# Date 2008-01-16 Time 06:28:58 PST -0800 (1200493738.13 s)
#phil __OFF__

Command line arguments: "../1159.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20386
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1159

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 85.9581, 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: 3.25, 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: (71.655, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99111
Completeness in resolution range: 0.954444
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9911

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: (71.655, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99111
Completeness in resolution range: 0.954444
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2611 [2152/2181]  1941   211   9.8%
  bin  2:  4.2611 -  3.3946 [2073/2089]  1863   210  10.1%
  bin  3:  3.3946 -  2.9691 [2032/2051]  1827   205  10.1%
  bin  4:  2.9691 -  2.6993 [2039/2069]  1838   201   9.9%
  bin  5:  2.6993 -  2.5068 [2022/2041]  1819   203  10.0%
  bin  6:  2.5068 -  2.3595 [1996/2021]  1790   206  10.3%
  bin  7:  2.3595 -  2.2418 [1986/2019]  1790   196   9.9%
  bin  8:  2.2418 -  2.1445 [1987/2018]  1793   194   9.8%
  bin  9:  2.1445 -  2.0621 [1985/2027]  1784   201  10.1%
  bin 10:  2.0621 -  1.9911 [1317/2008]  1185   132  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 5
        2.32 -     2.97: 1720
        2.97 -     3.61: 4492
        3.61 -     4.26: 9125
        4.26 -     4.90: 12694
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.105 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.174 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28031 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_1159/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/model_refine_001.geo

CPU time processing inputs: 9.03


============================ 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 = 71.655 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3263   r_free= 0.3237   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.048001                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.2874 0.2778       6.349      6.2928|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.2486 0.2479      6.4344      6.3989|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.2813 0.2618      6.3245      6.3558|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.2973 0.2880      6.2239      6.1808|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.3192 0.3499      6.0901      6.2221|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.3508 0.3309      6.0522      6.0196|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.3572 0.3343       6.041      6.0457|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.3652 0.3459      5.9602      5.9426|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.3594 0.3682      5.9299      5.9715|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.3726 0.4163      5.9199      5.9928|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.3885 0.4078      5.8868       5.925|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.3979 0.3690      5.8288      5.8644|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.3875 0.3992      5.7369      5.6563|
| 14:  2.0408 -  1.9911 0.53    694   80 0.3574 0.3663      5.6369      5.6267|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7529  1395   155  0.80  25.41   0.86     0.81      40428.17|
|  2:  4.7529 -  3.7919  1350   146  0.85  21.75   0.97     0.90      43621.50|
|  3:  3.7919 -  3.3182  1322   149  0.80  26.16   0.98     0.92      43813.09|
|  4:  3.3182 -  3.0174  1321   152  0.77  28.93   0.98     0.91      40341.06|
|  5:  3.0174 -  2.8026  1305   141  0.70  35.43   0.98     0.87      35782.67|
|  6:  2.8026 -  2.6383  1292   145  0.69  36.19   1.00     0.86      31335.37|
|  7:  2.6383 -  2.5068  1303   142  0.70  35.70   0.99     0.87      28509.90|
|  8:  2.5068 -  2.3981  1270   146  0.68  37.33   0.98     0.89      27151.07|
|  9:  2.3981 -  2.3061  1287   146  0.67  38.71   1.02     0.87      26636.49|
| 10:  2.3061 -  2.2268  1271   137  0.64  40.68   1.02     0.86      26520.37|
| 11:  2.2268 -  2.1573  1290   141  0.63  41.80   1.03     0.86      24942.72|
| 12:  2.1573 -  2.0958  1260   136  0.64  40.65   1.01     0.90      22475.23|
| 13:  2.0958 -  2.0408  1270   143  0.65  40.03   0.99     0.90      18074.67|
| 14:  2.0408 -  1.9911   694    80  0.67  38.25   1.04     0.85      13975.65|
|alpha:            min =        0.81 max =            0.92 mean =         0.88|
|beta:             min =    13975.65 max =        43813.09 mean =     30995.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.94 mean =        34.52|
|phase err.(test): min =        0.00 max =           89.70 mean =        33.98|
|-----------------------------------------------------------------------------|

============================== 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 = 4.689777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.784   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.747566              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.540   (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 |  1.680 -  2.002:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.002 -  2.324:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.324 -  2.646:       58 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.646 -  2.968:     1662 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.968 -  3.290:     1874 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2618 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4708 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4417 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5746 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6948 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.680 |       0.167 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3263   r_free= 0.3237   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.048001                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3129   r_free= 0.3113   ksol= 0.31   Bsol= 50.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,-1.91,-1.61,-0.00,-0.00,-0.00); trace/3= -0.57                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.027781                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.145740              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.088   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.112   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3129      final r-factor (work) = 0.1867          |
| start r-factor (free) = 0.3113      final r-factor (free) = 0.2089          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6684 = 4.15 * 0.50 * 6.0329 + 1.00 * 0.1629                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0167 = 4.15 * 0.50 * 5.7629 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1867      final r-factor (work) = 0.1731          |
| start r-factor (free) = 0.2089      final r-factor (free) = 0.2128          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2762 = 0.39 * 1.00 * 5.7629 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2333 = 0.39 * 1.00 * 5.4963 + 1.00 * 0.0689                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.67   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    63.67   16.76    None  None   None       |
|    Sol.    : 438    0      5.58    63.67   37.85    None  None   None       |
|    Mac.    : 2385   0      0.00    62.71   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.367:  260   |   5:    31.835 -  38.202:  100        |
|      1:     6.367 -  12.734: 1170   |   6:    38.202 -  44.569:   99        |
|      2:    12.734 -  19.101:  691   |   7:    44.569 -  50.936:   80        |
|      3:    19.101 -  25.468:  229   |   8:    50.936 -  57.303:   60        |
