# Date 2008-10-14 Time 09:11:02 PDT -0700 (1224000662.66 s)
#phil __OFF__

Command line arguments: "1l2h.mtz" "1l2h.pdb" "twin_law=h,-k,-l" "--overwrite"

HOST = chevy.lbl.gov
HOSTTYPE = x86_64-linux
USER = afonine
PID = 2730

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.4
  Release tag: 1
  cctbx tag: 2008_10_09_1338
  Platform: intel-linux-2.6-x86_64 linux
  User: afonine
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Nathaniel Echols,
  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.twinning.twin_law = h,-k,-l

Working crystal symmetry after inspecting all inputs:
  Unit cell: (53.89, 53.89, 77.36, 90, 90, 90)
  Space group: P 43 (No. 78)

  Monomer Library directory:
    "/net/chevy/raid1/afonine/PROJ/phenix/phenix-1.4-1/ext_ref_files/mon_lib"
  Total number of atoms: 1294
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1168
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 144, 1161
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 136, 'PCIS': 1}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 144, 1161
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 136, 'PCIS': 1}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1174
    Chain: " "
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 126
          Classifications: {'water': 126}
          Link IDs: {None: 125}
  Time building chain proxies: 1.10, per 1000 atoms: 0.85

  Number of scatterers: 1294
  At special positions: 0
  Unit cell: (53.89, 53.89, 77.36, 90, 90, 90)
  Space group: P 43 (No. 78)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       8     16.00
     O     351      8.00
     N     194      7.00
     C     741      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

F-obs:
  1l2h.mtz:FOBS,SIGFOBS

R-free flags:
  1l2h.mtz:FLAGS

Miller array info: 1l2h.mtz:FOBS,SIGFOBS
Observation type: xray.amplitude
Type of data: double, size=31781
Type of sigmas: double, size=31781
Number of Miller indices: 31781
Anomalous flag: False
Unit cell: (53.89, 53.89, 77.36, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 896
Resolution range: 18.63 1.53878
Completeness in resolution range: 0.97056
Completeness with d_max=infinity: 0.969998

Number of F-obs in resolution range:                   31781
Number of F-obs <= 0:                                  449
Refinement resolution range: d_max =  18.6300
                             d_min =   1.5388


Fobs statistics after all cutoffs applied:

Miller array info: None
Observation type: xray.amplitude
Type of data: double, size=31332
Type of sigmas: double, size=31332
Number of Miller indices: 31332
Anomalous flag: False
Unit cell: (53.89, 53.89, 77.36, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 859
Resolution range: 18.63 1.53878
Completeness in resolution range: 0.956848
Completeness with d_max=infinity: 0.956293
Miller array info: 1l2h.mtz:FLAGS
Observation type: None
Type of data: int, size=31781
Type of sigmas: None
Number of Miller indices: 31781
Anomalous flag: False
Unit cell: (53.89, 53.89, 77.36, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 896
Resolution range: 18.63 1.53878
Completeness in resolution range: 0.97056
Completeness with d_max=infinity: 0.969998

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 18.6313 -  3.3096 [2506/3334]  2414    92   3.7%
  bin  2:  3.3096 -  2.6293 [3276/3286]  3135   141   4.3%
  bin  3:  2.6293 -  2.2976 [3279/3281]  3143   136   4.1%
  bin  4:  2.2976 -  2.0879 [3263/3265]  3074   189   5.8%
  bin  5:  2.0879 -  1.9384 [3259/3265]  3105   154   4.7%
  bin  6:  1.9384 -  1.8242 [3257/3279]  3093   164   5.0%
  bin  7:  1.8242 -  1.7329 [3229/3266]  3053   176   5.5%
  bin  8:  1.7329 -  1.6575 [3181/3238]  3015   166   5.2%
  bin  9:  1.6575 -  1.5938 [3159/3272]  3010   149   4.7%
  bin 10:  1.5938 -  1.5388 [2923/3259]  2799   124   4.2%
                                overall 29841  1491   4.8%

No array of experimental phases found.


