Starting phenix.real_space_refine
on Sat Aug 23 00:25:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqg_36571/08_2025/8jqg_36571.map"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.075
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5548      2.51       5
     N    1494      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8708
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1061, 8708
          Classifications: {'peptide': 1061}
          Link IDs: {'PTRANS': 47, 'TRANS': 1013}
          Chain breaks: 4
  Time building chain proxies: 1.76, per 1000 atoms: 0.20
  Number of scatterers: 8708
  At special positions: 0
  Unit cell: (96.8, 101.2, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1622      8.00
     N    1494      7.00
     C    5548      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: 0.89
  Conformation dependent library (CDL) restraints added in 323.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2034

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 13 sheets defined
      33.6% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 115 through 136
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 162 through 170
    Processing helix  chain 'A' and resid 181 through 191
    Processing helix  chain 'A' and resid 198 through 221
      removed outlier: 5.940A  pdb=" N   SER A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE A 217 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LEU A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 257 through 260
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.620A  pdb=" N   VAL A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 3.636A  pdb=" N   ASN A 315 " --> pdb=" O   GLN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 4.035A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 393
    Processing helix  chain 'A' and resid 410 through 426
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'A' and resid 539 through 554
    Processing helix  chain 'A' and resid 609 through 620
      removed outlier: 3.718A  pdb=" N   LEU A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 652 through 663
    Processing helix  chain 'A' and resid 712 through 722
      removed outlier: 3.747A  pdb=" N   LYS A 722 " --> pdb=" O   SER A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 746
      removed outlier: 3.843A  pdb=" N   ARG A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 843
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 892 through 908
    Processing helix  chain 'A' and resid 927 through 934
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 970 through 979
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1034
      removed outlier: 4.195A  pdb=" N   LEU A1030 " --> pdb=" O   ALA A1026 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   GLY A1032 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1045
      removed outlier: 3.510A  pdb=" N   ARG A1044 " --> pdb=" O   PRO A1040 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55
      removed outlier: 6.358A  pdb=" N   THR A  37 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER A  32 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ARG A  41 " --> pdb=" O   MET A  28 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR A  29 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A  72 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 241
    Processing sheet with id=AA3, first strand: chain 'A' and resid 938 through 939
      removed outlier: 6.093A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   SER A 957 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLU A 954 " --> pdb=" O   LEU A 982 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ARG A 984 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   ARG A 956 " --> pdb=" O   ARG A 984 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   TYR A 986 " --> pdb=" O   ARG A 956 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   PHE A 958 " --> pdb=" O   TYR A 986 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   THR A 983 " --> pdb=" O   MET A1009 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ALA A1011 " --> pdb=" O   THR A 983 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   VAL A 985 " --> pdb=" O   ALA A1011 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   VAL A1010 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ILE A 323 " --> pdb=" O   VAL A1010 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   LEU A1012 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   SER A 325 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 358
      removed outlier: 6.329A  pdb=" N   VAL A 401 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   LYS A 454 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LEU A 403 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361
      removed outlier: 3.606A  pdb=" N   VAL A 369 " --> pdb=" O   TRP A 361 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE A 370 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ILE A 380 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 478 through 484
      removed outlier: 7.241A  pdb=" N   ARG A 493 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   ASP A 508 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   TYR A 495 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565
    Processing sheet with id=AA8, first strand: chain 'A' and resid 589 through 593
      removed outlier: 3.954A  pdb=" N   LEU A 605 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 624
    Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.641A  pdb=" N   LYS A 673 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.641A  pdb=" N   LYS A 673 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1124
      removed outlier: 6.780A  pdb=" N   LEU A1181 " --> pdb=" O   LEU A1068 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ALA A1070 " --> pdb=" O   SER A1179 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   SER A1179 " --> pdb=" O   ALA A1070 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1097 through 1100