|      4:    25.468 -  31.835:  113   |   9:    57.303 -  63.670:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1731 r_free = 0.2128             target_work(ml) = 5.503         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1725 r_free = 0.2127             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1725   r_free= 0.2127   ksol= 0.31   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,-1.91,-1.61,-0.00,-0.00,-0.00); trace/3= -0.57                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.500662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1702   r_free= 0.2090   ksol= 0.33   Bsol= 62.01   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,-2.69,-2.04,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.493857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.627181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.217   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516209              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.554   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1702      final r-factor (work) = 0.1284          |
| start r-factor (free) = 0.2090      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0625 = 3.63 * 0.50 * 5.5093 + 1.00 * 0.0709                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8133 = 3.63 * 0.50 * 5.3734 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8063 = 0.52 * 1.00 * 5.3734 + 1.00 * 0.0325                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7046 = 0.52 * 1.00 * 5.2216 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    77.87   17.33    None  None   None       |
|    all(noH): 2823   0      0.75    77.87   17.33    None  None   None       |
|    Sol.    : 438    0      5.62    74.58   40.22    None  None   None       |
|    Mac.    : 2385   0      0.75    77.87   13.13    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:     0.754 -   8.466:  619   |   5:    39.310 -  47.022:   96        |
|      1:     8.466 -  16.177: 1308   |   6:    47.022 -  54.733:   86        |
|      2:    16.177 -  23.888:  366   |   7:    54.733 -  62.444:   75        |
|      3:    23.888 -  31.599:  133   |   8:    62.444 -  70.155:   27        |
|      4:    31.599 -  39.310:  106   |   9:    70.155 -  77.866:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1642             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1641             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1641   ksol= 0.33   Bsol= 62.01   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,-2.69,-2.04,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1638   ksol= 0.33   Bsol= 62.01   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.55,-1.78,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199052                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.129995              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.976  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311522              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6288 = 2.13 * 0.50 * 5.2211 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5778 = 2.13 * 0.50 * 5.1802 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6229 = 0.31 * 1.00 * 5.1802 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6182 = 0.31 * 1.00 * 5.1666 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    79.11   17.13    None  None   None       |
|    all(noH): 2823   0      0.83    79.11   17.13    None  None   None       |
|    Sol.    : 438    0      2.98    75.86   39.71    None  None   None       |
|    Mac.    : 2385   0      0.83    79.11   12.99    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:     0.834 -   8.661:  663   |   5:    39.971 -  47.798:   94        |
|      1:     8.661 -  16.489: 1313   |   6:    47.798 -  55.626:   94        |
|      2:    16.489 -  24.316:  335   |   7:    55.626 -  63.453:   55        |
|      3:    24.316 -  32.143:  131   |   8:    63.453 -  71.280:   22        |
|      4:    32.143 -  39.971:  109   |   9:    71.280 -  79.108:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1598             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1597             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1597   ksol= 0.33   Bsol= 62.01   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.55,-1.78,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1597   ksol= 0.33   Bsol= 62.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.40,-1.63,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.604565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.958  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.455071              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.882  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3723 = 3.60 * 0.50 * 5.1664 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3445 = 3.60 * 0.50 * 5.1390 + 1.00 * 0.0827                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3472 = 0.46 * 1.00 * 5.1390 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3439 = 0.46 * 1.00 * 5.1312 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    81.92   16.99    None  None   None       |
|    all(noH): 2823   0      0.52    81.92   16.99    None  None   None       |
|    Sol.    : 438    0      3.60    78.24   39.39    None  None   None       |
|    Mac.    : 2385   0      0.52    81.92   12.87    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:     0.521 -   8.661:  707   |   5:    41.222 -  49.363:  101        |
|      1:     8.661 -  16.802: 1294   |   6:    49.363 -  57.503:   85        |
|      2:    16.802 -  24.942:  324   |   7:    57.503 -  65.643:   48        |
|      3:    24.942 -  33.082:  134   |   8:    65.643 -  73.784:   14        |
|      4:    33.082 -  41.222:  109   |   9:    73.784 -  81.924:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1593             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1078 r_free = 0.1594             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1594   ksol= 0.33   Bsol= 62.01   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.40,-1.63,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1593   ksol= 0.33   Bsol= 62.01   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.19,-1.41,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132318                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.100212              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.542  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.507662              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.307  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4718 = 2.10 * 0.50 * 5.1319 + 1.00 * 0.0827                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4657 = 2.10 * 0.50 * 5.1447 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7653 = 1.51 * 1.00 * 5.1447 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7716 = 1.51 * 1.00 * 5.1479 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.10   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    93.10   17.15    None  None   None       |
|    Sol.    : 438    0      4.66    84.84   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    93.10   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.310:  929   |   5:    46.549 -  55.858:  101        |
|      1:     9.310 -  18.620: 1183   |   6:    55.858 -  65.168:   63        |
|      2:    18.620 -  27.929:  253   |   7:    65.168 -  74.478:   25        |
|      3:    27.929 -  37.239:  140   |   8:    74.478 -  83.788:   11        |
