Starting phenix.real_space_refine
on Sat May  2 14:02:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i96_52753/05_2026/9i96_52753.map"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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      24      5.16       5
     C    3808      2.51       5
     N    1023      2.21       5
     O    1193      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6048
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4596
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 559, 4582
          Classifications: {'peptide': 559}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 538}
      Conformer: "B"
        Number of residues, atoms: 559, 4582
          Classifications: {'peptide': 559}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 538}
          bond proxies already assigned to first conformer: 4691
    Chain: "B"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1181
          Classifications: {'peptide': 150}
          Link IDs: {'PTRANS': 8, 'TRANS': 141}
    Chain: "C"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 149
          Classifications: {'peptide': 17}
          Link IDs: {'TRANS': 16}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 105
          Unusual residues: {'LMT': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'R06': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 6
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN A 367 " occ=0.63
      ... (14 atoms not shown)
      pdb=" ND2BASN A 367 " occ=0.37
  Time building chain proxies: 2.65, per 1000 atoms: 0.44
  Number of scatterers: 6048
  At special positions: 0
  Unit cell: (88.938, 80.19, 90.396, 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      24     16.00
     O    1193      8.00
     N    1023      7.00
     C    3808      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 520.8 milliseconds
  

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 3 sheets defined
      12.7% alpha, 51.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 675
      removed outlier: 3.589A  pdb=" N   SER A 673 " --> pdb=" O   PRO A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 774
    Processing helix  chain 'B' and resid 1010 through 1013
    Processing helix  chain 'B' and resid 1025 through 1038
      removed outlier: 3.728A  pdb=" N   ASN B1038 " --> pdb=" O   GLN B1034 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1112 through 1138
      removed outlier: 3.567A  pdb=" N   TYR B1128 " --> pdb=" O   VAL B1124 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP B1129 " --> pdb=" O   LYS B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1138 through 1149
      removed outlier: 4.343A  pdb=" N   ILE B1142 " --> pdb=" O   LYS B1138 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG B1143 " --> pdb=" O   LEU B1139 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER B1149 " --> pdb=" O   ALA B1145 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 252
      removed outlier: 5.376A  pdb=" N   TYR A 248 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE A 259 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA A 257 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 252 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA A 233 " --> pdb=" O   PHE A 754 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 8.362A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 13.270A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 13.187A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   GLN A 712 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   ASP A 706 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   TRP A 608 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   GLY A 580 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLY A 610 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   SER A 578 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR A 612 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN A 576 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   TRP A 614 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   ARG A 574 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   TYR A 504 " --> pdb=" O   MET A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 252
      removed outlier: 5.376A  pdb=" N   TYR A 248 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE A 259 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA A 257 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 252 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.144A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 11.653A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASP A 402 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   TYR A 504 " --> pdb=" O   MET A 497 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 1041 through 1043
