest distance to " CB  ASN A  39 " =    0.981
peak=    3.592 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.590 closest distance to " O   HOH Z 294 " =    1.599
peak=    3.586 closest distance to " CB  GLU A  46 " =    0.956
peak=    3.586 closest distance to " O   HOH Z 368 " =    1.969
peak=    3.585 closest distance to " OD1 ASN A  69 " =    2.595
peak=    3.585 closest distance to " CD2 TRP A 179 " =    1.274
peak=    3.581 closest distance to " O   HOH Z 193 " =    2.185
peak=    3.580 closest distance to " CG1 ILE A 151 " =    1.108
peak=    3.573 closest distance to " CB  LEU A 237 " =    0.804
peak=    3.567 closest distance to " N   ASN A 127 " =    1.298
peak=    3.564 closest distance to " CB  GLU A 277 " =    3.753
peak=    3.561 closest distance to " O   HOH Z 409 " =    2.455
peak=    3.553 closest distance to " O   HOH Z  44 " =    2.290
peak=    3.543 closest distance to " CB  MET A  47 " =    1.013
peak=    3.541 closest distance to " O   HOH Z 128 " =    2.256
peak=    3.540 closest distance to " CB  ALA A 114 " =    0.948
peak=    3.539 closest distance to " O   HOH Z   2 " =    1.482
peak=    3.521 closest distance to " O   HOH Z 359 " =    4.116
peak=    3.516 closest distance to " O   HOH Z 148 " =    3.407
peak=    3.510 closest distance to " O   HOH Z 116 " =    1.878
peak=    3.503 closest distance to " CE2 TYR A 186 " =    0.895
peak=    3.501 closest distance to " CB  ILE A 120 " =    1.330
peak=    3.501 closest distance to " CB  TYR A 169 " =    0.806
peak=    3.499 closest distance to " O   HOH Z 258 " =    2.175
peak=    3.499 closest distance to " CZ  PHE A  38 " =    1.252
peak=    3.498 closest distance to " CA  ALA A  51 " =    0.946
peak=    3.498 closest distance to " OG  SER A  62 " =    3.102
peak=    3.498 closest distance to " N   ARG A 156 " =    1.396
peak=    3.497 closest distance to " CA  ARG A 102 " =    1.185
peak=    3.495 closest distance to " CG1 VAL A 153 " =    0.948
peak=    3.495 closest distance to " CA  VAL A 125 " =    1.221
peak=    3.495 closest distance to " CD  LYS A 166 " =    1.351
peak=    3.489 closest distance to " O   HOH Z 394 " =    4.095
peak=    3.484 closest distance to " CA  THR A 221 " =    0.955
peak=    3.468 closest distance to " NE2 HIS A 207 " =    1.201
peak=    3.464 closest distance to " CB  TRP A 150 " =    1.192
peak=    3.460 closest distance to " C   ARG A 145 " =    1.689
peak=    3.459 closest distance to " O   MET A 105 " =    1.842
peak=    3.457 closest distance to " NH2AARG A 190 " =    1.931
peak=    3.443 closest distance to " CB  ALA A   1 " =    4.678
peak=    3.440 closest distance to " O   HOH Z 124 " =    1.871
peak=    3.436 closest distance to " CA  MET A 105 " =    0.968
peak=    3.435 closest distance to " CA  ALA A 154 " =    1.047
peak=    3.429 closest distance to " O   HOH Z   1 " =    1.743
peak=    3.424 closest distance to " O   THR A 220 " =    1.301
peak=    3.422 closest distance to " CA  ALA A 160 " =    0.975
peak=    3.420 closest distance to " O   HOH Z  63 " =    1.267
peak=    3.419 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.418 closest distance to " O   HOH Z 325 " =    2.358
peak=    3.417 closest distance to " N   ALA A   1 " =    2.161
peak=    3.414 closest distance to " O   ASN A  74 " =    1.517
peak=    3.413 closest distance to " O   HOH Z 327 " =    2.120
peak=    3.412 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.411 closest distance to " CZ  PHE A 192 " =    0.896
peak=    3.407 closest distance to " CG  ARG A 159 " =    0.938
peak=    3.403 closest distance to " O   HOH Z  61 " =    1.558
peak=    3.403 closest distance to " OD2 ASP A 286 " =    2.948
peak=    3.401 closest distance to " NE  ARG A  79 " =    1.148
peak=    3.399 closest distance to " CB  ALA A  34 " =    1.129
peak=    3.395 closest distance to " CG1 VAL A 189 " =    2.063
peak=    3.390 closest distance to " O  BHOH Z 338 " =    2.299
peak=    3.389 closest distance to " CG1 ILE A  33 " =    1.266
peak=    3.389 closest distance to " OG  SER A 135 " =    1.253
peak=    3.387 closest distance to " O   HOH Z 422 " =    2.738
peak=    3.386 closest distance to " N   SER A 271 " =    0.941
peak=    3.386 closest distance to " O   HOH Z 147 " =    1.800
peak=    3.382 closest distance to " O   THR A 251 " =    1.201
peak=    3.382 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.380 closest distance to " O   HOH Z  53 " =    2.478
peak=    3.377 closest distance to " O   HOH Z 389 " =    1.960
