# Date 2008-01-16 Time 04:47:42 PST -0800 (1200487662.21 s)
#phil __OFF__

Command line arguments: "../460.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32447
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 460

-------------------------------------------------------------------------------
  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: (69.5475, 47.6339, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98083
Completeness in resolution range: 0.935527
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             d_min =   1.9808

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: (69.5475, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98083
Completeness in resolution range: 0.935527
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.2383 [2206/2234]  1983   223  10.1%
  bin  2:  4.2383 -  3.3767 [2100/2123]  1889   211  10.0%
  bin  3:  3.3767 -  2.9536 [2069/2091]  1867   202   9.8%
  bin  4:  2.9536 -  2.6853 [2087/2106]  1876   211  10.1%
  bin  5:  2.6853 -  2.4938 [2027/2056]  1821   206  10.2%
  bin  6:  2.4938 -  2.3473 [2063/2105]  1857   206  10.0%
  bin  7:  2.3473 -  2.2302 [2023/2059]  1825   198   9.8%
  bin  8:  2.2302 -  2.1334 [2024/2062]  1816   208  10.3%
  bin  9:  2.1334 -  2.0515 [2028/2059]  1833   195   9.6%
  bin 10:  2.0515 -  1.9808 [ 962/2044]   863    99  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 18
        2.28 -     2.93: 1540
        2.93 -     3.59: 4424
        3.59 -     4.24: 9088
        4.24 -     4.90: 12913
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.623 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.711 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.886 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.887 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27978 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_460/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 69.5475 47.63395 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4338   r_free= 0.4276   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.236230                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.3331 0.3423      6.4813      6.4567|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.3596 0.3825        6.71      6.7784|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.4059 0.3630      6.6106      6.5477|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.4190 0.4236      6.4469      6.4318|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.4597 0.4209      6.3139      6.3072|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.4642 0.4932      6.2327      6.1562|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.4542 0.4388      6.1779      6.0882|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.4926 0.4553      6.1551       6.127|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.4828 0.4562      6.0883      6.0948|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.4961 0.4788      6.0779      6.0662|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.4976 0.4806      6.0026        6.01|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.4976 0.5014      5.9318      5.9751|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.5188 0.5546      5.8782      5.8354|
| 14:  2.0302 -  1.9808 0.30    377   55 0.4614 0.4571      5.8375      5.7259|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9625 -  4.7270  1429   158  0.75  30.11   0.84     0.76      56079.57|
|  2:  4.7270 -  3.7718  1386   154  0.75  30.57   0.93     0.84      82469.86|
|  3:  3.7718 -  3.3008  1336   149  0.68  37.57   0.90     0.83      85843.59|
|  4:  3.3008 -  3.0017  1343   145  0.60  43.53   0.93     0.77      75317.37|
|  5:  3.0017 -  2.7880  1313   152  0.55  48.05   0.90     0.71      59940.77|
|  6:  2.7880 -  2.6246  1335   143  0.51  51.20   0.92     0.67      54521.60|
|  7:  2.6246 -  2.4938  1294   152  0.51  50.99   0.94     0.68      49178.39|
|  8:  2.4938 -  2.3857  1340   140  0.51  51.31   0.91     0.69      44116.02|
|  9:  2.3857 -  2.2941  1312   147  0.52  50.77   0.92     0.72      40027.99|
| 10:  2.2941 -  2.2152  1306   145  0.51  51.83   0.93     0.71      37364.73|
| 11:  2.2152 -  2.1462  1285   151  0.44  57.07   0.93     0.66      39446.82|
| 12:  2.1462 -  2.0850  1305   140  0.37  62.09   0.93     0.57      40085.26|
| 13:  2.0850 -  2.0302  1269   128  0.32  66.37   0.91     0.50      37501.87|
| 14:  2.0302 -  1.9808   377    55  0.34  64.38   0.99     0.44      29441.82|
|alpha:            min =        0.44 max =            0.84 mean =         0.70|
|beta:             min =    29441.82 max =        85843.59 mean =     53745.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.63|
|phase err.(test): min =        0.00 max =           89.78 mean =        48.91|
|-----------------------------------------------------------------------------|

============================== 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 = 10.731368             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.004   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.372736              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.072   (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 |  1.623 -  1.950:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.950 -  2.278:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.278 -  2.606:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.606 -  2.934:     1503 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.934 -  3.261:     1881 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.261 -  3.589:     2543 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.589 -  3.917:     4696 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.917 -  4.244:     4392 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.244 -  4.572:     5865 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7048 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| 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  1.623 |       0.298 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4338   r_free= 0.4276   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.236230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4242   r_free= 0.4152   ksol= 0.31   Bsol= 50.00   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,2.05,3.47,0.00,0.00,0.00); trace/3= 0.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.226114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.163862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.619   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.780081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.766   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4242      final r-factor (work) = 0.2640          |
| start r-factor (free) = 0.4152      final r-factor (free) = 0.2893          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6921 = 9.16 * 0.50 * 6.2244 + 1.00 * 0.1722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6686 = 9.16 * 0.50 * 6.0127 + 1.00 * 0.1187                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2640      final r-factor (work) = 0.2413          |
| start r-factor (free) = 0.2893      final r-factor (free) = 0.2992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6967 = 0.78 * 1.00 * 6.0127 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5467 = 0.78 * 1.00 * 5.7910 + 1.00 * 0.0292                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.72   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    69.72   17.21    None  None   None       |
|    Sol.    : 438    0      4.14    68.23   38.64    None  None   None       |
|    Mac.    : 2385   0      0.00    69.72   13.27    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 -   6.972:  528   |   5:    34.861 -  41.833:  120        |
|      1:     6.972 -  13.944: 1002   |   6:    41.833 -  48.805:  105        |
|      2:    13.944 -  20.917:  542   |   7:    48.805 -  55.777:   82        |
|      3:    20.917 -  27.889:  276   |   8:    55.777 -  62.750:   33        |
