Starting phenix.real_space_refine
on Thu Jun 12 17:46:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9g_15931/06_2025/8b9g_15931.cif"
  }
  resolution = 2.86
  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=   0.005 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7745 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P      12      5.49       5
     S      48      5.16       5
     C    4890      2.51       5
     N    1333      2.21       5
     O    1494      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7782
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7545
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 953, 7534
          Classifications: {'peptide': 953}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 953, 7534
          Classifications: {'peptide': 953}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 7666
    Chain: "C"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 200
          Classifications: {'RNA': 10}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 7}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 37
          Unusual residues: {'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 2, 'water': 5}
          Link IDs: {None: 6}
  Time building chain proxies: 7.73, per 1000 atoms: 0.99
  Number of scatterers: 7782
  At special positions: 0
  Unit cell: (91.242, 92.886, 103.572, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      48     16.00
     P      12     15.00
     Al      1     13.00
     F       4      9.00
     O    1494      8.00
     N    1333      7.00
     C    4890      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: 1.75
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 7 sheets defined
      51.7% alpha, 14.2% beta
      0 base pairs and 2 stacking pairs defined.
    Time for finding SS restraints: 2.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 166 through 182
      removed outlier: 4.207A  pdb=" N   LYS A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   GLU A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'A' and resid 268 through 283
    Processing helix  chain 'A' and resid 352 through 371
    Processing helix  chain 'A' and resid 371 through 383
      removed outlier: 3.736A  pdb=" N   LYS A 383 " --> pdb=" O   GLU A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.669A  pdb=" N   ALA A 388 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 4.583A  pdb=" N   ALA A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLN A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 433
    Processing helix  chain 'A' and resid 442 through 457
    Processing helix  chain 'A' and resid 487 through 494
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 509 through 512
      removed outlier: 3.772A  pdb=" N   ARG A 512 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 509 through 512'
    Processing helix  chain 'A' and resid 513 through 530
    Processing helix  chain 'A' and resid 543 through 551
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 636 through 650
    Processing helix  chain 'A' and resid 662 through 675
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 3.780A  pdb=" N   VAL A 702 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 721
    Processing helix  chain 'A' and resid 758 through 767
    Processing helix  chain 'A' and resid 782 through 789
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 802 through 812
    Processing helix  chain 'A' and resid 816 through 823
    Processing helix  chain 'A' and resid 829 through 843
    Processing helix  chain 'A' and resid 853 through 861
    Processing helix  chain 'A' and resid 865 through 878
    Processing helix  chain 'A' and resid 880 through 892
    Processing helix  chain 'A' and resid 908 through 913
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 920 through 937
    Processing helix  chain 'A' and resid 939 through 951
    Processing helix  chain 'A' and resid 953 through 975
    Processing helix  chain 'A' and resid 977 through 982
      removed outlier: 3.755A  pdb=" N   ILE A 982 " --> pdb=" O   GLU A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1008
      removed outlier: 3.725A  pdb=" N   LEU A1006 " --> pdb=" O   ALA A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1077
    Processing helix  chain 'A' and resid 1086 through 1088
      No H-bonds generated for 'chain 'A' and resid 1086 through 1088'
    Processing helix  chain 'A' and resid 1101 through 1110
    Processing helix  chain 'A' and resid 1110 through 1125
      removed outlier: 3.951A  pdb=" N   ALA A1114 " --> pdb=" O   ALA A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1129
      removed outlier: 3.605A  pdb=" N   ILE A1129 " --> pdb=" O   PRO A1126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1126 through 1129'
    Processing helix  chain 'A' and resid 1133 through 1148
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264
      removed outlier: 6.148A  pdb=" N   TYR A 263 " --> pdb=" O   ASP A1099 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329
      removed outlier: 4.380A  pdb=" N   ALA A 329 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474
      removed outlier: 6.819A  pdb=" N   GLY A 466 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 8.592A  pdb=" N   THR A 486 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   SER A 468 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE A 436 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   CYS A 485 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   VAL A 438 " --> pdb=" O   CYS A 485 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ASN A 435 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ILE A 505 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   TYR A 437 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP A 507 " --> pdb=" O   TYR A 437 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   THR A 439 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 569