      removed outlier: 4.268A  pdb=" N   LEU B1018 " --> pdb=" O   LEU B1043 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ASN B1085 " --> pdb=" O   GLY B1058 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B1060 " --> pdb=" O   THR B1083 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR B1083 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE B1062 " --> pdb=" O   ILE B1081 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE B1081 " --> pdb=" O   ILE B1062 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LYS B1064 " --> pdb=" O   GLN B1079 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   GLN B1079 " --> pdb=" O   LYS B1064 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   THR B1066 " --> pdb=" O   GLU B1077 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   GLU B1077 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   SER B1068 " --> pdb=" O   THR B1075 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   THR B1075 " --> pdb=" O   SER B1068 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    899 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1007
        1.31 -     1.44: 1838
        1.44 -     1.57: 3309
        1.57 -     1.70: 2
        1.70 -     1.83: 43
  Bond restraints: 6199
  Sorted by residual:
  bond pdb=" C4  R06 C 101 "
       pdb=" N2  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.362  1.451 -0.089 2.00e-02 2.50e+03 1.98e+01
  bond pdb=" C2  R06 C 101 "
       pdb=" N1  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.364  1.449 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C7  R06 C 101 "
       pdb=" N3  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.451 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" N   ASP B1051 "
       pdb=" CA  ASP B1051 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.39e+00
  bond pdb=" C   ASP A 423 "
       pdb=" N   MET A 424 "
    ideal  model  delta    sigma   weight residual
    1.331  1.280  0.051 2.07e-02 2.33e+03 6.18e+00
  ... (remaining 6194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 7895
        2.42 -     4.83: 445
        4.83 -     7.25: 58
        7.25 -     9.67: 20
        9.67 -    12.09: 4
  Bond angle restraints: 8422
  Sorted by residual:
  angle pdb=" C   PRO A 253 "
        pdb=" N   ASN A 254 "
        pdb=" CA  ASN A 254 "
      ideal   model   delta    sigma   weight residual
     126.32  136.52  -10.20 1.74e+00 3.30e-01 3.44e+01
  angle pdb=" C   TYR A 516 "
        pdb=" N   VAL A 517 "
        pdb=" CA  VAL A 517 "
      ideal   model   delta    sigma   weight residual
     122.85  126.98   -4.13 8.70e-01 1.32e+00 2.25e+01
  angle pdb=" C   ASP A 322 "
        pdb=" N   GLN A 323 "
        pdb=" CA  GLN A 323 "
      ideal   model   delta    sigma   weight residual
     121.54  130.41   -8.87 1.91e+00 2.74e-01 2.15e+01
  angle pdb=" C   LYS B1050 "
        pdb=" N   ASP B1051 "
        pdb=" CA  ASP B1051 "
      ideal   model   delta    sigma   weight residual
     121.54  130.33   -8.79 1.91e+00 2.74e-01 2.12e+01
  angle pdb=" CA  PRO B1140 "
        pdb=" N   PRO B1140 "
        pdb=" CD  PRO B1140 "
      ideal   model   delta    sigma   weight residual
     112.00  106.05    5.95 1.40e+00 5.10e-01 1.80e+01
  ... (remaining 8417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.43: 3591
       29.43 -    58.86: 126
       58.86 -    88.30: 24
       88.30 -   117.73: 40
      117.73 -   147.16: 9
  Dihedral angle restraints: 3790
    sinusoidal: 1636
      harmonic: 2154
  Sorted by residual:
  dihedral pdb=" CA  PRO A 253 "
           pdb=" C   PRO A 253 "
           pdb=" N   ASN A 254 "
           pdb=" CA  ASN A 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.99  -27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  ARG B1093 "
           pdb=" C   ARG B1093 "
           pdb=" N   ASP B1094 "
           pdb=" CA  ASP B1094 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.17  -25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  PRO A 669 "
           pdb=" C   PRO A 669 "
           pdb=" N   LYS A 670 "
           pdb=" CA  LYS A 670 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 3787 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 726
       0.089 -    0.177: 135
       0.177 -    0.266: 23
       0.266 -    0.355: 4
       0.355 -    0.443: 2
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" C5' LMT A 801 "
            pdb=" C4' LMT A 801 "
            pdb=" C6' LMT A 801 "
            pdb=" O5' LMT A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.06   -0.44 2.00e-01 2.50e+01 4.91e+00
  chirality pdb=" C5' LMT A 803 "
            pdb=" C4' LMT A 803 "
            pdb=" C6' LMT A 803 "
            pdb=" O5' LMT A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.06   -0.44 2.00e-01 2.50e+01 4.90e+00
  chirality pdb=" CB  ILE A 752 "
            pdb=" CA  ILE A 752 "
            pdb=" CG1 ILE A 752 "
            pdb=" CG2 ILE A 752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.12e+00