|      4:    27.889 -  34.861:  131   |   9:    62.750 -  69.722:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2413 r_free = 0.2992             target_work(ml) = 5.804         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2410 r_free = 0.2996             target_work(ml) = 5.804         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2410   r_free= 0.2996   ksol= 0.31   Bsol= 50.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,2.05,3.47,0.00,0.00,0.00); trace/3= 0.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.803764                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2381   r_free= 0.2972   ksol= 0.33   Bsol= 71.90   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-0.26,0.65,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.799593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.829376              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.649   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.756   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2381      final r-factor (work) = 0.1687          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.2127          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1181 = 4.83 * 0.50 * 5.7976 + 1.00 * 0.1187                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7802 = 4.83 * 0.50 * 5.6766 + 1.00 * 0.0731                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1687      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2127      final r-factor (free) = 0.1953          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0192 = 0.35 * 1.00 * 5.6766 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9264 = 0.35 * 1.00 * 5.4386 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    71.22   17.18    None  None   None       |
|    all(noH): 2823   0      1.03    71.22   17.18    None  None   None       |
|    Sol.    : 438    0      5.73    71.22   40.38    None  None   None       |
|    Mac.    : 2385   0      1.03    69.71   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.035 -   8.053:  631   |   5:    36.129 -  43.148:   81        |
|      1:     8.053 -  15.072: 1182   |   6:    43.148 -  50.167:  108        |
|      2:    15.072 -  22.091:  422   |   7:    50.167 -  57.186:   83        |
|      3:    22.091 -  29.110:  144   |   8:    57.186 -  64.205:   49        |
|      4:    29.110 -  36.129:  105   |   9:    64.205 -  71.223:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1528 r_free = 0.1953             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1526 r_free = 0.1951             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1526   r_free= 0.1951   ksol= 0.33   Bsol= 71.90   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-0.26,0.65,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.400676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1525   r_free= 0.1946   ksol= 0.33   Bsol= 69.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.16,-0.06,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.399408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.066648              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.019   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.886853              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.033  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1525      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4142 = 3.07 * 0.50 * 5.4399 + 1.00 * 0.0731                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2334 = 3.07 * 0.50 * 5.3251 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7322 = 0.89 * 1.00 * 5.3251 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6539 = 0.89 * 1.00 * 5.2352 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    86.29   17.31    None  None   None       |
|    all(noH): 2823   0      0.52    86.29   17.31    None  None   None       |
|    Sol.    : 438    0      5.43    86.29   42.21    None  None   None       |
|    Mac.    : 2385   0      0.52    85.52   12.74    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:     0.520 -   9.097:  903   |   5:    43.406 -  51.983:  103        |
|      1:     9.097 -  17.674: 1159   |   6:    51.983 -  60.561:   78        |
|      2:    17.674 -  26.252:  274   |   7:    60.561 -  69.138:   51        |
|      3:    26.252 -  34.829:  123   |   8:    69.138 -  77.715:   27        |
|      4:    34.829 -  43.406:   98   |   9:    77.715 -  86.292:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1699             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1699             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1699   ksol= 0.33   Bsol= 69.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.16,-0.06,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1698   ksol= 0.33   Bsol= 69.58   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.43,-0.21,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.794347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.512558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.844  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0006 = 3.79 * 0.50 * 5.2353 + 1.00 * 0.0683                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9428 = 3.79 * 0.50 * 5.1973 + 1.00 * 0.0825                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6748 = 0.51 * 1.00 * 5.1973 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6605 = 0.51 * 1.00 * 5.1703 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.04   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    88.04   16.97    None  None   None       |
|    Sol.    : 438    0      0.00    88.04   41.39    None  None   None       |
|    Mac.    : 2385   0      0.00    87.35   12.48    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 -   8.804:  891   |   5:    44.022 -  52.826:   90        |
|      1:     8.804 -  17.609: 1195   |   6:    52.826 -  61.630:   81        |
|      2:    17.609 -  26.413:  263   |   7:    61.630 -  70.435:   44        |
|      3:    26.413 -  35.217:  122   |   8:    70.435 -  79.239:   20        |
|      4:    35.217 -  44.022:  112   |   9:    79.239 -  88.043:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1616             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1616             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1616   ksol= 0.33   Bsol= 69.58   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.43,-0.21,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.163953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1615   ksol= 0.32   Bsol= 62.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.28,-0.06,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.163922                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.888907              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.969  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.377160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.548  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9659 = 1.89 * 0.50 * 5.1706 + 1.00 * 0.0825                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9500 = 1.89 * 0.50 * 5.1767 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1396 = 1.38 * 1.00 * 5.1767 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1424 = 1.38 * 1.00 * 5.1781 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.15   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    97.15   16.85    None  None   None       |
|    Sol.    : 438    0      0.00    97.15   41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    95.11   12.35    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 -   9.715: 1134   |   5:    48.575 -  58.290:   83        |
|      1:     9.715 -  19.430: 1044   |   6:    58.290 -  68.004:   56        |
|      2:    19.430 -  29.145:  211   |   7:    68.004 -  77.719:   30        |
|      3:    29.145 -  38.860:  132   |   8:    77.719 -  87.434:   10        |