|      4:    37.239 -  46.549:  113   |   9:    83.788 -  93.097:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1614             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1615             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1615   ksol= 0.33   Bsol= 62.01   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.19,-1.41,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.0996 0.1339      5.3956      5.5407|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.0844 0.1074      5.4273      5.6042|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.1035 0.1534      5.4614      5.8695|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.1174 0.1581      5.4556       5.602|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.1336 0.1866      5.3429      5.5847|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.1224 0.1834      5.2283      5.4668|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.1225 0.1654      5.1733      5.3784|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.1135 0.1808      5.0467      5.3575|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.1136 0.1807      5.0285      5.3449|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.1076 0.1781      4.9525      5.2107|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.1162 0.1873      4.9723      5.3349|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.1097 0.1592       4.896      5.1048|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.1160 0.1854      4.8153      5.1086|
| 14:  2.0408 -  1.9911 0.53    694   80 0.0997 0.1720      4.6512      4.9658|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7529  1395   155  0.94   9.28   0.97     0.94       7325.96|
|  2:  4.7529 -  3.7919  1350   146  0.95   8.02   1.00     0.99       8913.10|
|  3:  3.7919 -  3.3182  1322   149  0.93  11.25   1.02     1.02      10224.25|
|  4:  3.3182 -  3.0174  1321   152  0.92  13.83   1.00     0.98      10739.45|
|  5:  3.0174 -  2.8026  1305   141  0.89  16.76   0.99     0.97       8882.04|
|  6:  2.8026 -  2.6383  1292   145  0.90  16.37   0.98     0.95       7511.56|
|  7:  2.6383 -  2.5068  1303   142  0.91  15.59   0.98     0.96       6438.39|
|  8:  2.5068 -  2.3981  1270   146  0.91  15.44   0.98     0.96       5268.00|
|  9:  2.3981 -  2.3061  1287   146  0.91  15.29   0.99     0.96       5069.51|
| 10:  2.3061 -  2.2268  1271   137  0.90  15.60   0.98     0.94       4407.37|
| 11:  2.2268 -  2.1573  1290   141  0.89  17.10   0.98     0.95       4760.48|
| 12:  2.1573 -  2.0958  1260   136  0.91  15.51   0.98     0.97       4248.39|
| 13:  2.0958 -  2.0408  1270   143  0.89  17.11   0.98     0.97       3648.72|
| 14:  2.0408 -  1.9911   694    80  0.91  15.03   0.96     0.92       2606.03|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2606.03 max =        10739.45 mean =      6602.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.36|
|phase err.(test): min =        0.00 max =           88.73 mean =        13.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1614   ksol= 0.32   Bsol= 62.02   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-2.00,-1.22,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153223                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1614   ksol= 0.32   Bsol= 62.02   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-2.00,-1.22,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153223                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.0994 0.1340      5.3947       5.542|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.0845 0.1074      5.4283      5.6047|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.1035 0.1533      5.4614      5.8692|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.1174 0.1582      5.4555       5.602|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.1336 0.1866      5.3428      5.5845|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.1224 0.1833      5.2283      5.4667|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.1224 0.1653      5.1732      5.3783|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.1134 0.1808      5.0466      5.3574|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.1136 0.1807      5.0286      5.3448|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.1076 0.1782      4.9527      5.2107|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.1162 0.1873      4.9724      5.3351|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.1097 0.1592      4.8961      5.1051|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.1160 0.1854      4.8152      5.1083|
| 14:  2.0408 -  1.9911 0.53    694   80 0.0997 0.1721      4.6514      4.9661|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7529  1395   155  0.94   9.29   0.97     0.94       7340.01|
|  2:  4.7529 -  3.7919  1350   146  0.95   8.03   1.00     0.99       8927.43|
|  3:  3.7919 -  3.3182  1322   149  0.93  11.26   1.02     1.02      10227.53|
|  4:  3.3182 -  3.0174  1321   152  0.92  13.83   1.00     0.98      10738.04|
|  5:  3.0174 -  2.8026  1305   141  0.89  16.76   0.99     0.97       8880.48|
|  6:  2.8026 -  2.6383  1292   145  0.90  16.37   0.99     0.96       7510.32|
|  7:  2.6383 -  2.5068  1303   142  0.91  15.59   0.99     0.96       6436.35|
|  8:  2.5068 -  2.3981  1270   146  0.91  15.44   0.99     0.97       5266.68|
|  9:  2.3981 -  2.3061  1287   146  0.91  15.29   1.00     0.96       5067.97|
| 10:  2.3061 -  2.2268  1271   137  0.90  15.60   0.99     0.95       4408.69|
| 11:  2.2268 -  2.1573  1290   141  0.89  17.10   0.99     0.96       4761.22|
| 12:  2.1573 -  2.0958  1260   136  0.91  15.52   0.99     0.98       4249.95|
| 13:  2.0958 -  2.0408  1270   143  0.89  17.11   0.99     0.98       3648.76|
| 14:  2.0408 -  1.9911   694    80  0.91  15.04   0.97     0.93       2607.15|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2607.15 max =        10738.04 mean =      6604.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.36|
|phase err.(test): min =        0.00 max =           88.72 mean =        13.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.10   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    93.10   17.15    None  None   None       |
|    Sol.    : 438    0      4.67    84.85   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    93.10   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.313:  929   |   5:    46.552 -  55.861:  101        |
|      1:     9.313 -  18.622: 1183   |   6:    55.861 -  65.171:   63        |
|      2:    18.622 -  27.932:  253   |   7:    65.171 -  74.481:   25        |
|      3:    27.932 -  37.242:  140   |   8:    74.481 -  83.790:   11        |
|      4:    37.242 -  46.552:  113   |   9:    83.790 -  93.100:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.665 - 4.669
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 303
   mapped sites are within: 0.708 - 4.669

peak=    5.851 closest distance to " O   HOH Z 111 " =    2.132
peak=    5.805 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.423 closest distance to " CG  PRO A  54 " =    1.244
peak=    4.986 closest distance to " O   HOH Z 232 " =    2.289
peak=    4.911 closest distance to " CB  SER A  63 " =    1.271
peak=    4.840 closest distance to " O   HOH Z 126 " =    1.913
peak=    4.820 closest distance to " CB  PRO A  54 " =    0.920
peak=    4.764 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.729 closest distance to " O   HOH Z  78 " =    1.728
peak=    4.714 closest distance to " O   HOH Z 298 " =    1.983
peak=    4.712 closest distance to " CG  PRO A 213 " =    1.199
peak=    4.706 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.581 closest distance to " NE2 GLN A  11 " =    1.070
peak=    4.570 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.529 closest distance to " CB  GLU A 128 " =    1.047
peak=    4.469 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.447 closest distance to " C   PRO A 198 " =    1.519
peak=    4.357 closest distance to " OD1 ASN A  69 " =    2.618
peak=    4.348 closest distance to " O   HOH Z  15 " =    2.162
peak=    4.325 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.299 closest distance to " CG  PRO A 198 " =    1.277
peak=    4.298 closest distance to " O   HOH Z 236 " =    2.115
peak=    4.226 closest distance to " O   HOH Z 369 " =    2.103
peak=    4.221 closest distance to " CG  PRO A  90 " =    1.085
peak=    4.180 closest distance to " CB  TYR A 169 " =    0.751
peak=    4.166 closest distance to " CA  MET A  40 " =    1.162
peak=    4.161 closest distance to " CB  ARG A  79 " =    1.415
