Starting phenix.real_space_refine
on Mon May 12 05:39:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqg_36571/05_2025/8jqg_36571_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqg_36571/05_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_36571/05_2025/8jqg_36571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqg_36571/05_2025/8jqg_36571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqg_36571/05_2025/8jqg_36571_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqg_36571/05_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-5687/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: 5.49, per 1000 atoms: 0.63
  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: 2.41
  Conformation dependent library (CDL) restraints added in 1.0 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: 1.42
  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: 3.61

  Time building geometry restraints manager: 2.78 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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.180
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8910  Z= 0.227
  Angle     :  0.823  14.328  12025  Z= 0.470
  Chirality :  0.046   0.201   1291
  Planarity :  0.005   0.058   1546
  Dihedral  : 17.222  89.606   3379
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 22.35
  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 

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

*********************** 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  : 1.002 
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: 0.2116
  time to fit residues: 48.7586
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  : 0.971 
-------------------------------------------------------------------------------
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 = 48)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.107471 restraints weight = 16623.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.111432 restraints weight = 8481.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114115 restraints weight = 5458.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
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 = 0.01   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
r_final: 0.3719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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= 0.124
  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 : 14.31
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  337)
  hydrogen bonds       : angle       5.63629 (  933)
  covalent geometry    : bond        0.00282 ( 8910)
  covalent geometry    : angle       0.62066 (12025)

*********************** 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  : 1.064 
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: 0.8547 (mmt) cc_final: 0.8220 (mmt)
REVERT: A  330 TYR cc_start: 0.6495 (p90) cc_final: 0.5874 (p90)
REVERT: A  730 ARG cc_start: 0.8169 (ptp-110) cc_final: 0.7852 (ptp-110)
REVERT: A 1013 ASN cc_start: 0.8618 (m-40) cc_final: 0.8059 (m-40)
REVERT: A 1015 GLN cc_start: 0.8479 (pm20) cc_final: 0.8247 (pm20)
REVERT: A 1022 GLN cc_start: 0.8474 (mt0) cc_final: 0.8015 (mt0)
  outliers start: 23
  outliers final: 11
  residues processed: 180
  average time/residue: 0.1954
  time to fit residues: 49.3077
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  : 1.046 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.132038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.102736 restraints weight = 16838.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.106695 restraints weight = 8335.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.109408 restraints weight = 5309.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3674 r_free = 0.3674    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
r_final: 0.3673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8910  Z= 0.137
  Angle     :  0.608   7.260  12025  Z= 0.308
  Chirality :  0.043   0.196   1291
  Planarity :  0.004   0.050   1546
  Dihedral  :  4.624  21.794   1166
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.08 %
    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: -0.24 (0.26), residues: 1051
  helix:  1.17 (0.29), residues: 326
  sheet: -0.75 (0.36), residues: 198
  loop : -0.71 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 408 
 PHE   0.024   0.001   PHE A 888 
 TYR   0.011   0.002   TYR A 321 
 ARG   0.006   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  337)
  hydrogen bonds       : angle       5.40963 (  933)
  covalent geometry    : bond        0.00317 ( 8910)
  covalent geometry    : angle       0.60818 (12025)

*********************** 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
  192 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8402 (pp20) cc_final: 0.8154 (tm-30)
REVERT: A  182 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7306 (p90)
REVERT: A  311 MET cc_start: 0.8839 (mmt) cc_final: 0.8493 (mmt)
REVERT: A  330 TYR cc_start: 0.6496 (p90) cc_final: 0.5712 (p90)
REVERT: A  561 PHE cc_start: 0.7441 (p90) cc_final: 0.7168 (p90)
REVERT: A  726 TYR cc_start: 0.8594 (t80) cc_final: 0.6809 (t80)
REVERT: A  730 ARG cc_start: 0.8253 (ptp-110) cc_final: 0.7822 (ptp-110)
REVERT: A 1009 MET cc_start: 0.6618 (mtt) cc_final: 0.6409 (mtt)
REVERT: A 1013 ASN cc_start: 0.8697 (m-40) cc_final: 0.8064 (m-40)
REVERT: A 1015 GLN cc_start: 0.8493 (pm20) cc_final: 0.8285 (pm20)
REVERT: A 1022 GLN cc_start: 0.8456 (mt0) cc_final: 0.7972 (mt0)
REVERT: A 1025 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7016 (t-90)
REVERT: A 1066 LYS cc_start: 0.8566 (tttt) cc_final: 0.8220 (tttt)
  outliers start: 33
  outliers final: 22
  residues processed: 182
  average time/residue: 0.2028
  time to fit residues: 51.5154
Evaluate side-chains
  169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  375 THR
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  716 LEU
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1080 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1176 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 87 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   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 214 GLN
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.133303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.104781 restraints weight = 16671.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.108777 restraints weight = 8347.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.111432 restraints weight = 5328.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2213