|      4:    38.860 -  48.575:  117   |   9:    87.434 -  97.149:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1630             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1630             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1630   ksol= 0.32   Bsol= 62.35   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.28,-0.06,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182372                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.0973 0.1294       5.386      5.5538|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.0839 0.1067      5.4193      5.6234|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.1071 0.1502      5.4746      5.8338|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.1270 0.1667      5.4721      5.6397|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.1375 0.1711      5.3617      5.5481|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.1295 0.2145      5.2567      5.5411|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.1313 0.1722      5.2094       5.395|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.1194 0.1720       5.125      5.3249|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.1206 0.2029      5.0585      5.3885|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.1177 0.1804      5.0007       5.201|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.1221 0.1923      4.9602      5.3284|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.1161 0.1661      4.9024      5.1345|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.1135 0.1751      4.8117      5.0268|
| 14:  2.0302 -  1.9808 0.30    377   55 0.1026 0.1853      4.7301      5.0057|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9625 -  4.7270  1429   158  0.94   9.32   0.96     0.94       7434.41|
|  2:  4.7270 -  3.7718  1386   154  0.95   7.92   1.00     0.99       8890.19|
|  3:  3.7718 -  3.3008  1336   149  0.93  11.32   1.02     1.01      10350.99|
|  4:  3.3008 -  3.0017  1343   145  0.91  14.42   1.00     0.99      10765.96|
|  5:  3.0017 -  2.7880  1313   152  0.90  16.58   0.99     0.96       9010.96|
|  6:  2.7880 -  2.6246  1335   143  0.89  17.42   0.98     0.95       7850.74|
|  7:  2.6246 -  2.4938  1294   152  0.90  16.42   0.98     0.95       6837.51|
|  8:  2.4938 -  2.3857  1340   140  0.90  16.55   0.98     0.95       6176.84|
|  9:  2.3857 -  2.2941  1312   147  0.90  16.78   0.99     0.94       5376.42|
| 10:  2.2941 -  2.2152  1306   145  0.90  16.60   0.98     0.93       4882.67|
| 11:  2.2152 -  2.1462  1285   151  0.89  16.93   0.97     0.93       4524.81|
| 12:  2.1462 -  2.0850  1305   140  0.90  16.57   0.98     0.98       4219.90|
| 13:  2.0850 -  2.0302  1269   128  0.90  16.92   0.97     0.95       3611.82|
| 14:  2.0302 -  1.9808   377    55  0.91  15.37   0.95     0.90       2946.40|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2946.40 max =        10765.96 mean =      6869.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.84|
|phase err.(test): min =        0.00 max =           88.65 mean =        14.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1629   ksol= 0.32   Bsol= 62.35   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.12,0.11,-0.00,0.00,0.00); trace/3= -1.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182546                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1629   ksol= 0.32   Bsol= 62.35   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.12,0.11,-0.00,0.00,0.00); trace/3= -1.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182546                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.0973 0.1296      5.3868      5.5552|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.0840 0.1067      5.4198      5.6234|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.1071 0.1502      5.4747      5.8342|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.1270 0.1667      5.4722      5.6397|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.1375 0.1711      5.3617      5.5478|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.1294 0.2145      5.2566      5.5409|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.1313 0.1723      5.2095      5.3951|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.1194 0.1720      5.1252      5.3249|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.1206 0.2029      5.0586      5.3885|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.1177 0.1805      5.0009      5.2013|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.1221 0.1923      4.9602      5.3284|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.1161 0.1661      4.9024      5.1344|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.1135 0.1751      4.8116      5.0265|
| 14:  2.0302 -  1.9808 0.30    377   55 0.1025 0.1853      4.7308      5.0061|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9625 -  4.7270  1429   158  0.94   9.33   0.97     0.94       7447.32|
|  2:  4.7270 -  3.7718  1386   154  0.95   7.92   1.00     0.99       8898.78|
|  3:  3.7718 -  3.3008  1336   149  0.93  11.33   1.02     1.02      10355.62|
|  4:  3.3008 -  3.0017  1343   145  0.91  14.42   1.01     0.99      10767.34|
|  5:  3.0017 -  2.7880  1313   152  0.90  16.58   1.00     0.97       9009.66|
|  6:  2.7880 -  2.6246  1335   143  0.89  17.42   0.98     0.96       7848.68|
|  7:  2.6246 -  2.4938  1294   152  0.90  16.42   0.99     0.96       6837.36|
|  8:  2.4938 -  2.3857  1340   140  0.90  16.56   0.99     0.95       6177.88|
|  9:  2.3857 -  2.2941  1312   147  0.90  16.79   0.99     0.95       5378.40|
| 10:  2.2941 -  2.2152  1306   145  0.90  16.61   0.98     0.94       4882.92|
| 11:  2.2152 -  2.1462  1285   151  0.89  16.93   0.98     0.94       4523.52|
| 12:  2.1462 -  2.0850  1305   140  0.90  16.57   0.99     0.99       4219.57|
| 13:  2.0850 -  2.0302  1269   128  0.90  16.92   0.98     0.96       3610.95|
| 14:  2.0302 -  1.9808   377    55  0.91  15.39   0.96     0.91       2946.24|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2946.24 max =        10767.34 mean =      6871.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.84|
|phase err.(test): min =        0.00 max =           88.66 mean =        14.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.15   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    97.15   16.85    None  None   None       |
|    Sol.    : 438    0      0.00    97.15   41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    95.11   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.718: 1134   |   5:    48.578 -  58.293:   83        |
|      1:     9.718 -  19.433: 1044   |   6:    58.293 -  68.007:   56        |
|      2:    19.433 -  29.148:  211   |   7:    68.007 -  77.722:   30        |
|      3:    29.148 -  38.863:  132   |   8:    77.722 -  87.437:   10        |
|      4:    38.863 -  48.578:  117   |   9:    87.437 -  97.152:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.442 - 5.138
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 294
   mapped sites are within: 0.721 - 5.138

peak=    5.437 closest distance to " O   HOH Z 113 " =    2.037
peak=    5.139 closest distance to " O   HOH Z 210 " =    1.109
peak=    5.104 closest distance to " CG  PRO A 280 " =    0.885
peak=    5.091 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.051 closest distance to " CG  PRO A  54 " =    1.357
peak=    4.989 closest distance to " CB  ARG A 190 " =    1.738
peak=    4.713 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.709 closest distance to " CB  ARG A 275 " =    0.944
peak=    4.708 closest distance to " CZ  PHE A 218 " =    1.084
peak=    4.687 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.664 closest distance to " CG  PRO A  90 " =    1.193
peak=    4.587 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.555 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.534 closest distance to " CB  SER A  63 " =    1.123
peak=    4.525 closest distance to " C   PRO A 198 " =    1.514
peak=    4.478 closest distance to " CA  ARG A  36 " =    1.077
peak=    4.440 closest distance to " CB  PRO A  54 " =    0.988
peak=    4.405 closest distance to " O   HOH Z 369 " =    2.260
peak=    4.376 closest distance to " CB  ARG A  79 " =    1.407
peak=    4.368 closest distance to " CD2 TRP A 179 " =    1.325
peak=    4.368 closest distance to " O  BHOH Z  74 " =    1.119
peak=    4.366 closest distance to " O   HOH Z 403 " =    1.799
peak=    4.355 closest distance to " O   HOH Z 142 " =    1.620
peak=    4.293 closest distance to " NE2 GLN A  11 " =    1.133
peak=    4.257 closest distance to " CB  GLU A 152 " =    1.158
peak=    4.238 closest distance to " O   HOH Z 232 " =    2.326
peak=    4.225 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.200 closest distance to " O   HOH Z 234 " =    3.837
