# Date 2008-01-16 Time 05:54:37 PST -0800 (1200491677.33 s)
#phil __OFF__

Command line arguments: "../930.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18892
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 930

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.3993, 86.822, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01102
Completeness in resolution range: 0.977837
Completeness with d_max=infinity: 0.974723

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   2.0110

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01102
Completeness in resolution range: 0.977837
Completeness with d_max=infinity: 0.974723

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.3025 [2101/2125]  1892   209   9.9%
  bin  2:  4.3025 -  3.4281 [2029/2048]  1826   203  10.0%
  bin  3:  3.4281 -  2.9986 [1993/2012]  1790   203  10.2%
  bin  4:  2.9986 -  2.7262 [1967/1997]  1773   194   9.9%
  bin  5:  2.7262 -  2.5317 [1962/1981]  1766   196  10.0%
  bin  6:  2.5317 -  2.3831 [1952/1977]  1756   196  10.0%
  bin  7:  2.3831 -  2.2641 [1970/1998]  1773   197  10.0%
  bin  8:  2.2641 -  2.1659 [1927/1963]  1735   192  10.0%
  bin  9:  2.1659 -  2.0827 [1916/1958]  1727   189   9.9%
  bin 10:  2.0827 -  2.0110 [1772/1974]  1592   180  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/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:
        1.79 -     2.41: 7
        2.41 -     3.04: 2112
        3.04 -     3.66: 4579
        3.66 -     4.28: 8928
        4.28 -     4.90: 12299
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.793 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.350 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27920 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_930/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.3993 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3115   r_free= 0.3032   ksol= 0.00   Bsol= 0.00   scale= 0.966    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.005748                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7984 0.99   1372  153 0.2751 0.2712      6.3107      6.2482|
|  2:  4.7984 -  3.8290 0.99   1314  145 0.2367 0.2275      6.3671      6.3521|
|  3:  3.8290 -  3.3510 0.99   1287  144 0.2565 0.2577      6.2745      6.2911|
|  4:  3.3510 -  3.0474 0.99   1278  143 0.2976 0.2753      6.2147      6.1601|
|  5:  3.0474 -  2.8305 0.99   1270  140 0.3152 0.2875       6.058      6.0253|
|  6:  2.8305 -  2.6645 0.99   1276  140 0.3302 0.3267      6.0181      5.9739|
|  7:  2.6645 -  2.5317 0.99   1250  140 0.3293 0.3100      5.9559      5.9089|
|  8:  2.5317 -  2.4220 0.98   1265  140 0.3443 0.3238      5.9555      5.9661|
|  9:  2.4220 -  2.3291 0.98   1257  138 0.3431 0.3453      5.8813      5.9107|
| 10:  2.3291 -  2.2490 0.99   1234  138 0.3613 0.3498       5.912      5.8341|
| 11:  2.2490 -  2.1789 0.98   1249  142 0.3541 0.3362       5.834      5.8426|
| 12:  2.1789 -  2.1168 0.97   1242  134 0.3702 0.3759      5.8102      5.8636|
| 13:  2.1168 -  2.0612 1.00   1233  141 0.3689 0.3777      5.7298      5.7004|
| 14:  2.0612 -  2.0110 0.86   1103  121 0.3712 0.3839      5.6498      5.6329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.7984  1372   153  0.80  25.35   0.86     0.81      39733.09|
|  2:  4.7984 -  3.8290  1314   145  0.85  20.68   0.97     0.91      39838.73|
|  3:  3.8290 -  3.3510  1287   144  0.83  23.27   0.99     0.93      37724.89|
|  4:  3.3510 -  3.0474  1278   143  0.80  26.23   0.98     0.92      33314.82|
|  5:  3.0474 -  2.8305  1270   140  0.75  31.37   0.99     0.89      29139.73|
|  6:  2.8305 -  2.6645  1276   140  0.74  32.14   0.99     0.89      26255.67|
|  7:  2.6645 -  2.5317  1250   140  0.72  33.58   1.00     0.89      24490.26|
|  8:  2.5317 -  2.4220  1265   140  0.72  33.72   1.01     0.91      23272.21|
|  9:  2.4220 -  2.3291  1257   138  0.72  33.60   1.01     0.91      21280.27|
| 10:  2.3291 -  2.2490  1234   138  0.71  34.63   1.04     0.91      19961.71|
| 11:  2.2490 -  2.1789  1249   142  0.71  35.29   1.04     0.93      19216.45|
| 12:  2.1789 -  2.1168  1242   134  0.70  35.81   1.02     0.94      18719.21|
| 13:  2.1168 -  2.0612  1233   141  0.69  36.72   1.02     0.93      16853.66|
| 14:  2.0612 -  2.0110  1103   121  0.68  37.46   1.02     0.89      13840.56|
|alpha:            min =        0.81 max =            0.94 mean =         0.90|
|beta:             min =    13840.56 max =        39838.73 mean =     26275.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.98 mean =        31.25|
|phase err.(test): min =        0.00 max =           89.97 mean =        31.13|
|-----------------------------------------------------------------------------|

============================== 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 = 3.711005              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.834   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.069   (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 |  1.793 -  2.103:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.103 -  2.414:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.414 -  2.725:      148 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.725 -  3.036:     1964 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.036 -  3.346:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.346 -  3.657:     2738 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.657 -  3.968:     4601 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.968 -  4.279:     4327 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.279 -  4.589:     5603 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.589 -  4.900:     6696 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.793 |       0.144 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3115   r_free= 0.3032   ksol= 0.00   Bsol= 0.00   scale= 0.966    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.005748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2992   r_free= 0.2923   ksol= 0.32   Bsol= 56.57   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.54,-1.14,0.00,-0.00,-0.00); trace/3= -0.81                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.982029                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.449949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.953   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.344406              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.941   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2992      final r-factor (work) = 0.1761          |
| start r-factor (free) = 0.2923      final r-factor (free) = 0.1933          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5008 = 3.45 * 0.50 * 5.9937 + 1.00 * 0.1618                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8930 = 3.45 * 0.50 * 5.6968 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1761      final r-factor (work) = 0.1632          |
| start r-factor (free) = 0.1933      final r-factor (free) = 0.1957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9685 = 0.34 * 1.00 * 5.6968 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9180 = 0.34 * 1.00 * 5.4335 + 1.00 * 0.0466                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.21   16.51    None  None   None       |
|    all(noH): 2823   0      0.00    74.21   16.51    None  None   None       |
|    Sol.    : 438    0      6.97    63.68   37.53    None  None   None       |
|    Mac.    : 2385   0      0.00    74.21   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.421:  411   |   5:    37.106 -  44.527:  126        |
|      1:     7.421 -  14.842: 1376   |   6:    44.527 -  51.948:   79        |
|      2:    14.842 -  22.264:  499   |   7:    51.948 -  59.370:   60        |
|      3:    22.264 -  29.685:  136   |   8:    59.370 -  66.791:    8        |