peak=    3.376 closest distance to " O   HOH Z 145 " =    1.690
peak=    3.371 closest distance to " O   ALA A 291 " =    1.437
peak=    3.367 closest distance to " CB  ALA A 248 " =    1.023
peak=    3.367 closest distance to " CD2 LEU A 255 " =    1.704
peak=    3.367 closest distance to " O   HOH Z 193 " =    1.909
peak=    3.366 closest distance to " CA  ALA A 233 " =    1.506
peak=    3.363 closest distance to " O   HOH Z 280 " =    3.120
peak=    3.363 closest distance to " CA  GLU A  46 " =    0.941
peak=    3.361 closest distance to " O   HOH Z 426 " =    1.891
peak=    3.356 closest distance to " O   HOH Z 371 " =    2.784
peak=    3.348 closest distance to " N   ASN A  39 " =    1.329
peak=    3.347 closest distance to " CG  PHE A 204 " =    0.950
peak=    3.344 closest distance to " CB  THR A  82 " =    1.389
peak=    3.342 closest distance to " CB  GLN A  88 " =    1.250
peak=    3.342 closest distance to " O   HOH Z 272 " =    2.532
peak=    3.338 closest distance to " CA  ALA A 291 " =    0.902
peak=    3.337 closest distance to " CA  TRP A  92 " =    1.107
peak=    3.335 closest distance to " O   HOH Z  68 " =    2.058
peak=    3.335 closest distance to " OG  SER A  62 " =    3.071
peak=    3.334 closest distance to " O   HOH Z 218 " =    4.624
peak=    3.334 closest distance to " O   HOH Z  80 " =    1.514
peak=    3.326 closest distance to " CA  ASN A  74 " =    1.359
peak=    3.325 closest distance to " O   HOH Z 345 " =    3.560
peak=    3.312 closest distance to " O   ASP A 191 " =    1.484
peak=    3.310 closest distance to " CA  GLY A 241 " =    0.792
peak=    3.310 closest distance to " CG  ARG A 138 " =    1.132
peak=    3.308 closest distance to " CA  SER A  95 " =    0.944
peak=    3.307 closest distance to " O   HOH Z 184 " =    1.495
peak=    3.307 closest distance to " O   HOH Z 368 " =    4.295
peak=    3.307 closest distance to " O   HOH Z 213 " =    2.864
peak=    3.301 closest distance to " CA  ASN A 127 " =    1.112
peak=    3.300 closest distance to " CB  ARG A 138 " =    1.009
peak=    3.300 closest distance to " O   HOH Z 108 " =    2.864
peak=    3.298 closest distance to " O   HOH Z 188 " =    2.367
peak=    3.298 closest distance to " CG AARG A 275 " =    1.261
peak=    3.297 closest distance to " O   HOH Z  57 " =    1.301
peak=    3.296 closest distance to " CG  GLU A  37 " =    0.927
peak=    3.294 closest distance to " O   HOH Z 403 " =    1.430
peak=    3.294 closest distance to " CB  SER A 276 " =    1.102
peak=    3.294 closest distance to " CB  PRO A 243 " =    1.225
peak=    3.293 closest distance to " O   HOH Z 126 " =    1.703
peak=    3.292 closest distance to " O   HOH Z  88 " =    3.640
peak=    3.290 closest distance to " O   HOH Z 185 " =    2.032
peak=    3.289 closest distance to " O   HOH Z 329 " =    4.061
peak=    3.286 closest distance to " CB  LYS A 117 " =    1.140
peak=    3.284 closest distance to " CG2 ILE A 151 " =    0.865
peak=    3.283 closest distance to " O   HOH Z 273 " =    2.811
peak=    3.281 closest distance to " N   VAL A 296 " =    1.740
peak=    3.277 closest distance to " ND1 HIS A  81 " =    1.706
peak=    3.275 closest distance to " CD  LYS A  76 " =    2.027
peak=    3.274 closest distance to " O   HOH Z 302 " =    1.905
peak=    3.273 closest distance to " O   HOH Z  85 " =    2.229
peak=    3.273 closest distance to " O   PRO A 213 " =    1.578
peak=    3.266 closest distance to " CB  ALA A 291 " =    1.170
peak=    3.265 closest distance to " OD2 ASP A  65 " =    3.118
peak=    3.263 closest distance to " CB  ALA A 160 " =    1.354
peak=    3.256 closest distance to " O   HOH Z  44 " =    2.841
peak=    3.247 closest distance to " O   HOH Z 130 " =    3.794
peak=    3.245 closest distance to " CE2 PHE A  16 " =    1.001
peak=    3.241 closest distance to " O   HOH Z 172 " =    3.061
peak=    3.235 closest distance to " CG  GLN A 278 " =    1.435
peak=    3.234 closest distance to " CA  ARG A  36 " =    1.224
peak=    3.234 closest distance to " CZ  PHE A 208 " =    1.095
peak=    3.231 closest distance to " CG  GLN A 144 " =    0.881
peak=    3.221 closest distance to " CG  MET A 113 " =    1.758
peak=    3.220 closest distance to " O   HOH Z 238 " =    3.569
peak=    3.218 closest distance to " CA  ASP A 162 " =    1.097
peak=    3.218 closest distance to " O   HOH Z 352 " =    1.693
peak=    3.217 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.216 closest distance to " CA  ALA A 299 " =    0.916
