Starting phenix.real_space_refine
on Sat Jan 18 10:31:22 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sfr_40449/01_2025/8sfr_40449.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      91      5.49       5
     S      23      5.16       5
     C    7395      2.51       5
     N    2050      2.21       5
     O    2486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12045
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 10138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1240, 10138
          Classifications: {'peptide': 1240}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1193}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 826
          Classifications: {'RNA': 39}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 17, 'rna3p_pyr': 15}
          Link IDs: {'rna2p': 7, 'rna3p': 31}
    Chain: "C"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 696
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    Chain: "D"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 385
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
  Time building chain proxies: 7.41, per 1000 atoms: 0.62
  Number of scatterers: 12045
  At special positions: 0
  Unit cell: (90.797, 106.624, 140.777, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P      91     15.00
     O    2486      8.00
     N    2050      7.00
     C    7395      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.33
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2368

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 9 sheets defined
      53.6% alpha, 10.8% beta
      40 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 4.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 26 through 35
      removed outlier: 3.875A  pdb=" N   GLN A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 67
      Proline residue:  A  52  - end of helix
      removed outlier: 3.787A  pdb=" N   ARG A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE A  57 " --> pdb=" O   ILE A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 86
      removed outlier: 3.549A  pdb=" N   GLU A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 112
      removed outlier: 3.862A  pdb=" N   TYR A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 140 through 147
      removed outlier: 3.579A  pdb=" N   LYS A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLN A 145 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 160
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 178
    Processing helix  chain 'A' and resid 188 through 196
    Processing helix  chain 'A' and resid 196 through 215
      removed outlier: 3.944A  pdb=" N   LYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 230
      removed outlier: 3.774A  pdb=" N   HIS A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
      removed outlier: 5.913A  pdb=" N   PHE A 243 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      Proline residue:  A 244  - end of helix
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.507A  pdb=" N   ILE A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
    Processing helix  chain 'A' and resid 289 through 297
    Processing helix  chain 'A' and resid 325 through 343
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.534A  pdb=" N   THR A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 356 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 370 through 379
    Processing helix  chain 'A' and resid 382 through 396
      removed outlier: 4.410A  pdb=" N   ARG A 386 " --> pdb=" O   TRP A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.801A  pdb=" N   HIS A 415 " --> pdb=" O   ARG A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 428
    Processing helix  chain 'A' and resid 428 through 452
      removed outlier: 3.507A  pdb=" N   SER A 432 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.510A  pdb=" N   LYS A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 508
    Processing helix  chain 'A' and resid 509 through 522
    Processing helix  chain 'A' and resid 570 through 574
      removed outlier: 4.157A  pdb=" N   GLY A 573 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 610
      Proline residue:  A 606  - end of helix
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 639 through 647
    Processing helix  chain 'A' and resid 656 through 664
      removed outlier: 3.789A  pdb=" N   ALA A 660 " --> pdb=" O   GLN A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 687
    Processing helix  chain 'A' and resid 700 through 704
    Processing helix  chain 'A' and resid 706 through 719
      Proline residue:  A 716  - end of helix
      removed outlier: 3.830A  pdb=" N   TYR A 719 " --> pdb=" O   ASN A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 737