peak=    4.141 closest distance to " CZ  PHE A 218 " =    1.068
peak=    4.138 closest distance to " CD  ARG A 159 " =    0.821
peak=    4.137 closest distance to " NH2 ARG A 156 " =    1.221
peak=    4.123 closest distance to " O   HOH Z 261 " =    2.030
peak=    4.118 closest distance to " CB  ARG A 190 " =    1.615
peak=    4.113 closest distance to " CB  TRP A 266 " =    0.978
peak=    4.058 closest distance to " CB  SER A   3 " =    1.352
peak=    4.043 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.040 closest distance to " O   HOH Z 234 " =    3.851
peak=    4.034 closest distance to " CB  ASN A 187 " =    1.341
peak=    4.028 closest distance to " CD1 LEU A 300 " =    1.191
peak=    3.992 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.988 closest distance to " O   HOH Z 316 " =    3.086
peak=    3.983 closest distance to " O   HOH Z 142 " =    1.593
peak=    3.974 closest distance to " O   MET A 105 " =    1.876
peak=    3.972 closest distance to " ND2 ASN A 187 " =    1.412
peak=    3.969 closest distance to " O   HOH Z 135 " =    1.743
peak=    3.952 closest distance to " O   HOH Z 368 " =    2.113
peak=    3.939 closest distance to " O   HOH Z 132 " =    2.622
peak=    3.939 closest distance to " CB  GLU A 152 " =    1.176
peak=    3.938 closest distance to " O   HOH Z 158 " =    2.979
peak=    3.935 closest distance to " O   HOH Z 427 " =    3.068
peak=    3.934 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.933 closest distance to " O   HOH Z 193 " =    1.906
peak=    3.915 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.913 closest distance to " CG1 ILE A  33 " =    1.259
peak=    3.908 closest distance to " O   HOH Z 272 " =    1.883
peak=    3.906 closest distance to " CD BLYS A 290 " =    0.978
peak=    3.900 closest distance to " O   HOH Z 108 " =    2.542
peak=    3.892 closest distance to " CB  VAL A 265 " =    1.226
peak=    3.891 closest distance to " CB  ASP A 140 " =    0.957
peak=    3.884 closest distance to " CB  GLU A 277 " =    3.691
peak=    3.875 closest distance to " O   HOH Z 303 " =    2.098
peak=    3.864 closest distance to " CA  PRO A  54 " =    1.353
peak=    3.862 closest distance to " CG2 VAL A 257 " =    0.935
peak=    3.854 closest distance to " CA  ALA A  51 " =    0.946
peak=    3.847 closest distance to " CB  SER A 216 " =    0.895
peak=    3.838 closest distance to " O   HOH Z 193 " =    1.776
peak=    3.836 closest distance to " NH1AARG A 145 " =    1.210
peak=    3.833 closest distance to " O   HOH Z 133 " =    2.363
peak=    3.818 closest distance to " O   HOH Z  20 " =    1.862
peak=    3.816 closest distance to " CA  THR A 264 " =    0.847
peak=    3.791 closest distance to " CB  VAL A 202 " =    1.614
peak=    3.791 closest distance to " O   HOH Z 411 " =    3.763
peak=    3.787 closest distance to " O   HOH Z 250 " =    1.529
peak=    3.787 closest distance to " O   HOH Z 197 " =    2.969
peak=    3.765 closest distance to " CA  ALA A  21 " =    1.241
peak=    3.765 closest distance to " CG2 THR A 221 " =    1.058
peak=    3.760 closest distance to " CA  THR A 221 " =    0.959
peak=    3.757 closest distance to " ND1 HIS A  86 " =    1.794
peak=    3.756 closest distance to " O   HOH Z 344 " =    3.237
peak=    3.747 closest distance to " CB  TRP A 179 " =    1.437
peak=    3.747 closest distance to " O   THR A 251 " =    1.295
peak=    3.747 closest distance to " NZ  LYS A 117 " =    3.309
peak=    3.746 closest distance to " CE  LYS A  76 " =    0.827
peak=    3.744 closest distance to " CZ  PHE A 192 " =    0.925
peak=    3.742 closest distance to " CD  ARG A  66 " =    2.295
peak=    3.742 closest distance to " O   HOH Z 203 " =    1.897
peak=    3.737 closest distance to " CD  LYS A 166 " =    1.279
peak=    3.724 closest distance to " CB  SER A 212 " =    1.076
peak=    3.722 closest distance to " O   HOH Z 346 " =    1.642
peak=    3.721 closest distance to " OD2 ASP A 286 " =    2.908
peak=    3.700 closest distance to " O   HOH Z 213 " =    1.926
peak=    3.698 closest distance to " O   HOH Z 214 " =    2.025
peak=    3.697 closest distance to " O   HOH Z 403 " =    1.725
peak=    3.688 closest distance to " O   HOH Z 189 " =    2.574
peak=    3.687 closest distance to " CG2BVAL A  41 " =    0.859
peak=    3.684 closest distance to " ND2 ASN A 110 " =    1.696
peak=    3.680 closest distance to " OD1 ASN A 217 " =    1.837
peak=    3.675 closest distance to " O   HOH Z  66 " =    2.104
peak=    3.668 closest distance to " O   HOH Z  54 " =    2.324
peak=    3.664 closest distance to " CA  ARG A  36 " =    1.145
peak=    3.664 closest distance to " O   HOH Z  21 " =    1.763
peak=    3.651 closest distance to " O   HOH Z 368 " =    3.667
peak=    3.644 closest distance to " CB  TYR A 169 " =    0.828
peak=    3.642 closest distance to " ND1 HIS A  81 " =    1.658
peak=    3.640 closest distance to " O   HOH Z  53 " =    2.553
peak=    3.630 closest distance to " CA  ASN A 215 " =    1.253
peak=    3.629 closest distance to " ND2 ASN A 249 " =    1.921
peak=    3.626 closest distance to " O   HOH Z 134 " =    1.346
peak=    3.624 closest distance to " O   HOH Z  88 " =    3.615
peak=    3.617 closest distance to " CG1BVAL A  72 " =    1.664
peak=    3.615 closest distance to " O   HOH Z 425 " =    2.051
peak=    3.615 closest distance to " CG  LEU A 167 " =    1.226
peak=    3.608 closest distance to " CB  MET A  40 " =    0.814
peak=    3.608 closest distance to " O   HOH Z 425 " =    1.301
peak=    3.600 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.599 closest distance to " O   HOH Z 245 " =    1.288
peak=    3.592 closest distance to " CG1 ILE A 151 " =    0.979
peak=    3.591 closest distance to " O   HOH Z  40 " =    1.890
peak=    3.590 closest distance to " O   ALA A 158 " =    1.290
peak=    3.585 closest distance to " CB  ASN A  39 " =    0.924
peak=    3.583 closest distance to " O   HOH Z  61 " =    1.615
peak=    3.583 closest distance to " O   HOH Z 371 " =    3.365
peak=    3.561 closest distance to " CD  ARG A  66 " =    2.345
peak=    3.556 closest distance to " CA  ALA A 158 " =    1.154
peak=    3.555 closest distance to " CD2 LEU A 297 " =    0.839
peak=    3.553 closest distance to " N   ARG A 156 " =    1.385
peak=    3.549 closest distance to " O   HOH Z 147 " =    1.778
peak=    3.548 closest distance to " O   HOH Z 171 " =    3.910
peak=    3.543 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.540 closest distance to " O   HOH Z   1 " =    2.095
peak=    3.537 closest distance to " CD1 ILE A 106 " =    0.781
peak=    3.534 closest distance to " O   HOH Z  49 " =    2.244
peak=    3.529 closest distance to " O   HOH Z 329 " =    3.787
peak=    3.528 closest distance to " NZ  LYS A 166 " =    3.087
peak=    3.521 closest distance to " N   ASN A 127 " =    1.273
peak=    3.519 closest distance to " O   HOH Z 426 " =    1.601
peak=    3.515 closest distance to " O   HOH Z 423 " =    1.816
peak=    3.508 closest distance to " CB  MET A  47 " =    0.981
peak=    3.497 closest distance to " CB  LEU A 143 " =    1.112
peak=    3.495 closest distance to " O   THR A 220 " =    1.270
peak=    3.471 closest distance to " O   HOH Z 133 " =    1.729
peak=    3.469 closest distance to " N   VAL A 126 " =    1.298
peak=    3.468 closest distance to " CE1 TYR A 186 " =    1.261
peak=    3.459 closest distance to " O   HOH Z 172 " =    3.629
peak=    3.458 closest distance to " CD  GLU A 152 " =    0.841
peak=    3.454 closest distance to " NH2BARG A 145 " =    2.213
peak=    3.449 closest distance to " CA  ASP A 140 " =    1.201
peak=    3.444 closest distance to " CB  LYS A 193 " =    0.958
peak=    3.443 closest distance to " O   HOH Z  97 " =    2.006
peak=    3.442 closest distance to " CG1 VAL A 153 " =    0.946
peak=    3.442 closest distance to " O   ALA A 165 " =    1.449
peak=    3.439 closest distance to " OG BSER A 164 " =    2.342
peak=    3.436 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.432 closest distance to " CB  ALA A 291 " =    1.309
peak=    3.427 closest distance to " CD  LYS A 119 " =    1.229