      removed outlier: 6.103A  pdb=" N   GLN A 567 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   THR A 779 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE A 569 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL A 730 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   PHE A 778 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL A 732 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA A 655 " --> pdb=" O   PHE A 731 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ILE A 733 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1012 through 1017
      removed outlier: 6.948A  pdb=" N   LYS A1020 " --> pdb=" O   LYS A1016 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ALA A1028 " --> pdb=" O   VAL A1061 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   CYS A1063 " --> pdb=" O   ALA A1028 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU A1030 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   GLN A1065 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL A1061 " --> pdb=" O   ARG A1057 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   ARG A1057 " --> pdb=" O   VAL A1061 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   CYS A1063 " --> pdb=" O   LYS A1055 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LYS A1055 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   GLN A1065 " --> pdb=" O   GLY A1053 " (cutoff:3.500A)

    377 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      2 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2546
        1.34 -     1.48: 1851
        1.48 -     1.61: 3470
        1.61 -     1.74: 0
        1.74 -     1.88: 77
  Bond restraints: 7944
  Sorted by residual:
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.877 -0.192 2.00e-02 2.50e+03 9.20e+01
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.865 -0.181 2.00e-02 2.50e+03 8.20e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.808 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.805 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" N   GLU A 585 "
       pdb=" CA  GLU A 585 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.40e-02 5.10e+03 3.98e+00
  ... (remaining 7939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.00: 10805
       14.00 -    28.00: 4
       28.00 -    42.01: 0
       42.01 -    56.01: 0
       56.01 -    70.01: 2
  Bond angle restraints: 10811
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  178.69  -70.01 3.00e+00 1.11e-01 5.45e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  178.75  -69.12 3.00e+00 1.11e-01 5.31e+02
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.59   89.09   20.50 3.00e+00 1.11e-01 4.67e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.02   88.71   20.31 3.00e+00 1.11e-01 4.58e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.69   90.05   19.64 3.00e+00 1.11e-01 4.29e+01
  ... (remaining 10806 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.93: 4680
       32.93 -    65.86: 186
       65.86 -    98.79: 17
       98.79 -   131.73: 1
      131.73 -   164.66: 1
  Dihedral angle restraints: 4885
    sinusoidal: 2087
      harmonic: 2798
  Sorted by residual:
  dihedral pdb=" O4'   U C   6 "
           pdb=" C1'   U C   6 "
           pdb=" N1    U C   6 "
           pdb=" C2    U C   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    4.66 -164.66     1      1.50e+01 4.44e-03 8.38e+01
  dihedral pdb=" C5' ADP A1201 "
           pdb=" O5' ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" O2A ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -164.32  104.33     1      2.00e+01 2.50e-03 2.99e+01
  dihedral pdb=" CA  THR A 722 "
           pdb=" C   THR A 722 "
           pdb=" N   SER A 723 "
           pdb=" CA  SER A 723 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 4882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 805
       0.035 -    0.071: 299
       0.071 -    0.106: 98
       0.106 -    0.141: 45
       0.141 -    0.176: 2
  Chirality restraints: 1249
  Sorted by residual:
  chirality pdb=" CA  GLU A1134 "
            pdb=" N   GLU A1134 "
            pdb=" C   GLU A1134 "
            pdb=" CB  GLU A1134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.78e-01
  chirality pdb=" CB  ILE A 719 "
            pdb=" CA  ILE A 719 "
            pdb=" CG1 ILE A 719 "
            pdb=" CG2 ILE A 719 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CB  THR A 414 "
            pdb=" CA  THR A 414 "
            pdb=" OG1 THR A 414 "
            pdb=" CG2 THR A 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 1246 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 261 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO A 262 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 262 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 262 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 865 "    0.031 5.00e-02 4.00e+02   4.75e-02 3.62e+00
        pdb=" N   PRO A 866 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 866 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 866 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 146 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   GLN A 146 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   GLN A 146 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 147 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 12
        2.29 -     2.94: 3313
        2.94 -     3.59: 11713
        3.59 -     4.25: 19485