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.784A  pdb=" N   PHE A 769 " --> pdb=" O   TRP A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 861 through 865
      removed outlier: 3.642A  pdb=" N   PHE A 864 " --> pdb=" O   ASP A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 939 through 956
      removed outlier: 4.180A  pdb=" N   LYS A 943 " --> pdb=" O   ASP A 939 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLN A 956 " --> pdb=" O   VAL A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 987
      removed outlier: 3.745A  pdb=" N   GLN A 974 " --> pdb=" O   GLY A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1025
      removed outlier: 3.643A  pdb=" N   GLU A1016 " --> pdb=" O   TYR A1012 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LYS A1017 " --> pdb=" O   GLN A1013 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   MET A1018 " --> pdb=" O   GLN A1014 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A1019 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS A1025 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1100
      removed outlier: 3.568A  pdb=" N   GLY A1100 " --> pdb=" O   HIS A1096 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1190
    Processing helix  chain 'A' and resid 1199 through 1206
      removed outlier: 4.095A  pdb=" N   ASN A1206 " --> pdb=" O   LYS A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1224
    Processing helix  chain 'A' and resid 1252 through 1254
      No H-bonds generated for 'chain 'A' and resid 1252 through 1254'
    Processing helix  chain 'A' and resid 1261 through 1284
    Processing helix  chain 'A' and resid 1294 through 1307
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532
      removed outlier: 4.333A  pdb=" N   PHE A 869 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   TYR A 563 " --> pdb=" O   ILE A 745 " (cutoff:3.500A)
      removed outlier: 11.191A  pdb=" N   ALA A 554 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   TYR A 595 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LEU A 556 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419
      removed outlier: 4.266A  pdb=" N   PHE A 365 " --> pdb=" O   ALA A 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628
    Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931
      removed outlier: 6.509A  pdb=" N   VAL A 919 " --> pdb=" O   LEU A 927 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLN A 929 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ILE A 917 " --> pdb=" O   GLN A 929 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 907 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1103 through 1107
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229
      removed outlier: 3.719A  pdb=" N   PHE A1249 " --> pdb=" O   SER A1239 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      96 hydrogen bonds
      188 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 6.79

  Time building geometry restraints manager: 3.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 3119
        1.33 -     1.45: 3194
        1.45 -     1.58: 5969
        1.58 -     1.70: 180
        1.70 -     1.82: 38
  Bond restraints: 12500
  Sorted by residual:
  bond pdb=" C   GLU A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 8.40e-03 1.42e+04 1.13e+01
  bond pdb=" CB  ASP A1021 "
       pdb=" CG  ASP A1021 "
    ideal  model  delta    sigma   weight residual
    1.516  1.472  0.044 2.50e-02 1.60e+03 3.06e+00
  bond pdb=" CG  ARG A 912 "
       pdb=" CD  ARG A 912 "
    ideal  model  delta    sigma   weight residual
    1.520  1.569 -0.049 3.00e-02 1.11e+03 2.71e+00
  bond pdb=" N1    U B  12 "
       pdb=" C2    U B  12 "
    ideal  model  delta    sigma   weight residual
    1.381  1.413 -0.032 2.00e-02 2.50e+03 2.58e+00
  bond pdb=" CG  LEU A 475 "
       pdb=" CD2 LEU A 475 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.51e+00
  ... (remaining 12495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.98: 17173
        4.98 -     9.96: 101
        9.96 -    14.94: 18
       14.94 -    19.92: 3
       19.92 -    24.90: 1
  Bond angle restraints: 17296
  Sorted by residual:
  angle pdb=" O3'  DG D   6 "
        pdb=" P    DA D   7 "
        pdb=" OP1  DA D   7 "
      ideal   model   delta    sigma   weight residual
     108.00  132.90  -24.90 3.00e+00 1.11e-01 6.89e+01
  angle pdb=" O3'  DC C   7 "
        pdb=" P    DA C   8 "
        pdb=" OP1  DA C   8 "
      ideal   model   delta    sigma   weight residual
     108.00  126.22  -18.22 3.00e+00 1.11e-01 3.69e+01
  angle pdb=" OP1  DA D   7 "
        pdb=" P    DA D   7 "
        pdb=" OP2  DA D   7 "
      ideal   model   delta    sigma   weight residual
     120.00  104.46   15.54 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" CA  LYS A  48 "
        pdb=" CB  LYS A  48 "
        pdb=" CG  LYS A  48 "