peak=    4.182 closest distance to " CG  PRO A 243 " =    1.111
peak=    4.178 closest distance to " O   HOH Z  43 " =    2.007
peak=    4.177 closest distance to " O   HOH Z 188 " =    2.884
peak=    4.155 closest distance to " CD  ARG A 269 " =    1.005
peak=    4.150 closest distance to " CZ3 TRP A 266 " =    1.108
peak=    4.069 closest distance to " CZ  PHE A  38 " =    1.242
peak=    4.051 closest distance to " O   HOH Z  49 " =    1.128
peak=    4.041 closest distance to " CB  GLU A 277 " =    3.762
peak=    4.023 closest distance to " O   HOH Z 126 " =    1.907
peak=    4.018 closest distance to " O   HOH Z  63 " =    1.889
peak=    4.013 closest distance to " O   HOH Z 287 " =    1.822
peak=    3.990 closest distance to " NZ  LYS A 117 " =    3.107
peak=    3.989 closest distance to " CB  ASN A 148 " =    1.410
peak=    3.982 closest distance to " O   SER A  87 " =    2.264
peak=    3.974 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.955 closest distance to " O   HOH Z 362 " =    3.597
peak=    3.944 closest distance to " ND2 ASN A 187 " =    1.510
peak=    3.937 closest distance to " O   HOH Z  40 " =    1.921
peak=    3.936 closest distance to " CA  ALA A  51 " =    1.001
peak=    3.936 closest distance to " O   HOH Z 402 " =    1.430
peak=    3.932 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.921 closest distance to " O   HOH Z 265 " =    2.022
peak=    3.919 closest distance to " O   HOH Z 368 " =    2.114
peak=    3.915 closest distance to " O   HOH Z  97 " =    2.001
peak=    3.911 closest distance to " O   HOH Z 214 " =    2.569
peak=    3.904 closest distance to " ND2 ASN A 249 " =    0.911
peak=    3.891 closest distance to " O   HOH Z 158 " =    3.066
peak=    3.884 closest distance to " CG2 ILE A 120 " =    1.208
peak=    3.871 closest distance to " CA  ALA A 160 " =    0.923
peak=    3.867 closest distance to " O   HOH Z 423 " =    1.931
peak=    3.864 closest distance to " CB  GLU A 128 " =    1.159
peak=    3.855 closest distance to " CG  ARG A  66 " =    2.544
peak=    3.841 closest distance to " O   HOH Z 346 " =    1.664
peak=    3.829 closest distance to " O   ASN A  74 " =    1.719
peak=    3.828 closest distance to " O   HOH Z 209 " =    2.300
peak=    3.824 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.821 closest distance to " O   HOH Z 412 " =    3.804
peak=    3.808 closest distance to " CG  MET A 185 " =    1.149
peak=    3.802 closest distance to " NH1AARG A 145 " =    1.359
peak=    3.799 closest distance to " O   HOH Z 316 " =    3.097
peak=    3.798 closest distance to " CB  TRP A 266 " =    1.033
peak=    3.796 closest distance to " O   HOH Z 248 " =    1.457
peak=    3.792 closest distance to " CD  LYS A 166 " =    1.346
peak=    3.787 closest distance to " CB  THR A  31 " =    1.542
peak=    3.776 closest distance to " O   THR A 220 " =    1.220
peak=    3.771 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.770 closest distance to " O   HOH Z 261 " =    2.174
peak=    3.762 closest distance to " CA  MET A 105 " =    1.085
peak=    3.760 closest distance to " OG BSER A 164 " =    2.274
peak=    3.752 closest distance to " O   HOH Z 303 " =    2.224
peak=    3.750 closest distance to " O   HOH Z  21 " =    1.875
peak=    3.748 closest distance to " O   HOH Z 406 " =    1.599
peak=    3.746 closest distance to " CB  LEU A 228 " =    1.132
peak=    3.744 closest distance to " O   HOH Z  15 " =    2.233
peak=    3.738 closest distance to " CB  VAL A 265 " =    1.215
peak=    3.735 closest distance to " O   HOH Z  44 " =    1.982
peak=    3.734 closest distance to " O   HOH Z 427 " =    2.995
peak=    3.727 closest distance to " O   HOH Z  19 " =    1.519
peak=    3.721 closest distance to " N   ASN A  39 " =    1.281
peak=    3.720 closest distance to " O   HOH Z 258 " =    2.075
peak=    3.719 closest distance to " O   HOH Z 389 " =    1.914
peak=    3.714 closest distance to " O   HOH Z 132 " =    2.799
peak=    3.693 closest distance to " O   HOH Z 361 " =    2.548
peak=    3.693 closest distance to " O   HOH Z 250 " =    1.422
peak=    3.692 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.686 closest distance to " O   HOH Z  78 " =    1.646
peak=    3.677 closest distance to " N   HIS A 108 " =    1.820
peak=    3.668 closest distance to " O   HOH Z 180 " =    2.203
peak=    3.665 closest distance to " O   HOH Z 353 " =    2.749
peak=    3.665 closest distance to " CG2 VAL A 257 " =    0.791
peak=    3.661 closest distance to " CG  GLU A  37 " =    0.933
peak=    3.660 closest distance to " OG BSER A 134 " =    2.789
peak=    3.656 closest distance to " O   HOH Z  80 " =    1.882
peak=    3.648 closest distance to " CB  ASN A  39 " =    0.843
peak=    3.644 closest distance to " CB  TYR A 169 " =    0.799
peak=    3.643 closest distance to " CB  ASN A 142 " =    1.123
peak=    3.641 closest distance to " O   HOH Z 251 " =    1.602
peak=    3.639 closest distance to " O  BHOH Z 338 " =    2.219
peak=    3.638 closest distance to " CD1 LEU A  96 " =    0.802
peak=    3.637 closest distance to " NZ  LYS A  48 " =    1.164
peak=    3.636 closest distance to " CA  ASN A 176 " =    1.376
peak=    3.632 closest distance to " O   HOH Z 365 " =    2.736
peak=    3.615 closest distance to " CA  VAL A 125 " =    1.200
peak=    3.611 closest distance to " CD  ARG A 159 " =    0.805
peak=    3.601 closest distance to " O   HOH Z  59 " =    2.363
peak=    3.599 closest distance to " O   HOH Z 359 " =    1.647
peak=    3.593 closest distance to " O   HOH Z 383 " =    2.053
peak=    3.588 closest distance to " O   ALA A 165 " =    1.450
peak=    3.586 closest distance to " CB  SER A 141 " =    1.107
peak=    3.585 closest distance to " CG1BVAL A  72 " =    1.860
peak=    3.583 closest distance to " CA  ALA A 295 " =    1.063
peak=    3.582 closest distance to " O   HOH Z 291 " =    1.447
peak=    3.581 closest distance to " O   HOH Z 392 " =    2.470
peak=    3.577 closest distance to " O   HOH Z 313 " =    1.972
peak=    3.570 closest distance to " CD1 ILE A 199 " =    1.158
peak=    3.561 closest distance to " O   HOH Z 128 " =    2.032
peak=    3.553 closest distance to " O   HOH Z 203 " =    1.778
peak=    3.552 closest distance to " CB  PHE A 204 " =    0.786
peak=    3.549 closest distance to " O   HOH Z 126 " =    1.534
peak=    3.545 closest distance to " O   HOH Z 185 " =    1.796
peak=    3.545 closest distance to " O   HOH Z 272 " =    1.842
peak=    3.540 closest distance to " CA  SER A  87 " =    1.074
peak=    3.539 closest distance to " CD2 LEU A 297 " =    0.917
peak=    3.538 closest distance to " O   HOH Z 227 " =    1.564
peak=    3.532 closest distance to " CB  THR A  52 " =    0.732
peak=    3.520 closest distance to " O   HOH Z 393 " =    3.065
peak=    3.519 closest distance to " O   TYR A 116 " =    1.444
peak=    3.515 closest distance to " CB  TRP A 179 " =    1.411
peak=    3.509 closest distance to " CA  TYR A 116 " =    1.346
peak=    3.507 closest distance to " O   HOH Z 345 " =    1.663
peak=    3.506 closest distance to " O   HOH Z 134 " =    1.242
peak=    3.504 closest distance to " CB  ALA A 248 " =    1.327
peak=    3.503 closest distance to " CG  LEU A 167 " =    1.159
peak=    3.500 closest distance to " OD1 ASN A  69 " =    2.423
peak=    3.497 closest distance to " CG1 VAL A 153 " =    1.023
peak=    3.495 closest distance to " O   THR A 182 " =    1.439
peak=    3.494 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.492 closest distance to " O   HOH Z 148 " =    3.456
peak=    3.488 closest distance to " NE2 GLN A  77 " =    3.286
peak=    3.480 closest distance to " O   HOH Z  97 " =    2.228
peak=    3.479 closest distance to " CB  PRO A  90 " =    1.103
peak=    3.478 closest distance to " O   HOH Z  61 " =    1.620
peak=    3.477 closest distance to " CA  ASN A 215 " =    0.998
peak=    3.474 closest distance to " O   HOH Z  63 " =    2.288
peak=    3.467 closest distance to " CB  GLN A  89 " =    1.351
peak=    3.461 closest distance to " O   HOH Z 325 " =    2.197
peak=    3.459 closest distance to " N   CYS A 260 " =    0.839
peak=    3.458 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.457 closest distance to " O   HOH Z 421 " =    1.881
peak=    3.456 closest distance to " NH2AARG A 275 " =    3.502