|      4:    29.685 -  37.106:  127   |   9:    66.791 -  74.212:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1632 r_free = 0.1957             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1626 r_free = 0.1951             target_work(ml) = 5.437         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.1951   ksol= 0.32   Bsol= 56.57   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.54,-1.14,0.00,-0.00,-0.00); trace/3= -0.81                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.437441                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1618   r_free= 0.1930   ksol= 0.33   Bsol= 65.63   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.46,-1.47,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.434978                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.100039              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.141   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.215   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1618      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1930      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7830 = 2.10 * 0.50 * 5.4445 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6483 = 2.10 * 0.50 * 5.3247 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8884 = 0.35 * 1.00 * 5.3247 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8374 = 0.35 * 1.00 * 5.2045 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    78.06   16.92    None  None   None       |
|    all(noH): 2823   0      1.47    78.06   16.92    None  None   None       |
|    Sol.    : 438    0      5.80    72.02   39.34    None  None   None       |
|    Mac.    : 2385   0      1.47    78.06   12.80    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:     1.473 -   9.132:  819   |   5:    39.767 -  47.426:  105        |
|      1:     9.132 -  16.790: 1189   |   6:    47.426 -  55.085:   85        |
|      2:    16.790 -  24.449:  305   |   7:    55.085 -  62.744:   67        |
|      3:    24.449 -  32.108:  128   |   8:    62.744 -  70.403:   19        |
|      4:    32.108 -  39.767:  102   |   9:    70.403 -  78.062:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1215 r_free = 0.1597             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1595             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1595   ksol= 0.33   Bsol= 65.63   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.46,-1.47,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.190736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1595   ksol= 0.33   Bsol= 65.63   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.73,-1.12,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191283                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.005644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.132  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.492166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.306  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2767 = 2.01 * 0.50 * 5.2048 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2393 = 2.01 * 0.50 * 5.1629 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5499 = 0.49 * 1.00 * 5.1629 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5433 = 0.49 * 1.00 * 5.1489 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    81.28   16.78    None  None   None       |
|    all(noH): 2823   0      0.46    81.28   16.78    None  None   None       |
|    Sol.    : 438    0      3.59    73.87   39.37    None  None   None       |
|    Mac.    : 2385   0      0.46    81.28   12.63    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:     0.462 -   8.544:  743   |   5:    40.871 -  48.952:  101        |
|      1:     8.544 -  16.626: 1266   |   6:    48.952 -  57.034:   90        |
|      2:    16.626 -  24.707:  313   |   7:    57.034 -  65.116:   54        |
|      3:    24.707 -  32.789:  126   |   8:    65.116 -  73.197:   14        |
|      4:    32.789 -  40.871:  112   |   9:    73.197 -  81.279:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1571             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1571             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1571   ksol= 0.33   Bsol= 65.63   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.73,-1.12,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149895                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1571   ksol= 0.32   Bsol= 59.31   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.67,-0.88,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.959036              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.089  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.405  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6804 = 2.96 * 0.50 * 5.1494 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6697 = 2.96 * 0.50 * 5.1320 + 1.00 * 0.0769                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4197 = 0.27 * 1.00 * 5.1320 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4184 = 0.27 * 1.00 * 5.1296 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    82.74   16.37    None  None   None       |
|    all(noH): 2823   0      0.61    82.74   16.37    None  None   None       |
|    Sol.    : 438    0      4.82    74.51   38.10    None  None   None       |
|    Mac.    : 2385   0      0.61    82.74   12.38    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:     0.612 -   8.825:  849   |   5:    41.676 -  49.888:   96        |
|      1:     8.825 -  17.037: 1205   |   6:    49.888 -  58.101:   85        |
|      2:    17.037 -  25.250:  289   |   7:    58.101 -  66.314:   35        |
|      3:    25.250 -  33.463:  129   |   8:    66.314 -  74.527:    6        |
|      4:    33.463 -  41.676:  126   |   9:    74.527 -  82.739:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1573             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1574             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1574   ksol= 0.32   Bsol= 59.31   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.67,-0.88,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.128678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1573   ksol= 0.32   Bsol= 59.31   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.54,-0.66,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.128705                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.729520              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.618  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.144350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.256  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5135 = 1.73 * 0.50 * 5.1304 + 1.00 * 0.0769                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5064 = 1.73 * 0.50 * 5.1425 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7508 = 0.14 * 1.00 * 5.1425 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7514 = 0.14 * 1.00 * 5.1560 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    79.35   15.81    None  None   None       |
|    all(noH): 2823   0      1.14    79.35   15.81    None  None   None       |
|    Sol.    : 438    0      5.60    72.38   35.97    None  None   None       |
|    Mac.    : 2385   0      1.14    79.35   12.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.139 -   8.961:  899   |   5:    40.246 -  48.068:   91        |
|      1:     8.961 -  16.782: 1170   |   6:    48.068 -  55.889:   78        |
|      2:    16.782 -  24.603:  280   |   7:    55.889 -  63.710:   25        |
|      3:    24.603 -  32.425:  133   |   8:    63.710 -  71.532:    5        |
|      4:    32.425 -  40.246:  138   |   9:    71.532 -  79.353:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1587             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1588             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1588   ksol= 0.32   Bsol= 59.31   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.54,-0.66,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156736                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7984 0.99   1372  153 0.1036 0.1315      5.4163      5.5247|