      ideal   model   delta    sigma   weight residual
     114.10  123.85   -9.75 2.00e+00 2.50e-01 2.38e+01
  angle pdb=" OP1  DA C   8 "
        pdb=" P    DA C   8 "
        pdb=" OP2  DA C   8 "
      ideal   model   delta    sigma   weight residual
     120.00  105.73   14.27 3.00e+00 1.11e-01 2.26e+01
  ... (remaining 17291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 6965
       35.54 -    71.09: 443
       71.09 -   106.63: 28
      106.63 -   142.18: 0
      142.18 -   177.72: 3
  Dihedral angle restraints: 7439
    sinusoidal: 3781
      harmonic: 3658
  Sorted by residual:
  dihedral pdb=" O4'   C B  11 "
           pdb=" C1'   C B  11 "
           pdb=" N1    C B  11 "
           pdb=" C2    C B  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.72 -177.72     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B  12 "
           pdb=" C1'   U B  12 "
           pdb=" N1    U B  12 "
           pdb=" C2    U B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  101.79   98.21     1      1.50e+01 4.44e-03 4.88e+01
  dihedral pdb=" CA  ALA A1007 "
           pdb=" C   ALA A1007 "
           pdb=" N   GLU A1008 "
           pdb=" CA  GLU A1008 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.46   27.54     0      5.00e+00 4.00e-02 3.03e+01
  ... (remaining 7436 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.141: 1890
       0.141 -    0.281: 26
       0.281 -    0.422: 10
       0.422 -    0.562: 2
       0.562 -    0.703: 2
  Chirality restraints: 1930
  Sorted by residual:
  chirality pdb=" P    DA D   7 "
            pdb=" OP1  DA D   7 "
            pdb=" OP2  DA D   7 "
            pdb=" O5'  DA D   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.05   -0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" P    DA C   8 "
            pdb=" OP1  DA C   8 "
            pdb=" OP2  DA C   8 "
            pdb=" O5'  DA C   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.61 2.00e-01 2.50e+01 9.16e+00
  chirality pdb=" CG  LEU A 645 "
            pdb=" CB  LEU A 645 "
            pdb=" CD1 LEU A 645 "
            pdb=" CD2 LEU A 645 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.13   -0.46 2.00e-01 2.50e+01 5.29e+00
  ... (remaining 1927 not shown)

  Planarity restraints: 1895
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 784 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.17e+01
        pdb=" C   GLN A 784 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   GLN A 784 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 785 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 908 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.92e+00
        pdb=" CG  ASP A 908 "   -0.052 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 908 "    0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 908 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D  11 "   -0.033 2.00e-02 2.50e+03   1.59e-02 6.28e+00
        pdb=" N1   DT D  11 "    0.030 2.00e-02 2.50e+03
        pdb=" C2   DT D  11 "    0.006 2.00e-02 2.50e+03
        pdb=" O2   DT D  11 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DT D  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DT D  11 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4   DT D  11 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5   DT D  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT D  11 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DT D  11 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1892 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1674
        2.75 -     3.29: 12343
        3.29 -     3.82: 23069
        3.82 -     4.36: 25824
        4.36 -     4.90: 40318
  Nonbonded interactions: 103228
  Sorted by model distance:
  nonbonded pdb=" O   ALA A1067 "
            pdb=" OG1 THR A1070 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   LYS A 370 "
            pdb=" OG1 THR A 373 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE A 605 "
            pdb=" OG  SER A 609 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   GLY A 767 "
            pdb=" OG  SER A 770 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   LYS A1282 "
            pdb=" NZ  LYS A1285 "
     model   vdw
     2.302 3.120
  ... (remaining 103223 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     34.400
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  12500  Z= 0.395
  Angle     :  1.026  24.904  17296  Z= 0.490
  Chirality :  0.062   0.703   1930
  Planarity :  0.005   0.050   1895
  Dihedral  : 20.280 177.720   5071
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 20.40 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.23), residues: 1234
  helix:  0.02 (0.20), residues: 601
  sheet: -0.70 (0.47), residues: 121
  loop : -0.22 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 382 
 HIS   0.008   0.001   HIS A 363 