peak=    3.451 closest distance to " CB  LEU A  83 " =    0.793
peak=    3.439 closest distance to " O   HOH Z 380 " =    1.999
peak=    3.437 closest distance to " CB  ASN A 110 " =    1.130
peak=    3.430 closest distance to " CB  SER A  62 " =    0.849
peak=    3.428 closest distance to " OD2 ASP A 298 " =    3.983
peak=    3.427 closest distance to " O   HOH Z 146 " =    2.309
peak=    3.425 closest distance to " NH2BARG A 145 " =    2.130
peak=    3.425 closest distance to " CG  GLN A  11 " =    1.506
peak=    3.417 closest distance to " O   THR A 251 " =    1.095
peak=    3.417 closest distance to " CB  ALA A 291 " =    1.111
peak=    3.413 closest distance to " CA  ALA A 154 " =    1.030
peak=    3.412 closest distance to " CA  THR A 264 " =    0.936
peak=    3.407 closest distance to " O   HOH Z 371 " =    3.022
peak=    3.403 closest distance to " CA  GLU A 152 " =    0.844
peak=    3.399 closest distance to " N   TYR A 116 " =    1.607
peak=    3.399 closest distance to " CB  PRO A 243 " =    1.475
peak=    3.399 closest distance to " CA  ALA A 100 " =    0.976
peak=    3.395 closest distance to " CB  ASP A 140 " =    1.179
peak=    3.391 closest distance to " O   HOH Z 422 " =    2.646
peak=    3.383 closest distance to " O   HOH Z 417 " =    3.068
peak=    3.382 closest distance to " O   HOH Z 285 " =    2.434
peak=    3.375 closest distance to " CA  SER A  32 " =    1.630
peak=    3.374 closest distance to " O   HOH Z 327 " =    1.624
peak=    3.373 closest distance to " OG  SER A  28 " =    1.430
peak=    3.370 closest distance to " O   HOH Z 298 " =    2.433
peak=    3.368 closest distance to " CA  ASN A 127 " =    1.221
peak=    3.361 closest distance to " CB  ASN A 148 " =    2.037
peak=    3.359 closest distance to " O   HOH Z  48 " =    1.637
peak=    3.354 closest distance to " N   ARG A 156 " =    1.478
peak=    3.347 closest distance to " CB  ASN A 215 " =    1.215
peak=    3.342 closest distance to " NH2 ARG A 156 " =    1.167
peak=    3.341 closest distance to " O   HOH Z 299 " =    4.419
peak=    3.341 closest distance to " CG2 ILE A  20 " =    1.276
peak=    3.334 closest distance to " O   HOH Z  88 " =    2.641
peak=    3.333 closest distance to " O   HOH Z 128 " =    2.361
peak=    3.333 closest distance to " O   HOH Z 421 " =    2.739
peak=    3.330 closest distance to " CA  ILE A 234 " =    0.979
peak=    3.326 closest distance to " O   HOH Z 199 " =    1.641
peak=    3.324 closest distance to " O   HOH Z 357 " =    2.149
peak=    3.324 closest distance to " CB  ASP A 298 " =    1.210
peak=    3.323 closest distance to " CG2 VAL A 197 " =    1.111
peak=    3.323 closest distance to " O   HOH Z 294 " =    1.551
peak=    3.323 closest distance to " CD  PRO A  54 " =    0.988
peak=    3.322 closest distance to " CA  ILE A 106 " =    0.835
peak=    3.318 closest distance to " OH  TYR A 116 " =    1.118
peak=    3.318 closest distance to " O   HOH Z 250 " =    1.530
peak=    3.316 closest distance to " CB  SER A  26 " =    1.838
peak=    3.312 closest distance to " CG1 ILE A  20 " =    1.260
peak=    3.306 closest distance to " O   HOH Z 366 " =    2.473
peak=    3.306 closest distance to " O   ASP A 191 " =    1.551
peak=    3.303 closest distance to " O   HOH Z 285 " =    1.874
peak=    3.298 closest distance to " O   ASP A 124 " =    1.318
peak=    3.294 closest distance to " O   HOH Z 271 " =    2.529
peak=    3.293 closest distance to " CE1 HIS A  81 " =    1.678
peak=    3.292 closest distance to " CG2 THR A 220 " =    0.765
peak=    3.289 closest distance to " CE1 TYR A 186 " =    1.292
peak=    3.282 closest distance to " CA  ALA A  21 " =    1.255
peak=    3.282 closest distance to " N   VAL A 265 " =    1.336
peak=    3.282 closest distance to " CB  SER A   3 " =    1.317
peak=    3.281 closest distance to " CA  MET A 188 " =    0.965
peak=    3.280 closest distance to " CB  MET A  47 " =    0.967
peak=    3.271 closest distance to " CD1 LEU A 300 " =    1.192
peak=    3.271 closest distance to " O   HOH Z   1 " =    2.438
peak=    3.271 closest distance to " CG2 THR A 221 " =    1.192
peak=    3.266 closest distance to " CA  GLU A  46 " =    1.069
peak=    3.264 closest distance to " CB  ALA A 114 " =    0.783
peak=    3.263 closest distance to " O   HOH Z 279 " =    2.191
peak=    3.261 closest distance to " N   ASP A 162 " =    1.182
peak=    3.261 closest distance to " O   HOH Z 425 " =    1.301
peak=    3.261 closest distance to " O   HOH Z 102 " =    1.254
peak=    3.253 closest distance to " O   HOH Z 227 " =    2.101
peak=    3.247 closest distance to " O   HOH Z 193 " =    1.727
peak=    3.244 closest distance to " CG  ARG A 138 " =    1.242
peak=    3.237 closest distance to " CB  ASP A 191 " =    1.257
peak=    3.235 closest distance to " CA  ASP A 162 " =    1.115
peak=    3.223 closest distance to " OG  SER A  22 " =    2.712
peak=    3.219 closest distance to " OE1 GLN A  73 " =    2.514
peak=    3.219 closest distance to " CA  ALA A  84 " =    1.190
peak=    3.217 closest distance to " O   HOH Z 109 " =    2.419
peak=    3.216 closest distance to " CA  ASP A 140 " =    1.278
peak=    3.214 closest distance to " CG2 THR A  29 " =    1.341
peak=    3.207 closest distance to " O   HOH Z 426 " =    1.569
peak=    3.203 closest distance to " O   HOH Z 411 " =    1.669
peak=    3.202 closest distance to " O   HOH Z 216 " =    5.138
peak=    3.199 closest distance to " O   HOH Z 336 " =    1.765
peak=    3.199 closest distance to " OG  SER A 135 " =    1.298
peak=    3.198 closest distance to " CB  SER A 273 " =    0.849
peak=    3.196 closest distance to " CD1AILE A 234 " =    0.826
peak=    3.191 closest distance to " O   HOH Z 391 " =    2.948
peak=    3.190 closest distance to " CA  ALA A 233 " =    1.530
peak=    3.184 closest distance to " CD  ARG A  66 " =    2.513
peak=    3.183 closest distance to " CB  LYS A 117 " =    1.164
peak=    3.180 closest distance to " O   HOH Z  85 " =    1.357
peak=    3.179 closest distance to " CA  LEU A  83 " =    1.241
peak=    3.173 closest distance to " N   PHE A 130 " =    1.287
peak=    3.167 closest distance to " O   HOH Z 286 " =    2.172
peak=    3.167 closest distance to " O   HOH Z 193 " =    1.963
peak=    3.166 closest distance to " O   HOH Z 193 " =    1.733
peak=    3.165 closest distance to " O   ALA A 158 " =    1.128
peak=    3.161 closest distance to " OE1 GLN A  55 " =    1.420
peak=    3.160 closest distance to " O   HOH Z 141 " =    1.681
peak=    3.160 closest distance to " CA  GLN A  94 " =    0.766
peak=    3.159 closest distance to " O   HOH Z 345 " =    3.802
peak=    3.151 closest distance to " CA  ASN A 217 " =    1.272
peak=    3.146 closest distance to " O   HOH Z  35 " =    2.417
peak=    3.144 closest distance to " O   HOH Z 132 " =    2.786
peak=    3.144 closest distance to " CB  PHE A 204 " =    0.721
peak=    3.143 closest distance to " CB  ALA A   9 " =    1.642
peak=    3.143 closest distance to " CA  THR A 221 " =    1.109
peak=    3.136 closest distance to " O   HOH Z 130 " =    2.283
peak=    3.136 closest distance to " O   HOH Z 305 " =    3.774
peak=    3.130 closest distance to " OD2 ASP A 286 " =    3.276
peak=    3.130 closest distance to " O   GLY A  91 " =    1.333
peak=    3.127 closest distance to " CB  TYR A 116 " =    0.783
peak=    3.125 closest distance to " O   HOH Z 371 " =    1.515
peak=    3.122 closest distance to " CB  ASN A 285 " =    0.956
peak=    3.118 closest distance to " CE1 HIS A  81 " =    1.404
peak=    3.116 closest distance to " CB  ALA A 227 " =    1.253
peak=    3.109 closest distance to " CB  ALA A   1 " =    4.941
peak=    3.109 closest distance to " CA  ALA A 248 " =    1.180
peak=    3.109 closest distance to " O   HOH Z 416 " =    2.997
peak=    3.108 closest distance to " O   HOH Z 183 " =    1.456
peak=    3.094 closest distance to " O   HOH Z 141 " =    1.637
peak=    3.094 closest distance to " O   HOH Z 368 " =    4.281
peak=    3.091 closest distance to " CA  LYS A 117 " =    1.210
peak=    3.082 closest distance to " O   HOH Z 394 " =    1.699
peak=    3.080 closest distance to " O   HOH Z 245 " =    1.325
peak=    3.077 closest distance to " CA  ARG A 156 " =    1.063
peak=    3.076 closest distance to " CB  ALA A 242 " =    0.985
peak=    3.044 closest distance to " CG2BVAL A  41 " =    0.822