peak=    3.215 closest distance to " O   THR A 182 " =    1.466
peak=    3.211 closest distance to " OD1 ASN A 217 " =    1.489
peak=    3.211 closest distance to " CA  LYS A 290 " =    1.267
peak=    3.208 closest distance to " O   HOH Z  40 " =    1.787
peak=    3.203 closest distance to " CB  ALA A   9 " =    1.630
peak=    3.200 closest distance to " O   HOH Z 286 " =    2.257
peak=    3.196 closest distance to " CD  GLN A 240 " =    1.734
peak=    3.195 closest distance to " CB  ALA A 114 " =    1.177
peak=    3.189 closest distance to " O   HOH Z 345 " =    1.778
peak=    3.183 closest distance to " OH  TYR A 214 " =    1.290
peak=    3.182 closest distance to " CA  ARG A 139 " =    1.032
peak=    3.178 closest distance to " O   HOH Z  88 " =    2.867
peak=    3.177 closest distance to " CA  ASN A 217 " =    1.245
peak=    3.175 closest distance to " CD2 LEU A 297 " =    0.901
peak=    3.174 closest distance to " OD1 ASP A 171 " =    1.243
peak=    3.174 closest distance to " CE3 TRP A  85 " =    0.980
peak=    3.166 closest distance to " O   HOH Z 166 " =    3.807
peak=    3.166 closest distance to " NH2 ARG A 219 " =    1.797
peak=    3.163 closest distance to " CG  GLN A  55 " =    2.181
peak=    3.162 closest distance to " CG BARG A 102 " =    1.933
peak=    3.161 closest distance to " O   HOH Z 112 " =    1.525
peak=    3.161 closest distance to " CB  LEU A  83 " =    0.780
peak=    3.161 closest distance to " CA  LYS A 117 " =    1.123
peak=    3.161 closest distance to " CD  ARG A 219 " =    1.114
peak=    3.156 closest distance to " CA  TYR A 186 " =    1.603
peak=    3.155 closest distance to " CB  SER A 245 " =    3.176
peak=    3.154 closest distance to " O   HOH Z 425 " =    2.050
peak=    3.154 closest distance to " CA  GLU A 152 " =    1.106
peak=    3.153 closest distance to " O  BHOH Z  74 " =    1.294
peak=    3.145 closest distance to " CB  ALA A  43 " =    0.806
peak=    3.142 closest distance to " O   HOH Z  59 " =    1.778
peak=    3.139 closest distance to " CG  GLU A 277 " =    1.979
peak=    3.133 closest distance to " CB  LEU A 300 " =    0.961
peak=    3.129 closest distance to " OD1BASN A 224 " =    2.325
peak=    3.129 closest distance to " CE2 TYR A 293 " =    0.987
peak=    3.125 closest distance to " O   HOH Z 128 " =    1.540
peak=    3.122 closest distance to " CD1 ILE A 106 " =    0.802
peak=    3.111 closest distance to " CB  SER A  62 " =    1.163
peak=    3.107 closest distance to " O   HOH Z 392 " =    1.360
peak=    3.106 closest distance to " CB  HIS A 108 " =    0.782
peak=    3.104 closest distance to " O   HOH Z 359 " =    1.486
peak=    3.102 closest distance to " CB  LYS A 193 " =    0.974
peak=    3.100 closest distance to " C   GLN A  88 " =    1.594
peak=    3.098 closest distance to " CB  ALA A  10 " =    0.854
peak=    3.095 closest distance to " CB  ASN A 285 " =    0.876
peak=    3.092 closest distance to " CA  ALA A 291 " =    3.633
peak=    3.074 closest distance to " ND2 ASN A 110 " =    1.656
peak=    3.074 closest distance to " CA  ASP A 140 " =    1.317
peak=    3.013 closest distance to " O   HOH Z 171 " =    3.816
peak=    3.012 closest distance to " O   HOH Z 128 " =    2.703

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 5.707
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.702 - 5.707

peak=   -4.370 closest distance to " CD  ARG A  14 " =    3.465
peak=   -4.348 closest distance to " CB  PRO A 243 " =    2.577
peak=   -4.335 closest distance to " O   PRO A 198 " =    1.255
peak=   -4.222 closest distance to " O   HOH Z 377 " =    1.913
peak=   -4.129 closest distance to " N   ALA A  43 " =    2.431
peak=   -4.098 closest distance to " O   HOH Z 231 " =    2.017
peak=   -4.072 closest distance to " CZ3 TRP A 179 " =    1.170
peak=   -4.061 closest distance to " O   HOH Z  38 " =    1.273
peak=   -4.025 closest distance to " O   HOH Z 407 " =    3.398
peak=   -4.018 closest distance to " CB  ALA A  43 " =    2.633
peak=   -4.016 closest distance to " CD  ARG A 156 " =    2.165
peak=   -4.009 closest distance to " CG2 ILE A  49 " =    2.767
peak=   -3.993 closest distance to " O   HOH Z 389 " =    2.172
peak=   -3.912 closest distance to " CG1 VAL A 250 " =    2.661
peak=   -3.912 closest distance to " OG BSER A 134 " =    1.373
peak=   -3.874 closest distance to " OE1 GLN A 223 " =    2.318
peak=   -3.873 closest distance to " O   HOH Z  52 " =    1.286
peak=   -3.873 closest distance to " CB  ALA A 158 " =    1.633