 PHE   0.031   0.002   PHE A 619 
 TYR   0.038   0.002   TYR A 526 
 ARG   0.006   0.001   ARG A 392 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  537 MET cc_start: 0.9387 (mmt) cc_final: 0.8844 (mmm)
REVERT: A  604 MET cc_start: 0.9314 (mmm) cc_final: 0.9097 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 52
  average time/residue: 0.2511
  time to fit residues: 19.9773
Evaluate side-chains
  49 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  969 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 102 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1206 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.041042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.029300 restraints weight = 81864.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.030486 restraints weight = 40809.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.031272 restraints weight = 27123.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12500  Z= 0.205
  Angle     :  0.614  10.342  17296  Z= 0.322
  Chirality :  0.040   0.211   1930
  Planarity :  0.004   0.039   1895
  Dihedral  : 20.195 179.371   2524
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.32 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.24), residues: 1234
  helix:  1.06 (0.21), residues: 597
  sheet: -0.60 (0.45), residues: 132
  loop :  0.03 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 363 
 PHE   0.013   0.001   PHE A 353 
 TYR   0.015   0.001   TYR A 526 
 ARG   0.004   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 1.337 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8898 (tpp) cc_final: 0.8343 (tmm)
REVERT: A  604 MET cc_start: 0.9292 (mmm) cc_final: 0.9042 (mmm)
REVERT: A  754 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7598 (t-90)
REVERT: A  786 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8292 (mp0)
REVERT: A  908 ASP cc_start: 0.7344 (t0) cc_final: 0.7129 (t0)
REVERT: A  912 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7743 (tpm170)
REVERT: A  969 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8172 (pp30)
REVERT: A 1092 GLU cc_start: 0.9684 (OUTLIER) cc_final: 0.9340 (mp0)
  outliers start: 17
  outliers final: 3
  residues processed: 64
  average time/residue: 0.2484
  time to fit residues: 24.4297
Evaluate side-chains
  54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 104 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 90 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 114 optimal weight:   20.0000
   chunk 69 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 ASN
** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 560 ASN
** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.038684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.027130 restraints weight = 88289.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.028214 restraints weight = 44748.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.028937 restraints weight = 30437.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061  12500  Z= 0.519
  Angle     :  0.765   9.567  17296  Z= 0.409
  Chirality :  0.045   0.206   1930
  Planarity :  0.004   0.040   1895
  Dihedral  : 20.327 179.611   2524
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.95 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1234
  helix:  1.04 (0.21), residues: 607
  sheet: -1.09 (0.45), residues: 121
  loop : -0.00 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 382 
 HIS   0.007   0.001   HIS A 191 
 PHE   0.021   0.002   PHE A1079 
 TYR   0.020   0.002   TYR A  61 
 ARG   0.006   0.001   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 48
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9028 (tpp) cc_final: 0.8256 (tmm)
REVERT: A   20 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: A   48 LYS cc_start: 0.9447 (pttm) cc_final: 0.9224 (ptpp)
REVERT: A  271 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8134 (p)
REVERT: A  507 MET cc_start: 0.9257 (ppp) cc_final: 0.9004 (ppp)
REVERT: A  604 MET cc_start: 0.9416 (mmm) cc_final: 0.9103 (mmm)
REVERT: A  786 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8383 (mp0)
REVERT: A  908 ASP cc_start: 0.7882 (t0) cc_final: 0.7571 (t0)
REVERT: A  969 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8460 (pp30)
REVERT: A 1055 MET cc_start: 0.9590 (pmm) cc_final: 0.9052 (pmm)
REVERT: A 1092 GLU cc_start: 0.9690 (OUTLIER) cc_final: 0.9320 (mp0)
  outliers start: 38
  outliers final: 15
  residues processed: 80
  average time/residue: 0.2729
  time to fit residues: 32.1688
Evaluate side-chains
  65 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1050 THR
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1235 ASP
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