peak=    3.033 closest distance to " CA  ARG A 275 " =    1.814
peak=    3.008 closest distance to " O   HOH Z   9 " =    2.470

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.927 - 5.970
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 223
   mapped sites are within: 0.927 - 5.970

peak=   -4.716 closest distance to " CD  GLN A  58 " =    0.977
peak=   -4.632 closest distance to " CD  ARG A  14 " =    3.430
peak=   -4.344 closest distance to " O   HOH Z 266 " =    5.426
peak=   -4.335 closest distance to " O   PRO A 198 " =    1.316
peak=   -4.329 closest distance to " CB  PRO A 243 " =    2.751
peak=   -4.263 closest distance to " CD  ARG A 156 " =    2.110
peak=   -4.235 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.221 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -4.158 closest distance to " O   HOH Z 231 " =    2.401
peak=   -4.154 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -4.149 closest distance to " CG2 ILE A  49 " =    2.736
peak=   -4.102 closest distance to " OXT GLY A 302 " =    2.973
peak=   -4.080 closest distance to " CD1 LEU A 101 " =    2.460
peak=   -4.068 closest distance to " O   HOH Z  10 " =    1.590
peak=   -4.057 closest distance to " CD2 TYR A 293 " =    1.910
peak=   -4.022 closest distance to " CE2 PHE A  61 " =    2.664
peak=   -4.019 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -3.943 closest distance to " O   HOH Z 377 " =    2.046
peak=   -3.939 closest distance to " O   HOH Z 196 " =    2.064
peak=   -3.917 closest distance to " O   HOH Z 210 " =    0.927
peak=   -3.915 closest distance to " CG  ARG A  66 " =    2.544
peak=   -3.905 closest distance to " O   HOH Z 166 " =    1.740
peak=   -3.900 closest distance to " CA  VAL A  67 " =    2.924
peak=   -3.896 closest distance to " O   HOH Z 348 " =    2.250
peak=   -3.882 closest distance to " O   HOH Z 198 " =    1.652
peak=   -3.869 closest distance to " OG  SER A  97 " =    2.226
peak=   -3.851 closest distance to " CH2 TRP A 179 " =    1.264
peak=   -3.840 closest distance to " O   VAL A  67 " =    2.819
peak=   -3.838 closest distance to " CE3 TRP A 150 " =    2.254
peak=   -3.779 closest distance to " O   SER A 210 " =    1.894
peak=   -3.764 closest distance to " O   HOH Z 374 " =    1.944
peak=   -3.751 closest distance to " O   HOH Z 394 " =    1.523
peak=   -3.746 closest distance to " CG  PRO A 243 " =    1.706
peak=   -3.716 closest distance to " CG  GLU A  53 " =    1.456
peak=   -3.715 closest distance to " N   ALA A  43 " =    2.662
peak=   -3.706 closest distance to " O   PRO A 163 " =    2.103
peak=   -3.706 closest distance to " CA  GLY A 241 " =    3.211
peak=   -3.705 closest distance to " OE1 GLN A 223 " =    2.017
peak=   -3.702 closest distance to " CA  GLY A 241 " =    2.414
peak=   -3.698 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.694 closest distance to " O   HOH Z 283 " =    2.343
peak=   -3.693 closest distance to " O   HOH Z 264 " =    1.740
peak=   -3.691 closest distance to " CB  ALA A 161 " =    2.614
peak=   -3.689 closest distance to " CZ  TYR A 169 " =    1.821
peak=   -3.682 closest distance to " CD  GLN A 223 " =    1.359
peak=   -3.681 closest distance to " CG1 VAL A 112 " =    2.781
peak=   -3.671 closest distance to " CG  ASP A 132 " =    2.379
peak=   -3.661 closest distance to " ND2 ASN A 249 " =    2.298
peak=   -3.655 closest distance to " O   HOH Z 372 " =    2.325
peak=   -3.653 closest distance to " CB  PHE A 192 " =    2.092
peak=   -3.645 closest distance to " O   ALA A  34 " =    2.353
peak=   -3.616 closest distance to " CG1AVAL A  41 " =    2.618
peak=   -3.611 closest distance to " O   HOH Z  13 " =    1.821
peak=   -3.600 closest distance to " O   HOH Z 102 " =    1.552
peak=   -3.588 closest distance to " CG  GLN A  11 " =    1.676
peak=   -3.585 closest distance to " O   HOH Z  71 " =    2.358
peak=   -3.583 closest distance to " CD  ARG A  79 " =    1.172
peak=   -3.581 closest distance to " CB  ALA A  10 " =    2.236
peak=   -3.576 closest distance to " O   HOH Z 165 " =    1.892
peak=   -3.573 closest distance to " ND2 ASN A  45 " =    1.187
peak=   -3.573 closest distance to " CD1 PHE A  59 " =    2.037
peak=   -3.563 closest distance to " OG BSER A 134 " =    1.306
peak=   -3.554 closest distance to " CG  GLU A 277 " =    1.173
peak=   -3.548 closest distance to " N   THR A  52 " =    1.688
peak=   -3.545 closest distance to " CB  ASN A  39 " =    2.386
peak=   -3.537 closest distance to " ND2 ASN A 187 " =    1.635
peak=   -3.535 closest distance to " CE BMET A  47 " =    1.710
peak=   -3.530 closest distance to " ND2BASN A 224 " =    1.828
peak=   -3.512 closest distance to " O   HOH Z 154 " =    1.677
peak=   -3.510 closest distance to " CE  MET A 105 " =    2.536
peak=   -3.510 closest distance to " OD1 ASN A 148 " =    1.433
peak=   -3.509 closest distance to " O   HOH Z 351 " =    1.582
peak=   -3.504 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.502 closest distance to " O   HOH Z 171 " =    2.310
peak=   -3.501 closest distance to " O   HOH Z 106 " =    1.961
peak=   -3.490 closest distance to " CD2 TYR A 247 " =    2.399
peak=   -3.489 closest distance to " CD  ARG A 195 " =    5.103
peak=   -3.485 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.484 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.481 closest distance to " CZ  PHE A 155 " =    1.147
peak=   -3.477 closest distance to " O   HOH Z 193 " =    1.336
peak=   -3.473 closest distance to " N   ALA A 248 " =    1.771
peak=   -3.473 closest distance to " CB  TRP A  85 " =    2.538
peak=   -3.473 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.471 closest distance to " ND2 ASN A  45 " =    1.905
peak=   -3.468 closest distance to " O   HOH Z 357 " =    2.129
peak=   -3.457 closest distance to " OD1 ASP A 191 " =    1.470
peak=   -3.455 closest distance to " O   HOH Z 185 " =    2.448
peak=   -3.454 closest distance to " O   HOH Z 421 " =    3.875
peak=   -3.434 closest distance to " CB  ALA A 291 " =    2.408
peak=   -3.430 closest distance to " C   ASN A 285 " =    2.275
peak=   -3.428 closest distance to " O   HOH Z 285 " =    1.534
peak=   -3.427 closest distance to " CG  GLN A  58 " =    1.116
peak=   -3.426 closest distance to " O   ALA A  10 " =    1.777
peak=   -3.418 closest distance to " CG  PHE A 283 " =    2.605
peak=   -3.415 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.413 closest distance to " CG  HIS A  86 " =    1.161
peak=   -3.408 closest distance to " CG2 VAL A 189 " =    2.220
peak=   -3.407 closest distance to " C   SER A 206 " =    1.530
peak=   -3.403 closest distance to " O   HOH Z 174 " =    2.397
peak=   -3.402 closest distance to " CA  GLY A 203 " =    2.363
peak=   -3.395 closest distance to " CB  ALA A  43 " =    2.591
peak=   -3.391 closest distance to " O   HOH Z 252 " =    3.853
peak=   -3.391 closest distance to " O   TRP A  92 " =    1.966
peak=   -3.384 closest distance to " CG  LEU A  83 " =    2.081
peak=   -3.383 closest distance to " CD2 HIS A 207 " =    2.314
peak=   -3.373 closest distance to " O   HOH Z 128 " =    2.626
peak=   -3.371 closest distance to " O   VAL A 174 " =    2.156
peak=   -3.364 closest distance to " O   HOH Z 290 " =    1.205
peak=   -3.360 closest distance to " O   HOH Z   6 " =    2.050
peak=   -3.351 closest distance to " O   HOH Z 211 " =    1.473
peak=   -3.349 closest distance to " O   HOH Z 366 " =    1.638
peak=   -3.346 closest distance to " NE2 GLN A  88 " =    1.159
peak=   -3.343 closest distance to " O   VAL A 189 " =    1.785
peak=   -3.342 closest distance to " O   HOH Z  60 " =    2.038
peak=   -3.339 closest distance to " N   ALA A 248 " =    2.177
peak=   -3.337 closest distance to " O   HOH Z 177 " =    1.841
peak=   -3.337 closest distance to " OD1 ASP A 171 " =    1.496
peak=   -3.334 closest distance to " O   VAL A 189 " =    2.663
peak=   -3.328 closest distance to " O   HOH Z 174 " =    3.648
peak=   -3.325 closest distance to " O   HOH Z  78 " =    1.866
peak=   -3.324 closest distance to " CD1 ILE A 151 " =    2.403
peak=   -3.322 closest distance to " O   HOH Z 113 " =    1.936
peak=   -3.322 closest distance to " O   HOH Z  37 " =    1.841
peak=   -3.321 closest distance to " CG1 VAL A 265 " =    2.651
peak=   -3.320 closest distance to " O   HOH Z 191 " =    5.970