  ... (remaining 887 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 778 "   -0.068 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO A 779 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 779 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 779 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 691 "   -0.060 5.00e-02 4.00e+02   9.25e-02 1.37e+01
        pdb=" N   PRO A 692 "    0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO A 692 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 692 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 245 "    0.060 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO A 246 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "    0.050 5.00e-02 4.00e+02
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1780
        2.84 -     3.36: 4786
        3.36 -     3.87: 10012
        3.87 -     4.39: 11458
        4.39 -     4.90: 20580
  Nonbonded interactions: 48616
  Sorted by model distance:
  nonbonded pdb=" CB  ALA C   1 "
            pdb=" N   NH2 C  18 "
     model   vdw
     2.326 3.540
  nonbonded pdb=" OH  TYR A 458 "
            pdb=" OD1 ASP A 550 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   MET A 772 "
            pdb=" OG  SER A 775 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   THR A 332 "
            pdb=" NE2 GLN A 357 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   GLU A 648 "
            pdb=" NE2 GLN A 770 "
     model   vdw
     2.376 3.120
  ... (remaining 48611 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=0.31 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:             3.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.110
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:9.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
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      :  0.008   0.089   6203  Z= 0.375
  Angle     :  1.243  12.085   8422  Z= 0.657
  Chirality :  0.076   0.443    890
  Planarity :  0.013   0.103   1090
  Dihedral  : 21.808 147.160   2416
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.29), residues: 724
  helix: -2.80 (0.37), residues: 84
  sheet:  0.44 (0.27), residues: 360
  loop : -1.41 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A 759 
 TYR   0.040   0.003   TYR A 628 
 PHE   0.057   0.004   PHE B1107 
 TRP   0.039   0.002   TRP A 444 
 HIS   0.014   0.002   HIS B1002 

Details of bonding type rmsd
  covalent geometry    : bond        0.00765 ( 6199)
  covalent geometry    : angle       1.24300 ( 8422)
  hydrogen bonds       : bond        0.09243 (  314)
  hydrogen bonds       : angle       6.82509 (  899)
  Misc. bond           : bond        0.03569 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 GLN cc_start: 0.8011 (mp-120) cc_final: 0.7778 (pm20)
REVERT: A  469 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.7957 (ptp-170)
REVERT: B 1074 GLN cc_start: 0.8596 (tt0) cc_final: 0.8239 (tt0)
REVERT: B 1079 GLN cc_start: 0.8293 (tp-100) cc_final: 0.8065 (mm-40)
  outliers start: 0
  outliers final: 1
  residues processed: 97
  average time/residue: 0.7003
  time to fit residues: 70.4812
Evaluate side-chains
  59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 262 HIS
A 513 GLN
A 712 GLN
A 755 ASN
A 770 GLN
A 781 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.068228 restraints weight = 27148.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 4.37
r_work: 0.2759 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6203  Z= 0.183
  Angle     :  0.742   8.224   8422  Z= 0.363
  Chirality :  0.052   0.506    890
  Planarity :  0.008   0.077   1090
  Dihedral  : 15.568 138.202   1024
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  8.28 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.31), residues: 724
  helix: -0.72 (0.53), residues: 83
  sheet:  0.44 (0.28), residues: 360
  loop : -0.94 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 774 
 TYR   0.014   0.001   TYR A 705 
 PHE   0.034   0.002   PHE A 754 
 TRP   0.017   0.001   TRP A 444 
 HIS   0.003   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6199)
  covalent geometry    : angle       0.74246 ( 8422)
  hydrogen bonds       : bond        0.03921 (  314)
  hydrogen bonds       : angle       5.53658 (  899)
  Misc. bond           : bond        0.00095 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  243 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7056 (p90)
REVERT: A  275 GLU cc_start: 0.8714 (tt0) cc_final: 0.8405 (tt0)
REVERT: A  281 GLN cc_start: 0.8303 (mp-120) cc_final: 0.8101 (pm20)
REVERT: B 1074 GLN cc_start: 0.8737 (tt0) cc_final: 0.8505 (tt0)
REVERT: B 1105 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (t)
REVERT: C    9 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7023 (mp0)
REVERT: C   12 ASP cc_start: 0.7989 (t0) cc_final: 0.7783 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 71
  average time/residue: 0.6481
  time to fit residues: 47.9590
Evaluate side-chains
  66 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN
A 522 GLN
A 712 GLN
A 755 ASN
