Starting phenix.real_space_refine
on Thu Mar 13 08:32:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqg_36571/03_2025/8jqg_36571_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqg_36571/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jqg_36571/03_2025/8jqg_36571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqg_36571/03_2025/8jqg_36571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqg_36571/03_2025/8jqg_36571_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqg_36571/03_2025/8jqg_36571_neut.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.30, per 1000 atoms: 0.61
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.07
  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: 3.21

  Time building geometry restraints manager: 2.88 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:             0.750
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.610
-------------------------------------------------------------------------------
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= 0.256
  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 : 22.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (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
 TRP   0.012   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.020   0.002   PHE A 221 
 TYR   0.043   0.002   TYR A 647 
 ARG   0.008   0.001   ARG A 850 

*********************** 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  : 0.977 
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: 0.6227 (p90)
REVERT: A  562 LEU cc_start: 0.7931 (tt) cc_final: 0.7709 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2173
  time to fit residues: 49.9599
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
A 637 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.135766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.107474 restraints weight = 16623.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.111425 restraints weight = 8480.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114109 restraints weight = 5460.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
r_final: 0.3710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8910  Z= 0.184
  Angle     :  0.621   7.462  12025  Z= 0.319
  Chirality :  0.042   0.140   1291
  Planarity :  0.004   0.046   1546
  Dihedral  :  4.662  22.191   1166
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 26.11 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.25), residues: 1051
  helix:  0.91 (0.28), residues: 332
  sheet: -0.70 (0.36), residues: 196
  loop : -0.84 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 578 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.039   0.002   PHE A1000 
 TYR   0.013   0.001   TYR A 617 
 ARG   0.005   0.000   ARG A 347 

*********************** 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
  187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.964 
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: 0.8551 (mmt) cc_final: 0.8226 (mmt)
REVERT: A  330 TYR cc_start: 0.6469 (p90) cc_final: 0.5854 (p90)
REVERT: A  730 ARG cc_start: 0.8169 (ptp-110) cc_final: 0.7878 (ptp-110)
REVERT: A 1013 ASN cc_start: 0.8585 (m-40) cc_final: 0.8054 (m-40)
REVERT: A 1015 GLN cc_start: 0.8450 (pm20) cc_final: 0.8231 (pm20)
REVERT: A 1022 GLN cc_start: 0.8463 (mt0) cc_final: 0.8015 (mt0)
  outliers start: 23
  outliers final: 11
  residues processed: 180
  average time/residue: 0.1941
  time to fit residues: 49.0811
Evaluate side-chains
  149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
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  384 ASP
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 1180 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.130378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.101415 restraints weight = 17031.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.105295 restraints weight = 8632.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.107806 restraints weight = 5571.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
r_final: 0.3638
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8910  Z= 0.257
  Angle     :  0.630   7.158  12025  Z= 0.321
  Chirality :  0.044   0.193   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.747  22.322   1166
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 24.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.26), residues: 1051
  helix:  1.10 (0.29), residues: 327
  sheet: -0.88 (0.36), residues: 198
  loop : -0.74 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 408 
 PHE   0.023   0.002   PHE A 888 
 TYR   0.011   0.002   TYR A1036 
 ARG   0.006   0.000   ARG A 850 

*********************** 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
  189 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 1.113 
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: A  251 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8601 (mm)
REVERT: A  330 TYR cc_start: 0.6588 (p90) cc_final: 0.5935 (p90)
REVERT: A  730 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7714 (ptp-110)
REVERT: A 1009 MET cc_start: 0.6783 (mtt) cc_final: 0.6342 (mtt)
REVERT: A 1022 GLN cc_start: 0.8579 (mt0) cc_final: 0.7984 (mt0)
REVERT: A 1066 LYS cc_start: 0.8577 (tttt) cc_final: 0.8237 (tttt)
  outliers start: 41
  outliers final: 24
  residues processed: 178
  average time/residue: 0.2696
  time to fit residues: 70.2200
Evaluate side-chains
  166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 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  250 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  348 CYS
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  578 TRP
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  845 LEU
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 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 1165 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1176 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 80 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.132859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.104221 restraints weight = 16657.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.108153 restraints weight = 8343.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.110787 restraints weight = 5334.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       74 |
|-----------------------------------------------------------------------------|
r_final: 0.3677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8910  Z= 0.180
  Angle     :  0.598   7.378  12025  Z= 0.300
  Chirality :  0.042   0.129   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.540  21.154   1166
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 26.22 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1051
  helix:  1.27 (0.29), residues: 327
  sheet: -0.65 (0.37), residues: 195
  loop : -0.72 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 578 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.021   0.001   PHE A 221 
 TYR   0.014   0.001   TYR A 206 
 ARG   0.006   0.000   ARG A 850 