|  2:  4.7984 -  3.8290 0.99   1314  145 0.0894 0.1117      5.4651      5.6494|
|  3:  3.8290 -  3.3510 0.99   1287  144 0.1048 0.1527      5.4836       5.869|
|  4:  3.3510 -  3.0474 0.99   1278  143 0.1227 0.1516      5.4627      5.5923|
|  5:  3.0474 -  2.8305 0.99   1270  140 0.1349 0.1716      5.3551       5.541|
|  6:  2.8305 -  2.6645 0.99   1276  140 0.1231 0.1925      5.2326       5.485|
|  7:  2.6645 -  2.5317 0.99   1250  140 0.1287 0.1703      5.1858      5.3937|
|  8:  2.5317 -  2.4220 0.98   1265  140 0.1175 0.1742      5.0901      5.3827|
|  9:  2.4220 -  2.3291 0.98   1257  138 0.1168 0.1705        5.04      5.2677|
| 10:  2.3291 -  2.2490 0.99   1234  138 0.1166 0.1870      4.9947      5.2642|
| 11:  2.2490 -  2.1789 0.98   1249  142 0.1183 0.1731      4.9568      5.2365|
| 12:  2.1789 -  2.1168 0.97   1242  134 0.1144 0.1736      4.9079      5.2303|
| 13:  2.1168 -  2.0612 1.00   1233  141 0.1128 0.1664      4.8047        5.07|
| 14:  2.0612 -  2.0110 0.86   1103  121 0.1081 0.1766      4.6723      4.9638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.7984  1372   153  0.94   9.51   0.97     0.94       7564.52|
|  2:  4.7984 -  3.8290  1314   145  0.95   8.10   1.00     0.98       9242.81|
|  3:  3.8290 -  3.3510  1287   144  0.94  11.02   1.01     1.00      10536.36|
|  4:  3.3510 -  3.0474  1278   143  0.92  13.51   0.99     0.98      10291.61|
|  5:  3.0474 -  2.8305  1270   140  0.90  15.92   0.98     0.96       8622.71|
|  6:  2.8305 -  2.6645  1276   140  0.90  15.86   0.98     0.95       7197.35|
|  7:  2.6645 -  2.5317  1250   140  0.90  15.92   0.98     0.95       6364.54|
|  8:  2.5317 -  2.4220  1265   140  0.91  14.79   0.98     0.96       5416.71|
|  9:  2.4220 -  2.3291  1257   138  0.91  15.36   0.99     0.95       5036.76|
| 10:  2.3291 -  2.2490  1234   138  0.90  15.76   0.99     0.95       4563.28|
| 11:  2.2490 -  2.1789  1249   142  0.90  16.29   0.98     0.94       4397.31|
| 12:  2.1789 -  2.1168  1242   134  0.91  15.14   0.99     0.98       4075.08|
| 13:  2.1168 -  2.0612  1233   141  0.91  15.41   0.99     0.98       3395.32|
| 14:  2.0612 -  2.0110  1103   121  0.91  14.50   0.96     0.92       2492.17|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2492.17 max =        10536.36 mean =      6445.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1587   ksol= 0.32   Bsol= 59.27   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.47,-0.54,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1587   ksol= 0.32   Bsol= 59.27   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.47,-0.54,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156755                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7984 0.99   1372  153 0.1036 0.1316      5.4165      5.5249|
|  2:  4.7984 -  3.8290 0.99   1314  145 0.0894 0.1117      5.4651      5.6493|
|  3:  3.8290 -  3.3510 0.99   1287  144 0.1048 0.1527      5.4835       5.869|
|  4:  3.3510 -  3.0474 0.99   1278  143 0.1227 0.1516      5.4627      5.5923|
|  5:  3.0474 -  2.8305 0.99   1270  140 0.1350 0.1716      5.3552       5.541|
|  6:  2.8305 -  2.6645 0.99   1276  140 0.1231 0.1924      5.2326      5.4848|
|  7:  2.6645 -  2.5317 0.99   1250  140 0.1287 0.1703      5.1857      5.3935|
|  8:  2.5317 -  2.4220 0.98   1265  140 0.1175 0.1743        5.09      5.3825|
|  9:  2.4220 -  2.3291 0.98   1257  138 0.1168 0.1705        5.04      5.2678|
| 10:  2.3291 -  2.2490 0.99   1234  138 0.1166 0.1871       4.995      5.2644|
| 11:  2.2490 -  2.1789 0.98   1249  142 0.1183 0.1732      4.9571       5.237|
| 12:  2.1789 -  2.1168 0.97   1242  134 0.1143 0.1738       4.908      5.2307|
| 13:  2.1168 -  2.0612 1.00   1233  141 0.1128 0.1663      4.8046      5.0698|
| 14:  2.0612 -  2.0110 0.86   1103  121 0.1081 0.1765      4.6721      4.9635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.7984  1372   153  0.94   9.52   0.97     0.94       7567.60|
|  2:  4.7984 -  3.8290  1314   145  0.95   8.10   1.00     0.98       9243.53|
|  3:  3.8290 -  3.3510  1287   144  0.94  11.02   1.01     1.00      10534.43|
|  4:  3.3510 -  3.0474  1278   143  0.92  13.51   0.99     0.98      10291.31|
|  5:  3.0474 -  2.8305  1270   140  0.90  15.92   0.99     0.96       8620.32|
|  6:  2.8305 -  2.6645  1276   140  0.90  15.86   0.98     0.95       7196.47|
|  7:  2.6645 -  2.5317  1250   140  0.90  15.92   0.98     0.96       6362.04|
|  8:  2.5317 -  2.4220  1265   140  0.91  14.79   0.98     0.96       5416.00|
|  9:  2.4220 -  2.3291  1257   138  0.91  15.36   0.99     0.96       5036.78|
| 10:  2.3291 -  2.2490  1234   138  0.90  15.76   0.99     0.95       4565.96|
| 11:  2.2490 -  2.1789  1249   142  0.90  16.29   0.99     0.95       4400.82|
| 12:  2.1789 -  2.1168  1242   134  0.91  15.14   0.99     0.98       4077.00|
| 13:  2.1168 -  2.0612  1233   141  0.91  15.41   0.99     0.98       3394.38|
| 14:  2.0612 -  2.0110  1103   121  0.91  14.50   0.96     0.92       2489.91|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2489.91 max =        10534.43 mean =      6445.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    79.31   15.77    None  None   None       |
|    all(noH): 2823   0      1.10    79.31   15.77    None  None   None       |
|    Sol.    : 438    0      5.56    72.34   35.93    None  None   None       |
|    Mac.    : 2385   0      1.10    79.31   12.07    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:     1.099 -   8.921:  899   |   5:    40.206 -  48.028:   91        |
|      1:     8.921 -  16.742: 1170   |   6:    48.028 -  55.849:   78        |
|      2:    16.742 -  24.564:  280   |   7:    55.849 -  63.671:   25        |
|      3:    24.564 -  32.385:  133   |   8:    63.671 -  71.492:    5        |
|      4:    32.385 -  40.206:  138   |   9:    71.492 -  79.313:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 4.829
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 302
   mapped sites are within: 0.700 - 4.829

peak=    5.786 closest distance to " NH2 ARG A  56 " =    2.370
peak=    5.772 closest distance to " CB  GLN A 223 " =    1.410
peak=    5.474 closest distance to " CG  PRO A  54 " =    1.357
peak=    4.986 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.852 closest distance to " O   HOH Z 126 " =    1.823
peak=    4.813 closest distance to " CB  SER A  63 " =    1.229
peak=    4.706 closest distance to " CG  PRO A 198 " =    1.361
peak=    4.701 closest distance to " O   HOH Z 232 " =    2.292
peak=    4.621 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.606 closest distance to " CB  PRO A  54 " =    0.941
peak=    4.594 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.592 closest distance to " C   PRO A 198 " =    1.510
peak=    4.569 closest distance to " CG  PRO A  90 " =    1.191
peak=    4.468 closest distance to " CB  GLN A 183 " =    1.217
peak=    4.450 closest distance to " CZ  PHE A 218 " =    1.071
peak=    4.446 closest distance to " CB  TYR A 169 " =    0.738
peak=    4.445 closest distance to " CB  ARG A 190 " =    1.649
peak=    4.412 closest distance to " O   HOH Z 298 " =    1.936
peak=    4.402 closest distance to " O   HOH Z 369 " =    2.039
peak=    4.381 closest distance to " CB  ASN A 148 " =    1.463
peak=    4.375 closest distance to " CB  ASN A 187 " =    1.287
peak=    4.371 closest distance to " CB  LEU A 228 " =    1.041
peak=    4.349 closest distance to " CG  PRO A 243 " =    1.068
peak=    4.283 closest distance to " NH2 ARG A 156 " =    1.167
peak=    4.282 closest distance to " O   HOH Z 236 " =    1.956
peak=    4.281 closest distance to " CA  TYR A  30 " =    0.919
peak=    4.255 closest distance to " O   HOH Z 234 " =    3.866
peak=    4.212 closest distance to " ND2 ASN A 187 " =    1.523