peak=   -3.857 closest distance to " CD2 LEU A 143 " =    2.622
peak=   -3.847 closest distance to " O   HOH Z 211 " =    0.971
peak=   -3.835 closest distance to " O   HOH Z  73 " =    1.948
peak=   -3.822 closest distance to " O   TYR A 247 " =    2.909
peak=   -3.820 closest distance to " CG1 VAL A 112 " =    2.590
peak=   -3.798 closest distance to " ND2 ASN A  45 " =    1.183
peak=   -3.759 closest distance to " CG1 VAL A 112 " =    3.085
peak=   -3.758 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -3.747 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.730 closest distance to " CB  TRP A  85 " =    2.472
peak=   -3.723 closest distance to " C   LEU A 143 " =    1.500
peak=   -3.722 closest distance to " CA  GLY A 241 " =    3.121
peak=   -3.708 closest distance to " O   HOH Z 411 " =    5.324
peak=   -3.704 closest distance to " O   HOH Z 231 " =    0.989
peak=   -3.704 closest distance to " CA  GLY A 241 " =    2.328
peak=   -3.689 closest distance to " O   HOH Z 290 " =    1.168
peak=   -3.667 closest distance to " CB  PRO A  54 " =    2.544
peak=   -3.664 closest distance to " CG  MET A 105 " =    0.938
peak=   -3.662 closest distance to " CG  GLN A  88 " =    0.870
peak=   -3.644 closest distance to " OG  SER A  97 " =    2.219
peak=   -3.643 closest distance to " O   HOH Z 111 " =    1.877
peak=   -3.639 closest distance to " O   VAL A  67 " =    2.622
peak=   -3.629 closest distance to " CB  ASP A  27 " =    2.558
peak=   -3.627 closest distance to " O   GLY A 203 " =    2.426
peak=   -3.625 closest distance to " CG2 THR A 178 " =    2.290
peak=   -3.624 closest distance to " CD1 LEU A 101 " =    2.338
peak=   -3.622 closest distance to " ND2 ASN A 249 " =    2.117
peak=   -3.616 closest distance to " O   HOH Z 198 " =    2.069
peak=   -3.612 closest distance to " OD1 ASP A 191 " =    1.805
peak=   -3.589 closest distance to " C   LEU A 222 " =    0.825
peak=   -3.582 closest distance to " O   ALA A  10 " =    1.710
peak=   -3.576 closest distance to " O   HOH Z 118 " =    1.187
peak=   -3.569 closest distance to " CE BMET A  47 " =    1.615
peak=   -3.567 closest distance to " O   HOH Z 337 " =    1.460
peak=   -3.556 closest distance to " O   HOH Z 394 " =    1.552
peak=   -3.555 closest distance to " OXT GLY A 302 " =    3.138
peak=   -3.552 closest distance to " NH2AARG A 275 " =    5.707
peak=   -3.547 closest distance to " OE1 GLN A  88 " =    1.118
peak=   -3.547 closest distance to " CB  ALA A   9 " =    2.455
peak=   -3.543 closest distance to " CA  GLY A  98 " =    1.979
peak=   -3.536 closest distance to " O   HOH Z 426 " =    1.616
peak=   -3.531 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.530 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.530 closest distance to " O   HOH Z 351 " =    1.543
peak=   -3.524 closest distance to " O   GLY A 211 " =    1.345
peak=   -3.523 closest distance to " O   HOH Z 198 " =    1.628
peak=   -3.516 closest distance to " O   HOH Z 281 " =    2.736
peak=   -3.515 closest distance to " CD  ARG A 195 " =    5.159
peak=   -3.513 closest distance to " O   VAL A 189 " =    2.476
peak=   -3.509 closest distance to " O   HOH Z  65 " =    1.224
peak=   -3.504 closest distance to " O   VAL A 125 " =    2.279
peak=   -3.500 closest distance to " O   HOH Z 313 " =    1.872
peak=   -3.494 closest distance to " O   HOH Z 275 " =    1.791
peak=   -3.493 closest distance to " N   THR A 157 " =    1.542
peak=   -3.489 closest distance to " O   HOH Z 435 " =    2.886
peak=   -3.483 closest distance to " CG2 THR A  18 " =    2.868
peak=   -3.477 closest distance to " OD1 ASN A 148 " =    1.499
peak=   -3.474 closest distance to " CE  MET A 105 " =    2.317
peak=   -3.469 closest distance to " CD  LYS A 289 " =    2.358
peak=   -3.467 closest distance to " O   PHE A 218 " =    1.465
peak=   -3.467 closest distance to " CB  ASP A 286 " =    2.024
peak=   -3.464 closest distance to " CD  GLN A  58 " =    0.926
peak=   -3.447 closest distance to " O   GLY A  17 " =    1.276
peak=   -3.430 closest distance to " CB  CYS A 254 " =    2.176
peak=   -3.424 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.421 closest distance to " CG1 VAL A 125 " =    1.820
peak=   -3.420 closest distance to " O   HOH Z  22 " =    2.264
peak=   -3.416 closest distance to " OG BSER A 134 " =    1.749
peak=   -3.414 closest distance to " NH1AARG A 275 " =    1.969
peak=   -3.414 closest distance to " OD1 ASP A 171 " =    1.638
peak=   -3.410 closest distance to " O   HOH Z 359 " =    3.227