*********************** 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
  194 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 1.116 
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: A  330 TYR cc_start: 0.6499 (p90) cc_final: 0.5698 (p90)
REVERT: A  726 TYR cc_start: 0.8568 (t80) cc_final: 0.6881 (t80)
REVERT: A  730 ARG cc_start: 0.8047 (ptp-110) cc_final: 0.7723 (ptp-110)
REVERT: A 1009 MET cc_start: 0.6760 (mtt) cc_final: 0.6559 (mtt)
REVERT: A 1013 ASN cc_start: 0.8626 (m-40) cc_final: 0.8088 (m-40)
REVERT: A 1022 GLN cc_start: 0.8345 (mt0) cc_final: 0.7934 (mt0)
REVERT: A 1025 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.6950 (t-90)
REVERT: A 1066 LYS cc_start: 0.8595 (tttt) cc_final: 0.8276 (tttt)
  outliers start: 33
  outliers final: 22
  residues processed: 186
  average time/residue: 0.2499
  time to fit residues: 65.9508
Evaluate side-chains
  171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 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  741 GLU
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:   40.0000
   chunk 89 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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 856 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.124389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.095595 restraints weight = 17157.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.099075 restraints weight = 8892.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.101463 restraints weight = 5881.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       74 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       74 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   8910  Z= 0.427
  Angle     :  0.740  15.106  12025  Z= 0.377
  Chirality :  0.046   0.157   1291
  Planarity :  0.005   0.045   1546
  Dihedral  :  5.103  23.158   1166
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 26.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.26), residues: 1051
  helix:  1.08 (0.29), residues: 323
  sheet: -1.01 (0.37), residues: 194
  loop : -0.84 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 361 
 HIS   0.009   0.002   HIS A 621 
 PHE   0.020   0.003   PHE A1084 
 TYR   0.020   0.002   TYR A 345 
 ARG   0.007   0.001   ARG A 850 

*********************** 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
  177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 129
  time to evaluate  : 0.991 
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  251 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: A  330 TYR cc_start: 0.6849 (p90) cc_final: 0.6147 (p90)
REVERT: A  561 PHE cc_start: 0.7719 (p90) cc_final: 0.7431 (p90)
REVERT: A  574 THR cc_start: 0.6481 (OUTLIER) cc_final: 0.6223 (p)
REVERT: A  997 TYR cc_start: 0.7917 (p90) cc_final: 0.7548 (p90)
REVERT: A 1009 MET cc_start: 0.7134 (mtt) cc_final: 0.6798 (mtt)
REVERT: A 1066 LYS cc_start: 0.8671 (tttt) cc_final: 0.8347 (tttt)
REVERT: A 1177 LEU cc_start: 0.9032 (mm) cc_final: 0.8768 (mm)
  outliers start: 48
  outliers final: 31
  residues processed: 162
  average time/residue: 0.2198
  time to fit residues: 50.7021
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   95 CYS
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  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  574 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  659 MET
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  887 GLU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  935 VAL
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
Chi-restraints excluded: chain A residue 1179 SER
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 94 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0070
   chunk 58 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 49 optimal weight:    8.9990
   overall best weight:    0.8000

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.130575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.101965 restraints weight = 16938.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.105831 restraints weight = 8568.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.108352 restraints weight = 5504.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       74 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
r_final: 0.3642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8910  Z= 0.193
  Angle     :  0.629   9.236  12025  Z= 0.313
  Chirality :  0.042   0.178   1291
  Planarity :  0.004   0.048   1546
  Dihedral  :  4.668  21.263   1166
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 29.12 %
    Favored  : 68.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.26), residues: 1051
  helix:  1.31 (0.29), residues: 326
  sheet: -0.96 (0.37), residues: 196
  loop : -0.86 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 578 
 HIS   0.006   0.001   HIS A 621 
 PHE   0.021   0.001   PHE A 221 
 TYR   0.010   0.001   TYR A1036 
 ARG   0.003   0.000   ARG A 850 