peak=    3.427 closest distance to " N   ASN A  39 " =    1.383
peak=    3.426 closest distance to " O   HOH Z 391 " =    2.957
peak=    3.426 closest distance to " CA  ALA A 160 " =    0.889
peak=    3.425 closest distance to " CA  ASP A 191 " =    0.788
peak=    3.424 closest distance to " CD1 LEU A  96 " =    0.708
peak=    3.423 closest distance to " O   HOH Z 193 " =    2.167
peak=    3.417 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.409 closest distance to " O   HOH Z 295 " =    1.454
peak=    3.408 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.405 closest distance to " O   HOH Z  64 " =    2.114
peak=    3.405 closest distance to " O   HOH Z 383 " =    2.113
peak=    3.403 closest distance to " CB  SER A 141 " =    0.997
peak=    3.402 closest distance to " O   HOH Z 305 " =    3.696
peak=    3.401 closest distance to " CZ  PHE A 208 " =    1.140
peak=    3.395 closest distance to " O   HOH Z 327 " =    1.933
peak=    3.393 closest distance to " CB  ILE A 120 " =    1.232
peak=    3.386 closest distance to " O   TRP A 274 " =    1.814
peak=    3.385 closest distance to " O   HOH Z  61 " =    1.518
peak=    3.383 closest distance to " CD  ARG A  14 " =    1.237
peak=    3.382 closest distance to " CG2 ILE A 120 " =    1.107
peak=    3.382 closest distance to " O   HOH Z 219 " =    1.838
peak=    3.380 closest distance to " O   HOH Z 281 " =    4.669
peak=    3.375 closest distance to " CG BARG A 275 " =    1.453
peak=    3.375 closest distance to " O   HOH Z 148 " =    3.301
peak=    3.363 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.358 closest distance to " CA  ALA A 154 " =    0.985
peak=    3.354 closest distance to " CB  ASN A 142 " =    0.974
peak=    3.352 closest distance to " CD  ARG A 219 " =    1.013
peak=    3.349 closest distance to " CD2 LEU A 255 " =    1.517
peak=    3.348 closest distance to " O   HOH Z 273 " =    2.782
peak=    3.346 closest distance to " CA  MET A 105 " =    1.039
peak=    3.339 closest distance to " O   HOH Z 247 " =    1.314
peak=    3.338 closest distance to " O   HOH Z 126 " =    1.925
peak=    3.337 closest distance to " CA  ALA A 291 " =    0.837
peak=    3.336 closest distance to " O   HOH Z 185 " =    1.862
peak=    3.336 closest distance to " CZ  PHE A 192 " =    0.743
peak=    3.325 closest distance to " O   HOH Z 403 " =    1.370
peak=    3.325 closest distance to " CA  ALA A 295 " =    1.085
peak=    3.324 closest distance to " CG2 VAL A 197 " =    1.168
peak=    3.323 closest distance to " CA  LYS A 117 " =    1.209
peak=    3.319 closest distance to " CD1 LEU A 228 " =    1.968
peak=    3.315 closest distance to " O   HOH Z 406 " =    1.637
peak=    3.314 closest distance to " O   HOH Z 128 " =    2.358
peak=    3.309 closest distance to " O   HOH Z  66 " =    2.071
peak=    3.307 closest distance to " O   HOH Z 359 " =    1.414
peak=    3.305 closest distance to " CB  ALA A 248 " =    1.010
peak=    3.303 closest distance to " O   HOH Z 209 " =    2.326
peak=    3.299 closest distance to " NH2AARG A 275 " =    3.692
peak=    3.296 closest distance to " O   HOH Z 183 " =    1.437
peak=    3.292 closest distance to " CB  ARG A 139 " =    0.899
peak=    3.291 closest distance to " CG1 VAL A 202 " =    2.014
peak=    3.291 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.287 closest distance to " O   HOH Z 199 " =    1.543
peak=    3.285 closest distance to " NE2 HIS A 115 " =    0.988
peak=    3.284 closest distance to " CG  ARG A 159 " =    0.951
peak=    3.281 closest distance to " O   HOH Z 227 " =    1.626
peak=    3.280 closest distance to " CG2 VAL A  78 " =    0.931
peak=    3.274 closest distance to " CB  ASN A 110 " =    1.224
peak=    3.273 closest distance to " O   HOH Z 163 " =    1.557
peak=    3.271 closest distance to " N   TYR A  15 " =    0.816
peak=    3.269 closest distance to " NE2 HIS A 207 " =    1.348
peak=    3.269 closest distance to " CB  LEU A 255 " =    0.782
peak=    3.266 closest distance to " O   HOH Z 116 " =    1.853
peak=    3.258 closest distance to " CB  ALA A 242 " =    0.928
peak=    3.252 closest distance to " CA  SER A  87 " =    1.049
peak=    3.248 closest distance to " O   HOH Z 263 " =    1.753
peak=    3.246 closest distance to " O   HOH Z 409 " =    3.120
peak=    3.246 closest distance to " OG  SER A  97 " =    3.551
peak=    3.245 closest distance to " O   HOH Z 109 " =    2.714
peak=    3.243 closest distance to " CA  GLY A 267 " =    1.150
peak=    3.240 closest distance to " CB  ALA A   9 " =    1.574
peak=    3.240 closest distance to " OE1 GLU A   2 " =    2.205
peak=    3.236 closest distance to " O   HOH Z  59 " =    2.186
peak=    3.235 closest distance to " O   HOH Z 345 " =    3.488
peak=    3.233 closest distance to " CG  MET A 185 " =    1.222
peak=    3.229 closest distance to " CB  PHE A  16 " =    0.989
peak=    3.226 closest distance to " O   HOH Z 271 " =    2.663
peak=    3.224 closest distance to " N   SER A 135 " =    1.389
peak=    3.223 closest distance to " CG  GLN A  88 " =    1.051
peak=    3.222 closest distance to " O   HOH Z 175 " =    3.612
peak=    3.221 closest distance to " O   HOH Z 419 " =    3.175
peak=    3.221 closest distance to " CE2 TYR A 293 " =    0.961
peak=    3.217 closest distance to " CB  ALA A 248 " =    1.312
peak=    3.215 closest distance to " CA  SER A 146 " =    1.818
peak=    3.215 closest distance to " CB  GLU A 152 " =    1.512
peak=    3.207 closest distance to " CB  TRP A 150 " =    1.306
peak=    3.205 closest distance to " CB  GLU A 236 " =    1.149
peak=    3.200 closest distance to " O   HOH Z 313 " =    1.743
peak=    3.200 closest distance to " CD2 TRP A 179 " =    1.369
peak=    3.199 closest distance to " N   SER A 134 " =    1.360
peak=    3.197 closest distance to " O   HOH Z 188 " =    2.287
peak=    3.187 closest distance to " CD1AILE A 234 " =    0.968
peak=    3.185 closest distance to " CA  ILE A  33 " =    1.670
peak=    3.185 closest distance to " CE2 TYR A 186 " =    0.871
peak=    3.184 closest distance to " O   HOH Z 421 " =    1.786
peak=    3.174 closest distance to " O   HOH Z 422 " =    2.675
peak=    3.173 closest distance to " CB  ALA A  71 " =    1.377
peak=    3.171 closest distance to " O   HOH Z   9 " =    2.130
peak=    3.171 closest distance to " CB  LYS A 117 " =    1.134
peak=    3.168 closest distance to " O   HOH Z 213 " =    2.355
peak=    3.168 closest distance to " O   HOH Z 112 " =    1.579
peak=    3.165 closest distance to " CG2 THR A 220 " =    0.933
peak=    3.155 closest distance to " CZ2 TRP A 179 " =    1.629
peak=    3.154 closest distance to " O   HOH Z  93 " =    2.783
peak=    3.154 closest distance to " CA  GLU A  46 " =    0.714
peak=    3.153 closest distance to " OG  SER A  22 " =    2.841
peak=    3.151 closest distance to " O   HOH Z  88 " =    3.012
peak=    3.150 closest distance to " C   TYR A 214 " =    1.470
peak=    3.149 closest distance to " O   GLY A  57 " =    2.606
peak=    3.149 closest distance to " CB  ALA A 114 " =    1.085
peak=    3.139 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.138 closest distance to " CA  ALA A 233 " =    1.371
peak=    3.137 closest distance to " OD1BASN A 224 " =    2.326
peak=    3.129 closest distance to " O   HOH Z  68 " =    1.603
peak=    3.129 closest distance to " O   SER A  87 " =    2.384
peak=    3.127 closest distance to " C   SER A  32 " =    1.070
peak=    3.120 closest distance to " OD1 ASP A 171 " =    1.230
peak=    3.111 closest distance to " O   TYR A 116 " =    1.298
peak=    3.111 closest distance to " CG  MET A 185 " =    1.076
peak=    3.107 closest distance to " CA  ASN A 217 " =    1.237
peak=    3.104 closest distance to " OD2 ASP A 200 " =    1.285
peak=    3.101 closest distance to " CD2 HIS A  81 " =    1.072
peak=    3.101 closest distance to " N   ASN A 252 " =    1.438
peak=    3.098 closest distance to " CB  ARG A 138 " =    1.033
peak=    3.097 closest distance to " CA  GLN A  88 " =    1.503
peak=    3.094 closest distance to " O   HOH Z 417 " =    2.079
peak=    3.092 closest distance to " CA  VAL A  41 " =    0.899