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= 0.122
  Angle     :  0.601   8.556  12025  Z= 0.302
  Chirality :  0.042   0.141   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.464  20.966   1166
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.01 %
    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: -0.11 (0.26), residues: 1051
  helix:  1.31 (0.29), residues: 327
  sheet: -0.60 (0.37), residues: 195
  loop : -0.70 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 578 
 HIS   0.008   0.001   HIS A 621 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.010   0.001   TYR A1036 
 ARG   0.007   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03228 (  337)
  hydrogen bonds       : angle       5.14897 (  933)
  covalent geometry    : bond        0.00277 ( 8910)
  covalent geometry    : angle       0.60124 (12025)

*********************** 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
  191 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8071 (m)
REVERT: A  730 ARG cc_start: 0.8081 (ptp-110) cc_final: 0.7589 (ptp-110)
REVERT: A 1009 MET cc_start: 0.6705 (mtt) cc_final: 0.6460 (mtt)
REVERT: A 1013 ASN cc_start: 0.8651 (m-40) cc_final: 0.8114 (m-40)
REVERT: A 1025 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7068 (t-90)
REVERT: A 1066 LYS cc_start: 0.8586 (tttt) cc_final: 0.8284 (tttt)
  outliers start: 35
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2065
  time to fit residues: 52.7135
Evaluate side-chains
  166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  329 THR
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  578 TRP
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1176 GLU
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:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 48 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 89 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.128894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.100092 restraints weight = 16950.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.103544 restraints weight = 9084.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.105888 restraints weight = 6100.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       75 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8910  Z= 0.278
  Angle     :  0.737  15.333  12025  Z= 0.374
  Chirality :  0.045   0.155   1291
  Planarity :  0.005   0.046   1546
  Dihedral  :  5.072  22.702   1166
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 26.94 %
    Favored  : 68.39 %
  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: -0.31 (0.26), residues: 1051
  helix:  1.30 (0.29), residues: 313
  sheet: -0.98 (0.37), residues: 195
  loop : -0.76 (0.26), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 361 
 HIS   0.007   0.002   HIS A 641 
 PHE   0.021   0.003   PHE A1084 
 TYR   0.015   0.002   TYR A 986 
 ARG   0.007   0.001   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03962 (  337)
  hydrogen bonds       : angle       5.76272 (  933)
  covalent geometry    : bond        0.00638 ( 8910)
  covalent geometry    : angle       0.73696 (12025)