*********************** 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
  165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.006 
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: 0.8356 (OUTLIER) cc_final: 0.7938 (tt)
REVERT: A  330 TYR cc_start: 0.6644 (p90) cc_final: 0.5814 (p90)
REVERT: A  619 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.3789 (tm-30)
REVERT: A  622 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5687 (pp)
REVERT: A  747 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7205 (mtm-85)
REVERT: A  997 TYR cc_start: 0.7679 (p90) cc_final: 0.7286 (p90)
REVERT: A 1009 MET cc_start: 0.6743 (mtt) cc_final: 0.6451 (mtt)
REVERT: A 1013 ASN cc_start: 0.8625 (m-40) cc_final: 0.8097 (m-40)
REVERT: A 1025 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7095 (t-90)
REVERT: A 1066 LYS cc_start: 0.8563 (tttt) cc_final: 0.8179 (tttt)
  outliers start: 27
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2061
  time to fit residues: 46.5825
Evaluate side-chains
  150 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  172 LEU
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  434 THR
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  741 GLU
Chi-restraints excluded: chain A residue  747 ARG
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 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 1182 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 77 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.132967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.104500 restraints weight = 16988.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.108458 restraints weight = 8517.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.111034 restraints weight = 5454.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2830

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= 0.194
  Angle     :  0.645  10.206  12025  Z= 0.320
  Chirality :  0.043   0.146   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.583  21.121   1166
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 29.22 %
    Favored  : 67.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1051
  helix:  1.52 (0.29), residues: 318
  sheet: -0.74 (0.38), residues: 196
  loop : -0.77 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 621 
 PHE   0.023   0.002   PHE A 221 
 TYR   0.009   0.001   TYR A1036 
 ARG   0.007   0.000   ARG A 850 

*********************** 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
  176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8014 (tt)
REVERT: A  434 THR cc_start: 0.6120 (OUTLIER) cc_final: 0.5864 (t)
REVERT: A  619 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.3432 (tm-30)
REVERT: A  622 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5580 (pp)
REVERT: A  673 LYS cc_start: 0.8681 (tmtt) cc_final: 0.8204 (tmtt)
REVERT: A  730 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7756 (ptp-110)
REVERT: A  747 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7193 (mtm-85)
REVERT: A  902 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8070 (p)
REVERT: A  997 TYR cc_start: 0.7680 (p90) cc_final: 0.7311 (p90)
REVERT: A 1009 MET cc_start: 0.6643 (mtt) cc_final: 0.6339 (mtt)
REVERT: A 1025 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.6922 (t-90)
REVERT: A 1066 LYS cc_start: 0.8585 (tttt) cc_final: 0.8194 (tttt)
REVERT: A 1141 MET cc_start: 0.8278 (mtm) cc_final: 0.8053 (mtm)
REVERT: A 1172 SER cc_start: 0.9374 (m) cc_final: 0.9116 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 170
  average time/residue: 0.2001
  time to fit residues: 47.9012
Evaluate side-chains
  159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  172 LEU
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  434 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  622 LEU
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  902 SER
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1025 HIS
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 1182 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 91 optimal weight:    0.2980
   chunk 89 optimal weight:    0.8980
   chunk 71 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.134758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.106513 restraints weight = 17163.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.110566 restraints weight = 8520.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.113245 restraints weight = 5416.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8910  Z= 0.181
  Angle     :  0.646  12.840  12025  Z= 0.322
  Chirality :  0.043   0.217   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.467  20.429   1166
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 29.84 %
    Favored  : 67.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1051
  helix:  1.59 (0.29), residues: 319
  sheet: -0.64 (0.38), residues: 196
  loop : -0.73 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 621 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.026   0.001   TYR A 206 
 ARG   0.005   0.000   ARG A 850 

*********************** 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
  169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 1.000 
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  172 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (tt)
REVERT: A  206 TYR cc_start: 0.8189 (t80) cc_final: 0.7983 (t80)
REVERT: A  619 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.3482 (tm-30)
REVERT: A  673 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8159 (tmtt)
REVERT: A  747 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7170 (mtm-85)
REVERT: A  850 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8061 (mmm160)
REVERT: A  902 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (p)
REVERT: A  997 TYR cc_start: 0.7624 (p90) cc_final: 0.7232 (p90)
REVERT: A 1009 MET cc_start: 0.6404 (mtt) cc_final: 0.6112 (mtt)
REVERT: A 1013 ASN cc_start: 0.8372 (m-40) cc_final: 0.8105 (m-40)
REVERT: A 1022 GLN cc_start: 0.8328 (mt0) cc_final: 0.7696 (mt0)
REVERT: A 1025 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.6811 (t-90)
REVERT: A 1141 MET cc_start: 0.8338 (mtm) cc_final: 0.8086 (mtm)
REVERT: A 1172 SER cc_start: 0.9351 (m) cc_final: 0.9113 (p)
  outliers start: 26
  outliers final: 14
  residues processed: 163
  average time/residue: 0.2114
  time to fit residues: 47.9867
Evaluate side-chains
  158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  172 LEU
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  431 THR
Chi-restraints excluded: chain A residue  434 THR
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  747 ARG
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  955 ILE
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1117 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    0.0870
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 96 optimal weight:    0.0070
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.135681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.107777 restraints weight = 17126.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.111794 restraints weight = 8472.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.114503 restraints weight = 5381.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3226