peak=   -3.315 closest distance to " C   THR A 279 " =    1.145
peak=   -3.313 closest distance to " OD2 ASP A 191 " =    1.573
peak=   -3.313 closest distance to " OG1 THR A 157 " =    2.904
peak=   -3.313 closest distance to " OD2 ASP A 171 " =    2.467
peak=   -3.311 closest distance to " O   HOH Z 114 " =    3.327
peak=   -3.308 closest distance to " OE1 GLN A 183 " =    1.605
peak=   -3.307 closest distance to " O   HOH Z 396 " =    2.047
peak=   -3.304 closest distance to " O   GLU A 152 " =    1.377
peak=   -3.304 closest distance to " CZ3 TRP A 274 " =    2.458
peak=   -3.303 closest distance to " CA  GLY A 241 " =    2.916
peak=   -3.301 closest distance to " O   HOH Z 292 " =    4.658
peak=   -3.298 closest distance to " O   HOH Z 116 " =    1.421
peak=   -3.290 closest distance to " NH2 ARG A 159 " =    2.257
peak=   -3.290 closest distance to " O   GLY A 196 " =    1.135
peak=   -3.287 closest distance to " O   HOH Z 145 " =    2.889
peak=   -3.286 closest distance to " CH2 TRP A 150 " =    1.140
peak=   -3.285 closest distance to " O   HOH Z 393 " =    1.318
peak=   -3.280 closest distance to " CA  GLY A 133 " =    2.412
peak=   -3.279 closest distance to " O   HOH Z 197 " =    2.059
peak=   -3.277 closest distance to " O   HOH Z 150 " =    1.213
peak=   -3.275 closest distance to " O   SER A  62 " =    2.142
peak=   -3.267 closest distance to " N   SER A 276 " =    1.480
peak=   -3.266 closest distance to " O   SER A 276 " =    1.710
peak=   -3.264 closest distance to " OD1 ASN A 301 " =    1.966
peak=   -3.264 closest distance to " C   LEU A 143 " =    1.134
peak=   -3.263 closest distance to " CG1 VAL A  78 " =    2.737
peak=   -3.258 closest distance to " CZ  PHE A  38 " =    2.346
peak=   -3.256 closest distance to " CD2 PHE A  61 " =    2.158
peak=   -3.255 closest distance to " CG1 VAL A 125 " =    1.978
peak=   -3.254 closest distance to " OE1 GLN A  88 " =    1.102
peak=   -3.252 closest distance to " O   HOH Z 156 " =    3.500
peak=   -3.252 closest distance to " CZ  PHE A  38 " =    1.997
peak=   -3.248 closest distance to " NE  ARG A  66 " =    4.296
peak=   -3.245 closest distance to " CZ  TYR A 172 " =    1.905
peak=   -3.245 closest distance to " NH2AARG A 275 " =    5.216
peak=   -3.244 closest distance to " O   HOH Z   6 " =    1.581
peak=   -3.240 closest distance to " O   HOH Z 407 " =    2.904
peak=   -3.239 closest distance to " C   GLY A 262 " =    2.041
peak=   -3.239 closest distance to " CD  GLU A 236 " =    1.129
peak=   -3.234 closest distance to " OG BSER A 134 " =    1.972
peak=   -3.229 closest distance to " CD1 ILE A 106 " =    2.251
peak=   -3.227 closest distance to " CB  ARG A 219 " =    2.331
peak=   -3.225 closest distance to " CG  GLN A 103 " =    2.468
peak=   -3.215 closest distance to " CG  TRP A 266 " =    1.976
peak=   -3.210 closest distance to " O   HOH Z   9 " =    2.054
peak=   -3.206 closest distance to " CB  ALA A 291 " =    2.147
peak=   -3.205 closest distance to " O   SER A   3 " =    1.072
peak=   -3.199 closest distance to " O   GLY A  80 " =    2.600
peak=   -3.192 closest distance to " O   HOH Z  19 " =    2.354
peak=   -3.190 closest distance to " O   ALA A 292 " =    2.218
peak=   -3.188 closest distance to " O   TYR A 186 " =    1.753
peak=   -3.187 closest distance to " O   HOH Z 252 " =    4.103
peak=   -3.186 closest distance to " CB  PHE A  16 " =    2.475
peak=   -3.185 closest distance to " O   TRP A  70 " =    1.644
peak=   -3.184 closest distance to " O   HOH Z  63 " =    1.343
peak=   -3.181 closest distance to " O   HOH Z 216 " =    1.522
peak=   -3.178 closest distance to " O   ASN A 252 " =    1.446
peak=   -3.177 closest distance to " O   HOH Z 426 " =    1.632
peak=   -3.177 closest distance to " CD  LYS A 289 " =    2.374
peak=   -3.175 closest distance to " CD  PRO A 243 " =    2.104
peak=   -3.175 closest distance to " NH2 ARG A  79 " =    2.269
peak=   -3.172 closest distance to " O   HOH Z 418 " =    1.375
peak=   -3.170 closest distance to " CG  ASN A 148 " =    2.394
peak=   -3.170 closest distance to " CG1BVAL A  41 " =    2.762
peak=   -3.167 closest distance to " CG  ARG A 269 " =    2.358
peak=   -3.165 closest distance to " C   GLY A  17 " =    1.127
peak=   -3.164 closest distance to " CG1 VAL A  67 " =    3.181
peak=   -3.163 closest distance to " CB  ALA A 114 " =    2.561
peak=   -3.159 closest distance to " N   ALA A 226 " =    1.993
peak=   -3.154 closest distance to " OG BSER A 210 " =    2.193
peak=   -3.150 closest distance to " CG  ASP A 286 " =    1.552
peak=   -3.150 closest distance to " CD2 LEU A 237 " =    2.898
peak=   -3.149 closest distance to " CG2BVAL A  41 " =    1.923
peak=   -3.148 closest distance to " CB  ALA A   9 " =    2.456
peak=   -3.144 closest distance to " CA  ILE A 263 " =    1.162
peak=   -3.140 closest distance to " OD2 ASP A 171 " =    1.794
peak=   -3.131 closest distance to " O   HOH Z  44 " =    2.405
peak=   -3.130 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.128 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.122 closest distance to " O   HOH Z  38 " =    1.689
peak=   -3.115 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.114 closest distance to " O   HOH Z  64 " =    1.658
peak=   -3.111 closest distance to " NE2 GLN A 223 " =    1.176
peak=   -3.108 closest distance to " NE1 TRP A 266 " =    2.507
peak=   -3.093 closest distance to " O   HOH Z 423 " =    2.394
peak=   -3.086 closest distance to " CD  PRO A 213 " =    2.176
peak=   -3.083 closest distance to " OH  TYR A 172 " =    2.065
peak=   -3.082 closest distance to " O   GLN A 240 " =    2.562
peak=   -3.081 closest distance to " O   HOH Z 278 " =    1.375
peak=   -3.070 closest distance to " NH2 ARG A  66 " =    3.544
peak=   -3.062 closest distance to " O   HOH Z 134 " =    2.988
peak=   -3.060 closest distance to " O   HOH Z  51 " =    1.979
peak=   -3.059 closest distance to " O   HOH Z 350 " =    1.949
peak=   -3.028 closest distance to " O   HOH Z 340 " =    1.776
peak=   -3.026 closest distance to " CA  GLY A 133 " =    2.125
peak=   -3.025 closest distance to " CB  ASP A 286 " =    1.836

================= 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    :  0.4338 0.4276   6.236230e+00   6.215357e+00
   1_bss:  0.4242 0.4152   6.226114e+00   6.201607e+00
   1_xyz:  0.2640 0.2893   5.847162e+00   5.933640e+00
   1_adp:  0.2413 0.2992   5.803569e+00   5.960290e+00
   1_occ:  0.2410 0.2996   5.803764e+00   5.961684e+00
   2_bss:  0.2381 0.2972   5.799593e+00   5.957967e+00
   2_xyz:  0.1687 0.2127   5.484566e+00   5.674216e+00
   2_adp:  0.1528 0.1953   5.401450e+00   5.600484e+00
   2_occ:  0.1526 0.1951   5.400676e+00   5.599986e+00
   3_bss:  0.1525 0.1946   5.399408e+00   5.597649e+00
   3_xyz:  0.1276 0.1719   5.254763e+00   5.469925e+00
   3_adp:  0.1223 0.1699   5.228536e+00   5.455121e+00
   3_occ:  0.1222 0.1699   5.228702e+00   5.455406e+00
   4_bss:  0.1224 0.1698   5.228676e+00   5.455000e+00
   4_xyz:  0.1136 0.1632   5.174248e+00   5.417943e+00
   4_adp:  0.1125 0.1616   5.164651e+00   5.407419e+00
   4_occ:  0.1124 0.1616   5.163953e+00   5.406939e+00
   5_bss:  0.1123 0.1615   5.163922e+00   5.407116e+00
   5_xyz:  0.1152 0.1622   5.181328e+00   5.415203e+00
   5_adp:  0.1149 0.1630   5.182521e+00   5.421245e+00
   5_occ:  0.1148 0.1630   5.182372e+00   5.421190e+00
   5_bss:  0.1147 0.1629   5.182546e+00   5.421321e+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:  0.308  50.001  -2.762   2.046   3.468   0.000   0.000   0.000
   1_xyz:  0.308  50.001  -2.762   2.046   3.468   0.000   0.000   0.000
   1_adp:  0.308  50.001  -2.762   2.046   3.468   0.000   0.000   0.000
   1_occ:  0.308  50.001  -2.762   2.046   3.468   0.000   0.000   0.000
   2_bss:  0.331  71.898  -2.885  -0.263   0.647  -0.000   0.000   0.000
   2_xyz:  0.331  71.898  -2.885  -0.263   0.647  -0.000   0.000   0.000
   2_adp:  0.331  71.898  -2.885  -0.263   0.647  -0.000   0.000   0.000
   2_occ:  0.331  71.898  -2.885  -0.263   0.647  -0.000   0.000   0.000
   3_bss:  0.332  69.578  -2.848  -1.165  -0.061  -0.000  -0.000  -0.000
   3_xyz:  0.332  69.578  -2.848  -1.165  -0.061  -0.000  -0.000  -0.000
   3_adp:  0.332  69.578  -2.848  -1.165  -0.061  -0.000  -0.000  -0.000