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

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

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

  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.04 seconds
  Histogram of bond lengths:
        1.02 -     1.21: 86
        1.21 -     1.40: 378
        1.40 -     1.59: 563
        1.59 -     1.77: 150
        1.77 -     1.96: 11
  Bond restraints sorted by residual:
                 atom i - atom j                ideal  model  delta   weight residual
  pdb=" C   PRO A  57 " - pdb=" N   VAL A  58 " 1.329  1.507 -0.178 5.10e+03 1.62e+02
  pdb=" CA  TRP A  42 " - pdb=" CB  TRP A  42 " 1.530  1.780 -0.250 2.50e+03 1.56e+02
  pdb=" C   SER A  13 " - pdb=" N   GLN A  14 " 1.329  1.157  0.172 5.10e+03 1.50e+02
  pdb=" C   LEU A  18 " - pdb=" N   VAL A  19 " 1.329  1.500 -0.171 5.10e+03 1.50e+02
  pdb=" ND1 HIS A  30 " - pdb=" CE1 HIS A  30 " 1.321  1.199  0.122 1.00e+04 1.49e+02
  ... (remaining 1183 not shown)
  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 281
        2.75 -     3.29: 1264
        3.29 -     3.83: 2416
        3.83 -     4.36: 3330
        4.36 -     4.90: 5032
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb=" O   HOH    11 " - pdb=" O   HOH    72 "  2.218 3.040
  pdb=" O   HOH    81 " - pdb=" O   HOH    89 "  2.261 3.040
  pdb=" O   HOH    99 " - pdb=" O   HOH   118 "  2.290 3.040
  pdb=" O   HOH    78 " - pdb=" O   HOH    88 "  2.296 3.040
  pdb=" OE1 GLN A 116 " - pdb=" O   HOH    29 "  2.315 3.040
  ... (remaining 12318 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.05 -    18.02: 352
       18.02 -    35.98: 57
       35.98 -    53.94: 32
       53.94 -    71.90: 8
       71.90 -    89.86: 9
  Dihedral angle restraints sorted by residual:
  pdb=" CA  GLU A 128 "
  pdb=" C   GLU A 128 "
  pdb=" N   ASN A 129 "
  pdb=" CA  ASN A 129 "
      ideal   model   delta periodicty    weight residual
     180.00  155.09   24.91     1       4.00e-02 2.48e+01
  pdb=" CA  PRO A 131 "
  pdb=" C   PRO A 131 "
  pdb=" N   VAL A 132 "
  pdb=" CA  VAL A 132 "
      ideal   model   delta periodicty    weight residual
     180.00  156.24   23.76     1       4.00e-02 2.26e+01
  pdb=" CA  LEU A  10 "
  pdb=" C   LEU A  10 "
  pdb=" N   ARG A  11 "
  pdb=" CA  ARG A  11 "
      ideal   model   delta periodicty    weight residual
     180.00  156.72   23.28     1       4.00e-02 2.17e+01
  ... (remaining 455 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       8     15.96       2
   O     351      7.97       2
   N     194      6.97       2
   C     741      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 =================

Refinement flags and selection counts:
  individual_sites       =  True (1294 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 1294 aniso = 0)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (14 atoms)
  group_anomalous        = False

n_use            =  1294
n_use_u_iso      =  1294
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 =  1294

==================== 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/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001.eff

Writing geometry restraints to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001.geo

CPU time processing inputs: 3.43


============================ 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 = 53.88999939 53.88999939 77.36000061 90 90 90
    space_group = "P 43"
  }
  input {
    pdb {
      file_name = "/net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h.pdb"
    }
    xray_data {
      file_name = "1l2h.mtz"
      labels = "FOBS,SIGFOBS"
      r_free_flags {
        file_name = "1l2h.mtz"
        label = "FLAGS"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "1l2h_refine"
    serial = 1
  }
  twinning {
    twin_law = "h,-k,-l"
  }
}
#phil __OFF__