peak=    4.186 closest distance to " CB  ARG A  79 " =    1.325
peak=    4.137 closest distance to " CB  GLU A 128 " =    1.030
peak=    4.121 closest distance to " CB  TRP A 266 " =    0.913
peak=    4.118 closest distance to " CB  GLU A 277 " =    3.692
peak=    4.115 closest distance to " CD1 LEU A 300 " =    1.233
peak=    4.108 closest distance to " O   HOH Z  15 " =    2.154
peak=    4.066 closest distance to " CB  ASP A 124 " =    0.708
peak=    4.053 closest distance to " O   HOH Z  40 " =    1.818
peak=    4.050 closest distance to " OD1 ASN A  69 " =    2.569
peak=    4.015 closest distance to " O   HOH Z 423 " =    1.923
peak=    3.996 closest distance to " O   HOH Z  78 " =    1.669
peak=    3.979 closest distance to " O   HOH Z 303 " =    2.144
peak=    3.976 closest distance to " CB  VAL A 202 " =    1.536
peak=    3.967 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.963 closest distance to " O   HOH Z 189 " =    2.610
peak=    3.956 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.947 closest distance to " CB  GLU A  46 " =    0.958
peak=    3.938 closest distance to " O   HOH Z 158 " =    3.098
peak=    3.932 closest distance to " O   HOH Z 250 " =    1.532
peak=    3.925 closest distance to " O   HOH Z 197 " =    2.950
peak=    3.900 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.899 closest distance to " O   HOH Z  21 " =    1.843
peak=    3.891 closest distance to " CG2 VAL A 257 " =    0.931
peak=    3.884 closest distance to " O   HOH Z  63 " =    2.099
peak=    3.878 closest distance to " CA  ALA A  51 " =    0.852
peak=    3.873 closest distance to " CA  ARG A 195 " =    1.205
peak=    3.871 closest distance to " O   HOH Z 147 " =    1.840
peak=    3.870 closest distance to " O   HOH Z 368 " =    2.050
peak=    3.854 closest distance to " O   HOH Z  19 " =    2.382
peak=    3.850 closest distance to " CA  ARG A  36 " =    1.130
peak=    3.841 closest distance to " CA  THR A 264 " =    0.909
peak=    3.839 closest distance to " CB  ILE A 120 " =    1.151
peak=    3.836 closest distance to " CB  SER A   3 " =    1.336
peak=    3.826 closest distance to " NH1AARG A 145 " =    1.277
peak=    3.801 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.799 closest distance to " O   HOH Z  44 " =    2.168
peak=    3.793 closest distance to " O   HOH Z 261 " =    2.029
peak=    3.791 closest distance to " O   HOH Z 346 " =    1.568
peak=    3.767 closest distance to " CB  VAL A 265 " =    1.259
peak=    3.767 closest distance to " CG2 ILE A 120 " =    1.118
peak=    3.760 closest distance to " O   HOH Z 272 " =    1.895
peak=    3.760 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.757 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.747 closest distance to " CA  ASP A 124 " =    0.720
peak=    3.747 closest distance to " O   SER A  87 " =    2.284
peak=    3.744 closest distance to " O   HOH Z 265 " =    2.286
peak=    3.744 closest distance to " CA  ASP A 191 " =    0.776
peak=    3.737 closest distance to " O   HOH Z 402 " =    1.491
peak=    3.735 closest distance to " O   HOH Z 389 " =    1.975
peak=    3.734 closest distance to " CG1BVAL A  72 " =    1.758
peak=    3.726 closest distance to " CD  LYS A 166 " =    1.298
peak=    3.721 closest distance to " O   HOH Z 214 " =    2.062
peak=    3.720 closest distance to " O   HOH Z 203 " =    1.852
peak=    3.703 closest distance to " CA  ASN A 215 " =    1.155
peak=    3.695 closest distance to " O   MET A 105 " =    1.834
peak=    3.690 closest distance to " O   HOH Z 193 " =    2.035
peak=    3.676 closest distance to " O   HOH Z 406 " =    1.665
peak=    3.670 closest distance to " O   HOH Z  43 " =    1.942
peak=    3.669 closest distance to " CB  ASN A 142 " =    1.041
peak=    3.668 closest distance to " O   HOH Z  66 " =    2.181
peak=    3.667 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.663 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.655 closest distance to " O   TRP A 274 " =    1.915
peak=    3.655 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.650 closest distance to " CA  SER A  87 " =    1.063
peak=    3.635 closest distance to " O   HOH Z 426 " =    1.576
peak=    3.633 closest distance to " N   GLY A  98 " =    1.129
peak=    3.630 closest distance to " O   HOH Z 383 " =    2.023
peak=    3.629 closest distance to " O   HOH Z 234 " =    1.821
peak=    3.626 closest distance to " CB  ALA A 291 " =    1.241
peak=    3.618 closest distance to " CD1 LEU A  96 " =    0.716
peak=    3.617 closest distance to " CB  MET A  40 " =    0.798
peak=    3.616 closest distance to " O   HOH Z 427 " =    3.120
peak=    3.615 closest distance to " CD1 ILE A 106 " =    0.865
peak=    3.610 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.609 closest distance to " CZ  PHE A 192 " =    0.958
peak=    3.608 closest distance to " O   HOH Z   1 " =    2.150
peak=    3.606 closest distance to " CG1 ILE A  33 " =    1.301
peak=    3.604 closest distance to " O   HOH Z 133 " =    2.390
peak=    3.598 closest distance to " O   THR A 251 " =    1.167
peak=    3.598 closest distance to " NE2 GLN A  11 " =    1.059
peak=    3.596 closest distance to " CD  ARG A 159 " =    0.778
peak=    3.594 closest distance to " O   HOH Z 280 " =    2.972
peak=    3.594 closest distance to " CA  THR A 221 " =    0.922
peak=    3.592 closest distance to " O   HOH Z 108 " =    2.875
peak=    3.592 closest distance to " CG2 THR A 221 " =    0.960
peak=    3.568 closest distance to " O   HOH Z 180 " =    2.088
peak=    3.567 closest distance to " CD2 LEU A 297 " =    0.852
peak=    3.567 closest distance to " CB  LEU A 143 " =    1.115
peak=    3.564 closest distance to " O   HOH Z  97 " =    1.966
peak=    3.563 closest distance to " O   HOH Z 344 " =    3.246
peak=    3.563 closest distance to " NE2 GLN A  77 " =    3.389
peak=    3.554 closest distance to " O   HOH Z 142 " =    1.591
peak=    3.554 closest distance to " N   ARG A 156 " =    1.460
peak=    3.551 closest distance to " CD2 TRP A 179 " =    1.288
peak=    3.546 closest distance to " O   HOH Z 172 " =    3.853
peak=    3.543 closest distance to " O   HOH Z  10 " =    1.795
peak=    3.530 closest distance to " O   HOH Z 294 " =    1.540
peak=    3.530 closest distance to " CB  GLN A 103 " =    0.841
peak=    3.523 closest distance to " O   HOH Z 185 " =    1.824
peak=    3.522 closest distance to " O   HOH Z 305 " =    3.728
peak=    3.522 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.520 closest distance to " CD  ARG A  66 " =    2.478
peak=    3.518 closest distance to " CG AARG A 275 " =    1.127
peak=    3.513 closest distance to " CB  TRP A 179 " =    1.421
peak=    3.508 closest distance to " CB  MET A  47 " =    0.975
peak=    3.507 closest distance to " NH2BARG A 145 " =    2.180
peak=    3.507 closest distance to " OD2 ASP A 286 " =    2.922
peak=    3.502 closest distance to " CB  ALA A 242 " =    0.852
peak=    3.500 closest distance to " O   HOH Z 213 " =    1.876
peak=    3.497 closest distance to " O   HOH Z 316 " =    3.179
peak=    3.487 closest distance to " O   HOH Z 135 " =    1.735
peak=    3.484 closest distance to " CB  SER A 141 " =    0.989
peak=    3.480 closest distance to " CA  ASP A 162 " =    1.000
peak=    3.480 closest distance to " O   HOH Z 295 " =    1.507
peak=    3.471 closest distance to " O   HOH Z 421 " =    1.737
peak=    3.469 closest distance to " O   HOH Z 411 " =    3.789
peak=    3.468 closest distance to " O   HOH Z 313 " =    1.874
peak=    3.462 closest distance to " CB  ALA A 114 " =    1.110
peak=    3.458 closest distance to " N   ASN A  39 " =    1.273
peak=    3.456 closest distance to " O   HOH Z 403 " =    1.383
peak=    3.445 closest distance to " O   HOH Z 368 " =    3.650
peak=    3.441 closest distance to " CB  PRO A 198 " =    1.034
peak=    3.435 closest distance to " O   HOH Z 411 " =    1.811
peak=    3.433 closest distance to " O   HOH Z  62 " =    2.227
peak=    3.425 closest distance to " O   HOH Z 132 " =    2.722