      removed outlier: 3.812A  pdb=" N   ASN A1097 " --> pdb=" O   ILE A1089 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA A1149 " --> pdb=" O   VAL A1136 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLU A1138 " --> pdb=" O   PHE A1147 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   PHE A1147 " --> pdb=" O   GLU A1138 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.04 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: 2304
        1.33 -     1.45: 1673
        1.45 -     1.58: 4863
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8910
  Sorted by residual:
  bond pdb=" N   VAL A 635 "
       pdb=" CA  VAL A 635 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 8.70e-03 1.32e+04 1.99e+01
  bond pdb=" CE1 HIS A 641 "
       pdb=" NE2 HIS A 641 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.61e+01
  bond pdb=" N   ASP A 224 "
       pdb=" CA  ASP A 224 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.23e-02 6.61e+03 1.05e+01
  bond pdb=" CA  LEU A 562 "
       pdb=" C   LEU A 562 "
    ideal  model  delta    sigma   weight residual
    1.523  1.563 -0.040 1.34e-02 5.57e+03 8.85e+00
  bond pdb=" N   TYR A1036 "
       pdb=" CA  TYR A1036 "
    ideal  model  delta    sigma   weight residual
    1.458  1.422  0.035 1.22e-02 6.72e+03 8.29e+00
  ... (remaining 8905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 11850
        2.87 -     5.73: 145
        5.73 -     8.60: 25
        8.60 -    11.46: 4
       11.46 -    14.33: 1
  Bond angle restraints: 12025
  Sorted by residual:
  angle pdb=" N   PHE A 221 "
        pdb=" CA  PHE A 221 "
        pdb=" C   PHE A 221 "
      ideal   model   delta    sigma   weight residual
     112.87  105.56    7.31 1.20e+00 6.94e-01 3.71e+01
  angle pdb=" N   LEU A 218 "
        pdb=" CA  LEU A 218 "
        pdb=" C   LEU A 218 "
      ideal   model   delta    sigma   weight residual
     112.38  105.16    7.22 1.22e+00 6.72e-01 3.50e+01
  angle pdb=" N   ARG A 540 "
        pdb=" CA  ARG A 540 "
        pdb=" C   ARG A 540 "
      ideal   model   delta    sigma   weight residual
     111.28  105.07    6.21 1.09e+00 8.42e-01 3.25e+01
  angle pdb=" N   PHE A 577 "
        pdb=" CA  PHE A 577 "
        pdb=" C   PHE A 577 "
      ideal   model   delta    sigma   weight residual
     108.41  117.50   -9.09 1.63e+00 3.76e-01 3.11e+01
  angle pdb=" N   PHE A 182 "
        pdb=" CA  PHE A 182 "
        pdb=" C   PHE A 182 "
      ideal   model   delta    sigma   weight residual
     111.82  105.76    6.06 1.16e+00 7.43e-01 2.73e+01
  ... (remaining 12020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4588
       17.92 -    35.84: 645
       35.84 -    53.76: 145
       53.76 -    71.68: 25
       71.68 -    89.61: 10
  Dihedral angle restraints: 5413
    sinusoidal: 2281
      harmonic: 3132
  Sorted by residual:
  dihedral pdb=" CA  THR A 632 "
           pdb=" C   THR A 632 "
           pdb=" N   ASP A 633 "
           pdb=" CA  ASP A 633 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.76  -25.24     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  THR A 560 "
           pdb=" C   THR A 560 "
           pdb=" N   PHE A 561 "
           pdb=" CA  PHE A 561 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.13  -21.87     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  TYR A 321 "
           pdb=" C   TYR A 321 "
           pdb=" N   TRP A 322 "
           pdb=" CA  TRP A 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.06   17.94     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 5410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 896
       0.040 -    0.081: 260
       0.081 -    0.121: 109
       0.121 -    0.161: 22
       0.161 -    0.201: 4
  Chirality restraints: 1291
  Sorted by residual:
  chirality pdb=" CA  MET A 210 "
            pdb=" N   MET A 210 "
            pdb=" C   MET A 210 "
            pdb=" CB  MET A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  LEU A 601 "
            pdb=" N   LEU A 601 "
            pdb=" C   LEU A 601 "
            pdb=" CB  LEU A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.20e-01
  chirality pdb=" CA  HIS A 527 "
            pdb=" N   HIS A 527 "
            pdb=" C   HIS A 527 "
            pdb=" CB  HIS A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  ... (remaining 1288 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 647 "   -0.016 2.00e-02 2.50e+03   1.78e-02 6.32e+00
        pdb=" CG  TYR A 647 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 647 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 647 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 647 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 647 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 647 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 647 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 561 "   -0.012 2.00e-02 2.50e+03   2.39e-02 5.70e+00
        pdb=" C   PHE A 561 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 561 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 562 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  37 "   -0.039 5.00e-02 4.00e+02   5.84e-02 5.47e+00
        pdb=" N   PRO A  38 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A  38 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  38 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1222
        2.75 -     3.29: 9082
        3.29 -     3.83: 14998
        3.83 -     4.36: 17376
        4.36 -     4.90: 29274
  Nonbonded interactions: 71952
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 400 "
            pdb=" OH  TYR A1036 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG1 THR A 632 "
            pdb=" OD2 ASP A 633 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   SER A 580 "