*********************** 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
  181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 136
  time to evaluate  : 1.094 
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  251 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8707 (mm)
REVERT: A  330 TYR cc_start: 0.6751 (p90) cc_final: 0.6151 (p90)
REVERT: A  561 PHE cc_start: 0.7605 (p90) cc_final: 0.7350 (p90)
REVERT: A  574 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6644 (p)
REVERT: A  997 TYR cc_start: 0.7864 (p90) cc_final: 0.7480 (p90)
REVERT: A 1009 MET cc_start: 0.7081 (mtt) cc_final: 0.6766 (mtt)
REVERT: A 1022 GLN cc_start: 0.8713 (mt0) cc_final: 0.8084 (mt0)
REVERT: A 1066 LYS cc_start: 0.8598 (tttt) cc_final: 0.8272 (tttt)
REVERT: A 1177 LEU cc_start: 0.9059 (mm) cc_final: 0.8819 (mm)
  outliers start: 45
  outliers final: 28
  residues processed: 164
  average time/residue: 0.1943
  time to fit residues: 45.0949
Evaluate side-chains
  149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  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  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  852 ILE
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1062 THR
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 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 = 0.3848 r_free = 0.3848 target = 0.127134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.098459 restraints weight = 17116.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.102180 restraints weight = 8777.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.104617 restraints weight = 5702.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       75 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8910  Z= 0.185
  Angle     :  0.667  11.005  12025  Z= 0.332
  Chirality :  0.043   0.163   1291
  Planarity :  0.004   0.045   1546
  Dihedral  :  4.852  21.581   1166
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 28.19 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.39 (0.26), residues: 1051
  helix:  1.19 (0.29), residues: 324
  sheet: -0.99 (0.37), residues: 190
  loop : -0.85 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 578 
 HIS   0.006   0.001   HIS A 621 
 PHE   0.022   0.002   PHE A 221 
 TYR   0.011   0.002   TYR A 206 
 ARG   0.003   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  337)
  hydrogen bonds       : angle       5.43409 (  933)
  covalent geometry    : bond        0.00432 ( 8910)
  covalent geometry    : angle       0.66652 (12025)

*********************** 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
  168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.960 
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: 0.8230 (OUTLIER) cc_final: 0.7777 (tt)
REVERT: A  251 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8675 (mm)
REVERT: A  330 TYR cc_start: 0.6790 (p90) cc_final: 0.6047 (p90)
REVERT: A  561 PHE cc_start: 0.7478 (p90) cc_final: 0.7164 (p90)
REVERT: A  619 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.3479 (tm-30)
REVERT: A  622 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5404 (pp)
REVERT: A  747 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7245 (mtm-85)
REVERT: A  997 TYR cc_start: 0.7820 (p90) cc_final: 0.7446 (p90)
REVERT: A 1009 MET cc_start: 0.6864 (mtt) cc_final: 0.6503 (mtt)
REVERT: A 1013 ASN cc_start: 0.8811 (m-40) cc_final: 0.7915 (m-40)
REVERT: A 1022 GLN cc_start: 0.8592 (mt0) cc_final: 0.7876 (mt0)
REVERT: A 1066 LYS cc_start: 0.8552 (tttt) cc_final: 0.8167 (tttt)
  outliers start: 39
  outliers final: 24
  residues processed: 160
  average time/residue: 0.2120
  time to fit residues: 48.0625
Evaluate side-chains
  150 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  401 VAL
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  659 MET
Chi-restraints excluded: chain A residue  747 ARG
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  955 ILE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1175 ILE
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0070
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 77 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.2834

-------------------------------------------------------------------------------
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 = 0.135084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.106834 restraints weight = 16914.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110777 restraints weight = 8409.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.113461 restraints weight = 5356.278|
|-----------------------------------------------------------------------------|
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:       77 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       81 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8910  Z= 0.109
  Angle     :  0.631   9.212  12025  Z= 0.311
  Chirality :  0.042   0.150   1291
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.524  19.809   1166
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 29.84 %
    Favored  : 67.98 %
  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:  1.49 (0.29), residues: 320
  sheet: -0.86 (0.36), residues: 217
  loop : -0.73 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 361 
 HIS   0.005   0.001   HIS A 408 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.010   0.001   TYR A 206 
 ARG   0.008   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  337)
  hydrogen bonds       : angle       5.07486 (  933)
  covalent geometry    : bond        0.00249 ( 8910)
  covalent geometry    : angle       0.63054 (12025)