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= 0.176
  Angle     :  0.660  11.892  12025  Z= 0.329
  Chirality :  0.043   0.245   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.420  20.257   1166
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 30.88 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.26), residues: 1051
  helix:  1.71 (0.30), residues: 318
  sheet: -0.64 (0.37), residues: 201
  loop : -0.74 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 361 
 HIS   0.009   0.001   HIS A 408 
 PHE   0.024   0.001   PHE A 221 
 TYR   0.026   0.001   TYR A 206 
 ARG   0.005   0.000   ARG A1071 

*********************** 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
  162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 1.119 
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  619 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.3605 (tm-30)
REVERT: A  673 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8138 (tmtt)
REVERT: A  747 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7190 (mtm-85)
REVERT: A  850 ARG cc_start: 0.8357 (mmm160) cc_final: 0.7973 (mmm160)
REVERT: A  902 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (p)
REVERT: A  945 ASP cc_start: 0.7896 (p0) cc_final: 0.7451 (t0)
REVERT: A  997 TYR cc_start: 0.7610 (p90) cc_final: 0.7238 (p90)
REVERT: A 1025 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.6847 (t-90)
REVERT: A 1141 MET cc_start: 0.8306 (mtm) cc_final: 0.8031 (mtm)
REVERT: A 1172 SER cc_start: 0.9340 (m) cc_final: 0.9107 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2263
  time to fit residues: 49.7505
Evaluate side-chains
  159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  250 LEU
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  434 THR
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  717 VAL
Chi-restraints excluded: chain A residue  747 ARG
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  955 ILE
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1117 GLN
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 48 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0870
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 99 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   chunk 79 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0030
   overall best weight:    0.3568

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.137031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.109189 restraints weight = 17171.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.113317 restraints weight = 8465.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.116026 restraints weight = 5321.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3770 r_free = 0.3770    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 = 0.3770 r_free = 0.3770    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       88 |
|-----------------------------------------------------------------------------|
r_final: 0.3770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8910  Z= 0.177
  Angle     :  0.661  11.612  12025  Z= 0.330
  Chirality :  0.042   0.138   1291
  Planarity :  0.004   0.052   1546
  Dihedral  :  4.345  19.560   1166
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 31.09 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1051
  helix:  1.74 (0.30), residues: 319
  sheet: -0.51 (0.37), residues: 206
  loop : -0.72 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 145 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.026   0.001   PHE A 221 
 TYR   0.027   0.001   TYR A 206 
 ARG   0.006   0.000   ARG A1071 

********************** 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
  162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.059 
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  619 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.3793 (tm-30)
REVERT: A  673 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8107 (tmtt)
REVERT: A  721 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: A  902 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8120 (p)
REVERT: A  945 ASP cc_start: 0.7891 (p0) cc_final: 0.7347 (t0)
REVERT: A 1025 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.6817 (t-90)
REVERT: A 1141 MET cc_start: 0.8277 (mtm) cc_final: 0.8010 (mtm)
REVERT: A 1172 SER cc_start: 0.9333 (m) cc_final: 0.9089 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 156
  average time/residue: 0.2159
  time to fit residues: 49.1680
Evaluate side-chains
  157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  434 THR
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  717 VAL
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  955 ILE
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1112 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 75 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 66 optimal weight:    0.5980
   chunk 95 optimal weight:    0.2980
   chunk 79 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   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**
** A1013 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.135657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.107553 restraints weight = 17147.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.111491 restraints weight = 8534.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.114213 restraints weight = 5449.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       88 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8910  Z= 0.190
  Angle     :  0.664  11.568  12025  Z= 0.330
  Chirality :  0.043   0.156   1291
  Planarity :  0.004   0.052   1546
  Dihedral  :  4.337  19.399   1166
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 30.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.26), residues: 1051
  helix:  1.69 (0.29), residues: 325
  sheet: -0.56 (0.37), residues: 206
  loop : -0.78 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 145 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.026   0.001   PHE A 221 
 TYR   0.021   0.001   TYR A 206 
 ARG   0.010   0.000   ARG A 850 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3373.55 seconds
wall clock time: 61 minutes 12.52 seconds (3672.52 seconds total)