=============================== refinement start ==============================


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


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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.2286   r_free= 0.2607   ksol= 0.47   Bsol= 34.39   scale= 0.386   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.37,-2.74,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.077528           |
| twin fraction: 0.38  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 18.6313 -  3.8666 0.98   1285   46 0.1935 0.2164        None        None|
|  2:  3.8666 -  3.0735 0.98   1920   74 0.1735 0.2043        None        None|
|  3:  3.0735 -  2.6863 0.98   1961   90 0.2078 0.2773        None        None|
|  4:  2.6863 -  2.4413 0.98   1960   87 0.2431 0.2711        None        None|
|  5:  2.4413 -  2.2666 0.98   1956   90 0.2414 0.2528        None        None|
|  6:  2.2666 -  2.1332 0.98   1915  110 0.2213 0.2306        None        None|
|  7:  2.1332 -  2.0265 0.98   1958  123 0.2354 0.2548        None        None|
|  8:  2.0265 -  1.9384 0.98   1916   92 0.2518 0.3114        None        None|
|  9:  1.9384 -  1.8638 0.98   1916  114 0.2609 0.3154        None        None|
| 10:  1.8638 -  1.7996 0.98   1909  101 0.2837 0.2930        None        None|
| 11:  1.7996 -  1.7433 0.98   1914  104 0.2911 0.3061        None        None|
| 12:  1.7433 -  1.6935 0.98   1914  107 0.2973 0.3190        None        None|
| 13:  1.6935 -  1.6490 0.98   1910  107 0.3050 0.3149        None        None|
| 14:  1.6490 -  1.6088 0.98   1880   80 0.3255 0.2889        None        None|
| 15:  1.6088 -  1.5722 0.98   1808   97 0.3301 0.3267        None        None|
| 16:  1.5722 -  1.5388 0.98   1719   69 0.3764 0.3503        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 18.6313 -  3.8666  1285    46  0.75  31.65   None     0.83       2977.33|
|  2:  3.8666 -  3.0735  1920    74  0.74  32.54   None     0.85       2882.03|
|  3:  3.0735 -  2.6863  1961    90  0.73  34.22   None     0.82       1495.21|
|  4:  2.6863 -  2.4413  1960    87  0.71  35.91   None     0.80        858.38|
|  5:  2.4413 -  2.2666  1956    90  0.72  35.21   None     0.82        647.86|
|  6:  2.2666 -  2.1332  1915   110  0.71  35.78   None     0.85        539.04|
|  7:  2.1332 -  2.0265  1958   123  0.67  39.15   None     0.86        429.56|
|  8:  2.0265 -  1.9384  1916    92  0.66  39.98   None     0.86        318.39|
|  9:  1.9384 -  1.8638  1916   114  0.66  39.73   None     0.85        230.07|
| 10:  1.8638 -  1.7996  1909   101  0.64  41.73   None     0.85        168.39|
| 11:  1.7996 -  1.7433  1914   104  0.63  42.19   None     0.85        125.46|
| 12:  1.7433 -  1.6935  1914   107  0.63  42.34   None     0.84         95.09|
| 13:  1.6935 -  1.6490  1910   107  0.63  42.07   None     0.85         73.75|
| 14:  1.6490 -  1.6088  1880    80  0.62  43.52   None     0.86         60.04|
| 15:  1.6088 -  1.5722  1808    97  0.62  43.41   None     0.89         51.53|
| 16:  1.5722 -  1.5388  1719    69  0.61  44.38   None     0.89         45.55|
|alpha:            min =        0.80 max =            0.89 mean =         0.85|
|beta:             min =       43.86 max =         3552.55 mean =       668.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.90 mean =        38.89|
|phase err.(test): min =        0.01 max =           89.28 mean =        40.50|
|-----------------------------------------------------------------------------|