        4.25 -     4.90: 31715
  Nonbonded interactions: 66238
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 414 "
            pdb=" F4  ALF A1202 "
     model   vdw
     1.632 2.990
  nonbonded pdb=" OD2 ASP A 507 "
            pdb=" F4  ALF A1202 "
     model   vdw
     1.858 2.990
  nonbonded pdb=" O2A ADP A1201 "
            pdb=" O   HOH A1301 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" O   ILE A 574 "
            pdb=" OG1 THR A 578 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OG1 THR A 414 "
            pdb="AL   ALF A1202 "
     model   vdw
     2.167 2.760
  ... (remaining 66233 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.680
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
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      :  0.005   0.192   7944  Z= 0.241
  Angle     :  1.198  70.010  10811  Z= 0.470
  Chirality :  0.045   0.176   1249
  Planarity :  0.005   0.049   1358
  Dihedral  : 17.073 164.658   3063
  Min Nonbonded Distance : 1.632

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.43 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.52 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.28), residues: 947
  helix:  1.76 (0.24), residues: 449
  sheet:  0.08 (0.41), residues: 165
  loop :  0.17 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 932 
 HIS   0.004   0.001   HIS A 162 
 PHE   0.018   0.002   PHE A 667 
 TYR   0.018   0.002   TYR A 890 
 ARG   0.004   0.001   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11087 (  377)
  hydrogen bonds       : angle       4.78750 ( 1080)
  covalent geometry    : bond        0.00503 ( 7944)
  covalent geometry    : angle       1.19771 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.916 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 48
  average time/residue: 1.5413
  time to fit residues: 78.3944
Evaluate side-chains
  32 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 196 HIS
A 339 HIS
A 342 ASN
A 435 ASN
A 621 GLN
A 625 ASN
A 965 GLN
A1011 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.062251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.047890 restraints weight = 36327.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 4.19
r_work: 0.2786 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7944  Z= 0.178
  Angle     :  0.634   9.462  10811  Z= 0.313
  Chirality :  0.044   0.165   1249
  Planarity :  0.004   0.050   1358
  Dihedral  : 10.543 160.758   1207
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.69 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.45 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.28), residues: 947
  helix:  1.97 (0.25), residues: 450
  sheet:  0.29 (0.42), residues: 159
  loop :  0.16 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 663 
 HIS   0.005   0.001   HIS A 646 
 PHE   0.016   0.001   PHE A 667 
 TYR   0.008   0.001   TYR A 467 
 ARG   0.007   0.001   ARG A 934 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  377)
  hydrogen bonds       : angle       4.21078 ( 1080)
  covalent geometry    : bond        0.00417 ( 7944)
  covalent geometry    : angle       0.63442 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 27
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  865 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7555 (mp0)
REVERT: A  942 MET cc_start: 0.8382 (mmm) cc_final: 0.7900 (mtp)
REVERT: A  950 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7913 (tppp)
REVERT: A  954 MET cc_start: 0.8439 (ttm) cc_final: 0.8170 (ttm)
  outliers start: 18
  outliers final: 3
  residues processed: 44
  average time/residue: 1.3301
  time to fit residues: 63.0565
Evaluate side-chains
  31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 16 optimal weight:    0.1980
   chunk 40 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.064054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.048900 restraints weight = 55318.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 5.14
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7944  Z= 0.106
  Angle     :  0.556   8.536  10811  Z= 0.274
  Chirality :  0.041   0.163   1249
  Planarity :  0.004   0.050   1358
  Dihedral  : 10.139 155.959   1204
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.59 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.85 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.28), residues: 947
  helix:  2.14 (0.24), residues: 452
  sheet:  0.31 (0.43), residues: 159
  loop :  0.18 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.004   0.001   TYR A 467 
 ARG   0.007   0.000   ARG A 934 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  377)
  hydrogen bonds       : angle       3.97693 ( 1080)
  covalent geometry    : bond        0.00240 ( 7944)
  covalent geometry    : angle       0.55591 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  805 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7248 (ttm)
REVERT: A  843 MET cc_start: 0.8214 (ttm) cc_final: 0.7955 (ttp)
REVERT: A  865 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7368 (mp0)
REVERT: A  942 MET cc_start: 0.8410 (mmm) cc_final: 0.7904 (mtp)
REVERT: A  950 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7999 (tppp)
  outliers start: 13
  outliers final: 1
  residues processed: 38
  average time/residue: 1.5821
  time to fit residues: 63.9250
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 MET
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0980
   chunk 91 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.063587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.048954 restraints weight = 40991.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 4.32
r_work: 0.2829 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7944  Z= 0.107