peak=    3.083 closest distance to " CA  ALA A 248 " =    1.245
peak=    3.083 closest distance to " N   GLY A  98 " =    1.161
peak=    3.083 closest distance to " O   HOH Z 353 " =    2.752
peak=    3.081 closest distance to " O   HOH Z 387 " =    3.170
peak=    3.077 closest distance to " CG2 ILE A 234 " =    0.877
peak=    3.075 closest distance to " CB  PHE A 283 " =    0.853
peak=    3.074 closest distance to " CA  TYR A 116 " =    1.418
peak=    3.065 closest distance to " O   HOH Z 302 " =    2.017
peak=    3.063 closest distance to " N   GLN A 278 " =    0.983
peak=    3.063 closest distance to " O   HOH Z 128 " =    2.206
peak=    3.057 closest distance to " O   HOH Z 365 " =    3.038
peak=    3.053 closest distance to " CB  ALA A 100 " =    1.232
peak=    3.047 closest distance to " O   HOH Z 234 " =    1.763
peak=    3.046 closest distance to " CG BARG A 102 " =    1.873
peak=    3.037 closest distance to " O   HOH Z 271 " =    2.363
peak=    3.001 closest distance to " O   HOH Z 258 " =    1.924

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.813 - 5.546
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.813 - 5.546

peak=   -4.446 closest distance to " O   HOH Z 266 " =    4.936
peak=   -4.378 closest distance to " O   VAL A  67 " =    2.786
peak=   -4.342 closest distance to " CB  PRO A 243 " =    2.613
peak=   -4.325 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.227 closest distance to " O   HOH Z 377 " =    2.020
peak=   -4.207 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -4.183 closest distance to " O   HOH Z  10 " =    1.581
peak=   -4.161 closest distance to " OE1 GLN A 223 " =    1.995
peak=   -4.149 closest distance to " N   ALA A  43 " =    2.544
peak=   -4.105 closest distance to " O   HOH Z 372 " =    2.473
peak=   -4.089 closest distance to " C   ASN A 187 " =    1.916
peak=   -4.051 closest distance to " CD  ARG A  14 " =    3.351
peak=   -4.045 closest distance to " O   HOH Z  52 " =    1.438
peak=   -4.035 closest distance to " O   HOH Z 198 " =    2.240
peak=   -4.030 closest distance to " O   PRO A 198 " =    1.310
peak=   -4.006 closest distance to " O   HOH Z 231 " =    2.192
peak=   -3.981 closest distance to " CB  ALA A 161 " =    2.660
peak=   -3.969 closest distance to " CZ3 TRP A 179 " =    1.117
peak=   -3.929 closest distance to " O   HOH Z 389 " =    1.893
peak=   -3.905 closest distance to " O   HOH Z 118 " =    3.213
peak=   -3.869 closest distance to " O   HOH Z  43 " =    1.493
peak=   -3.862 closest distance to " CG1 VAL A 250 " =    2.616
peak=   -3.853 closest distance to " O   HOH Z  38 " =    1.284
peak=   -3.851 closest distance to " C   HIS A 108 " =    1.049
peak=   -3.850 closest distance to " NH2AARG A 275 " =    5.546
peak=   -3.819 closest distance to " O   HOH Z 353 " =    2.127
peak=   -3.814 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.803 closest distance to " O   HOH Z  73 " =    2.144
peak=   -3.786 closest distance to " CB  ALA A  43 " =    2.605
peak=   -3.775 closest distance to " O   HOH Z 290 " =    1.287
peak=   -3.775 closest distance to " ND2 ASN A  45 " =    1.017
peak=   -3.753 closest distance to " ND2 ASN A  45 " =    1.725
peak=   -3.750 closest distance to " CG1 VAL A 112 " =    2.883
peak=   -3.744 closest distance to " CD2 LEU A 300 " =    2.928
peak=   -3.730 closest distance to " O   PRO A 163 " =    2.102
peak=   -3.730 closest distance to " O   HOH Z 185 " =    2.325
peak=   -3.716 closest distance to " CG1 VAL A 112 " =    2.611
peak=   -3.713 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.698 closest distance to " C   ASN A 285 " =    2.563
peak=   -3.693 closest distance to " CD1 LEU A 228 " =    2.405
peak=   -3.691 closest distance to " OG BSER A 134 " =    1.242
peak=   -3.691 closest distance to " OD1 ASN A 148 " =    1.583
peak=   -3.684 closest distance to " CB  ALA A 291 " =    2.271
peak=   -3.683 closest distance to " CA  GLY A 241 " =    3.086
peak=   -3.673 closest distance to " O   HOH Z 394 " =    1.486
peak=   -3.672 closest distance to " CD  GLN A  58 " =    1.072
peak=   -3.670 closest distance to " CD1 LEU A 101 " =    2.456
peak=   -3.642 closest distance to " CB  ALA A 291 " =    2.299
peak=   -3.629 closest distance to " CG  MET A 105 " =    0.989
peak=   -3.620 closest distance to " CD2 TYR A 293 " =    2.013
peak=   -3.620 closest distance to " CG  ARG A 269 " =    2.515
peak=   -3.607 closest distance to " CG  PHE A 283 " =    2.814
peak=   -3.604 closest distance to " CA  GLY A 203 " =    2.319
peak=   -3.593 closest distance to " CE  MET A 105 " =    2.242
peak=   -3.587 closest distance to " CG2 ILE A 263 " =    2.388
peak=   -3.572 closest distance to " O   HOH Z 435 " =    2.736
peak=   -3.572 closest distance to " O   HOH Z 393 " =    1.438
peak=   -3.568 closest distance to " ND2 ASN A 249 " =    2.370
peak=   -3.564 closest distance to " O   HOH Z 103 " =    1.824
peak=   -3.555 closest distance to " O   HOH Z 243 " =    2.165
peak=   -3.553 closest distance to " O   HOH Z 111 " =    2.140
peak=   -3.553 closest distance to " CB  ASN A  39 " =    2.267
peak=   -3.542 closest distance to " CD  ARG A 139 " =    1.564
peak=   -3.540 closest distance to " O   HOH Z 196 " =    2.078
peak=   -3.535 closest distance to " OD2 ASP A 171 " =    1.785
peak=   -3.532 closest distance to " O   HOH Z 407 " =    3.379
peak=   -3.524 closest distance to " O   GLY A 211 " =    1.518
peak=   -3.524 closest distance to " CD2 PHE A  61 " =    2.557
peak=   -3.523 closest distance to " OXT GLY A 302 " =    2.936
peak=   -3.521 closest distance to " CG  GLU A  53 " =    1.343
peak=   -3.520 closest distance to " C   ALA A 158 " =    1.308
peak=   -3.515 closest distance to " OG BSER A 134 " =    1.780
peak=   -3.508 closest distance to " CZ  PHE A  59 " =    1.667
peak=   -3.508 closest distance to " O   HOH Z 351 " =    1.478
peak=   -3.502 closest distance to " CD2 PHE A  59 " =    2.578
peak=   -3.496 closest distance to " O   HOH Z 198 " =    1.472
peak=   -3.494 closest distance to " NH2 ARG A  66 " =    2.025
peak=   -3.490 closest distance to " N   ALA A 226 " =    2.171
peak=   -3.488 closest distance to " CG  ARG A  66 " =    2.355
peak=   -3.484 closest distance to " NE2 GLN A  88 " =    1.959
peak=   -3.483 closest distance to " O   HOH Z 426 " =    1.663
peak=   -3.480 closest distance to " CD  ARG A 195 " =    5.159
peak=   -3.478 closest distance to " CE2 PHE A 218 " =    2.428
peak=   -3.476 closest distance to " OD1 ASP A 191 " =    1.663
peak=   -3.473 closest distance to " O   HOH Z 350 " =    1.828
peak=   -3.469 closest distance to " C   LEU A 143 " =    1.199
peak=   -3.463 closest distance to " O   ASN A 209 " =    2.060
peak=   -3.459 closest distance to " O   HOH Z  60 " =    2.573
peak=   -3.443 closest distance to " O   HOH Z 292 " =    4.669
peak=   -3.440 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.438 closest distance to " O   HOH Z 275 " =    1.564
peak=   -3.429 closest distance to " OG  SER A  62 " =    1.704
peak=   -3.410 closest distance to " CZ  TYR A 169 " =    1.763
peak=   -3.406 closest distance to " CB  TRP A  85 " =    2.383
peak=   -3.403 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.401 closest distance to " SG ACYS A 201 " =    2.040
peak=   -3.398 closest distance to " OD1 ASN A 187 " =    1.574
peak=   -3.396 closest distance to " O   HOH Z 252 " =    4.190
peak=   -3.391 closest distance to " O   HOH Z  19 " =    2.455
peak=   -3.386 closest distance to " O   HOH Z 311 " =    3.747
peak=   -3.383 closest distance to " CB  PHE A 192 " =    2.016
peak=   -3.371 closest distance to " NH2 ARG A 159 " =    2.405
peak=   -3.363 closest distance to " CG2 ILE A  49 " =    2.738
peak=   -3.357 closest distance to " O   HOH Z 313 " =    2.045
peak=   -3.355 closest distance to " O   HOH Z  93 " =    2.253
peak=   -3.354 closest distance to " O   HOH Z 211 " =    1.609
peak=   -3.349 closest distance to " CE3 TRP A 150 " =    2.075
peak=   -3.346 closest distance to " CG1 VAL A 125 " =    1.980