peak=   -3.401 closest distance to " O   HOH Z 185 " =    2.295
peak=   -3.396 closest distance to " O   HOH Z 353 " =    2.087
peak=   -3.392 closest distance to " O   HOH Z  10 " =    1.485
peak=   -3.388 closest distance to " O   HOH Z 243 " =    1.887
peak=   -3.386 closest distance to " CB  PRO A 163 " =    2.564
peak=   -3.384 closest distance to " O   HOH Z 241 " =    1.325
peak=   -3.380 closest distance to " CD1 PHE A  59 " =    1.909
peak=   -3.377 closest distance to " C   ASN A 285 " =    2.484
peak=   -3.373 closest distance to " ND2 ASN A 187 " =    1.571
peak=   -3.362 closest distance to " O   ILE A  49 " =    1.758
peak=   -3.360 closest distance to " N   SER A 212 " =    2.079
peak=   -3.351 closest distance to " O   HOH Z 174 " =    2.681
peak=   -3.340 closest distance to " O   HOH Z  43 " =    1.554
peak=   -3.339 closest distance to " ND2 ASN A  45 " =    2.072
peak=   -3.336 closest distance to " NZ  LYS A 166 " =    1.229
peak=   -3.334 closest distance to " CD1 LEU A 228 " =    2.453
peak=   -3.328 closest distance to " O   HOH Z 252 " =    4.019
peak=   -3.324 closest distance to " NH2BARG A 275 " =    1.918
peak=   -3.321 closest distance to " CG  TRP A 266 " =    1.708
peak=   -3.320 closest distance to " O   HOH Z  53 " =    1.679
peak=   -3.318 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.316 closest distance to " O   HOH Z 417 " =    2.821
peak=   -3.315 closest distance to " O   HOH Z   9 " =    2.002
peak=   -3.315 closest distance to " CD2 PHE A  61 " =    2.004
peak=   -3.313 closest distance to " CG1 VAL A 197 " =    2.309
peak=   -3.312 closest distance to " O   HOH Z 219 " =    4.587
peak=   -3.300 closest distance to " O   HOH Z 177 " =    1.805
peak=   -3.295 closest distance to " CG  LEU A 282 " =    2.482
peak=   -3.290 closest distance to " O   HOH Z 372 " =    2.488
peak=   -3.280 closest distance to " O   SER A  62 " =    2.312
peak=   -3.279 closest distance to " O   HOH Z 298 " =    2.347
peak=   -3.278 closest distance to " OH  TYR A 172 " =    1.771
peak=   -3.278 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.278 closest distance to " CG  ARG A 269 " =    2.539
peak=   -3.273 closest distance to " O   HOH Z 345 " =    2.319
peak=   -3.268 closest distance to " OH  TYR A 247 " =    2.169
peak=   -3.264 closest distance to " NE  ARG A  36 " =    2.060
peak=   -3.264 closest distance to " C   GLY A  13 " =    0.900
peak=   -3.258 closest distance to " O   HOH Z  51 " =    1.190
peak=   -3.257 closest distance to " CG2 VAL A 189 " =    1.983
peak=   -3.255 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.255 closest distance to " O   HOH Z 102 " =    1.607
peak=   -3.253 closest distance to " O   PRO A 243 " =    2.418
peak=   -3.251 closest distance to " O   HOH Z 196 " =    2.240
peak=   -3.247 closest distance to " O   SER A  22 " =    2.549
peak=   -3.246 closest distance to " CE3 TRP A 150 " =    2.226
peak=   -3.245 closest distance to " OG  SER A  87 " =    1.388
peak=   -3.242 closest distance to " CG  LEU A  83 " =    1.985
peak=   -3.241 closest distance to " O   HOH Z 191 " =    5.696
peak=   -3.240 closest distance to " O   HOH Z 275 " =    1.586
peak=   -3.237 closest distance to " O   HOH Z 184 " =    1.674
peak=   -3.234 closest distance to " CB  ALA A 248 " =    2.447
peak=   -3.233 closest distance to " O   HOH Z 216 " =    1.605
peak=   -3.231 closest distance to " NH2 ARG A  79 " =    1.556
peak=   -3.227 closest distance to " O   ALA A  34 " =    2.692
peak=   -3.225 closest distance to " CD  ARG A  79 " =    1.100
peak=   -3.219 closest distance to " O   ASP A  27 " =    1.877
peak=   -3.215 closest distance to " CB  ALA A 227 " =    2.393
peak=   -3.215 closest distance to " O   HOH Z 409 " =    4.655
peak=   -3.206 closest distance to " O   HOH Z  11 " =    1.812
peak=   -3.201 closest distance to " C   PHE A  59 " =    1.254
peak=   -3.200 closest distance to " O   ILE A 109 " =    2.668
peak=   -3.199 closest distance to " O   ARG A  56 " =    1.843
peak=   -3.195 closest distance to " CD2 LEU A 300 " =    2.699
peak=   -3.190 closest distance to " O   HOH Z  51 " =    1.743
peak=   -3.189 closest distance to " CE1 TYR A 169 " =    2.657
peak=   -3.188 closest distance to " CA  SER A  62 " =    2.714
peak=   -3.182 closest distance to " C   GLU A 236 " =    0.904
peak=   -3.180 closest distance to " O   HOH Z  85 " =    2.271
peak=   -3.180 closest distance to " O   GLN A 240 " =    2.455