*********************** 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
  174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.024 
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  330 TYR cc_start: 0.6626 (p90) cc_final: 0.5951 (p90)
REVERT: A  339 GLU cc_start: 0.7823 (tp30) cc_final: 0.7531 (pt0)
REVERT: A  619 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.3297 (tm-30)
REVERT: A  673 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8215 (tmtt)
REVERT: A  997 TYR cc_start: 0.7586 (p90) cc_final: 0.7207 (p90)
REVERT: A 1022 GLN cc_start: 0.8269 (mt0) cc_final: 0.7832 (mt0)
REVERT: A 1025 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6444 (t-90)
REVERT: A 1172 SER cc_start: 0.9352 (m) cc_final: 0.9037 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 169
  average time/residue: 0.1971
  time to fit residues: 47.1303
Evaluate side-chains
  151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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  250 LEU
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 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  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 1182 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 91 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0870
   chunk 25 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.135071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.107047 restraints weight = 17144.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.111060 restraints weight = 8479.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.113725 restraints weight = 5372.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3737 r_free = 0.3737    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       81 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3737 r_free = 0.3737    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8910  Z= 0.116
  Angle     :  0.657  11.824  12025  Z= 0.322
  Chirality :  0.043   0.182   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.457  20.425   1166
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 31.09 %
    Favored  : 66.53 %
  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:  1.60 (0.29), residues: 319
  sheet: -0.77 (0.38), residues: 197
  loop : -0.70 (0.27), residues: 535

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   0.024   0.001   PHE A 221 
 TYR   0.009   0.001   TYR A 753 
 ARG   0.006   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  337)
  hydrogen bonds       : angle       5.04597 (  933)
  covalent geometry    : bond        0.00272 ( 8910)
  covalent geometry    : angle       0.65696 (12025)

*********************** 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
  165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 1.110 
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: 0.6702 (p90) cc_final: 0.6189 (p90)
REVERT: A  619 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.3326 (tm-30)
REVERT: A  673 LYS cc_start: 0.8670 (tmtt) cc_final: 0.8191 (tmtt)
REVERT: A  997 TYR cc_start: 0.7619 (p90) cc_final: 0.7233 (p90)
REVERT: A 1009 MET cc_start: 0.6418 (mtt) cc_final: 0.6081 (mtt)
REVERT: A 1022 GLN cc_start: 0.8306 (mt0) cc_final: 0.7823 (mt0)
REVERT: A 1025 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.6879 (t-90)
REVERT: A 1172 SER cc_start: 0.9348 (m) cc_final: 0.9111 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 158
  average time/residue: 0.1969
  time to fit residues: 44.1333
Evaluate side-chains
  158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
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  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  578 TRP
Chi-restraints excluded: chain A residue  619 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  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 1182 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0980
   chunk 96 optimal weight:    0.2980
   chunk 91 optimal weight:    0.0070
   overall best weight:    0.8600

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.134234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.106189 restraints weight = 17108.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.110150 restraints weight = 8511.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.112761 restraints weight = 5384.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8910  Z= 0.130
  Angle     :  0.671  11.367  12025  Z= 0.330
  Chirality :  0.043   0.264   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.468  19.958   1166
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 30.57 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.01 (0.26), residues: 1051
  helix:  1.62 (0.29), residues: 319
  sheet: -0.68 (0.38), residues: 197
  loop : -0.71 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 361 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.025   0.001   PHE A 221 
 TYR   0.016   0.001   TYR A 753 
 ARG   0.005   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  337)
  hydrogen bonds       : angle       5.11886 (  933)
  covalent geometry    : bond        0.00305 ( 8910)
  covalent geometry    : angle       0.67118 (12025)