A1105 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.040689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.029058 restraints weight = 82919.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.030239 restraints weight = 41309.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.031023 restraints weight = 27349.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12500  Z= 0.173
  Angle     :  0.593  10.579  17296  Z= 0.308
  Chirality :  0.039   0.171   1930
  Planarity :  0.003   0.037   1895
  Dihedral  : 20.076 178.152   2524
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.13 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1234
  helix:  1.50 (0.21), residues: 613
  sheet: -0.92 (0.45), residues: 121
  loop :  0.12 (0.30), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 382 
 HIS   0.006   0.001   HIS A 754 
 PHE   0.013   0.001   PHE A1052 
 TYR   0.015   0.001   TYR A  61 
 ARG   0.007   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8973 (tpp) cc_final: 0.8171 (tmm)
REVERT: A   20 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8055 (tm-30)
REVERT: A   48 LYS cc_start: 0.9424 (pttm) cc_final: 0.9196 (ptpp)
REVERT: A  271 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8269 (p)
REVERT: A  507 MET cc_start: 0.9234 (ppp) cc_final: 0.9029 (ppp)
REVERT: A  537 MET cc_start: 0.9283 (mmt) cc_final: 0.8589 (mmm)
REVERT: A  604 MET cc_start: 0.9259 (mmm) cc_final: 0.8915 (mmm)
REVERT: A  754 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7725 (t-170)
REVERT: A  786 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8294 (mp0)
REVERT: A  908 ASP cc_start: 0.7780 (t0) cc_final: 0.7481 (t0)
REVERT: A  969 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8389 (pp30)
REVERT: A 1055 MET cc_start: 0.9557 (pmm) cc_final: 0.9263 (pmm)
REVERT: A 1092 GLU cc_start: 0.9703 (OUTLIER) cc_final: 0.9342 (mp0)
REVERT: A 1119 MET cc_start: 0.9168 (mmp) cc_final: 0.8875 (mmp)
  outliers start: 27
  outliers final: 12
  residues processed: 73
  average time/residue: 0.2614
  time to fit residues: 28.4731
Evaluate side-chains
  66 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  933 ASN
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1046 THR
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1235 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 121 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 120 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   overall best weight:    3.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 946 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.039642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.028021 restraints weight = 85429.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.029193 restraints weight = 42965.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.029941 restraints weight = 28561.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12500  Z= 0.306
  Angle     :  0.631  10.147  17296  Z= 0.332
  Chirality :  0.041   0.276   1930
  Planarity :  0.003   0.033   1895
  Dihedral  : 20.040 179.924   2524
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.40 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.25), residues: 1234
  helix:  1.48 (0.21), residues: 619
  sheet: -0.99 (0.45), residues: 121
  loop :  0.02 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.013   0.001   PHE A1052 
 TYR   0.019   0.001   TYR A  61 
 ARG   0.004   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 52
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9029 (tpp) cc_final: 0.8179 (tmm)
REVERT: A   20 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: A   48 LYS cc_start: 0.9441 (pttm) cc_final: 0.9226 (ptpp)
REVERT: A  165 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8636 (t80)
REVERT: A  271 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8236 (p)
REVERT: A  507 MET cc_start: 0.9204 (ppp) cc_final: 0.8974 (ppp)
REVERT: A  604 MET cc_start: 0.9330 (mmm) cc_final: 0.8996 (mmm)
REVERT: A  754 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7834 (t-90)
REVERT: A  786 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8351 (mp0)
REVERT: A  908 ASP cc_start: 0.7943 (t0) cc_final: 0.7672 (t0)
REVERT: A  912 ARG cc_start: 0.8156 (tpm170) cc_final: 0.7840 (tpm170)
REVERT: A  933 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7995 (t0)
REVERT: A  969 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8296 (pp30)
REVERT: A 1046 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8947 (p)
REVERT: A 1092 GLU cc_start: 0.9709 (OUTLIER) cc_final: 0.9347 (mp0)
  outliers start: 37
  outliers final: 19
  residues processed: 84
  average time/residue: 0.2375
  time to fit residues: 29.8426
Evaluate side-chains
  76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 ASN
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1046 THR
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1235 ASP