peak=   -3.178 closest distance to " CD1 LEU A   5 " =    2.619
peak=   -3.178 closest distance to " O   HOH Z   2 " =    1.974
peak=   -3.174 closest distance to " ND2 ASN A  60 " =    4.061
peak=   -3.166 closest distance to " CG  TYR A 186 " =    2.401
peak=   -3.160 closest distance to " O   HOH Z  90 " =    1.608
peak=   -3.160 closest distance to " O   ALA A 180 " =    1.298
peak=   -3.159 closest distance to " O   HOH Z  70 " =    2.175
peak=   -3.155 closest distance to " CB  ALA A 114 " =    2.558
peak=   -3.154 closest distance to " O   HOH Z  60 " =    1.514
peak=   -3.153 closest distance to " O   HOH Z 108 " =    1.428
peak=   -3.148 closest distance to " O   HOH Z 266 " =    5.120
peak=   -3.145 closest distance to " SG ACYS A 201 " =    2.368
peak=   -3.142 closest distance to " O   SER A 135 " =    1.392
peak=   -3.142 closest distance to " CG2 THR A 221 " =    2.211
peak=   -3.135 closest distance to " CD1 LEU A 297 " =    2.611
peak=   -3.134 closest distance to " CB  PHE A 192 " =    1.837
peak=   -3.134 closest distance to " CD1 TRP A 179 " =    1.018
peak=   -3.133 closest distance to " O   HOH Z 179 " =    2.295
peak=   -3.132 closest distance to " O   HOH Z 318 " =    2.018
peak=   -3.132 closest distance to " CG  PRO A 163 " =    2.376
peak=   -3.128 closest distance to " OD2 ASP A 171 " =    1.818
peak=   -3.127 closest distance to " O   GLY A  80 " =    2.443
peak=   -3.124 closest distance to " CB  ALA A 100 " =    2.291
peak=   -3.120 closest distance to " N   ALA A 248 " =    1.631
peak=   -3.116 closest distance to " O   HOH Z 384 " =    2.659
peak=   -3.112 closest distance to " O   HOH Z 222 " =    1.134
peak=   -3.104 closest distance to " O   HOH Z 114 " =    1.541
peak=   -3.103 closest distance to " O   HOH Z 377 " =    0.991
peak=   -3.092 closest distance to " O   HOH Z  49 " =    1.461
peak=   -3.090 closest distance to " O   HOH Z 114 " =    0.702
peak=   -3.086 closest distance to " O   PRO A 198 " =    1.422
peak=   -3.086 closest distance to " O   HOH Z 250 " =    1.475
peak=   -3.083 closest distance to " N   ALA A 226 " =    2.186
peak=   -3.081 closest distance to " CH2 TRP A 123 " =    2.198
peak=   -3.067 closest distance to " O   VAL A 189 " =    1.625
peak=   -3.063 closest distance to " O   HOH Z 103 " =    1.849
peak=   -3.051 closest distance to " CA  SER A 135 " =    1.237
peak=   -3.044 closest distance to " O   HOH Z 357 " =    1.997
peak=   -3.035 closest distance to " CG  GLU A  53 " =    1.744
peak=   -3.034 closest distance to " CD2 PHE A 192 " =    2.319
peak=   -3.032 closest distance to " O   TRP A  70 " =    1.405
peak=   -3.029 closest distance to " ND2 ASN A  60 " =    1.964
peak=   -3.015 closest distance to " O   ASN A 209 " =    1.975
peak=   -3.015 closest distance to " CB  ALA A  10 " =    2.262
peak=   -3.012 closest distance to " CD1 ILE A 239 " =    2.312

================= 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    :  0.4364 0.4281   6.239013e+00   6.220286e+00
   1_bss:  0.4281 0.4219   6.229944e+00   6.209734e+00
   1_xyz:  0.2565 0.2866   5.828163e+00   5.909488e+00
   1_adp:  0.2345 0.2951   5.781791e+00   5.937582e+00
   1_occ:  0.2341 0.2947   5.780809e+00   5.937365e+00
   2_bss:  0.2318 0.2946   5.781772e+00   5.937517e+00
   2_xyz:  0.1653 0.2180   5.485937e+00   5.689402e+00
   2_adp:  0.1513 0.2022   5.409138e+00   5.622374e+00
   2_occ:  0.1511 0.2019   5.408155e+00   5.621727e+00
   3_bss:  0.1512 0.2019   5.406704e+00   5.619334e+00
   3_xyz:  0.1388 0.1865   5.331256e+00   5.544812e+00
   3_adp:  0.1326 0.1829   5.298261e+00   5.520498e+00
   3_occ:  0.1325 0.1829   5.298131e+00   5.520661e+00
   4_bss:  0.1325 0.1830   5.297719e+00   5.520785e+00
   4_xyz:  0.1203 0.1726   5.222267e+00   5.468541e+00
   4_adp:  0.1188 0.1677   5.203253e+00   5.442153e+00
   4_occ:  0.1188 0.1677   5.203216e+00   5.442314e+00
   5_bss:  0.1191 0.1667   5.201640e+00   5.438385e+00
   5_xyz:  0.1167 0.1650   5.191385e+00   5.432815e+00
   5_adp:  0.1162 0.1638   5.187230e+00   5.428155e+00
   5_occ:  0.1161 0.1638   5.187187e+00   5.428196e+00
   5_bss:  0.1161 0.1638   5.187187e+00   5.428196e+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:  0.327  71.892   2.313  -1.403   1.512  -0.000   0.000   0.000
   1_xyz:  0.327  71.892   2.313  -1.403   1.512  -0.000   0.000   0.000
   1_adp:  0.327  71.892   2.313  -1.403   1.512  -0.000   0.000   0.000
   1_occ:  0.327  71.892   2.313  -1.403   1.512  -0.000   0.000   0.000