peak=    3.423 closest distance to " CB  ALA A   1 " =    4.829
peak=    3.421 closest distance to " CG  GLN A  11 " =    1.515
peak=    3.417 closest distance to " CD  ARG A 219 " =    1.051
peak=    3.417 closest distance to " O  BHOH Z 338 " =    2.358
peak=    3.416 closest distance to " O   HOH Z 425 " =    1.975
peak=    3.412 closest distance to " O   HOH Z 285 " =    2.879
peak=    3.402 closest distance to " CG  MET A 185 " =    1.137
peak=    3.400 closest distance to " OD1 ASN A 217 " =    1.678
peak=    3.398 closest distance to " N   ASN A 127 " =    1.236
peak=    3.396 closest distance to " CB  ALA A 248 " =    0.984
peak=    3.395 closest distance to " NZ  LYS A 117 " =    3.264
peak=    3.394 closest distance to " O   HOH Z 148 " =    3.265
peak=    3.389 closest distance to " CA  ALA A 233 " =    1.457
peak=    3.388 closest distance to " CB  SER A 216 " =    0.762
peak=    3.382 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.381 closest distance to " N   VAL A 126 " =    1.426
peak=    3.377 closest distance to " C   TYR A 214 " =    1.548
peak=    3.375 closest distance to " CZ2 TRP A 179 " =    1.769
peak=    3.374 closest distance to " CG  LYS A  76 " =    1.004
peak=    3.372 closest distance to " OG1 THR A 294 " =    2.453
peak=    3.372 closest distance to " CA  MET A 105 " =    0.967
peak=    3.368 closest distance to " CA  GLY A 241 " =    0.767
peak=    3.362 closest distance to " CG2 THR A 220 " =    0.786
peak=    3.354 closest distance to " CB  SER A 212 " =    1.207
peak=    3.353 closest distance to " CD BLYS A 290 " =    1.002
peak=    3.350 closest distance to " O   HOH Z  97 " =    2.510
peak=    3.345 closest distance to " O   ALA A 165 " =    1.464
peak=    3.342 closest distance to " ND1 HIS A  81 " =    1.694
peak=    3.341 closest distance to " CG1 ILE A 151 " =    1.037
peak=    3.339 closest distance to " O   HOH Z 248 " =    1.688
peak=    3.334 closest distance to " O   HOH Z 171 " =    2.437
peak=    3.331 closest distance to " O   HOH Z 387 " =    3.010
peak=    3.325 closest distance to " CA  ALA A  84 " =    1.243
peak=    3.321 closest distance to " O   HOH Z 126 " =    1.693
peak=    3.320 closest distance to " O   HOH Z 371 " =    3.092
peak=    3.317 closest distance to " CA  ASN A 176 " =    1.245
peak=    3.315 closest distance to " O   HOH Z  48 " =    1.796
peak=    3.308 closest distance to " CG BARG A 275 " =    1.389
peak=    3.308 closest distance to " O   HOH Z 287 " =    1.785
peak=    3.307 closest distance to " CB  GLN A  89 " =    1.204
peak=    3.307 closest distance to " CG2 VAL A 197 " =    1.076
peak=    3.302 closest distance to " CG  LEU A 167 " =    1.217
peak=    3.301 closest distance to " O   HOH Z  88 " =    3.416
peak=    3.299 closest distance to " O   HOH Z 193 " =    1.695
peak=    3.297 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.295 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.289 closest distance to " CB  ARG A 139 " =    0.882
peak=    3.286 closest distance to " O   HOH Z 171 " =    3.894
peak=    3.285 closest distance to " O   HOH Z  68 " =    1.710
peak=    3.285 closest distance to " CA  ASN A 217 " =    1.297
peak=    3.284 closest distance to " O   HOH Z 273 " =    2.796
peak=    3.276 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.275 closest distance to " O   HOH Z  20 " =    1.623
peak=    3.268 closest distance to " O   HOH Z 227 " =    1.703
peak=    3.267 closest distance to " O   THR A 220 " =    1.217
peak=    3.266 closest distance to " CB  ASN A 215 " =    1.168
peak=    3.265 closest distance to " ND2 ASN A 249 " =    0.866
peak=    3.261 closest distance to " CA  VAL A  41 " =    0.874
peak=    3.260 closest distance to " CB  TYR A 116 " =    0.824
peak=    3.260 closest distance to " CB  ASP A 298 " =    1.202
peak=    3.259 closest distance to " CA  GLU A 152 " =    0.895
peak=    3.258 closest distance to " CD  LYS A 119 " =    1.468
peak=    3.258 closest distance to " O   ASP A 124 " =    1.146
peak=    3.256 closest distance to " CA  ILE A 106 " =    0.803
peak=    3.253 closest distance to " CZ  PHE A  38 " =    1.275
peak=    3.253 closest distance to " CG2 ILE A  20 " =    1.280
peak=    3.247 closest distance to " CG  MET A 185 " =    0.993
peak=    3.246 closest distance to " CB  ALA A 248 " =    1.228
peak=    3.245 closest distance to " O   HOH Z  49 " =    2.318
peak=    3.242 closest distance to " O   HOH Z 173 " =    2.030
peak=    3.240 closest distance to " O   TYR A 116 " =    1.339
peak=    3.234 closest distance to " CA  THR A 221 " =    1.317
peak=    3.234 closest distance to " O   HOH Z 245 " =    1.345
peak=    3.233 closest distance to " CA  GLN A 223 " =    0.875
peak=    3.232 closest distance to " CG  GLU A  37 " =    0.853
peak=    3.231 closest distance to " CA  ASP A 140 " =    1.257
peak=    3.225 closest distance to " OG BSER A 164 " =    2.434
peak=    3.223 closest distance to " CA  MET A  40 " =    1.107
peak=    3.222 closest distance to " CB  SER A  26 " =    1.726
peak=    3.219 closest distance to " CA  TYR A 116 " =    1.421
peak=    3.219 closest distance to " O   HOH Z 163 " =    1.626
peak=    3.216 closest distance to " O   HOH Z  88 " =    1.667
peak=    3.211 closest distance to " CB  LYS A 193 " =    0.922
peak=    3.210 closest distance to " CB  ALA A  34 " =    0.994
peak=    3.208 closest distance to " CA  ALA A 154 " =    0.908
peak=    3.201 closest distance to " ND2 ASN A 110 " =    1.574
peak=    3.198 closest distance to " CB  ALA A   9 " =    1.566
peak=    3.197 closest distance to " C   SER A  32 " =    1.022
peak=    3.196 closest distance to " CB  GLN A 278 " =    0.846
peak=    3.193 closest distance to " CB  SER A  28 " =    1.074
peak=    3.193 closest distance to " N   SER A 135 " =    1.394
peak=    3.192 closest distance to " CE  MET A 113 " =    1.688
peak=    3.192 closest distance to " O   HOH Z  49 " =    3.076
peak=    3.192 closest distance to " O   HOH Z 188 " =    2.234
peak=    3.186 closest distance to " CG2BVAL A  41 " =    0.843
peak=    3.185 closest distance to " CB  TYR A 169 " =    1.223
peak=    3.184 closest distance to " O   HOH Z  80 " =    1.633
peak=    3.183 closest distance to " CB  LEU A  83 " =    0.784
peak=    3.181 closest distance to " O   HOH Z 359 " =    1.519
peak=    3.181 closest distance to " O   HOH Z 199 " =    1.598
peak=    3.178 closest distance to " O   HOH Z 133 " =    1.610
peak=    3.177 closest distance to " O   HOH Z 345 " =    1.739
peak=    3.175 closest distance to " CB  PHE A 204 " =    0.892
peak=    3.167 closest distance to " CA  GLY A 267 " =    0.975
peak=    3.164 closest distance to " CG BARG A 102 " =    1.891
peak=    3.164 closest distance to " O   HOH Z 128 " =    2.220
peak=    3.163 closest distance to " OG  SER A  28 " =    1.532
peak=    3.163 closest distance to " CB  PHE A  16 " =    1.084
peak=    3.163 closest distance to " O   HOH Z 384 " =    2.743
peak=    3.158 closest distance to " O   HOH Z 116 " =    1.824
peak=    3.153 closest distance to " OG BSER A 134 " =    2.878
peak=    3.153 closest distance to " N   ARG A 190 " =    1.000
peak=    3.150 closest distance to " O   ALA A 158 " =    1.246
peak=    3.147 closest distance to " O   HOH Z 313 " =    1.754
peak=    3.146 closest distance to " CB  PRO A 243 " =    1.673
peak=    3.146 closest distance to " CA  ALA A 248 " =    1.181
peak=    3.145 closest distance to " O   HOH Z 419 " =    1.859
peak=    3.143 closest distance to " OG  SER A 245 " =    1.654
peak=    3.143 closest distance to " O   HOH Z 353 " =    2.694
peak=    3.141 closest distance to " OG  SER A  22 " =    2.696
peak=    3.138 closest distance to " N   TYR A  15 " =    0.700
peak=    3.131 closest distance to " O   HOH Z 139 " =    4.701
peak=    3.123 closest distance to " ND1 HIS A  86 " =    1.687
peak=    3.119 closest distance to " CB  THR A 157 " =    1.118
peak=    3.115 closest distance to " CB  SER A 210 " =    0.779