            pdb=" OG  SER A 580 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   SER A 296 "
            pdb=" OG  SER A1164 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE A 749 "
            pdb=" OH  TYR A 753 "
     model   vdw
     2.238 3.040
  ... (remaining 71947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.01 max=1.00 mean=0.99
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:             0.530
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.870
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
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      :  0.004   0.041   8910  Z= 0.227
  Angle     :  0.823  14.328  12025  Z= 0.470
  Chirality :  0.046   0.201   1291
  Planarity :  0.005   0.058   1546
  Dihedral  : 17.222  89.606   3379
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.15 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.25), residues: 1051
  helix:  0.49 (0.29), residues: 320
  sheet: -0.96 (0.38), residues: 175
  loop : -0.85 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 850 
 TYR   0.043   0.002   TYR A 647 
 PHE   0.020   0.002   PHE A 221 
 TRP   0.012   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8910)
  covalent geometry    : angle       0.82300 (12025)
  hydrogen bonds       : bond        0.14395 (  337)
  hydrogen bonds       : angle       6.79543 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 TYR cc_start: 0.6614 (p90) cc_final: 0.6222 (p90)
REVERT: A  562 LEU cc_start: 0.7931 (tt) cc_final: 0.7717 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0838
  time to fit residues: 19.5465
Evaluate side-chains
  140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 263 ASN
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.136444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.108022 restraints weight = 16751.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.112049 restraints weight = 8479.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.114677 restraints weight = 5412.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.116416 restraints weight = 4049.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.117255 restraints weight = 3355.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8910  Z= 0.121
  Angle     :  0.614   7.444  12025  Z= 0.317
  Chirality :  0.042   0.143   1291
  Planarity :  0.004   0.046   1546
  Dihedral  :  4.654  22.223   1166
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 25.91 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.25), residues: 1051
  helix:  0.92 (0.28), residues: 331
  sheet: -0.70 (0.36), residues: 196
  loop : -0.84 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.012   0.001   TYR A 617 
 PHE   0.039   0.002   PHE A1000 
 TRP   0.019   0.001   TRP A 578 
 HIS   0.004   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8910)
  covalent geometry    : angle       0.61416 (12025)
  hydrogen bonds       : bond        0.03825 (  337)
  hydrogen bonds       : angle       5.62302 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 MET cc_start: 0.8560 (mmt) cc_final: 0.8245 (mmt)
REVERT: A  330 TYR cc_start: 0.6497 (p90) cc_final: 0.5865 (p90)
REVERT: A  730 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7856 (ptp-110)
REVERT: A 1013 ASN cc_start: 0.8662 (m-40) cc_final: 0.8100 (m-40)
REVERT: A 1015 GLN cc_start: 0.8527 (pm20) cc_final: 0.8295 (pm20)
REVERT: A 1022 GLN cc_start: 0.8453 (mt0) cc_final: 0.7992 (mt0)
  outliers start: 22
  outliers final: 11
  residues processed: 177
  average time/residue: 0.0811
  time to fit residues: 20.6340
Evaluate side-chains
  150 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1180 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.130103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.100384 restraints weight = 17164.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.104191 restraints weight = 8709.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.106789 restraints weight = 5656.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.108513 restraints weight = 4255.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.109509 restraints weight = 3526.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
r_final: 0.3648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8910  Z= 0.198
  Angle     :  0.648   7.449  12025  Z= 0.331
  Chirality :  0.044   0.208   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.825  22.642   1166
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.87 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.26), residues: 1051
  helix:  1.05 (0.29), residues: 326
  sheet: -1.00 (0.36), residues: 204
  loop : -0.77 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 850 
 TYR   0.011   0.002   TYR A 986 
 PHE   0.019   0.002   PHE A 888 
 TRP   0.021   0.002   TRP A 578 
 HIS   0.006   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8910)
  covalent geometry    : angle       0.64813 (12025)
  hydrogen bonds       : bond        0.03722 (  337)
  hydrogen bonds       : angle       5.62932 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 149
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8617 (mm)
REVERT: A  330 TYR cc_start: 0.6681 (p90) cc_final: 0.6001 (p90)
REVERT: A  697 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5354 (mtm110)
REVERT: A  730 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.7755 (ptp-110)
REVERT: A 1009 MET cc_start: 0.6843 (mtt) cc_final: 0.6401 (mtt)
REVERT: A 1066 LYS cc_start: 0.8557 (tttt) cc_final: 0.8255 (tttt)
REVERT: A 1177 LEU cc_start: 0.9006 (mm) cc_final: 0.8783 (mm)
  outliers start: 42
  outliers final: 26
  residues processed: 177
  average time/residue: 0.0890
  time to fit residues: 22.5385
Evaluate side-chains
  166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  697 ARG
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1080 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 93 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0070