  Angle     :  0.546   8.776  10811  Z= 0.266
  Chirality :  0.041   0.160   1249
  Planarity :  0.004   0.048   1358
  Dihedral  : 10.052 155.792   1203
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.80 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.45 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.28), residues: 947
  helix:  2.19 (0.24), residues: 452
  sheet:  0.29 (0.43), residues: 160
  loop :  0.29 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.016   0.001   PHE A 667 
 TYR   0.005   0.001   TYR A 467 
 ARG   0.008   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  377)
  hydrogen bonds       : angle       3.93948 ( 1080)
  covalent geometry    : bond        0.00244 ( 7944)
  covalent geometry    : angle       0.54559 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  865 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7793 (mp0)
REVERT: A  942 MET cc_start: 0.8532 (mmm) cc_final: 0.7957 (mtm)
REVERT: A  950 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8255 (tppp)
  outliers start: 10
  outliers final: 2
  residues processed: 35
  average time/residue: 1.4144
  time to fit residues: 52.9630
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0670
   chunk 80 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.1520

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

Flipped N/Q/H residues before XYZ refinement:
** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.048699 restraints weight = 33826.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 4.03
r_work: 0.2817 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7944  Z= 0.111
  Angle     :  0.546   9.316  10811  Z= 0.264
  Chirality :  0.041   0.158   1249
  Planarity :  0.004   0.049   1358
  Dihedral  :  9.990 155.592   1203
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.69 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.33 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.28), residues: 947
  helix:  2.26 (0.24), residues: 451
  sheet:  0.22 (0.43), residues: 160
  loop :  0.36 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.006   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03116 (  377)
  hydrogen bonds       : angle       3.88744 ( 1080)
  covalent geometry    : bond        0.00257 ( 7944)
  covalent geometry    : angle       0.54551 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  865 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7638 (mp0)
REVERT: A  942 MET cc_start: 0.8473 (mmm) cc_final: 0.7949 (mtm)
REVERT: A  950 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (tppp)
  outliers start: 10
  outliers final: 2
  residues processed: 33
  average time/residue: 1.3920
  time to fit residues: 49.5686
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 972 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.062837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.047580 restraints weight = 57949.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 5.06
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7944  Z= 0.116
  Angle     :  0.546   9.589  10811  Z= 0.264
  Chirality :  0.042   0.154   1249
  Planarity :  0.004   0.048   1358
  Dihedral  :  9.936 156.333   1203
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.59 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.45 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.29), residues: 947
  helix:  2.27 (0.24), residues: 451
  sheet:  0.23 (0.45), residues: 150
  loop :  0.44 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.006   0.001   TYR A 467 
 ARG   0.006   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03217 (  377)
  hydrogen bonds       : angle       3.87969 ( 1080)
  covalent geometry    : bond        0.00270 ( 7944)
  covalent geometry    : angle       0.54574 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  865 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7728 (mp0)
REVERT: A  942 MET cc_start: 0.8503 (mmm) cc_final: 0.7968 (mtm)
  outliers start: 10
  outliers final: 2
  residues processed: 34
  average time/residue: 1.4340
  time to fit residues: 52.1248
Evaluate side-chains
  29 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0570
   chunk 82 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.8106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.047105 restraints weight = 53115.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 4.82
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7944  Z= 0.142
  Angle     :  0.558   9.829  10811  Z= 0.269
  Chirality :  0.042   0.152   1249
  Planarity :  0.004   0.049   1358
  Dihedral  :  9.932 157.651   1203
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.80 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 17.04 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.29), residues: 947
  helix:  2.26 (0.24), residues: 451
  sheet:  0.19 (0.45), residues: 150
  loop :  0.44 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 691 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.007   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  377)
  hydrogen bonds       : angle       3.93399 ( 1080)
  covalent geometry    : bond        0.00335 ( 7944)
  covalent geometry    : angle       0.55763 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A  865 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7754 (mp0)
REVERT: A  942 MET cc_start: 0.8561 (mmm) cc_final: 0.8014 (mtm)
REVERT: A  950 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8426 (tppp)
  outliers start: 5
  outliers final: 2
  residues processed: 30
  average time/residue: 1.4773
  time to fit residues: 47.5294