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 109 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 99 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.039201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.027666 restraints weight = 87163.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.028811 restraints weight = 43993.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.029543 restraints weight = 29355.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12500  Z= 0.382
  Angle     :  0.674  10.508  17296  Z= 0.356
  Chirality :  0.042   0.166   1930
  Planarity :  0.004   0.034   1895
  Dihedral  : 20.139 178.173   2524
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.68 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1234
  helix:  1.32 (0.21), residues: 619
  sheet: -1.17 (0.45), residues: 121
  loop : -0.07 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.016   0.002   PHE A 655 
 TYR   0.019   0.002   TYR A  61 
 ARG   0.004   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 54
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9090 (tpp) cc_final: 0.8075 (tmm)
REVERT: A   20 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: A  165 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8670 (t80)
REVERT: A  271 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8089 (p)
REVERT: A  507 MET cc_start: 0.9195 (ppp) cc_final: 0.8939 (ppp)
REVERT: A  604 MET cc_start: 0.9314 (mmm) cc_final: 0.9045 (mmm)
REVERT: A  754 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7777 (t-170)
REVERT: A  786 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8335 (mp0)
REVERT: A  908 ASP cc_start: 0.8129 (t0) cc_final: 0.7699 (t0)
REVERT: A 1046 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (p)
REVERT: A 1092 GLU cc_start: 0.9700 (OUTLIER) cc_final: 0.9339 (mp0)
REVERT: A 1194 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.8920 (mmm-85)
  outliers start: 41
  outliers final: 23
  residues processed: 87
  average time/residue: 0.2753
  time to fit residues: 35.1729
Evaluate side-chains
  79 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 49
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 ASN
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1046 THR
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1173 TYR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1194 ARG
Chi-restraints excluded: chain A residue 1235 ASP
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  64 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.039990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.028414 restraints weight = 84824.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.029601 restraints weight = 42609.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.030355 restraints weight = 28356.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12500  Z= 0.236
  Angle     :  0.619  13.605  17296  Z= 0.320
  Chirality :  0.040   0.162   1930
  Planarity :  0.003   0.033   1895
  Dihedral  : 20.033 178.272   2524
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.40 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1234
  helix:  1.52 (0.21), residues: 620
  sheet: -1.10 (0.44), residues: 123
  loop : -0.02 (0.30), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.011   0.001   PHE A1052 
 TYR   0.017   0.001   TYR A  61 
 ARG   0.004   0.000   ARG A 951 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 53
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9068 (tpp) cc_final: 0.8044 (tmm)
REVERT: A   20 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: A  145 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9026 (mp10)
REVERT: A  165 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8607 (t80)
REVERT: A  271 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8144 (p)
REVERT: A  507 MET cc_start: 0.9205 (ppp) cc_final: 0.8940 (ppp)
REVERT: A  604 MET cc_start: 0.9260 (mmm) cc_final: 0.8953 (mmm)
REVERT: A  610 THR cc_start: 0.9715 (OUTLIER) cc_final: 0.9399 (p)
REVERT: A  754 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.8025 (t-90)
REVERT: A  786 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8325 (mp0)
REVERT: A  908 ASP cc_start: 0.8018 (t0) cc_final: 0.7584 (t0)
REVERT: A  912 ARG cc_start: 0.8064 (tpm170) cc_final: 0.7763 (tpm170)
REVERT: A  933 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8319 (t0)
REVERT: A  969 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8016 (pp30)
REVERT: A 1046 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8945 (p)
REVERT: A 1074 ASP cc_start: 0.9571 (OUTLIER) cc_final: 0.8776 (p0)
REVERT: A 1092 GLU cc_start: 0.9730 (OUTLIER) cc_final: 0.9377 (mp0)
REVERT: A 1225 MET cc_start: 0.8990 (tpt) cc_final: 0.8743 (tpt)
  outliers start: 38
  outliers final: 21
  residues processed: 85