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


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.026:   284 |   0.010 -   2.018:   437 |  2.218 -  2.487:       23 |
| 0.026 - 0.052:   275 |   2.018 -   4.026:   374 |  2.487 -  2.755:      258 |
| 0.052 - 0.078:   199 |   4.026 -   6.034:   309 |  2.755 -  3.023:      631 |
| 0.078 - 0.104:   181 |   6.034 -   8.042:   204 |  3.023 -  3.291:      633 |
| 0.104 - 0.130:   115 |   8.042 -  10.050:   134 |  3.291 -  3.559:      969 |
| 0.130 - 0.156:    74 |  10.050 -  12.058:    80 |  3.559 -  3.827:     1447 |
| 0.156 - 0.182:    42 |  12.058 -  14.066:    37 |  3.827 -  4.095:     1557 |
| 0.182 - 0.208:    12 |  14.066 -  16.075:    11 |  4.095 -  4.363:     1773 |
| 0.208 - 0.234:     4 |  16.075 -  18.083:     5 |  4.363 -  4.632:     2267 |
| 0.234 - 0.260:     2 |  18.083 -  20.091:     2 |  4.632 -  4.900:     2765 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     1188 |   0.081    0.260  0.000 |      16.206 |              |
|     angle |     1593 |   5.762   20.091  0.010 |      10.747 |              |
| chirality |      173 |   0.378    0.969  0.001 |       3.572 |        2.523 |
| planarity |      206 |   0.029    0.073  0.000 |       9.372 |              |
|  dihedral |      458 |  22.033   89.863  0.054 |       2.306 |              |
| nonbonded |     1188 |   4.127    4.900  2.218 |       0.208 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      22.97   22.97   22.97    None  None   None       |
|    all(noH): 1294   0      22.97   22.97   22.97    None  None   None       |
|    Sol.    : 126    0      22.97   22.97   22.97    None  None   None       |
|    Mac.    : 1168   0      22.97   22.97   22.97    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:    22.974 -  22.974: 1294   |   5:    22.974 -  22.974:    0        |
|      1:    22.974 -  22.974:    0   |   6:    22.974 -  22.974:    0        |
|      2:    22.974 -  22.974:    0   |   7:    22.974 -  22.974:    0        |
|      3:    22.974 -  22.974:    0   |   8:    22.974 -  22.974:    0        |
|      4:    22.974 -  22.974:    0   |   9:    22.974 -  22.974:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      12.01   31.98   22.21    None  None   None       |
|    all(noH): 1294   0      12.01   31.98   22.21    None  None   None       |
|    Sol.    : 126    0      12.22   31.96   21.34    None  None   None       |
|    Mac.    : 1168   0      12.01   31.98   22.30    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:    12.006 -  14.004:  127   |   5:    21.992 -  23.989:  123        |
|      1:    14.004 -  16.001:  112   |   6:    23.989 -  25.986:  139        |
|      2:    16.001 -  17.998:  142   |   7:    25.986 -  27.983:  119        |
|      3:    17.998 -  19.995:  124   |   8:    27.983 -  29.980:  123        |
|      4:    19.995 -  21.992:  126   |   9:    29.980 -  31.977:  159        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.2870   r_free= 0.3188   ksol= 0.47   Bsol= 34.39   scale= 0.386   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.37,-2.74,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.097334           |
| twin fraction: 0.38  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.2456   r_free= 0.2747   ksol= 0.46   Bsol= 37.40   scale= 0.404   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.59,-3.18,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.085931           |
| twin fraction: 0.39  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.978088             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.520   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.239714              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 72.406   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2456      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.2747      final r-factor (free) = 0.2880          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2957 = 17.98 * 0.50 * 0.0859 + 1.00 * 2.5233                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.6431 = 17.98 * 0.50 * 0.0597 + 1.00 * 0.1063                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.1813          |
| start r-factor (free) = 0.2880      final r-factor (free) = 0.2293          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0194 = 0.24 * 1.00 * 0.0597 + 1.00 * 0.0051                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0098 = 0.24 * 1.00 * 0.0366 + 1.00 * 0.0010                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      14.28   68.20   25.60    None  None   None       |
|    all(noH): 1294   0      14.28   68.20   25.60    None  None   None       |
|    Sol.    : 126    0      15.03   42.00   28.21    None  None   None       |
|    Mac.    : 1168   0      14.28   68.20   25.32    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:    14.281 -  19.673:  229   |   5:    41.240 -  46.631:   37        |
|      1:    19.673 -  25.064:  507   |   6:    46.631 -  52.023:    9        |
|      2:    25.064 -  30.456:  310   |   7:    52.023 -  57.415:    3        |
|      3:    30.456 -  35.848:  126   |   8:    57.415 -  62.806:    0        |
|      4:    35.848 -  41.240:   70   |   9:    62.806 -  68.198:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1813 r_free = 0.2293     target_work(twin_lsq_f) = 0.037         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1813 r_free = 0.2291     target_work(twin_lsq_f) = 0.037         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1813   r_free= 0.2291   ksol= 0.46   Bsol= 37.40   scale= 0.404   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.59,-3.18,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.036629           |
| twin fraction: 0.39  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1807   r_free= 0.2287   ksol= 0.44   Bsol= 50.11   scale= 0.393   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,0.80,-3.68,0.00,-0.00,-0.00); trace/3= -0.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.037380           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.660011             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.921   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.219531              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 157.384  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1807      final r-factor (work) = 0.1753          |