B1033 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.086896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.065559 restraints weight = 23737.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.02
r_work: 0.2711 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6203  Z= 0.193
  Angle     :  0.670   9.524   8422  Z= 0.340
  Chirality :  0.049   0.294    890
  Planarity :  0.006   0.066   1090
  Dihedral  : 13.861 142.730   1021
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  9.53 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.31), residues: 724
  helix:  0.33 (0.58), residues: 83
  sheet:  0.46 (0.27), residues: 358
  loop : -0.73 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 774 
 TYR   0.014   0.001   TYR A 705 
 PHE   0.029   0.002   PHE A 754 
 TRP   0.014   0.001   TRP A 444 
 HIS   0.010   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 6199)
  covalent geometry    : angle       0.67003 ( 8422)
  hydrogen bonds       : bond        0.03950 (  314)
  hydrogen bonds       : angle       5.43458 (  899)
  Misc. bond           : bond        0.00085 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8785 (tt0) cc_final: 0.8537 (tt0)
REVERT: A  281 GLN cc_start: 0.8382 (mp-120) cc_final: 0.8169 (pm20)
REVERT: A  499 MET cc_start: 0.8298 (mpp) cc_final: 0.7875 (pmm)
REVERT: B 1077 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (mm-30)
REVERT: C    9 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7047 (mp0)
REVERT: C   12 ASP cc_start: 0.8242 (t0) cc_final: 0.7989 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 66
  average time/residue: 0.6710
  time to fit residues: 46.1946
Evaluate side-chains
  68 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1077 GLU
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN
A 712 GLN
B1038 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.086688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.065117 restraints weight = 23546.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 3.95
r_work: 0.2688 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6203  Z= 0.217
  Angle     :  0.647   7.700   8422  Z= 0.331
  Chirality :  0.049   0.243    890
  Planarity :  0.006   0.061   1090
  Dihedral  : 12.739 146.719   1021
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.94 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.31), residues: 724
  helix:  0.64 (0.59), residues: 82
  sheet:  0.39 (0.27), residues: 358
  loop : -0.63 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 574 
 TYR   0.014   0.001   TYR A 705 
 PHE   0.030   0.002   PHE A 754 
 TRP   0.012   0.001   TRP A 444 
 HIS   0.008   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6199)
  covalent geometry    : angle       0.64749 ( 8422)
  hydrogen bonds       : bond        0.03908 (  314)
  hydrogen bonds       : angle       5.41910 (  899)
  Misc. bond           : bond        0.00103 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.8321 (mp-120) cc_final: 0.8049 (pm20)
REVERT: A  499 MET cc_start: 0.8291 (mpp) cc_final: 0.7917 (pmm)
REVERT: C    9 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6995 (mp0)
REVERT: C   12 ASP cc_start: 0.8165 (t0) cc_final: 0.7897 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 63
  average time/residue: 0.6505
  time to fit residues: 42.7517
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1077 GLU
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0670
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN
A 712 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.088729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.067064 restraints weight = 24230.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 4.03
r_work: 0.2730 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6203  Z= 0.123
  Angle     :  0.562   5.857   8422  Z= 0.294
  Chirality :  0.045   0.162    890
  Planarity :  0.005   0.055   1090
  Dihedral  : 11.371 139.483   1021
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.88 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.31), residues: 724
  helix:  1.13 (0.60), residues: 82
  sheet:  0.41 (0.27), residues: 357
  loop : -0.53 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.008   0.001   PHE A 276 
 TRP   0.007   0.001   TRP A 444 
 HIS   0.007   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6199)
  covalent geometry    : angle       0.56198 ( 8422)
  hydrogen bonds       : bond        0.03337 (  314)
  hydrogen bonds       : angle       5.15689 (  899)
  Misc. bond           : bond        0.00096 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8699 (tt0) cc_final: 0.8405 (tt0)
REVERT: A  281 GLN cc_start: 0.8293 (mp-120) cc_final: 0.8016 (pm20)
REVERT: A  469 ARG cc_start: 0.8196 (ptp-110) cc_final: 0.7903 (ptp-170)
REVERT: A  499 MET cc_start: 0.8324 (mpp) cc_final: 0.7988 (pmm)
REVERT: B 1007 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8722 (p)
REVERT: B 1077 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (mm-30)
REVERT: C    9 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7131 (mp0)