peak=    3.113 closest distance to " O   HOH Z 250 " =    1.442
peak=    3.111 closest distance to " NZ  LYS A  48 " =    1.310
peak=    3.111 closest distance to " CA  GLN A  88 " =    1.307
peak=    3.111 closest distance to " OG1 THR A 294 " =    1.678
peak=    3.109 closest distance to " O   ASN A  74 " =    1.570
peak=    3.106 closest distance to " N   GLN A 278 " =    0.987
peak=    3.105 closest distance to " O   HOH Z 417 " =    3.265
peak=    3.103 closest distance to " O   HOH Z 299 " =    2.477
peak=    3.102 closest distance to " OH  TYR A  30 " =    1.098
peak=    3.096 closest distance to " O   ASN A 209 " =    1.285
peak=    3.092 closest distance to " O   HOH Z 329 " =    3.846
peak=    3.088 closest distance to " CD1AILE A 234 " =    0.927
peak=    3.060 closest distance to " CA  ALA A 158 " =    1.185
peak=    3.057 closest distance to " O   HOH Z 425 " =    1.312
peak=    3.055 closest distance to " OH  TYR A 116 " =    1.049
peak=    3.015 closest distance to " O   HOH Z 361 " =    3.193

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 5.519
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 196
   mapped sites are within: 0.782 - 5.519

peak=   -4.654 closest distance to " CD  GLN A  58 " =    0.909
peak=   -4.603 closest distance to " O   HOH Z 290 " =    1.023
peak=   -4.545 closest distance to " CB  PRO A 243 " =    2.655
peak=   -4.498 closest distance to " O   HOH Z 266 " =    5.151
peak=   -4.325 closest distance to " CD  ARG A 156 " =    2.083
peak=   -4.193 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -4.182 closest distance to " O   VAL A  67 " =    2.640
peak=   -4.065 closest distance to " C   HIS A 108 " =    1.101
peak=   -4.063 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -4.059 closest distance to " O   ILE A 109 " =    2.624
peak=   -4.012 closest distance to " O   HOH Z  10 " =    1.594
peak=   -4.009 closest distance to " OG  SER A  97 " =    2.313
peak=   -3.975 closest distance to " O   HOH Z 196 " =    1.967
peak=   -3.974 closest distance to " CG  GLN A 223 " =    1.864
peak=   -3.962 closest distance to " N   ALA A  43 " =    2.580
peak=   -3.948 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.945 closest distance to " O   HOH Z 372 " =    2.462
peak=   -3.909 closest distance to " O   HOH Z 231 " =    2.323
peak=   -3.900 closest distance to " O   HOH Z  52 " =    1.431
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    1.573
peak=   -3.867 closest distance to " O   HOH Z 114 " =    3.339
peak=   -3.856 closest distance to " CD  ARG A  14 " =    3.294
peak=   -3.794 closest distance to " O   HOH Z  73 " =    2.246
peak=   -3.776 closest distance to " CD  GLN A 223 " =    0.800
peak=   -3.764 closest distance to " NH2AARG A 275 " =    5.409
peak=   -3.757 closest distance to " CE2 TYR A  30 " =    2.767
peak=   -3.750 closest distance to " O   HOH Z 351 " =    1.448
peak=   -3.748 closest distance to " CD2 PHE A  61 " =    2.499
peak=   -3.738 closest distance to " O   HOH Z 394 " =    1.474
peak=   -3.734 closest distance to " CG2 ILE A 263 " =    2.388
peak=   -3.724 closest distance to " CG1 VAL A 250 " =    2.719
peak=   -3.701 closest distance to " NH2 ARG A  79 " =    1.588
peak=   -3.690 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.687 closest distance to " ND2 ASN A  45 " =    1.083
peak=   -3.670 closest distance to " O   HOH Z 353 " =    2.176
peak=   -3.669 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.654 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.653 closest distance to " CG  ARG A 269 " =    2.400
peak=   -3.634 closest distance to " CD2 PHE A 192 " =    2.038
peak=   -3.626 closest distance to " CA  GLY A 241 " =    3.157
peak=   -3.615 closest distance to " O   HOH Z 311 " =    3.703
peak=   -3.613 closest distance to " NH2 ARG A 159 " =    2.321
peak=   -3.612 closest distance to " CD1 PHE A  59 " =    1.990
peak=   -3.610 closest distance to " O   VAL A  67 " =    2.840
peak=   -3.610 closest distance to " CB  ASP A 132 " =    2.337
peak=   -3.607 closest distance to " CG1 VAL A 112 " =    2.833
peak=   -3.605 closest distance to " O   HOH Z 211 " =    1.626
peak=   -3.600 closest distance to " NE2 GLN A 103 " =    1.791
peak=   -3.598 closest distance to " O   HOH Z 377 " =    1.916
peak=   -3.595 closest distance to " CD1 LEU A 101 " =    2.454
peak=   -3.590 closest distance to " O   HOH Z 389 " =    1.857
peak=   -3.584 closest distance to " O   HOH Z 377 " =    1.333
peak=   -3.578 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.574 closest distance to " OXT GLY A 302 " =    2.889
peak=   -3.570 closest distance to " CD1 ILE A 239 " =    2.086
peak=   -3.566 closest distance to " O   HOH Z 185 " =    2.436
peak=   -3.556 closest distance to " CA  ASP A 298 " =    1.128
peak=   -3.544 closest distance to " CD2 LEU A 300 " =    2.909
peak=   -3.538 closest distance to " C   SER A 206 " =    1.506
peak=   -3.530 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.528 closest distance to " N   SER A 212 " =    1.944
peak=   -3.518 closest distance to " C   ASN A 187 " =    1.946
peak=   -3.512 closest distance to " CB  ALA A  43 " =    2.563
peak=   -3.508 closest distance to " O   ALA A  10 " =    1.703
peak=   -3.503 closest distance to " O   HOH Z  38 " =    1.359
peak=   -3.502 closest distance to " O   HOH Z 198 " =    2.201
peak=   -3.501 closest distance to " CG  ARG A  66 " =    2.453
peak=   -3.498 closest distance to " ND2 ASN A 249 " =    2.435
peak=   -3.498 closest distance to " C   ALA A 158 " =    1.376
peak=   -3.485 closest distance to " N   ALA A 226 " =    2.125
peak=   -3.483 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.463 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.457 closest distance to " O   HOH Z  60 " =    2.377
peak=   -3.452 closest distance to " OG BSER A 134 " =    1.273
peak=   -3.451 closest distance to " CD1 LEU A 101 " =    2.956
peak=   -3.450 closest distance to " CB  ALA A 291 " =    2.208
peak=   -3.449 closest distance to " CE3 TRP A 150 " =    2.094
peak=   -3.449 closest distance to " CB  PRO A 163 " =    2.553
peak=   -3.447 closest distance to " CZ3 TRP A 274 " =    0.992
peak=   -3.444 closest distance to " CB  ASN A  39 " =    2.307
peak=   -3.441 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.441 closest distance to " CG  MET A 105 " =    0.942
peak=   -3.426 closest distance to " O   HOH Z 241 " =    1.238
peak=   -3.425 closest distance to " O   HOH Z  43 " =    1.541
peak=   -3.424 closest distance to " C   ASN A 285 " =    2.454
peak=   -3.420 closest distance to " O   HOH Z  76 " =    2.047
peak=   -3.417 closest distance to " O   HOH Z 292 " =    4.637
peak=   -3.413 closest distance to " CG  GLU A 277 " =    1.125
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.816
peak=   -3.408 closest distance to " O   HOH Z 407 " =    3.340
peak=   -3.408 closest distance to " SG ACYS A 201 " =    2.077
peak=   -3.402 closest distance to " O   GLY A 211 " =    1.375
peak=   -3.397 closest distance to " OE1 GLN A  88 " =    1.219
peak=   -3.394 closest distance to " O   VAL A 189 " =    2.621
peak=   -3.381 closest distance to " NE2 GLN A 194 " =    1.820
peak=   -3.376 closest distance to " CD1 LEU A   5 " =    2.529
peak=   -3.375 closest distance to " CD  GLU A 152 " =    0.867
peak=   -3.371 closest distance to " CE  MET A 105 " =    2.138
peak=   -3.366 closest distance to " O   HOH Z 298 " =    2.569
peak=   -3.365 closest distance to " OG BSER A 134 " =    1.909
peak=   -3.361 closest distance to " OD2 ASP A 171 " =    1.890
peak=   -3.355 closest distance to " O   HOH Z 177 " =    1.768
peak=   -3.348 closest distance to " OG  SER A  62 " =    1.643
peak=   -3.347 closest distance to " CD1 LEU A 228 " =    2.384
peak=   -3.346 closest distance to " O   HOH Z 198 " =    1.094
peak=   -3.334 closest distance to " C   MET A 188 " =    1.445
peak=   -3.330 closest distance to " O   HOH Z 393 " =    1.340