| start r-factor (free) = 0.2287      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.3990 = 15.66 * 0.50 * 0.0374 + 1.00 * 0.1063                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.3401 = 15.66 * 0.50 * 0.0342 + 1.00 * 0.0720                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1753      final r-factor (work) = 0.1733          |
| start r-factor (free) = 0.2172      final r-factor (free) = 0.2146          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0085 = 0.22 * 1.00 * 0.0342 + 1.00 * 0.0010                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0084 = 0.22 * 1.00 * 0.0333 + 1.00 * 0.0011                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      13.41   82.92   25.66    None  None   None       |
|    all(noH): 1294   0      13.41   82.92   25.66    None  None   None       |
|    Sol.    : 126    0      14.85   41.96   28.40    None  None   None       |
|    Mac.    : 1168   0      13.41   82.92   25.36    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:    13.409 -  20.360:  350   |   5:    48.164 -  55.115:   15        |
|      1:    20.360 -  27.311:  536   |   6:    55.115 -  62.066:    6        |
|      2:    27.311 -  34.262:  239   |   7:    62.066 -  69.017:    0        |
|      3:    34.262 -  41.213:   97   |   8:    69.017 -  75.967:    2        |
|      4:    41.213 -  48.164:   48   |   9:    75.967 -  82.918:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1733 r_free = 0.2146     target_work(twin_lsq_f) = 0.033         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1733 r_free = 0.2144     target_work(twin_lsq_f) = 0.033         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2144   ksol= 0.44   Bsol= 50.11   scale= 0.393   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,0.80,-3.68,0.00,-0.00,-0.00); trace/3= -0.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.033308           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2143   ksol= 0.45   Bsol= 51.00   scale= 0.396   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.21,1.21,-3.38,0.00,-0.00,-0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.033291           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.801908             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.521  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.238816              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 172.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1733      final r-factor (work) = 0.1741          |
| start r-factor (free) = 0.2143      final r-factor (free) = 0.2162          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.3351 = 15.80 * 0.50 * 0.0333 + 1.00 * 0.0720                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.3213 = 15.80 * 0.50 * 0.0321 + 1.00 * 0.0681                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1741      final r-factor (work) = 0.1731          |
| start r-factor (free) = 0.2162      final r-factor (free) = 0.2148          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0087 = 0.24 * 1.00 * 0.0321 + 1.00 * 0.0011                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0087 = 0.24 * 1.00 * 0.0317 + 1.00 * 0.0011                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      12.92   85.71   25.64    None  None   None       |
|    all(noH): 1294   0      12.92   85.71   25.64    None  None   None       |
|    Sol.    : 126    0      14.64   43.38   28.49    None  None   None       |
|    Mac.    : 1168   0      12.92   85.71   25.33    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:    12.919 -  20.198:  359   |   5:    49.315 -  56.594:   14        |
|      1:    20.198 -  27.477:  541   |   6:    56.594 -  63.873:    6        |
|      2:    27.477 -  34.757:  228   |   7:    63.873 -  71.153:    0        |
|      3:    34.757 -  42.036:   97   |   8:    71.153 -  78.432:    1        |
|      4:    42.036 -  49.315:   46   |   9:    78.432 -  85.711:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1731 r_free = 0.2148     target_work(twin_lsq_f) = 0.032         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1731 r_free = 0.2147     target_work(twin_lsq_f) = 0.032         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2147   ksol= 0.45   Bsol= 51.00   scale= 0.396   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.21,1.21,-3.38,0.00,-0.00,-0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.031677           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 18.6313 -  3.8666 0.98   1285   46 0.1285 0.1991        None        None|
|  2:  3.8666 -  3.0735 0.98   1920   74 0.1145 0.2023        None        None|
|  3:  3.0735 -  2.6863 0.98   1961   90 0.1540 0.2035        None        None|
|  4:  2.6863 -  2.4413 0.98   1960   87 0.1870 0.1983        None        None|
|  5:  2.4413 -  2.2666 0.98   1956   90 0.1880 0.1714        None        None|
|  6:  2.2666 -  2.1332 0.98   1915  110 0.1856 0.2052        None        None|
|  7:  2.1332 -  2.0265 0.98   1958  123 0.1881 0.1827        None        None|
|  8:  2.0265 -  1.9384 0.98   1916   92 0.1964 0.2617        None        None|
|  9:  1.9384 -  1.8638 0.98   1916  114 0.2055 0.2509        None        None|
| 10:  1.8638 -  1.7996 0.98   1909  101 0.2187 0.2128        None        None|
| 11:  1.7996 -  1.7433 0.98   1914  104 0.2251 0.2721        None        None|
| 12:  1.7433 -  1.6935 0.98   1914  107 0.2347 0.3043        None        None|
| 13:  1.6935 -  1.6490 0.98   1910  107 0.2429 0.2678        None        None|
| 14:  1.6490 -  1.6088 0.98   1880   80 0.2669 0.2810        None        None|
| 15:  1.6088 -  1.5722 0.98   1808   97 0.2915 0.2325        None        None|