  average time/residue: 0.2529
  time to fit residues: 32.1278
Evaluate side-chains
  83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 ASN
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1046 THR
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1074 ASP
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1173 TYR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 128 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.039902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.028329 restraints weight = 85692.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.029493 restraints weight = 42985.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.030263 restraints weight = 28706.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12500  Z= 0.289
  Angle     :  0.643  13.623  17296  Z= 0.334
  Chirality :  0.041   0.291   1930
  Planarity :  0.003   0.033   1895
  Dihedral  : 20.011 177.531   2524
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.12 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1234
  helix:  1.50 (0.21), residues: 620
  sheet: -1.06 (0.45), residues: 121
  loop : -0.00 (0.30), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.011   0.001   PHE A1052 
 TYR   0.018   0.001   TYR A  61 
 ARG   0.006   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 52
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9124 (tpp) cc_final: 0.8534 (tmm)
REVERT: A   20 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: A  165 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8611 (t80)
REVERT: A  271 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8147 (p)
REVERT: A  363 HIS cc_start: 0.9447 (OUTLIER) cc_final: 0.9070 (t70)
REVERT: A  507 MET cc_start: 0.9198 (ppp) cc_final: 0.8928 (ppp)
REVERT: A  604 MET cc_start: 0.9275 (mmm) cc_final: 0.8968 (mmm)
REVERT: A  610 THR cc_start: 0.9726 (OUTLIER) cc_final: 0.9419 (p)
REVERT: A  754 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7833 (t-170)
REVERT: A  786 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8317 (mp0)
REVERT: A  908 ASP cc_start: 0.8109 (t0) cc_final: 0.7646 (t0)
REVERT: A  912 ARG cc_start: 0.8167 (tpm170) cc_final: 0.7843 (tpm170)
REVERT: A  933 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8190 (t0)
REVERT: A  951 ARG cc_start: 0.9103 (tpp-160) cc_final: 0.8895 (tpp-160)
REVERT: A 1046 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8940 (p)
REVERT: A 1074 ASP cc_start: 0.9573 (OUTLIER) cc_final: 0.8778 (p0)
REVERT: A 1092 GLU cc_start: 0.9721 (OUTLIER) cc_final: 0.9361 (mp0)
REVERT: A 1194 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8937 (mmm-85)
REVERT: A 1225 MET cc_start: 0.9029 (tpt) cc_final: 0.8782 (tpt)
  outliers start: 39
  outliers final: 23
  residues processed: 84
  average time/residue: 0.2518
  time to fit residues: 31.5958
Evaluate side-chains
  85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 51
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  363 HIS
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 ASN
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1046 THR
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1074 ASP
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1194 ARG
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 42 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 105 optimal weight:    0.2980
   chunk 102 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 123 optimal weight:   10.0000
   overall best weight:    1.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 206 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.040779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.029182 restraints weight = 83418.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.030396 restraints weight = 41985.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.031179 restraints weight = 27869.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12500  Z= 0.186
  Angle     :  0.617  14.946  17296  Z= 0.311
  Chirality :  0.040   0.284   1930
  Planarity :  0.003   0.033   1895
  Dihedral  : 19.877 177.958   2524
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.57 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1234
  helix:  1.68 (0.21), residues: 620
  sheet: -0.93 (0.46), residues: 123
  loop :  0.06 (0.30), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.010   0.001   PHE A1052 
 TYR   0.016   0.001   TYR A 595 
 ARG   0.005   0.000   ARG A 313 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9081 (tpp) cc_final: 0.8553 (tmm)
REVERT: A   20 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8199 (tm-30)
REVERT: A  145 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9029 (mp10)
REVERT: A  165 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8537 (t80)
REVERT: A  271 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8215 (p)