peak=   -3.325 closest distance to " CG  GLU A  53 " =    1.468
peak=   -3.324 closest distance to " CD  ARG A  79 " =    1.121
peak=   -3.323 closest distance to " CE BMET A  47 " =    1.998
peak=   -3.322 closest distance to " NH2 ARG A  79 " =    2.000
peak=   -3.317 closest distance to " O   HOH Z 253 " =    4.086
peak=   -3.317 closest distance to " N   ASP A 171 " =    2.385
peak=   -3.309 closest distance to " CG2 VAL A 189 " =    2.139
peak=   -3.309 closest distance to " O   HOH Z  51 " =    1.476
peak=   -3.308 closest distance to " CG1 VAL A 125 " =    2.009
peak=   -3.305 closest distance to " O   PRO A 163 " =    2.149
peak=   -3.303 closest distance to " OD1 ASP A 171 " =    1.542
peak=   -3.299 closest distance to " CB  ALA A 248 " =    2.468
peak=   -3.292 closest distance to " NH1 ARG A 195 " =    2.540
peak=   -3.290 closest distance to " O   GLY A 196 " =    1.176
peak=   -3.289 closest distance to " CG  TRP A 266 " =    1.880
peak=   -3.288 closest distance to " CB  ASP A 286 " =    1.965
peak=   -3.283 closest distance to " CD  ARG A 195 " =    5.122
peak=   -3.279 closest distance to " CZ  PHE A 155 " =    1.144
peak=   -3.277 closest distance to " O   HOH Z 435 " =    2.766
peak=   -3.275 closest distance to " O   HOH Z 222 " =    1.272
peak=   -3.268 closest distance to " NE1 TRP A 266 " =    2.381
peak=   -3.265 closest distance to " O   HOH Z   6 " =    1.440
peak=   -3.265 closest distance to " CG  PHE A 283 " =    2.770
peak=   -3.260 closest distance to " O   HOH Z 232 " =    1.586
peak=   -3.259 closest distance to " CD2 LEU A 237 " =    2.883
peak=   -3.258 closest distance to " CD  PRO A 213 " =    2.195
peak=   -3.255 closest distance to " O   HOH Z 264 " =    1.780
peak=   -3.254 closest distance to " CB  ALA A 248 " =    2.138
peak=   -3.253 closest distance to " CD  PRO A 243 " =    2.152
peak=   -3.249 closest distance to " O   HOH Z 234 " =    4.370
peak=   -3.247 closest distance to " N   THR A  52 " =    1.683
peak=   -3.245 closest distance to " CD1 PHE A  16 " =    2.634
peak=   -3.242 closest distance to " O   HOH Z 128 " =    2.617
peak=   -3.237 closest distance to " O   HOH Z 426 " =    1.638
peak=   -3.232 closest distance to " CB  TRP A  85 " =    2.444
peak=   -3.230 closest distance to " O   HOH Z 275 " =    1.540
peak=   -3.229 closest distance to " OG BSER A 210 " =    2.257
peak=   -3.228 closest distance to " O   HOH Z 165 " =    1.835
peak=   -3.222 closest distance to " CE2 PHE A 218 " =    2.491
peak=   -3.217 closest distance to " O   HOH Z  37 " =    1.873
peak=   -3.216 closest distance to " CA  GLY A 203 " =    2.389
peak=   -3.215 closest distance to " CG1 VAL A 197 " =    2.215
peak=   -3.214 closest distance to " ND2 ASN A  60 " =    1.256
peak=   -3.204 closest distance to " O   HOH Z 166 " =    1.675
peak=   -3.203 closest distance to " O   HOH Z 295 " =    1.621
peak=   -3.197 closest distance to " O   HOH Z 313 " =    2.061
peak=   -3.192 closest distance to " N   GLN A  58 " =    1.760
peak=   -3.191 closest distance to " CB  PHE A 208 " =    2.307
peak=   -3.186 closest distance to " CH2 TRP A 177 " =    2.097
peak=   -3.184 closest distance to " CG2 ILE A  20 " =    2.855
peak=   -3.184 closest distance to " O   HOH Z 114 " =    1.416
peak=   -3.183 closest distance to " O   HOH Z  13 " =    1.515
peak=   -3.180 closest distance to " CA  GLY A 241 " =    2.828
peak=   -3.180 closest distance to " O   HOH Z  11 " =    1.788
peak=   -3.178 closest distance to " O   HOH Z 313 " =    1.036
peak=   -3.177 closest distance to " NE2 GLN A  88 " =    1.848
peak=   -3.176 closest distance to " CD1 LEU A 297 " =    2.440
peak=   -3.176 closest distance to " CG2 THR A 221 " =    2.068
peak=   -3.176 closest distance to " CG1 VAL A  67 " =    2.945
peak=   -3.171 closest distance to " CE3 TRP A 274 " =    2.626
peak=   -3.169 closest distance to " N   THR A 157 " =    1.624
peak=   -3.154 closest distance to " O   HOH Z  71 " =    1.616
peak=   -3.152 closest distance to " C   GLY A  13 " =    0.952
peak=   -3.150 closest distance to " CD1 ILE A 151 " =    2.410
peak=   -3.146 closest distance to " O   PRO A 198 " =    2.012
peak=   -3.144 closest distance to " OD2 ASP A  50 " =    2.209
peak=   -3.140 closest distance to " O   GLY A  17 " =    1.293
peak=   -3.137 closest distance to " O   HOH Z 193 " =    2.163
peak=   -3.129 closest distance to " NH2 ARG A  66 " =    2.086
peak=   -3.125 closest distance to " CD1 ILE A 239 " =    2.377
peak=   -3.122 closest distance to " CG  LEU A  83 " =    1.935
peak=   -3.120 closest distance to " O   HOH Z 317 " =    2.301
peak=   -3.108 closest distance to " O   HOH Z 351 " =    1.408
peak=   -3.101 closest distance to " O   HOH Z 123 " =    2.533
peak=   -3.098 closest distance to " O   HOH Z 357 " =    2.006
peak=   -3.096 closest distance to " O   HOH Z 421 " =    3.225
peak=   -3.090 closest distance to " O   HOH Z  77 " =    2.076
peak=   -3.088 closest distance to " N   SER A   3 " =    1.974
peak=   -3.083 closest distance to " O   HOH Z 174 " =    4.158
peak=   -3.081 closest distance to " O   ALA A 292 " =    1.993
peak=   -3.080 closest distance to " CG  GLN A  11 " =    1.489
peak=   -3.077 closest distance to " CG2BVAL A  41 " =    1.926
peak=   -3.072 closest distance to " O   HOH Z 283 " =    5.519
peak=   -3.062 closest distance to " CE3 TRP A  70 " =    1.883

================= 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    :  0.3115 0.3032   6.005748e+00   5.986588e+00
   1_bss:  0.2992 0.2923   5.982029e+00   5.958672e+00
   1_xyz:  0.1761 0.1933   5.491637e+00   5.579281e+00
   1_adp:  0.1632 0.1957   5.439587e+00   5.597405e+00
   1_occ:  0.1626 0.1951   5.437441e+00   5.595652e+00
   2_bss:  0.1618 0.1930   5.434978e+00   5.590401e+00
   2_xyz:  0.1282 0.1639   5.234678e+00   5.432346e+00
   2_adp:  0.1215 0.1597   5.190888e+00   5.403572e+00
   2_occ:  0.1214 0.1595   5.190736e+00   5.403832e+00
   3_bss:  0.1214 0.1595   5.191283e+00   5.404020e+00
   3_xyz:  0.1143 0.1571   5.154013e+00   5.388603e+00
   3_adp:  0.1133 0.1571   5.149718e+00   5.388164e+00
   3_occ:  0.1133 0.1571   5.149895e+00   5.388655e+00
   4_bss:  0.1132 0.1571   5.149846e+00   5.388734e+00
   4_xyz:  0.1088 0.1580   5.129840e+00   5.386129e+00
   4_adp:  0.1089 0.1573   5.128333e+00   5.383227e+00
   4_occ:  0.1089 0.1574   5.128678e+00   5.383923e+00
   5_bss:  0.1088 0.1573   5.128705e+00   5.383936e+00
   5_xyz:  0.1121 0.1587   5.150224e+00   5.396228e+00
   5_adp:  0.1136 0.1587   5.156582e+00   5.397847e+00
   5_occ:  0.1136 0.1588   5.156736e+00   5.398135e+00
   5_bss:  0.1136 0.1587   5.156755e+00   5.398138e+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:  0.316  56.566  -1.822   0.543  -1.141   0.000  -0.000  -0.000
   1_xyz:  0.316  56.566  -1.822   0.543  -1.141   0.000  -0.000  -0.000
   1_adp:  0.316  56.566  -1.822   0.543  -1.141   0.000  -0.000  -0.000
   1_occ:  0.316  56.566  -1.822   0.543  -1.141   0.000  -0.000  -0.000
   2_bss:  0.332  65.634  -2.589  -1.457  -1.467  -0.000  -0.000  -0.000
   2_xyz:  0.332  65.634  -2.589  -1.457  -1.467  -0.000  -0.000  -0.000
   2_adp:  0.332  65.634  -2.589  -1.457  -1.467  -0.000  -0.000  -0.000
   2_occ:  0.332  65.634  -2.589  -1.457  -1.467  -0.000  -0.000  -0.000
   3_bss:  0.332  65.634  -2.351  -1.728  -1.124  -0.000  -0.000  -0.000
   3_xyz:  0.332  65.634  -2.351  -1.728  -1.124  -0.000  -0.000  -0.000
   3_adp:  0.332  65.634  -2.351  -1.728  -1.124  -0.000  -0.000  -0.000
   3_occ:  0.332  65.634  -2.351  -1.728  -1.124  -0.000  -0.000  -0.000
   4_bss:  0.323  59.313  -2.120  -1.668  -0.879  -0.000  -0.000  -0.000
   4_xyz:  0.323  59.313  -2.120  -1.668  -0.879  -0.000  -0.000  -0.000
   4_adp:  0.323  59.313  -2.120  -1.668  -0.879  -0.000  -0.000  -0.000
   4_occ:  0.323  59.313  -2.120  -1.668  -0.879  -0.000  -0.000  -0.000
   5_bss:  0.323  59.313  -1.920  -1.538  -0.660  -0.000  -0.000  -0.000