   2_bss:  0.345  76.130  -0.776  -2.585  -0.425  -0.000  -0.000  -0.000
   2_xyz:  0.345  76.130  -0.776  -2.585  -0.425  -0.000  -0.000  -0.000
   2_adp:  0.345  76.130  -0.776  -2.585  -0.425  -0.000  -0.000  -0.000
   2_occ:  0.345  76.130  -0.776  -2.585  -0.425  -0.000  -0.000  -0.000
   3_bss:  0.336  69.007  -1.577  -2.610  -0.703  -0.000  -0.000  -0.000
   3_xyz:  0.336  69.007  -1.577  -2.610  -0.703  -0.000  -0.000  -0.000
   3_adp:  0.336  69.007  -1.577  -2.610  -0.703  -0.000  -0.000  -0.000
   3_occ:  0.336  69.007  -1.577  -2.610  -0.703  -0.000  -0.000  -0.000
   4_bss:  0.330  72.955  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   4_xyz:  0.330  72.955  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   4_adp:  0.330  72.955  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   4_occ:  0.330  72.955  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   5_bss:  0.324  67.444  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   5_xyz:  0.324  67.444  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   5_adp:  0.324  67.444  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   5_occ:  0.324  67.444  -1.919  -2.741  -0.919  -0.000  -0.000  -0.000
   5_bss:  0.324  67.441  -1.916  -2.739  -0.917  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.753 0.5239  0.6823    54919.296
   1_bss:  49.016 0.5322  0.7200    53263.357
   1_xyz:  28.770 0.7723  0.9766    21359.010
   1_adp:  30.045 0.7572  0.9622    22570.776
   1_occ:  30.052 0.7570  0.9614    22510.050
   2_bss:  30.001 0.7577  0.8962    22543.617
   2_xyz:  21.472 0.8463  0.9678    12140.386
   2_adp:  19.414 0.8672  0.9804    10564.525
   2_occ:  19.397 0.8674  0.9803    10538.961
   3_bss:  19.351 0.8676  0.9672    10449.140
   3_xyz:  17.461 0.8854  0.9746     8828.688
   3_adp:  16.893 0.8906  0.9709     8375.437
   3_occ:  16.891 0.8906  0.9709     8376.579
   4_bss:  16.886 0.8906  0.9631     8375.394
   4_xyz:  15.733 0.9004  0.9694     7460.281
   4_adp:  15.101 0.9061  0.9682     7091.487
   4_occ:  15.104 0.9061  0.9681     7086.790
   5_bss:  15.045 0.9064  0.9680     6989.121
   5_xyz:  14.853 0.9083  0.9684     6917.930
   5_adp:  14.727 0.9095  0.9645     6858.278
   5_occ:  14.729 0.9094  0.9645     6857.685
   5_bss:  14.729 0.9094  0.9645     6857.685
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6267e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6267e-01
   1_xyz:   1.446  0.012  0.098 16.233  0.006  4.118   1.1700e-01
   1_adp:   1.446  0.012  0.098 16.233  0.006  4.118   1.1700e-01
   1_occ:   1.446  0.012  0.098 16.233  0.006  4.118   1.1700e-01
   2_bss:   1.446  0.012  0.098 16.233  0.006  4.118   1.1700e-01
   2_xyz:   1.108  0.009  0.079 14.483  0.004  4.112   6.9968e-02
   2_adp:   1.108  0.009  0.079 14.483  0.004  4.112   6.9968e-02
   2_occ:   1.108  0.009  0.079 14.483  0.004  4.112   6.9968e-02
   3_bss:   1.108  0.009  0.079 14.483  0.004  4.112   6.9968e-02
   3_xyz:   0.908  0.006  0.066 14.230  0.003  4.117   4.9918e-02
   3_adp:   0.908  0.006  0.066 14.230  0.003  4.117   4.9918e-02
   3_occ:   0.908  0.006  0.066 14.230  0.003  4.117   4.9918e-02
   4_bss:   0.908  0.006  0.066 14.230  0.003  4.117   4.9918e-02
   4_xyz:   1.095  0.009  0.080 14.460  0.004  4.114   6.9947e-02
   4_adp:   1.095  0.009  0.080 14.460  0.004  4.114   6.9947e-02
   4_occ:   1.095  0.009  0.080 14.460  0.004  4.114   6.9947e-02
   5_bss:   1.095  0.009  0.080 14.460  0.004  4.114   6.9947e-02
   5_xyz:   1.037  0.009  0.077 14.321  0.004  4.117   6.4712e-02
   5_adp:   1.037  0.009  0.077 14.321  0.004  4.117   6.4712e-02
   5_occ:   1.037  0.009  0.077 14.321  0.004  4.117   6.4712e-02
   5_bss:   1.037  0.009  0.077 14.321  0.004  4.117   6.4712e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4314e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4314e-01
   1_xyz:  10.262  0.080  0.374 83.685  0.059  2.066   9.4735e-02
   1_adp:  10.262  0.080  0.374 83.685  0.059  2.066   9.4735e-02
   1_occ:  10.262  0.080  0.374 83.685  0.059  2.066   9.4735e-02
   2_bss:  10.262  0.080  0.374 83.685  0.059  2.066   9.4735e-02
   2_xyz:   7.769  0.070  0.235 80.273  0.028  2.308   5.5813e-02
   2_adp:   7.769  0.070  0.235 80.273  0.028  2.308   5.5813e-02
   2_occ:   7.769  0.070  0.235 80.273  0.028  2.308   5.5813e-02
   3_bss:   7.769  0.070  0.235 80.273  0.028  2.308   5.5813e-02
   3_xyz:   8.668  0.044  0.234 79.531  0.033  2.428   3.6048e-02
   3_adp:   8.668  0.044  0.234 79.531  0.033  2.428   3.6048e-02