| 16:  1.5722 -  1.5388 0.98   1719   69 0.3471 0.4138        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 18.6313 -  3.8666  1285    46  0.75  31.65   None     0.83       2977.33|
|  2:  3.8666 -  3.0735  1920    74  0.74  32.54   None     0.85       2882.03|
|  3:  3.0735 -  2.6863  1961    90  0.73  34.22   None     0.82       1495.21|
|  4:  2.6863 -  2.4413  1960    87  0.71  35.91   None     0.80        858.38|
|  5:  2.4413 -  2.2666  1956    90  0.72  35.21   None     0.82        647.86|
|  6:  2.2666 -  2.1332  1915   110  0.71  35.78   None     0.85        539.04|
|  7:  2.1332 -  2.0265  1958   123  0.67  39.15   None     0.86        429.56|
|  8:  2.0265 -  1.9384  1916    92  0.66  39.98   None     0.86        318.39|
|  9:  1.9384 -  1.8638  1916   114  0.66  39.73   None     0.85        230.07|
| 10:  1.8638 -  1.7996  1909   101  0.64  41.73   None     0.85        168.39|
| 11:  1.7996 -  1.7433  1914   104  0.63  42.19   None     0.85        125.46|
| 12:  1.7433 -  1.6935  1914   107  0.63  42.34   None     0.84         95.09|
| 13:  1.6935 -  1.6490  1910   107  0.63  42.07   None     0.85         73.75|
| 14:  1.6490 -  1.6088  1880    80  0.62  43.52   None     0.86         60.04|
| 15:  1.6088 -  1.5722  1808    97  0.62  43.41   None     0.89         51.53|
| 16:  1.5722 -  1.5388  1719    69  0.61  44.38   None     0.89         45.55|
|alpha:            min =        0.80 max =            0.89 mean =         0.85|
|beta:             min =       43.86 max =         3552.55 mean =       668.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.90 mean =        38.89|
|phase err.(test): min =        0.01 max =           89.28 mean =        40.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1732   r_free= 0.2149   ksol= 0.45   Bsol= 50.84   scale= 0.396   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.26,-3.25,0.00,-0.00,-0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.031670           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.54 - 18.63 A; n_refl. = 31332)------------------------------|
|                                                                             |
| r_work= 0.1732   r_free= 0.2149   ksol= 0.45   Bsol= 50.84   scale= 0.396   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.26,-3.25,0.00,-0.00,-0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.031670           |
| twin fraction: 0.37  twin operator: h,-k,-l                                 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 18.6313 -  3.8666 0.98   1285   46 0.1286 0.1993        None        None|
|  2:  3.8666 -  3.0735 0.98   1920   74 0.1145 0.2020        None        None|
|  3:  3.0735 -  2.6863 0.98   1961   90 0.1542 0.2041        None        None|
|  4:  2.6863 -  2.4413 0.98   1960   87 0.1874 0.1988        None        None|
|  5:  2.4413 -  2.2666 0.98   1956   90 0.1883 0.1719        None        None|
|  6:  2.2666 -  2.1332 0.98   1915  110 0.1849 0.2046        None        None|
|  7:  2.1332 -  2.0265 0.98   1958  123 0.1873 0.1821        None        None|
|  8:  2.0265 -  1.9384 0.98   1916   92 0.1958 0.2612        None        None|
|  9:  1.9384 -  1.8638 0.98   1916  114 0.2050 0.2504        None        None|
| 10:  1.8638 -  1.7996 0.98   1909  101 0.2187 0.2128        None        None|
| 11:  1.7996 -  1.7433 0.98   1914  104 0.2252 0.2740        None        None|
| 12:  1.7433 -  1.6935 0.98   1914  107 0.2352 0.3057        None        None|
| 13:  1.6935 -  1.6490 0.98   1910  107 0.2440 0.2697        None        None|
| 14:  1.6490 -  1.6088 0.98   1880   80 0.2688 0.2814        None        None|
| 15:  1.6088 -  1.5722 0.98   1808   97 0.2938 0.2340        None        None|
| 16:  1.5722 -  1.5388 0.98   1719   69 0.3511 0.4191        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 18.6313 -  3.8666  1285    46  0.75  31.65   None     0.83       2977.33|
|  2:  3.8666 -  3.0735  1920    74  0.74  32.54   None     0.85       2882.03|
|  3:  3.0735 -  2.6863  1961    90  0.73  34.22   None     0.82       1495.21|
|  4:  2.6863 -  2.4413  1960    87  0.71  35.91   None     0.80        858.38|
|  5:  2.4413 -  2.2666  1956    90  0.72  35.21   None     0.82        647.86|
|  6:  2.2666 -  2.1332  1915   110  0.71  35.78   None     0.85        539.04|
|  7:  2.1332 -  2.0265  1958   123  0.67  39.15   None     0.86        429.56|
|  8:  2.0265 -  1.9384  1916    92  0.66  39.98   None     0.86        318.39|
|  9:  1.9384 -  1.8638  1916   114  0.66  39.73   None     0.85        230.07|
| 10:  1.8638 -  1.7996  1909   101  0.64  41.73   None     0.85        168.39|
| 11:  1.7996 -  1.7433  1914   104  0.63  42.19   None     0.85        125.46|
| 12:  1.7433 -  1.6935  1914   107  0.63  42.34   None     0.84         95.09|
| 13:  1.6935 -  1.6490  1910   107  0.63  42.07   None     0.85         73.75|
| 14:  1.6490 -  1.6088  1880    80  0.62  43.52   None     0.86         60.04|
| 15:  1.6088 -  1.5722  1808    97  0.62  43.41   None     0.89         51.53|
| 16:  1.5722 -  1.5388  1719    69  0.61  44.38   None     0.89         45.55|
|alpha:            min =        0.80 max =            0.89 mean =         0.85|
|beta:             min =       43.86 max =         3552.55 mean =       668.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.90 mean =        38.89|
|phase err.(test): min =        0.01 max =           89.28 mean =        40.50|
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 1294   0      12.76   85.55   25.47    None  None   None       |
|    all(noH): 1294   0      12.76   85.55   25.47    None  None   None       |
|    Sol.    : 126    0      14.48   43.21   28.33    None  None   None       |
|    Mac.    : 1168   0      12.76   85.55   25.16    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:    12.756 -  20.036:  359   |   5:    49.152 -  56.432:   14        |
|      1:    20.036 -  27.315:  541   |   6:    56.432 -  63.711:    6        |
|      2:    27.315 -  34.594:  228   |   7:    63.711 -  70.990:    0        |
|      3:    34.594 -  41.873:   97   |   8:    70.990 -  78.269:    1        |
|      4:    41.873 -  49.152:   46   |   9:    78.269 -  85.548:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