peak=   -3.336 closest distance to " CG2 VAL A 189 " =    2.119
peak=   -3.336 closest distance to " O   ALA A  10 " =    1.733
peak=   -3.330 closest distance to " CG1 VAL A 197 " =    2.339
peak=   -3.328 closest distance to " O   VAL A 189 " =    2.554
peak=   -3.327 closest distance to " O   HOH Z 348 " =    2.256
peak=   -3.327 closest distance to " ND2BASN A 224 " =    1.664
peak=   -3.325 closest distance to " CG  TRP A 266 " =    1.797
peak=   -3.322 closest distance to " O   HOH Z 298 " =    2.605
peak=   -3.321 closest distance to " O   HOH Z 189 " =    1.929
peak=   -3.313 closest distance to " NH1 ARG A 195 " =    2.625
peak=   -3.311 closest distance to " CD  PRO A 213 " =    2.224
peak=   -3.310 closest distance to " OH  TYR A 169 " =    1.091
peak=   -3.308 closest distance to " O   HOH Z 128 " =    2.509
peak=   -3.308 closest distance to " CE BMET A  47 " =    2.266
peak=   -3.304 closest distance to " OE1 GLN A  88 " =    1.240
peak=   -3.299 closest distance to " CB  PRO A 163 " =    2.544
peak=   -3.289 closest distance to " O   HOH Z  11 " =    1.792
peak=   -3.288 closest distance to " O   HOH Z 166 " =    1.851
peak=   -3.285 closest distance to " O   HOH Z 380 " =    5.106
peak=   -3.282 closest distance to " CA  SER A 135 " =    1.310
peak=   -3.279 closest distance to " O   HOH Z 417 " =    2.554
peak=   -3.276 closest distance to " O   HOH Z 253 " =    4.135
peak=   -3.273 closest distance to " O   HOH Z 241 " =    1.367
peak=   -3.273 closest distance to " O   GLY A  80 " =    2.609
peak=   -3.269 closest distance to " CG  PRO A 243 " =    1.744
peak=   -3.268 closest distance to " O   HOH Z   6 " =    2.224
peak=   -3.266 closest distance to " O   HOH Z 396 " =    1.765
peak=   -3.257 closest distance to " CD1 ILE A 239 " =    2.056
peak=   -3.256 closest distance to " CA  GLY A  98 " =    2.101
peak=   -3.253 closest distance to " CB  ASP A 132 " =    2.291
peak=   -3.253 closest distance to " OE2 GLU A   2 " =    1.801
peak=   -3.251 closest distance to " ND2 ASN A  60 " =    1.446
peak=   -3.251 closest distance to " CE3 TRP A 274 " =    2.447
peak=   -3.251 closest distance to " CG2 THR A 221 " =    2.270
peak=   -3.250 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.246 closest distance to " O   HOH Z  51 " =    1.595
peak=   -3.238 closest distance to " CD2 LEU A 167 " =    1.807
peak=   -3.238 closest distance to " O   HOH Z  13 " =    1.541
peak=   -3.231 closest distance to " CG  LEU A  83 " =    1.948
peak=   -3.231 closest distance to " O   HOH Z 174 " =    3.055
peak=   -3.228 closest distance to " CB  TYR A  15 " =    2.210
peak=   -3.218 closest distance to " CD2 TYR A 247 " =    2.442
peak=   -3.214 closest distance to " CB  ALA A   9 " =    2.558
peak=   -3.214 closest distance to " O   HOH Z 298 " =    1.253
peak=   -3.209 closest distance to " CG  PRO A 163 " =    2.463
peak=   -3.208 closest distance to " O   SER A 135 " =    1.505
peak=   -3.204 closest distance to " O   HOH Z  76 " =    1.958
peak=   -3.200 closest distance to " O   HOH Z 436 " =    1.441
peak=   -3.198 closest distance to " N   THR A 157 " =    1.556
peak=   -3.196 closest distance to " CD2 LEU A 237 " =    2.246
peak=   -3.195 closest distance to " O   HOH Z 193 " =    1.636
peak=   -3.191 closest distance to " C   SER A 206 " =    1.481
peak=   -3.190 closest distance to " O   HOH Z  90 " =    1.639
peak=   -3.187 closest distance to " NH2 ARG A  79 " =    1.550
peak=   -3.187 closest distance to " O   HOH Z 234 " =    4.351
peak=   -3.185 closest distance to " CB  ASP A 286 " =    2.216
peak=   -3.183 closest distance to " CD2 TRP A 274 " =    2.491
peak=   -3.183 closest distance to " O   PHE A 218 " =    1.589
peak=   -3.181 closest distance to " O   VAL A 125 " =    2.346
peak=   -3.181 closest distance to " O   TRP A  70 " =    1.519
peak=   -3.181 closest distance to " CD1 LEU A 297 " =    2.555
peak=   -3.176 closest distance to " O   GLY A 196 " =    1.179
peak=   -3.173 closest distance to " O   HOH Z  88 " =    2.277
peak=   -3.167 closest distance to " CZ  PHE A  38 " =    2.397
peak=   -3.165 closest distance to " CE  MET A  93 " =    1.540
peak=   -3.163 closest distance to " CH2 TRP A 177 " =    2.176
peak=   -3.158 closest distance to " O   HOH Z   6 " =    1.610
peak=   -3.154 closest distance to " CB  CYS A 254 " =    2.489
peak=   -3.152 closest distance to " CA  GLY A 241 " =    2.279
peak=   -3.144 closest distance to " O   HOH Z 324 " =    2.301
peak=   -3.142 closest distance to " C   GLY A  17 " =    1.234
peak=   -3.139 closest distance to " O   GLN A 240 " =    2.457
peak=   -3.139 closest distance to " CD2 LEU A 237 " =    2.865
peak=   -3.129 closest distance to " SG  CYS A 254 " =    2.866
peak=   -3.128 closest distance to " NE2 GLN A 103 " =    1.742
peak=   -3.126 closest distance to " O   HOH Z 295 " =    1.530
peak=   -3.123 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.119 closest distance to " N   ALA A 248 " =    1.598
peak=   -3.116 closest distance to " O   ALA A  34 " =    2.584
peak=   -3.112 closest distance to " O   ASN A 301 " =    1.450
peak=   -3.099 closest distance to " O   HOH Z 388 " =    1.988
peak=   -3.095 closest distance to " O   HOH Z 106 " =    1.987
peak=   -3.078 closest distance to " CE3 TRP A  70 " =    1.846
peak=   -3.073 closest distance to " OD1 ASP A 171 " =    1.570
peak=   -3.073 closest distance to " O   HOH Z 414 " =    1.707
peak=   -3.066 closest distance to " ND2 ASN A  60 " =    1.870
peak=   -3.058 closest distance to " O   SER A 164 " =    2.046
peak=   -3.052 closest distance to " O   HOH Z 166 " =    1.601
peak=   -3.023 closest distance to " O   GLY A  80 " =    2.313

================= 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    :  0.3263 0.3237   6.048001e+00   6.052688e+00
   1_bss:  0.3129 0.3113   6.027781e+00   6.027719e+00
   1_xyz:  0.1867 0.2089   5.553471e+00   5.654614e+00
   1_adp:  0.1731 0.2128   5.503249e+00   5.672636e+00
   1_occ:  0.1725 0.2127   5.500662e+00   5.670224e+00
   2_bss:  0.1702 0.2090   5.493857e+00   5.663284e+00
   2_xyz:  0.1284 0.1709   5.253672e+00   5.470385e+00
   2_adp:  0.1202 0.1642   5.200235e+00   5.433306e+00
   2_occ:  0.1201 0.1641   5.200029e+00   5.433378e+00
   3_bss:  0.1202 0.1638   5.199052e+00   5.431072e+00
   3_xyz:  0.1146 0.1613   5.170011e+00   5.411716e+00
   3_adp:  0.1137 0.1598   5.160757e+00   5.401470e+00
   3_occ:  0.1137 0.1597   5.160802e+00   5.401873e+00
   4_bss:  0.1136 0.1597   5.160629e+00   5.401667e+00
   4_xyz:  0.1082 0.1591   5.133589e+00   5.393075e+00
   4_adp:  0.1078 0.1593   5.132026e+00   5.393009e+00
   4_occ:  0.1078 0.1594   5.132221e+00   5.393492e+00
   5_bss:  0.1077 0.1593   5.132318e+00   5.393502e+00
   5_xyz:  0.1108 0.1600   5.150993e+00   5.403338e+00
   5_adp:  0.1103 0.1614   5.152890e+00   5.409178e+00
   5_occ:  0.1103 0.1615   5.153195e+00   5.409711e+00
   5_bss:  0.1103 0.1614   5.153223e+00   5.409787e+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:  0.311  50.000   1.814  -1.910  -1.612  -0.000  -0.000  -0.000
   1_xyz:  0.311  50.000   1.814  -1.910  -1.612  -0.000  -0.000  -0.000
   1_adp:  0.311  50.000   1.814  -1.910  -1.612  -0.000  -0.000  -0.000
   1_occ:  0.311  50.000   1.814  -1.910  -1.612  -0.000  -0.000  -0.000
   2_bss:  0.335  62.013  -1.361  -2.689  -2.045  -0.000  -0.000  -0.000
   2_xyz:  0.335  62.013  -1.361  -2.689  -2.045  -0.000  -0.000  -0.000
   2_adp:  0.335  62.013  -1.361  -2.689  -2.045  -0.000  -0.000  -0.000
   2_occ:  0.335  62.013  -1.361  -2.689  -2.045  -0.000  -0.000  -0.000
   3_bss:  0.330  62.013  -1.965  -2.547  -1.783  -0.000  -0.000  -0.000
   3_xyz:  0.330  62.013  -1.965  -2.547  -1.783  -0.000  -0.000  -0.000
   3_adp:  0.330  62.013  -1.965  -2.547  -1.783  -0.000  -0.000  -0.000
   3_occ:  0.330  62.013  -1.965  -2.547  -1.783  -0.000  -0.000  -0.000
   4_bss:  0.326  62.013  -2.117  -2.397  -1.632  -0.000  -0.000  -0.000
   4_xyz:  0.326  62.013  -2.117  -2.397  -1.632  -0.000  -0.000  -0.000
   4_adp:  0.326  62.013  -2.117  -2.397  -1.632  -0.000  -0.000  -0.000