   chunk 4 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6400

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

Flipped N/Q/H residues before XYZ refinement:
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.132790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.104175 restraints weight = 16986.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.108152 restraints weight = 8410.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.110798 restraints weight = 5332.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.112558 restraints weight = 3957.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.113206 restraints weight = 3249.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       67 |
|-----------------------------------------------------------------------------|
r_final: 0.3713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8910  Z= 0.115
  Angle     :  0.592   7.768  12025  Z= 0.299
  Chirality :  0.042   0.131   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.575  21.269   1166
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.74 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.26), residues: 1051
  helix:  1.25 (0.29), residues: 327
  sheet: -0.71 (0.37), residues: 196
  loop : -0.71 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 850 
 TYR   0.016   0.001   TYR A 206 
 PHE   0.021   0.001   PHE A 888 
 TRP   0.023   0.001   TRP A 578 
 HIS   0.004   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8910)
  covalent geometry    : angle       0.59183 (12025)
  hydrogen bonds       : bond        0.03251 (  337)
  hydrogen bonds       : angle       5.23810 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8187 (tm-30)
REVERT: A  330 TYR cc_start: 0.6482 (p90) cc_final: 0.5794 (p90)
REVERT: A  726 TYR cc_start: 0.8581 (t80) cc_final: 0.6736 (t80)
REVERT: A  730 ARG cc_start: 0.8071 (ptp-110) cc_final: 0.7635 (ptp-110)
REVERT: A 1022 GLN cc_start: 0.8356 (mt0) cc_final: 0.7880 (mt0)
REVERT: A 1025 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.6933 (t-90)
REVERT: A 1066 LYS cc_start: 0.8536 (tttt) cc_final: 0.8254 (tttt)
  outliers start: 31
  outliers final: 19
  residues processed: 183
  average time/residue: 0.0965
  time to fit residues: 24.8054
Evaluate side-chains
  164 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   72 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 105 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.128861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.100164 restraints weight = 17098.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.103959 restraints weight = 8647.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.106480 restraints weight = 5575.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.108102 restraints weight = 4191.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109095 restraints weight = 3484.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       67 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       73 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8910  Z= 0.177
  Angle     :  0.643  11.356  12025  Z= 0.323
  Chirality :  0.043   0.140   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.707  22.121   1166
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.84 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.26), residues: 1051
  helix:  1.25 (0.29), residues: 327
  sheet: -0.80 (0.38), residues: 195
  loop : -0.72 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 850 
 TYR   0.016   0.002   TYR A 345 
 PHE   0.020   0.002   PHE A 221 
 TRP   0.022   0.002   TRP A 578 
 HIS   0.008   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8910)
  covalent geometry    : angle       0.64281 (12025)
  hydrogen bonds       : bond        0.03479 (  337)
  hydrogen bonds       : angle       5.33713 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 152
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (tm-30)
REVERT: A  269 MET cc_start: 0.7915 (mmm) cc_final: 0.7651 (mtt)
REVERT: A  330 TYR cc_start: 0.6581 (p90) cc_final: 0.5892 (p90)
REVERT: A  574 THR cc_start: 0.6479 (OUTLIER) cc_final: 0.6224 (p)
REVERT: A  730 ARG cc_start: 0.8226 (ptp-110) cc_final: 0.7744 (ptp-110)
REVERT: A 1025 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7440 (t-90)
REVERT: A 1066 LYS cc_start: 0.8485 (tttt) cc_final: 0.8130 (tttt)
  outliers start: 37
  outliers final: 23
  residues processed: 177
  average time/residue: 0.0924
  time to fit residues: 23.1276
Evaluate side-chains
  162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   72 GLU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1080 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:   30.0000
   chunk 44 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.131354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.102734 restraints weight = 16897.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.106578 restraints weight = 8471.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.109157 restraints weight = 5442.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.110837 restraints weight = 4072.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.111821 restraints weight = 3374.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       73 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       79 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8910  Z= 0.143
  Angle     :  0.630   9.659  12025  Z= 0.317
  Chirality :  0.043   0.165   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.623  21.562   1166
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 27.88 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.26), residues: 1051
  helix:  1.36 (0.29), residues: 326
  sheet: -0.78 (0.38), residues: 195
  loop : -0.74 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 850 
 TYR   0.017   0.002   TYR A 345 
 PHE   0.022   0.002   PHE A 221 
 TRP   0.029   0.002   TRP A 361 