   3_occ:   8.668  0.044  0.234 79.531  0.033  2.428   3.6048e-02
   4_bss:   8.668  0.044  0.234 79.531  0.033  2.428   3.6048e-02
   4_xyz:   8.771  0.049  0.258 82.973  0.031  2.315   4.9258e-02
   4_adp:   8.771  0.049  0.258 82.973  0.031  2.315   4.9258e-02
   4_occ:   8.771  0.049  0.258 82.973  0.031  2.315   4.9258e-02
   5_bss:   8.771  0.049  0.258 82.973  0.031  2.315   4.9258e-02
   5_xyz:   8.621  0.047  0.241 82.322  0.029  2.353   4.6631e-02
   5_adp:   8.621  0.047  0.241 82.322  0.029  2.353   4.6631e-02
   5_occ:   8.621  0.047  0.241 82.322  0.029  2.353   4.6631e-02
   5_bss:   8.621  0.047  0.241 82.322  0.029  2.353   4.6631e-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:  80.86   0.00  17.38  80.86   0.00  13.28  67.46   3.39  39.68
   1_occ:  80.86   0.00  17.38  80.86   0.00  13.28  67.46   3.39  39.68
   2_bss:  80.86   0.00  17.38  80.86   0.00  13.28  67.46   3.39  39.68
   2_xyz:  80.86   0.00  17.38  80.86   0.00  13.28  67.46   3.39  39.68
   2_adp:  92.22   0.00  17.42  92.22   0.00  13.21  69.58   5.56  40.37
   2_occ:  92.22   0.00  17.42  92.22   0.00  13.21  69.58   5.56  40.37
   3_bss:  92.22   0.00  17.42  92.22   0.00  13.21  69.58   5.56  40.37
   3_xyz:  92.22   0.00  17.42  92.22   0.00  13.21  69.58   5.56  40.37
   3_adp:  98.61   0.00  18.46  87.12   0.00  13.43  98.61   5.42  45.84
   3_occ:  98.61   0.00  18.46  87.12   0.00  13.43  98.61   5.42  45.84
   4_bss:  98.61   0.00  18.46  87.12   0.00  13.43  98.61   5.42  45.84
   4_xyz:  98.61   0.00  18.46  87.12   0.00  13.43  98.61   5.42  45.84
   4_adp:  94.35   0.29  17.66  84.27   0.29  13.09  94.35   3.46  42.54
   4_occ:  94.35   0.29  17.66  84.27   0.29  13.09  94.35   3.46  42.54
   5_bss:  94.35   0.29  17.66  84.27   0.29  13.09  94.35   3.46  42.54
   5_xyz:  94.35   0.29  17.66  84.27   0.29  13.09  94.35   3.46  42.54
   5_adp:  94.25   0.15  17.41  85.65   0.15  12.96  94.25   4.02  41.62
   5_occ:  94.25   0.15  17.41  85.65   0.15  12.96  94.25   4.02  41.62
   5_bss:  94.24   0.14  17.40  85.65   0.14  12.96  94.24   4.02  41.62
------------------------------------------------------------------------
 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:    1.312    0.024    0.469
   1_adp:    1.312    0.024    0.469
   1_occ:    1.312    0.024    0.469
   2_bss:    1.312    0.024    0.469
   2_xyz:    1.269    0.025    0.553
   2_adp:    1.269    0.025    0.553
   2_occ:    1.269    0.025    0.553
   3_bss:    1.269    0.025    0.553
   3_xyz:    1.266    0.046    0.591
   3_adp:    1.266    0.046    0.591
   3_occ:    1.266    0.046    0.591
   4_bss:    1.266    0.046    0.591
   4_xyz:    1.316    0.051    0.621
   4_adp:    1.316    0.051    0.621
   4_occ:    1.316    0.051    0.621
   5_bss:    1.316    0.051    0.621
   5_xyz:    1.497    0.100    0.633
   5_adp:    1.497    0.100    0.633
   5_occ:    1.497    0.100    0.633
   5_bss:    1.497    0.100    0.633
------------------------------------------------------------------------

CPU time actual refinement: 346.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/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_1251/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1251/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.20 
  Macro-tasks:
    bulk solvent and scale       = 45.03  
    individual site refinement   = 141.70 
    weights calculation          = 29.85  
    collect and process          = 6.58   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 223.24 
  Micro-tasks:
    mask                            = 1.90   
    f_calc                          = 110.88 
    alpha_beta                      = 8.42   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 118.70 
    fmodel                         = 7.28   
    r_factors                      = 0.29   
    phase_errors                   = 10.66  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 259.56 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.934 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    629 calls, 110.53 s
gradients_fft:          574 calls, 105.40 s

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

# Date 2008-01-16 Time 06:48:03 PST -0800 (1200494883.76 s)
Start R-work = 0.4364, R-free = 0.4281 (no bulk solvent and anisotropic scale)
Final R-work = 0.1391, R-free = 0.1833 (no bulk solvent and anisotropic scale)

Start R-work = 0.4281, R-free = 0.4219
Final R-work = 0.1161, R-free = 0.1638