   4_occ:  0.326  62.013  -2.117  -2.397  -1.632  -0.000  -0.000  -0.000
   5_bss:  0.326  62.013  -1.977  -2.193  -1.405  -0.000  -0.000  -0.000
   5_xyz:  0.326  62.013  -1.977  -2.193  -1.405  -0.000  -0.000  -0.000
   5_adp:  0.326  62.013  -1.977  -2.193  -1.405  -0.000  -0.000  -0.000
   5_occ:  0.326  62.013  -1.977  -2.193  -1.405  -0.000  -0.000  -0.000
   5_bss:  0.321  62.016  -1.823  -2.002  -1.224  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.466 0.7104  0.8781    30994.036
   1_bss:  33.293 0.7220  0.8799    28216.286
   1_xyz:  19.922 0.8638  1.0001    11274.170
   1_adp:  20.557 0.8569  0.9987    11692.503
   1_occ:  20.512 0.8572  0.9989    11607.125
   2_bss:  20.261 0.8597  0.9510    11404.385
   2_xyz:  15.757 0.9003  0.9735     7576.618
   2_adp:  14.880 0.9078  0.9730     6968.549
   2_occ:  14.875 0.9079  0.9728     6965.205
   3_bss:  14.849 0.9080  0.9698     6926.078
   3_xyz:  14.373 0.9122  0.9703     6612.599
   3_adp:  14.130 0.9142  0.9670     6504.460
   3_occ:  14.137 0.9142  0.9669     6505.467
   4_bss:  14.138 0.9142  0.9685     6502.143
   4_xyz:  14.013 0.9151  0.9694     6428.704
   4_adp:  14.005 0.9152  0.9645     6428.858
   4_occ:  14.014 0.9151  0.9643     6432.536
   5_bss:  14.017 0.9151  0.9708     6432.751
   5_xyz:  14.165 0.9140  0.9691     6538.185
   5_adp:  14.301 0.9129  0.9623     6596.840
   5_occ:  14.311 0.9128  0.9622     6602.415
   5_bss:  14.315 0.9128  0.9682     6604.504
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6287e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6287e-01
   1_xyz:   1.101  0.008  0.073 15.166  0.004  4.117   7.0923e-02
   1_adp:   1.101  0.008  0.073 15.166  0.004  4.117   7.0923e-02
   1_occ:   1.101  0.008  0.073 15.166  0.004  4.117   7.0923e-02
   2_bss:   1.101  0.008  0.073 15.166  0.004  4.117   7.0923e-02
   2_xyz:   1.074  0.009  0.077 14.680  0.004  4.131   6.8261e-02
   2_adp:   1.074  0.009  0.077 14.680  0.004  4.131   6.8261e-02
   2_occ:   1.074  0.009  0.077 14.680  0.004  4.131   6.8261e-02
   3_bss:   1.074  0.009  0.077 14.680  0.004  4.131   6.8261e-02
   3_xyz:   1.000  0.008  0.075 14.583  0.004  4.115   6.0887e-02
   3_adp:   1.000  0.008  0.075 14.583  0.004  4.115   6.0887e-02
   3_occ:   1.000  0.008  0.075 14.583  0.004  4.115   6.0887e-02
   4_bss:   1.000  0.008  0.075 14.583  0.004  4.115   6.0887e-02
   4_xyz:   1.168  0.012  0.087 14.965  0.005  4.118   8.2677e-02
   4_adp:   1.168  0.012  0.087 14.965  0.005  4.118   8.2677e-02
   4_occ:   1.168  0.012  0.087 14.965  0.005  4.118   8.2677e-02
   5_bss:   1.168  0.012  0.087 14.965  0.005  4.118   8.2677e-02
   5_xyz:   1.025  0.009  0.077 14.626  0.004  4.117   6.3166e-02
   5_adp:   1.025  0.009  0.077 14.626  0.004  4.117   6.3166e-02
   5_occ:   1.025  0.009  0.077 14.626  0.004  4.117   6.3166e-02
   5_bss:   1.025  0.009  0.077 14.626  0.004  4.117   6.3166e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.680   2.4275e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.680   2.4275e-01
   1_xyz:   9.117  0.045  0.255 87.483  0.028  2.316   1.2504e-01
   1_adp:   9.117  0.045  0.255 87.483  0.028  2.316   1.2504e-01
   1_occ:   9.117  0.045  0.255 87.483  0.028  2.316   1.2504e-01
   2_bss:   9.117  0.045  0.255 87.483  0.028  2.316   1.2504e-01
   2_xyz:   7.963  0.047  0.227 83.080  0.039  2.320   1.0086e-01
   2_adp:   7.963  0.047  0.227 83.080  0.039  2.320   1.0086e-01
   2_occ:   7.963  0.047  0.227 83.080  0.039  2.320   1.0086e-01
   3_bss:   7.963  0.047  0.227 83.080  0.039  2.320   1.0086e-01
   3_xyz:   7.960  0.042  0.229 82.953  0.040  2.347   4.1137e-02
   3_adp:   7.960  0.042  0.229 82.953  0.040  2.347   4.1137e-02
   3_occ:   7.960  0.042  0.229 82.953  0.040  2.347   4.1137e-02
   4_bss:   7.960  0.042  0.229 82.953  0.040  2.347   4.1137e-02
   4_xyz:   7.486  0.049  0.271 82.934  0.042  2.280   6.6517e-02
   4_adp:   7.486  0.049  0.271 82.934  0.042  2.280   6.6517e-02
   4_occ:   7.486  0.049  0.271 82.934  0.042  2.280   6.6517e-02
   5_bss:   7.486  0.049  0.271 82.934  0.042  2.280   6.6517e-02
   5_xyz:   7.652  0.043  0.234 83.491  0.039  2.356   4.1814e-02
   5_adp:   7.652  0.043  0.234 83.491  0.039  2.356   4.1814e-02
   5_occ:   7.652  0.043  0.234 83.491  0.039  2.356   4.1814e-02
   5_bss:   7.652  0.043  0.234 83.491  0.039  2.356   4.1814e-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:  63.67   0.00  16.76  62.71   0.00  12.88  63.67   5.58  37.85
   1_occ:  63.67   0.00  16.76  62.71   0.00  12.88  63.67   5.58  37.85
   2_bss:  63.67   0.00  16.76  62.71   0.00  12.88  63.67   5.58  37.85
   2_xyz:  63.67   0.00  16.76  62.71   0.00  12.88  63.67   5.58  37.85
   2_adp:  77.87   0.75  17.33  77.87   0.75  13.13  74.58   5.62  40.22
   2_occ:  77.87   0.75  17.33  77.87   0.75  13.13  74.58   5.62  40.22
   3_bss:  77.87   0.75  17.33  77.87   0.75  13.13  74.58   5.62  40.22
   3_xyz:  77.87   0.75  17.33  77.87   0.75  13.13  74.58   5.62  40.22
   3_adp:  79.11   0.83  17.13  79.11   0.83  12.99  75.86   2.98  39.71
   3_occ:  79.11   0.83  17.13  79.11   0.83  12.99  75.86   2.98  39.71
   4_bss:  79.11   0.83  17.13  79.11   0.83  12.99  75.86   2.98  39.71
   4_xyz:  79.11   0.83  17.13  79.11   0.83  12.99  75.86   2.98  39.71
   4_adp:  81.92   0.52  16.99  81.92   0.52  12.87  78.24   3.60  39.39
   4_occ:  81.92   0.52  16.99  81.92   0.52  12.87  78.24   3.60  39.39
   5_bss:  81.92   0.52  16.99  81.92   0.52  12.87  78.24   3.60  39.39
   5_xyz:  81.92   0.52  16.99  81.92   0.52  12.87  78.24   3.60  39.39
   5_adp:  93.10   0.00  17.15  93.10   0.00  12.86  84.84   4.66  40.53
   5_occ:  93.10   0.00  17.15  93.10   0.00  12.86  84.84   4.66  40.53
   5_bss:  93.10   0.00  17.15  93.10   0.00  12.86  84.85   4.67  40.54
------------------------------------------------------------------------
 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:    1.272    0.014    0.309
   1_adp:    1.272    0.014    0.309
   1_occ:    1.272    0.014    0.309
   2_bss:    1.272    0.014    0.309
   2_xyz:    0.870    0.030    0.380
   2_adp:    0.870    0.030    0.380
   2_occ:    0.870    0.030    0.380
   3_bss:    0.870    0.030    0.380
   3_xyz:    0.915    0.032    0.402
   3_adp:    0.915    0.032    0.402
   3_occ:    0.915    0.032    0.402
   4_bss:    0.915    0.032    0.402
   4_xyz:    0.918    0.037    0.415
   4_adp:    0.918    0.037    0.415
   4_occ:    0.918    0.037    0.415
   5_bss:    0.918    0.037    0.415
   5_xyz:    0.930    0.040    0.417
   5_adp:    0.930    0.040    0.417
   5_occ:    0.930    0.040    0.417
   5_bss:    0.930    0.040    0.417
------------------------------------------------------------------------

CPU time actual refinement: 318.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/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_1159/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1159/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.89 
  Macro-tasks:
    bulk solvent and scale       = 38.07  
    individual site refinement   = 134.93 
    weights calculation          = 28.22  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.81 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 99.76  
    alpha_beta                      = 7.92   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 110.23 
    fmodel                         = 6.56   
    r_factors                      = 0.23   
    phase_errors                   = 11.28  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 238.46 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.465 micro seconds
Total CPU time: 5.52 minutes
from_scatterers_fft:    646 calls, 99.40 s
gradients_fft:          591 calls, 96.34 s

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

# Date 2008-01-16 Time 06:34:27 PST -0800 (1200494067.85 s)
Start R-work = 0.3263, R-free = 0.3237 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1791 (no bulk solvent and anisotropic scale)

Start R-work = 0.3129, R-free = 0.3113
Final R-work = 0.1103, R-free = 0.1614