 HIS   0.006   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8910)
  covalent geometry    : angle       0.63037 (12025)
  hydrogen bonds       : bond        0.03350 (  337)
  hydrogen bonds       : angle       5.25312 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 147
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 TYR cc_start: 0.6538 (p90) cc_final: 0.5752 (p90)
REVERT: A  619 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.3163 (tm-30)
REVERT: A  622 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5683 (pp)
REVERT: A  730 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7691 (ptp-110)
REVERT: A  902 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (p)
REVERT: A 1025 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7104 (t-90)
REVERT: A 1066 LYS cc_start: 0.8495 (tttt) cc_final: 0.8080 (tttt)
  outliers start: 38
  outliers final: 24
  residues processed: 176
  average time/residue: 0.0900
  time to fit residues: 22.4807
Evaluate side-chains
  164 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1080 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.131483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.102789 restraints weight = 16922.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.106598 restraints weight = 8551.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.109170 restraints weight = 5510.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.110775 restraints weight = 4132.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111926 restraints weight = 3443.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       79 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8910  Z= 0.141
  Angle     :  0.637  11.093  12025  Z= 0.320
  Chirality :  0.043   0.149   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.584  21.381   1166
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 28.19 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.26), residues: 1051
  helix:  1.45 (0.29), residues: 319
  sheet: -0.98 (0.36), residues: 204
  loop : -0.67 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 850 
 TYR   0.018   0.001   TYR A 345 
 PHE   0.022   0.001   PHE A 221 
 TRP   0.024   0.002   TRP A 578 
 HIS   0.006   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8910)
  covalent geometry    : angle       0.63744 (12025)
  hydrogen bonds       : bond        0.03379 (  337)
  hydrogen bonds       : angle       5.27476 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: A  619 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.3039 (tm-30)
REVERT: A  622 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5433 (pp)
REVERT: A  730 ARG cc_start: 0.8179 (ptp-110) cc_final: 0.7664 (ptp-110)
REVERT: A  902 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8067 (p)
REVERT: A 1025 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7108 (t-90)
REVERT: A 1066 LYS cc_start: 0.8519 (tttt) cc_final: 0.8158 (tttt)
  outliers start: 40
  outliers final: 31
  residues processed: 170
  average time/residue: 0.0887
  time to fit residues: 21.5492
Evaluate side-chains
  171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1080 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   chunk 56 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN
A1039 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.132346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.103784 restraints weight = 16690.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.107570 restraints weight = 8484.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110094 restraints weight = 5482.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.111648 restraints weight = 4126.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.112808 restraints weight = 3454.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       82 |
|-----------------------------------------------------------------------------|
r_final: 0.3721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8910  Z= 0.135
  Angle     :  0.631   9.071  12025  Z= 0.316
  Chirality :  0.043   0.139   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.501  20.559   1166
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 28.19 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.26), residues: 1051
  helix:  1.58 (0.29), residues: 319
  sheet: -1.04 (0.35), residues: 215
  loop : -0.64 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 850 
 TYR   0.016   0.001   TYR A 345 
 PHE   0.023   0.001   PHE A 221 
 TRP   0.023   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8910)
  covalent geometry    : angle       0.63081 (12025)
  hydrogen bonds       : bond        0.03289 (  337)
  hydrogen bonds       : angle       5.16707 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8019 (tt)
REVERT: A  251 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8580 (mm)
REVERT: A  619 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.3281 (tm-30)
REVERT: A  622 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5533 (pp)
REVERT: A  730 ARG cc_start: 0.8014 (ptp-110) cc_final: 0.7633 (ptp-110)
REVERT: A  747 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7065 (mtm-85)
REVERT: A 1025 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7008 (t-90)
REVERT: A 1172 SER cc_start: 0.9408 (m) cc_final: 0.9135 (p)
  outliers start: 39
  outliers final: 30
  residues processed: 168
  average time/residue: 0.0953
  time to fit residues: 22.0525
Evaluate side-chains
  171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  747 ARG
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1117 GLN
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0050