   3_occ:  0.332  69.578  -2.848  -1.165  -0.061  -0.000  -0.000  -0.000
   4_bss:  0.332  69.578  -2.656  -1.426  -0.210  -0.000  -0.000  -0.000
   4_xyz:  0.332  69.578  -2.656  -1.426  -0.210  -0.000  -0.000  -0.000
   4_adp:  0.332  69.578  -2.656  -1.426  -0.210  -0.000  -0.000  -0.000
   4_occ:  0.332  69.578  -2.656  -1.426  -0.210  -0.000  -0.000  -0.000
   5_bss:  0.321  62.351  -2.373  -1.281  -0.056  -0.000  -0.000  -0.000
   5_xyz:  0.321  62.351  -2.373  -1.281  -0.056  -0.000  -0.000  -0.000
   5_adp:  0.321  62.351  -2.373  -1.281  -0.056  -0.000  -0.000  -0.000
   5_occ:  0.321  62.351  -2.373  -1.281  -0.056  -0.000  -0.000  -0.000
   5_bss:  0.321  62.354  -2.162  -1.118   0.113  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.660 0.5381  0.6973    53736.613
   1_bss:  47.414 0.5519  0.7413    50456.754
   1_xyz:  30.003 0.7582  0.9626    22367.130
   1_adp:  31.354 0.7425  0.9450    24130.461
   1_occ:  31.432 0.7416  0.9436    24219.136
   2_bss:  31.014 0.7464  0.8960    23840.829
   2_xyz:  21.044 0.8507  0.9745    11677.098
   2_adp:  18.908 0.8720  0.9767    10017.932
   2_occ:  18.893 0.8722  0.9767    10003.496
   3_bss:  18.783 0.8731  0.9598     9910.614
   3_xyz:  16.048 0.8975  0.9731     7598.084
   3_adp:  15.665 0.9011  0.9653     7441.164
   3_occ:  15.669 0.9011  0.9651     7444.375
   4_bss:  15.651 0.9012  0.9630     7433.373
   4_xyz:  14.844 0.9080  0.9671     6827.071
   4_adp:  14.598 0.9102  0.9608     6706.921
   4_occ:  14.588 0.9103  0.9608     6699.657
   5_bss:  14.594 0.9102  0.9673     6697.987
   5_xyz:  14.691 0.9097  0.9662     6795.739
   5_adp:  14.788 0.9089  0.9575     6869.108
   5_occ:  14.785 0.9090  0.9575     6868.975
   5_bss:  14.790 0.9089  0.9637     6870.950
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7218e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7218e-01
   1_xyz:   1.487  0.013  0.091 15.380  0.006  4.114   1.1872e-01
   1_adp:   1.487  0.013  0.091 15.380  0.006  4.114   1.1872e-01
   1_occ:   1.487  0.013  0.091 15.380  0.006  4.114   1.1872e-01
   2_bss:   1.487  0.013  0.091 15.380  0.006  4.114   1.1872e-01
   2_xyz:   1.114  0.009  0.079 14.547  0.005  4.134   7.3088e-02
   2_adp:   1.114  0.009  0.079 14.547  0.005  4.134   7.3088e-02
   2_occ:   1.114  0.009  0.079 14.547  0.005  4.134   7.3088e-02
   3_bss:   1.114  0.009  0.079 14.547  0.005  4.134   7.3088e-02
   3_xyz:   1.088  0.009  0.079 14.646  0.004  4.117   6.8332e-02
   3_adp:   1.088  0.009  0.079 14.646  0.004  4.117   6.8332e-02
   3_occ:   1.088  0.009  0.079 14.646  0.004  4.117   6.8332e-02
   4_bss:   1.088  0.009  0.079 14.646  0.004  4.117   6.8332e-02
   4_xyz:   1.178  0.011  0.088 14.726  0.005  4.115   8.2548e-02
   4_adp:   1.178  0.011  0.088 14.726  0.005  4.115   8.2548e-02
   4_occ:   1.178  0.011  0.088 14.726  0.005  4.115   8.2548e-02
   5_bss:   1.178  0.011  0.088 14.726  0.005  4.115   8.2548e-02
   5_xyz:   1.017  0.008  0.078 14.327  0.004  4.115   6.0799e-02
   5_adp:   1.017  0.008  0.078 14.327  0.004  4.115   6.0799e-02
   5_occ:   1.017  0.008  0.078 14.327  0.004  4.115   6.0799e-02
   5_bss:   1.017  0.008  0.078 14.327  0.004  4.115   6.0799e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.623   2.4341e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.623   2.4341e-01
   1_xyz:   9.820  0.108  0.342 84.752  0.032  1.970   1.2160e-01
   1_adp:   9.820  0.108  0.342 84.752  0.032  1.970   1.2160e-01
   1_occ:   9.820  0.108  0.342 84.752  0.032  1.970   1.2160e-01
   2_bss:   9.820  0.108  0.342 84.752  0.032  1.970   1.2160e-01
   2_xyz:   7.645  0.062  0.258 81.202  0.047  2.285   1.4038e-01
   2_adp:   7.645  0.062  0.258 81.202  0.047  2.285   1.4038e-01
   2_occ:   7.645  0.062  0.258 81.202  0.047  2.285   1.4038e-01
   3_bss:   7.645  0.062  0.258 81.202  0.047  2.285   1.4038e-01
   3_xyz:   8.267  0.042  0.239 82.274  0.032  2.263   4.7417e-02
   3_adp:   8.267  0.042  0.239 82.274  0.032  2.263   4.7417e-02
   3_occ:   8.267  0.042  0.239 82.274  0.032  2.263   4.7417e-02
   4_bss:   8.267  0.042  0.239 82.274  0.032  2.263   4.7417e-02
   4_xyz:   8.670  0.053  0.317 82.395  0.035  2.325   6.2302e-02
   4_adp:   8.670  0.053  0.317 82.395  0.035  2.325   6.2302e-02
   4_occ:   8.670  0.053  0.317 82.395  0.035  2.325   6.2302e-02
   5_bss:   8.670  0.053  0.317 82.395  0.035  2.325   6.2302e-02
   5_xyz:   7.608  0.041  0.258 81.487  0.035  2.402   3.9675e-02
   5_adp:   7.608  0.041  0.258 81.487  0.035  2.402   3.9675e-02
   5_occ:   7.608  0.041  0.258 81.487  0.035  2.402   3.9675e-02
   5_bss:   7.608  0.041  0.258 81.487  0.035  2.402   3.9675e-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:  69.72   0.00  17.21  69.72   0.00  13.27  68.23   4.14  38.64
   1_occ:  69.72   0.00  17.21  69.72   0.00  13.27  68.23   4.14  38.64
   2_bss:  69.72   0.00  17.21  69.72   0.00  13.27  68.23   4.14  38.64
   2_xyz:  69.72   0.00  17.21  69.72   0.00  13.27  68.23   4.14  38.64
   2_adp:  71.22   1.03  17.18  69.71   1.03  12.91  71.22   5.73  40.38
   2_occ:  71.22   1.03  17.18  69.71   1.03  12.91  71.22   5.73  40.38
   3_bss:  71.22   1.03  17.18  69.71   1.03  12.91  71.22   5.73  40.38
   3_xyz:  71.22   1.03  17.18  69.71   1.03  12.91  71.22   5.73  40.38
   3_adp:  86.29   0.52  17.31  85.52   0.52  12.74  86.29   5.43  42.21
   3_occ:  86.29   0.52  17.31  85.52   0.52  12.74  86.29   5.43  42.21
   4_bss:  86.29   0.52  17.31  85.52   0.52  12.74  86.29   5.43  42.21
   4_xyz:  86.29   0.52  17.31  85.52   0.52  12.74  86.29   5.43  42.21
   4_adp:  88.04   0.00  16.97  87.35   0.00  12.48  88.04   0.00  41.39
   4_occ:  88.04   0.00  16.97  87.35   0.00  12.48  88.04   0.00  41.39
   5_bss:  88.04   0.00  16.97  87.35   0.00  12.48  88.04   0.00  41.39
   5_xyz:  88.04   0.00  16.97  87.35   0.00  12.48  88.04   0.00  41.39
   5_adp:  97.15   0.00  16.85  95.11   0.00  12.35  97.15   0.00  41.36
   5_occ:  97.15   0.00  16.85  95.11   0.00  12.35  97.15   0.00  41.36
   5_bss:  97.15   0.00  16.85  95.11   0.00  12.35  97.15   0.00  41.36
------------------------------------------------------------------------
 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:    1.495    0.020    0.445
   1_adp:    1.495    0.020    0.445
   1_occ:    1.495    0.020    0.445
   2_bss:    1.495    0.020    0.445
   2_xyz:    1.157    0.065    0.558
   2_adp:    1.157    0.065    0.558
   2_occ:    1.157    0.065    0.558
   3_bss:    1.157    0.065    0.558
   3_xyz:    1.168    0.038    0.628
   3_adp:    1.168    0.038    0.628
   3_occ:    1.168    0.038    0.628
   4_bss:    1.168    0.038    0.628
   4_xyz:    1.169    0.068    0.650
   4_adp:    1.169    0.068    0.650
   4_occ:    1.169    0.068    0.650
   5_bss:    1.169    0.068    0.650
   5_xyz:    1.303    0.090    0.656
   5_adp:    1.303    0.090    0.656
   5_occ:    1.303    0.090    0.656
   5_bss:    1.303    0.090    0.656
------------------------------------------------------------------------

CPU time actual refinement: 332.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/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_460/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_460/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.16 
  Macro-tasks:
    bulk solvent and scale       = 38.35  
    individual site refinement   = 138.78 
    weights calculation          = 29.27  
    collect and process          = 6.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 213.17 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 106.36 
    alpha_beta                      = 8.29   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 114.93 
    fmodel                         = 6.54   
    r_factors                      = 0.20   
    phase_errors                   = 10.83  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 250.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.718 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    638 calls, 106.00 s
gradients_fft:          583 calls, 101.62 s

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

# Date 2008-01-16 Time 04:53:27 PST -0800 (1200488007.06 s)
Start R-work = 0.4338, R-free = 0.4276 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.4242, R-free = 0.4152
Final R-work = 0.1147, R-free = 0.1629