*********************** 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
  161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 1.106 
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: 0.6758 (p90) cc_final: 0.6056 (p90)
REVERT: A  409 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.6880 (p)
REVERT: A  619 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.3447 (tm-30)
REVERT: A  673 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8186 (tmtt)
REVERT: A  850 ARG cc_start: 0.8461 (mmm160) cc_final: 0.8141 (mmm160)
REVERT: A  853 LEU cc_start: 0.8078 (pt) cc_final: 0.7732 (pp)
REVERT: A  997 TYR cc_start: 0.7697 (p90) cc_final: 0.7303 (p90)
REVERT: A 1009 MET cc_start: 0.6688 (mtt) cc_final: 0.6371 (mtt)
REVERT: A 1013 ASN cc_start: 0.8600 (m110) cc_final: 0.8038 (t0)
REVERT: A 1022 GLN cc_start: 0.8388 (mt0) cc_final: 0.7877 (mt0)
REVERT: A 1025 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.6983 (t-90)
REVERT: A 1172 SER cc_start: 0.9357 (m) cc_final: 0.9125 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1999
  time to fit residues: 43.6962
Evaluate side-chains
  155 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  305 LYS
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  409 CYS
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  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 1182 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0670
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.136305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.108269 restraints weight = 17215.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.112311 restraints weight = 8487.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.114920 restraints weight = 5352.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8910  Z= 0.120
  Angle     :  0.670  11.373  12025  Z= 0.332
  Chirality :  0.043   0.245   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.420  19.160   1166
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 31.19 %
    Favored  : 66.74 %
  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:  0.03 (0.26), residues: 1051
  helix:  1.63 (0.29), residues: 318
  sheet: -0.42 (0.38), residues: 201
  loop : -0.77 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 361 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.026   0.001   PHE A 221 
 TYR   0.011   0.001   TYR A 753 
 ARG   0.005   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  337)
  hydrogen bonds       : angle       5.10581 (  933)
  covalent geometry    : bond        0.00280 ( 8910)
  covalent geometry    : angle       0.66979 (12025)

********************** 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
  167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.076 
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  330 TYR cc_start: 0.6674 (p90) cc_final: 0.5946 (p90)
REVERT: A  345 TYR cc_start: 0.6922 (m-10) cc_final: 0.6659 (m-80)
REVERT: A  619 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.3456 (tm-30)
REVERT: A  673 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8135 (tmtt)
REVERT: A  747 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (mtm-85)
REVERT: A  850 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8124 (mmm160)
REVERT: A  906 ILE cc_start: 0.8232 (mt) cc_final: 0.7952 (tt)
REVERT: A  997 TYR cc_start: 0.7635 (p90) cc_final: 0.7294 (p90)
REVERT: A 1009 MET cc_start: 0.6417 (mtt) cc_final: 0.6099 (mtt)
REVERT: A 1013 ASN cc_start: 0.8597 (m110) cc_final: 0.8034 (m-40)
REVERT: A 1022 GLN cc_start: 0.8305 (mt0) cc_final: 0.7808 (mt0)
REVERT: A 1025 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.6910 (t-90)
REVERT: A 1061 MET cc_start: 0.7071 (ttp) cc_final: 0.6866 (ptm)
REVERT: A 1172 SER cc_start: 0.9342 (m) cc_final: 0.9100 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 162
  average time/residue: 0.2126
  time to fit residues: 47.5320
Evaluate side-chains
  157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  578 TRP
Chi-restraints excluded: chain A residue  619 GLU
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  876 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 1182 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0070
   chunk 65 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.9402

-------------------------------------------------------------------------------
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
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.134660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.106484 restraints weight = 17054.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.110441 restraints weight = 8459.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.113057 restraints weight = 5379.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       88 |
|-----------------------------------------------------------------------------|
r_final: 0.3732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8910  Z= 0.136
  Angle     :  0.673  11.282  12025  Z= 0.335
  Chirality :  0.043   0.248   1291
  Planarity :  0.004   0.051   1546
  Dihedral  :  4.482  18.934   1166
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 31.40 %
    Favored  : 66.22 %
  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:  1.57 (0.29), residues: 318
  sheet: -0.60 (0.37), residues: 197
  loop : -0.72 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 361 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.026   0.001   PHE A 221 
 TYR   0.016   0.001   TYR A 206 
 ARG   0.004   0.000   ARG A 850 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  337)
  hydrogen bonds       : angle       5.16434 (  933)
  covalent geometry    : bond        0.00322 ( 8910)
  covalent geometry    : angle       0.67277 (12025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3196.71 seconds
wall clock time: 56 minutes 56.78 seconds (3416.78 seconds total)