   chunk 82 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.133152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.104897 restraints weight = 16656.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.108813 restraints weight = 8352.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.111378 restraints weight = 5345.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.113150 restraints weight = 3990.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.114132 restraints weight = 3280.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       82 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
r_final: 0.3739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8910  Z= 0.130
  Angle     :  0.636   8.761  12025  Z= 0.321
  Chirality :  0.043   0.139   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.461  20.664   1166
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 28.70 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.26), residues: 1051
  helix:  1.61 (0.29), residues: 319
  sheet: -0.92 (0.37), residues: 197
  loop : -0.71 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 850 
 TYR   0.016   0.001   TYR A 345 
 PHE   0.023   0.001   PHE A 221 
 TRP   0.023   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8910)
  covalent geometry    : angle       0.63632 (12025)
  hydrogen bonds       : bond        0.03239 (  337)
  hydrogen bonds       : angle       5.09408 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8071 (tt)
REVERT: A  619 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.3316 (tm-30)
REVERT: A  673 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8217 (tmtt)
REVERT: A  730 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7618 (ptp-110)
REVERT: A  747 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7096 (mtm-85)
REVERT: A 1025 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7063 (t-90)
  outliers start: 40
  outliers final: 33
  residues processed: 167
  average time/residue: 0.0911
  time to fit residues: 21.2982
Evaluate side-chains
  176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  747 ARG
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1117 GLN
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 83 optimal weight:    0.3980
   chunk 98 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 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 = 0.3948 r_free = 0.3948 target = 0.134575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.106155 restraints weight = 16737.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.110094 restraints weight = 8402.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.112691 restraints weight = 5396.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.114462 restraints weight = 4036.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.115457 restraints weight = 3318.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8910  Z= 0.123
  Angle     :  0.655  12.425  12025  Z= 0.328
  Chirality :  0.043   0.193   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.400  20.134   1166
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 29.43 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.26), residues: 1051
  helix:  1.67 (0.29), residues: 319
  sheet: -0.76 (0.36), residues: 212
  loop : -0.66 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 850 
 TYR   0.018   0.001   TYR A 206 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.022   0.001   TRP A 578 
 HIS   0.007   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8910)
  covalent geometry    : angle       0.65527 (12025)
  hydrogen bonds       : bond        0.03340 (  337)
  hydrogen bonds       : angle       5.07685 (  933)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: A  339 GLU cc_start: 0.7960 (tp30) cc_final: 0.7654 (pt0)
REVERT: A  619 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.3409 (tm-30)
REVERT: A  673 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8174 (tmtt)
REVERT: A  684 PHE cc_start: 0.8579 (p90) cc_final: 0.8361 (p90)
REVERT: A  730 ARG cc_start: 0.8025 (ptp-110) cc_final: 0.7657 (ptp-110)
REVERT: A  747 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7079 (mtm-85)
REVERT: A 1025 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.6933 (t-90)
REVERT: A 1172 SER cc_start: 0.9376 (m) cc_final: 0.9115 (p)
  outliers start: 33
  outliers final: 29
  residues processed: 167
  average time/residue: 0.0905
  time to fit residues: 21.0947
Evaluate side-chains
  176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  747 ARG
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1117 GLN
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0070
   chunk 98 optimal weight:    0.4980
   chunk 97 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.8600

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.134387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.105934 restraints weight = 16805.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.109798 restraints weight = 8475.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.112446 restraints weight = 5454.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.114053 restraints weight = 4069.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.115152 restraints weight = 3384.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8910  Z= 0.133
  Angle     :  0.666  11.830  12025  Z= 0.335
  Chirality :  0.043   0.230   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.412  19.506   1166
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 29.43 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1051
  helix:  1.63 (0.29), residues: 319
  sheet: -0.74 (0.36), residues: 198
  loop : -0.74 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 850 
 TYR   0.013   0.001   TYR A 345 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.045   0.002   TRP A 145 
 HIS   0.007   0.001   HIS A 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8910)
  covalent geometry    : angle       0.66587 (12025)
  hydrogen bonds       : bond        0.03475 (  337)
  hydrogen bonds       : angle       5.12784 (  933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1685.88 seconds
wall clock time: 29 minutes 53.65 seconds (1793.65 seconds total)