================= 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 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    :  0.2286 0.2607   7.752792e-02   8.774489e-02
   1_bss:  0.2456 0.2747   8.593096e-02   9.114814e-02
   1_xyz:  0.2371 0.2880   5.972329e-02   1.033241e-01
   1_adp:  0.1813 0.2293   3.664907e-02   7.363350e-02
   1_occ:  0.1813 0.2291   3.662873e-02   7.377746e-02
   2_bss:  0.1807 0.2287   3.737991e-02   7.489591e-02
   2_xyz:  0.1753 0.2172   3.423734e-02   6.802994e-02
   2_adp:  0.1733 0.2146   3.331927e-02   6.646929e-02
   2_occ:  0.1733 0.2144   3.330831e-02   6.654513e-02
   3_bss:  0.1733 0.2143   3.329135e-02   6.666735e-02
   3_xyz:  0.1741 0.2162   3.205124e-02   6.919888e-02
   3_adp:  0.1731 0.2148   3.168135e-02   6.829404e-02
   3_occ:  0.1731 0.2147   3.167676e-02   6.841356e-02
   3_bss:  0.1732 0.2149   3.166952e-02   6.842581e-02
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.468  34.394   1.368   1.368  -2.736   0.000   0.000   0.000
   1_bss:  0.459  37.396   1.591   1.591  -3.182   0.000   0.000   0.000
   1_xyz:  0.459  37.396   1.591   1.591  -3.182   0.000   0.000   0.000
   1_adp:  0.459  37.396   1.591   1.591  -3.182   0.000   0.000   0.000
   1_occ:  0.459  37.396   1.591   1.591  -3.182   0.000   0.000   0.000
   2_bss:  0.441  50.107   0.799   0.799  -3.684   0.000  -0.000  -0.000
   2_xyz:  0.441  50.107   0.799   0.799  -3.684   0.000  -0.000  -0.000
   2_adp:  0.441  50.107   0.799   0.799  -3.684   0.000  -0.000  -0.000
   2_occ:  0.441  50.107   0.799   0.799  -3.684   0.000  -0.000  -0.000
   3_bss:  0.448  50.999   1.209   1.209  -3.384   0.000  -0.000  -0.000
   3_xyz:  0.448  50.999   1.209   1.209  -3.384   0.000  -0.000  -0.000
   3_adp:  0.448  50.999   1.209   1.209  -3.384   0.000  -0.000  -0.000
   3_occ:  0.448  50.999   1.209   1.209  -3.384   0.000  -0.000  -0.000
   3_bss:  0.449  50.843   1.261   1.261  -3.253   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.967 0.6704  0.8481      665.453
   1_bss:  38.967 0.6704  0.8481      665.453
   1_xyz:  38.967 0.6704  0.8481      665.453
   1_adp:  38.967 0.6704  0.8481      665.453
   1_occ:  38.967 0.6704  0.8481      665.453
   2_bss:  38.967 0.6704  0.8481      665.453
   2_xyz:  38.967 0.6704  0.8481      665.453
   2_adp:  38.967 0.6704  0.8481      665.453
   2_occ:  38.967 0.6704  0.8481      665.453
   3_bss:  38.967 0.6704  0.8481      665.453
   3_xyz:  38.967 0.6704  0.8481      665.453
   3_adp:  38.967 0.6704  0.8481      665.453
   3_occ:  38.967 0.6704  0.8481      665.453
   3_bss:  38.967 0.6704  0.8481      665.453
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   5.762  0.081  0.378 22.033  0.029  4.127   2.5233e+00
   1_bss:   5.762  0.081  0.378 22.033  0.029  4.127   2.5233e+00
   1_xyz:   1.236  0.009  0.072 19.677  0.006  4.143   1.0628e-01
   1_adp:   1.236  0.009  0.072 19.677  0.006  4.143   1.0628e-01
   1_occ:   1.236  0.009  0.072 19.677  0.006  4.143   1.0628e-01
   2_bss:   1.236  0.009  0.072 19.677  0.006  4.143   1.0628e-01
   2_xyz:   0.963  0.005  0.061 18.180  0.004  4.146   7.2037e-02
   2_adp:   0.963  0.005  0.061 18.180  0.004  4.146   7.2037e-02
   2_occ:   0.963  0.005  0.061 18.180  0.004  4.146   7.2037e-02
   3_bss:   0.963  0.005  0.061 18.180  0.004  4.146   7.2037e-02
   3_xyz:   0.934  0.005  0.059 17.475  0.004  4.151   6.8074e-02
   3_adp:   0.934  0.005  0.059 17.475  0.004  4.151   6.8074e-02
   3_occ:   0.934  0.005  0.059 17.475  0.004  4.151   6.8074e-02
   3_bss:   0.934  0.005  0.059 17.475  0.004  4.151   6.8074e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  20.091  0.260  0.969 89.863  0.073  2.218   2.1915e+00
   1_bss:  20.091  0.260  0.969 89.863  0.073  2.218   2.1915e+00
   1_xyz:   8.687  0.038  0.224 86.702  0.043  2.189   2.1648e-01
   1_adp:   8.687  0.038  0.224 86.702  0.043  2.189   2.1648e-01
   1_occ:   8.687  0.038  0.224 86.702  0.043  2.189   2.1648e-01
   2_bss:   8.687  0.038  0.224 86.702  0.043  2.189   2.1648e-01
   2_xyz:   5.797  0.024  0.207 86.339  0.047  2.328   6.7992e-02
   2_adp:   5.797  0.024  0.207 86.339  0.047  2.328   6.7992e-02
   2_occ:   5.797  0.024  0.207 86.339  0.047  2.328   6.7992e-02
   3_bss:   5.797  0.024  0.207 86.339  0.047  2.328   6.7992e-02
   3_xyz:   5.607  0.024  0.204 85.853  0.038  2.321   4.3448e-02
   3_adp:   5.607  0.024  0.204 85.853  0.038  2.321   4.3448e-02
   3_occ:   5.607  0.024  0.204 85.853  0.038  2.321   4.3448e-02
   3_bss:   5.607  0.024  0.204 85.853  0.038  2.321   4.3448e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  22.97  22.97  22.97  22.97  22.97  22.97  22.97  22.97  22.97
   1_bss:  35.93  15.96  26.16  35.93  15.96  26.25  35.91  16.18  25.29
   1_xyz:  35.93  15.96  26.16  35.93  15.96  26.25  35.91  16.18  25.29
   1_adp:  68.20  14.28  25.60  68.20  14.28  25.32  42.00  15.03  28.21
   1_occ:  68.20  14.28  25.60  68.20  14.28  25.32  42.00  15.03  28.21
   2_bss:  68.02  14.10  25.42  68.02  14.10  25.14  41.82  14.85  28.03
   2_xyz:  68.02  14.10  25.42  68.02  14.10  25.14  41.82  14.85  28.03
   2_adp:  82.92  13.41  25.66  82.92  13.41  25.36  41.96  14.85  28.40
   2_occ:  82.92  13.41  25.66  82.92  13.41  25.36  41.96  14.85  28.40
   3_bss:  82.75  13.24  25.49  82.75  13.24  25.19  41.79  14.68  28.24
   3_xyz:  82.75  13.24  25.49  82.75  13.24  25.19  41.79  14.68  28.24
   3_adp:  85.71  12.92  25.64  85.71  12.92  25.33  43.38  14.64  28.49
   3_occ:  85.71  12.92  25.64  85.71  12.92  25.33  43.38  14.64  28.49
   3_bss:  85.55  12.76  25.47  85.55  12.76  25.16  43.21  14.48  28.33
------------------------------------------------------------------------
 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:    0.531    0.014    0.165
   1_adp:    0.531    0.014    0.165
   1_occ:    0.531    0.014    0.165
   2_bss:    0.531    0.014    0.165
   2_xyz:    0.639    0.012    0.177
   2_adp:    0.639    0.012    0.177
   2_occ:    0.639    0.012    0.177
   3_bss:    0.639    0.012    0.177
   3_xyz:    0.924    0.014    0.202
   3_adp:    0.924    0.014    0.202
   3_occ:    0.924    0.014    0.202
   3_bss:    0.924    0.014    0.202
------------------------------------------------------------------------