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.062796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.048264 restraints weight = 44140.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 4.44
r_work: 0.2817 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7944  Z= 0.103
  Angle     :  0.549   9.863  10811  Z= 0.261
  Chirality :  0.041   0.154   1249
  Planarity :  0.004   0.048   1358
  Dihedral  :  9.853 155.612   1203
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.69 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 16.92 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.29), residues: 947
  helix:  2.30 (0.24), residues: 452
  sheet:  0.22 (0.45), residues: 150
  loop :  0.48 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 663 
 HIS   0.003   0.000   HIS A 746 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.005   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03110 (  377)
  hydrogen bonds       : angle       3.85610 ( 1080)
  covalent geometry    : bond        0.00235 ( 7944)
  covalent geometry    : angle       0.54941 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  494 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: A  865 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7867 (mp0)
REVERT: A  942 MET cc_start: 0.8538 (mmm) cc_final: 0.7974 (mtm)
  outliers start: 6
  outliers final: 2
  residues processed: 34
  average time/residue: 1.3469
  time to fit residues: 49.4837
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0000
   overall best weight:    1.6990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.047287 restraints weight = 47401.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 4.61
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7944  Z= 0.136
  Angle     :  0.566  11.105  10811  Z= 0.269
  Chirality :  0.042   0.151   1249
  Planarity :  0.004   0.048   1358
  Dihedral  :  9.854 157.599   1203
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.80 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 17.28 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.29), residues: 947
  helix:  2.27 (0.24), residues: 452
  sheet:  0.19 (0.45), residues: 149
  loop :  0.45 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.007   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  377)
  hydrogen bonds       : angle       3.92116 ( 1080)
  covalent geometry    : bond        0.00323 ( 7944)
  covalent geometry    : angle       0.56572 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A  494 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8961 (mm)
REVERT: A  865 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7752 (mp0)
REVERT: A  942 MET cc_start: 0.8594 (mmm) cc_final: 0.8012 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 30
  average time/residue: 1.4759
  time to fit residues: 47.7187
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  865 GLU
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 78 optimal weight:   20.0000
   chunk 71 optimal weight:    0.0020
   chunk 23 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.063021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.048144 restraints weight = 49967.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 4.73
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7944  Z= 0.101
  Angle     :  0.567  14.967  10811  Z= 0.265
  Chirality :  0.041   0.155   1249
  Planarity :  0.004   0.049   1358
  Dihedral  :  9.789 154.832   1203
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.80 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 17.52 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 947
  helix:  2.35 (0.24), residues: 452
  sheet:  0.26 (0.45), residues: 149
  loop :  0.46 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 663 
 HIS   0.003   0.000   HIS A 746 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.005   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03041 (  377)
  hydrogen bonds       : angle       3.82297 ( 1080)
  covalent geometry    : bond        0.00234 ( 7944)
  covalent geometry    : angle       0.56701 (10811)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A  494 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8943 (mm)
REVERT: A  942 MET cc_start: 0.8464 (mmm) cc_final: 0.7868 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 1.5754
  time to fit residues: 50.8605
Evaluate side-chains
  30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0010
   chunk 49 optimal weight:    0.0980
   chunk 88 optimal weight:    0.0030
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.064002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.048635 restraints weight = 70693.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 5.52
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7944  Z= 0.086
  Angle     :  0.540  13.356  10811  Z= 0.255
  Chirality :  0.040   0.155   1249
  Planarity :  0.004   0.048   1358
  Dihedral  :  9.727 152.263   1203
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.69 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 17.52 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  2.02 (0.29), residues: 947
  helix:  2.47 (0.24), residues: 452
  sheet:  0.25 (0.44), residues: 159
  loop :  0.40 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 663 
 HIS   0.003   0.000   HIS A 746 
 PHE   0.015   0.001   PHE A 667 
 TYR   0.004   0.001   TYR A 467 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02771 (  377)
  hydrogen bonds       : angle       3.76244 ( 1080)
  covalent geometry    : bond        0.00191 ( 7944)
  covalent geometry    : angle       0.53987 (10811)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4819.49 seconds
wall clock time: 85 minutes 45.47 seconds (5145.47 seconds total)