   5_xyz:  0.323  59.313  -1.920  -1.538  -0.660  -0.000  -0.000  -0.000
   5_adp:  0.323  59.313  -1.920  -1.538  -0.660  -0.000  -0.000  -0.000
   5_occ:  0.323  59.313  -1.920  -1.538  -0.660  -0.000  -0.000  -0.000
   5_bss:  0.323  59.273  -1.848  -1.470  -0.542  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.241 0.7475  0.9034    26275.217
   1_bss:  30.278 0.7565  0.8912    23742.474
   1_xyz:  18.090 0.8808  0.9930     9461.751
   1_adp:  18.633 0.8752  0.9834     9753.989
   1_occ:  18.592 0.8756  0.9831     9690.461
   2_bss:  18.448 0.8768  0.9495     9542.722
   2_xyz:  14.895 0.9076  0.9662     6819.015
   2_adp:  14.219 0.9133  0.9619     6418.908
   2_occ:  14.223 0.9132  0.9616     6421.982
   3_bss:  14.230 0.9133  0.9652     6444.209
   3_xyz:  13.868 0.9162  0.9676     6256.728
   3_adp:  13.836 0.9166  0.9606     6257.943
   3_occ:  13.847 0.9165  0.9605     6264.471
   4_bss:  13.850 0.9165  0.9667     6264.872
   4_xyz:  13.813 0.9167  0.9672     6263.059
   4_adp:  13.732 0.9174  0.9607     6239.767
   4_occ:  13.745 0.9174  0.9605     6247.986
   5_bss:  13.745 0.9174  0.9669     6248.537
   5_xyz:  13.952 0.9159  0.9656     6394.158
   5_adp:  13.957 0.9159  0.9602     6441.125
   5_occ:  13.965 0.9158  0.9601     6445.268
   5_bss:  13.966 0.9158  0.9617     6445.302
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6180e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6180e-01
   1_xyz:   1.064  0.008  0.070 14.929  0.004  4.117   6.6191e-02
   1_adp:   1.064  0.008  0.070 14.929  0.004  4.117   6.6191e-02
   1_occ:   1.064  0.008  0.070 14.929  0.004  4.117   6.6191e-02
   2_bss:   1.064  0.008  0.070 14.929  0.004  4.117   6.6191e-02
   2_xyz:   0.988  0.007  0.074 14.476  0.004  4.129   5.7285e-02
   2_adp:   0.988  0.007  0.074 14.476  0.004  4.129   5.7285e-02
   2_occ:   0.988  0.007  0.074 14.476  0.004  4.129   5.7285e-02
   3_bss:   0.988  0.007  0.074 14.476  0.004  4.129   5.7285e-02
   3_xyz:   1.012  0.008  0.077 14.578  0.004  4.114   6.1826e-02
   3_adp:   1.012  0.008  0.077 14.578  0.004  4.114   6.1826e-02
   3_occ:   1.012  0.008  0.077 14.578  0.004  4.114   6.1826e-02
   4_bss:   1.012  0.008  0.077 14.578  0.004  4.114   6.1826e-02
   4_xyz:   1.120  0.011  0.086 14.775  0.004  4.118   7.6917e-02
   4_adp:   1.120  0.011  0.086 14.775  0.004  4.118   7.6917e-02
   4_occ:   1.120  0.011  0.086 14.775  0.004  4.118   7.6917e-02
   5_bss:   1.120  0.011  0.086 14.775  0.004  4.118   7.6917e-02
   5_xyz:   0.986  0.008  0.076 14.482  0.004  4.117   5.9341e-02
   5_adp:   0.986  0.008  0.076 14.482  0.004  4.117   5.9341e-02
   5_occ:   0.986  0.008  0.076 14.482  0.004  4.117   5.9341e-02
   5_bss:   0.986  0.008  0.076 14.482  0.004  4.117   5.9341e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.793   2.4345e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.793   2.4345e-01
   1_xyz:   8.449  0.042  0.230 83.353  0.025  2.272   1.1745e-01
   1_adp:   8.449  0.042  0.230 83.353  0.025  2.272   1.1745e-01
   1_occ:   8.449  0.042  0.230 83.353  0.025  2.272   1.1745e-01
   2_bss:   8.449  0.042  0.230 83.353  0.025  2.272   1.1745e-01
   2_xyz:   6.891  0.045  0.222 83.073  0.042  2.340   4.5529e-02
   2_adp:   6.891  0.045  0.222 83.073  0.042  2.340   4.5529e-02
   2_occ:   6.891  0.045  0.222 83.073  0.042  2.340   4.5529e-02
   3_bss:   6.891  0.045  0.222 83.073  0.042  2.340   4.5529e-02
   3_xyz:   7.424  0.042  0.244 82.652  0.040  2.367   4.2097e-02
   3_adp:   7.424  0.042  0.244 82.652  0.040  2.367   4.2097e-02
   3_occ:   7.424  0.042  0.244 82.652  0.040  2.367   4.2097e-02
   4_bss:   7.424  0.042  0.244 82.652  0.040  2.367   4.2097e-02
   4_xyz:   7.724  0.049  0.281 82.177  0.039  2.330   5.8506e-02
   4_adp:   7.724  0.049  0.281 82.177  0.039  2.330   5.8506e-02
   4_occ:   7.724  0.049  0.281 82.177  0.039  2.330   5.8506e-02
   5_bss:   7.724  0.049  0.281 82.177  0.039  2.330   5.8506e-02
   5_xyz:   7.203  0.043  0.235 82.363  0.036  2.390   3.7959e-02
   5_adp:   7.203  0.043  0.235 82.363  0.036  2.390   3.7959e-02
   5_occ:   7.203  0.043  0.235 82.363  0.036  2.390   3.7959e-02
   5_bss:   7.203  0.043  0.235 82.363  0.036  2.390   3.7959e-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:  74.21   0.00  16.51  74.21   0.00  12.64  63.68   6.97  37.53
   1_occ:  74.21   0.00  16.51  74.21   0.00  12.64  63.68   6.97  37.53
   2_bss:  74.21   0.00  16.51  74.21   0.00  12.64  63.68   6.97  37.53
   2_xyz:  74.21   0.00  16.51  74.21   0.00  12.64  63.68   6.97  37.53
   2_adp:  78.06   1.47  16.92  78.06   1.47  12.80  72.02   5.80  39.34
   2_occ:  78.06   1.47  16.92  78.06   1.47  12.80  72.02   5.80  39.34
   3_bss:  78.06   1.47  16.92  78.06   1.47  12.80  72.02   5.80  39.34
   3_xyz:  78.06   1.47  16.92  78.06   1.47  12.80  72.02   5.80  39.34
   3_adp:  81.28   0.46  16.78  81.28   0.46  12.63  73.87   3.59  39.37
   3_occ:  81.28   0.46  16.78  81.28   0.46  12.63  73.87   3.59  39.37
   4_bss:  81.28   0.46  16.78  81.28   0.46  12.63  73.87   3.59  39.37
   4_xyz:  81.28   0.46  16.78  81.28   0.46  12.63  73.87   3.59  39.37
   4_adp:  82.74   0.61  16.37  82.74   0.61  12.38  74.51   4.82  38.10
   4_occ:  82.74   0.61  16.37  82.74   0.61  12.38  74.51   4.82  38.10
   5_bss:  82.74   0.61  16.37  82.74   0.61  12.38  74.51   4.82  38.10
   5_xyz:  82.74   0.61  16.37  82.74   0.61  12.38  74.51   4.82  38.10
   5_adp:  79.35   1.14  15.81  79.35   1.14  12.11  72.38   5.60  35.97
   5_occ:  79.35   1.14  15.81  79.35   1.14  12.11  72.38   5.60  35.97
   5_bss:  79.31   1.10  15.77  79.31   1.10  12.07  72.34   5.56  35.93
------------------------------------------------------------------------
 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:    1.150    0.026    0.306
   1_adp:    1.150    0.026    0.306
   1_occ:    1.150    0.026    0.306
   2_bss:    1.150    0.026    0.306
   2_xyz:    0.803    0.036    0.347
   2_adp:    0.803    0.036    0.347
   2_occ:    0.803    0.036    0.347
   3_bss:    0.803    0.036    0.347
   3_xyz:    0.870    0.044    0.374
   3_adp:    0.870    0.044    0.374
   3_occ:    0.870    0.044    0.374
   4_bss:    0.870    0.044    0.374
   4_xyz:    0.917    0.018    0.388
   4_adp:    0.917    0.018    0.388
   4_occ:    0.917    0.018    0.388
   5_bss:    0.917    0.018    0.388
   5_xyz:    0.965    0.024    0.390
   5_adp:    0.965    0.024    0.390
   5_occ:    0.965    0.024    0.390
   5_bss:    0.965    0.024    0.390
------------------------------------------------------------------------

CPU time actual refinement: 327.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/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_930/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_930/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.20 
  Macro-tasks:
    bulk solvent and scale       = 39.69  
    individual site refinement   = 134.41 
    weights calculation          = 29.84  
    collect and process          = 6.70   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 210.77 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 102.87 
    alpha_beta                      = 8.18   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 111.50 
    fmodel                         = 6.92   
    r_factors                      = 0.14   
    phase_errors                   = 11.32  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 243.53 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.669 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    627 calls, 102.47 s
gradients_fft:          572 calls,  98.19 s

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

# Date 2008-01-16 Time 06:00:16 PST -0800 (1200492016.96 s)
Start R-work = 0.3115, R-free = 0.3032 (no bulk solvent and anisotropic scale)
Final R-work = 0.1344, R-free = 0.1758 (no bulk solvent and anisotropic scale)

Start R-work = 0.2992, R-free = 0.2923
Final R-work = 0.1136, R-free = 0.1587