CPU time actual refinement: 256.90


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

Writing refined structure to PDB file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001.pdb
n_use            =  1294
n_use_u_iso      =  1294
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  14
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  1294

Writing 2mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001_2mFo-DFc.map
Writing mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001_mFo-DFc.map
Writing map coefficients to MTZ file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/twinning/1l2h_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 256.81 
  Macro-tasks:
    weights calculation          = 19.25  
    collect and process          = 2.82   
    model show statistics        = 0.27   
    TOTAL for macro-tasks        = 22.34  
  Micro-tasks:
    mask                            = 0.00   
    f_calc                          = 0.00   
    alpha_beta                      = 0.00   
    target                          = 0.00   
    gradients_wrt_atomic_parameters = 79.63  
    fmodel                         = 0.00   
    r_factors                      = 0.00   
    phase_errors                   = 0.00   
    foms                           = 0.00   
    TOTAL for micro-tasks          = 79.63  
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 8.008 micro seconds
Total CPU time: 4.51 minutes
from_scatterers_fft:    435 calls, 84.44 s
gradients_fft:          367 calls, 75.64 s

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

# Date 2008-10-14 Time 09:15:32 PDT -0700 (1224000932.34 s)
wall clock time: 269.68 s

Start R-work = 0.2286, R-free = 0.2607 (no bulk solvent and anisotropic scale)
Final R-work = 0.1798, R-free = 0.2209 (no bulk solvent and anisotropic scale)

Start R-work = 0.2456, R-free = 0.2747
Final R-work = 0.1732, R-free = 0.2149