REVERT: A  363 HIS cc_start: 0.9459 (OUTLIER) cc_final: 0.9061 (t70)
REVERT: A  507 MET cc_start: 0.9198 (ppp) cc_final: 0.8927 (ppp)
REVERT: A  604 MET cc_start: 0.9236 (mmm) cc_final: 0.8915 (mmm)
REVERT: A  754 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7997 (t-170)
REVERT: A  786 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8212 (mp0)
REVERT: A  908 ASP cc_start: 0.7978 (t0) cc_final: 0.7533 (t0)
REVERT: A  912 ARG cc_start: 0.8173 (tpm170) cc_final: 0.7972 (tpm170)
REVERT: A  969 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7933 (pp30)
REVERT: A 1074 ASP cc_start: 0.9583 (OUTLIER) cc_final: 0.8798 (p0)
REVERT: A 1092 GLU cc_start: 0.9726 (OUTLIER) cc_final: 0.9367 (mp0)
REVERT: A 1225 MET cc_start: 0.8960 (tpt) cc_final: 0.8680 (tpt)
  outliers start: 31
  outliers final: 20
  residues processed: 78
  average time/residue: 0.2557
  time to fit residues: 29.8083
Evaluate side-chains
  81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 52
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  363 HIS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1074 ASP
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 119 optimal weight:    0.5980
   chunk 36 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 104 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.041380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.029787 restraints weight = 82242.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.031014 restraints weight = 41467.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.031804 restraints weight = 27559.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12500  Z= 0.166
  Angle     :  0.626  15.376  17296  Z= 0.312
  Chirality :  0.040   0.308   1930
  Planarity :  0.003   0.032   1895
  Dihedral  : 19.745 178.351   2524
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 22.02 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.25), residues: 1234
  helix:  1.73 (0.21), residues: 619
  sheet: -0.77 (0.46), residues: 123
  loop :  0.07 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.010   0.001   PHE A1113 
 TYR   0.017   0.001   TYR A 595 
 ARG   0.004   0.000   ARG A 951 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 54
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9087 (tpp) cc_final: 0.8066 (tmm)
REVERT: A   20 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: A  145 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9088 (mp10)
REVERT: A  165 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8546 (t80)
REVERT: A  271 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8277 (p)
REVERT: A  363 HIS cc_start: 0.9478 (OUTLIER) cc_final: 0.9076 (t70)
REVERT: A  507 MET cc_start: 0.9211 (ppp) cc_final: 0.8951 (ppp)
REVERT: A  604 MET cc_start: 0.9243 (mmm) cc_final: 0.8891 (mmm)
REVERT: A  754 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.8061 (t-170)
REVERT: A  786 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8156 (mp0)
REVERT: A  908 ASP cc_start: 0.7951 (t0) cc_final: 0.7529 (t0)
REVERT: A  912 ARG cc_start: 0.8159 (tpm170) cc_final: 0.7938 (tpm170)
REVERT: A  969 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8084 (pp30)
REVERT: A 1074 ASP cc_start: 0.9595 (OUTLIER) cc_final: 0.8761 (p0)
REVERT: A 1092 GLU cc_start: 0.9716 (OUTLIER) cc_final: 0.9355 (mp0)
REVERT: A 1225 MET cc_start: 0.8932 (tpt) cc_final: 0.8653 (tpt)
  outliers start: 26
  outliers final: 17
  residues processed: 75
  average time/residue: 0.2524
  time to fit residues: 28.9430
Evaluate side-chains
  79 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  363 HIS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1074 ASP
Chi-restraints excluded: chain A residue 1088 ILE
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1307 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.040411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.028778 restraints weight = 84663.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.029983 restraints weight = 42195.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.030764 restraints weight = 28032.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12500  Z= 0.267
  Angle     :  0.650  14.849  17296  Z= 0.331
  Chirality :  0.040   0.286   1930
  Planarity :  0.003   0.033   1895
  Dihedral  : 19.789 176.927   2524
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 22.11 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.25), residues: 1234
  helix:  1.72 (0.21), residues: 619
  sheet: -0.89 (0.46), residues: 123
  loop :  0.08 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.011   0.001   PHE A1113 
 TYR   0.017   0.001   TYR A  61 
 ARG   0.004   0.000   ARG A 951 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3355.99 seconds
wall clock time: 61 minutes 38.79 seconds (3698.79 seconds total)