REVERT: C   12 ASP cc_start: 0.8302 (t0) cc_final: 0.8057 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 67
  average time/residue: 0.6099
  time to fit residues: 42.7663
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1077 GLU
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.087676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.065612 restraints weight = 29604.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 4.30
r_work: 0.2689 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6203  Z= 0.152
  Angle     :  0.564   6.175   8422  Z= 0.298
  Chirality :  0.046   0.154    890
  Planarity :  0.005   0.053   1090
  Dihedral  : 10.916 133.256   1021
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.66 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.32), residues: 724
  helix:  1.30 (0.59), residues: 82
  sheet:  0.46 (0.27), residues: 357
  loop : -0.46 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.030   0.002   PHE A 754 
 TRP   0.011   0.001   TRP A 444 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6199)
  covalent geometry    : angle       0.56424 ( 8422)
  hydrogen bonds       : bond        0.03474 (  314)
  hydrogen bonds       : angle       5.15477 (  899)
  Misc. bond           : bond        0.00088 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.8328 (mp-120) cc_final: 0.8056 (pm20)
REVERT: A  469 ARG cc_start: 0.8240 (ptp-110) cc_final: 0.7965 (ptp-170)
REVERT: A  499 MET cc_start: 0.8273 (mpp) cc_final: 0.7984 (pmm)
REVERT: B 1007 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8777 (p)
REVERT: B 1077 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (mm-30)
REVERT: C    9 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7107 (mp0)
REVERT: C   12 ASP cc_start: 0.8403 (t0) cc_final: 0.8167 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 0.6319
  time to fit residues: 40.9375
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1077 GLU
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.089236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.066444 restraints weight = 26233.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 4.00
r_work: 0.2744 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6203  Z= 0.228
  Angle     :  0.604   6.621   8422  Z= 0.317
  Chirality :  0.047   0.159    890
  Planarity :  0.005   0.054   1090
  Dihedral  : 10.970 132.826   1021
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.81 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.32), residues: 724
  helix:  1.04 (0.56), residues: 88
  sheet:  0.41 (0.27), residues: 358
  loop : -0.40 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 574 
 TYR   0.014   0.001   TYR A 705 
 PHE   0.007   0.001   PHE B1103 
 TRP   0.011   0.001   TRP A 444 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 6199)
  covalent geometry    : angle       0.60400 ( 8422)
  hydrogen bonds       : bond        0.03808 (  314)
  hydrogen bonds       : angle       5.27059 (  899)
  Misc. bond           : bond        0.00096 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  243 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7208 (p90)
REVERT: A  281 GLN cc_start: 0.8402 (mp-120) cc_final: 0.8164 (pm20)
REVERT: A  469 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.7887 (ptp-170)
REVERT: A  499 MET cc_start: 0.8277 (mpp) cc_final: 0.8005 (pmm)
REVERT: B 1007 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8836 (p)
REVERT: C    9 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7060 (mp0)
REVERT: C   12 ASP cc_start: 0.8428 (t0) cc_final: 0.8212 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 61
  average time/residue: 0.6009
  time to fit residues: 38.4081
Evaluate side-chains
  62 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.068055 restraints weight = 20262.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.60
r_work: 0.2788 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6203  Z= 0.167
  Angle     :  0.577   6.313   8422  Z= 0.306
  Chirality :  0.046   0.157    890
  Planarity :  0.005   0.051   1090
  Dihedral  : 10.791 130.477   1021
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.97 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.32), residues: 724
  helix:  1.17 (0.56), residues: 88
  sheet:  0.42 (0.27), residues: 358
  loop : -0.39 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.029   0.001   PHE A 754 
 TRP   0.009   0.001   TRP A 444 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6199)
  covalent geometry    : angle       0.57704 ( 8422)
  hydrogen bonds       : bond        0.03538 (  314)
  hydrogen bonds       : angle       5.18807 (  899)
  Misc. bond           : bond        0.00086 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8792 (tt0) cc_final: 0.8573 (tt0)
REVERT: A  281 GLN cc_start: 0.8362 (mp-120) cc_final: 0.8158 (pm20)
REVERT: A  469 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.8058 (ptp-170)
REVERT: A  499 MET cc_start: 0.8300 (mpp) cc_final: 0.8039 (pmm)
REVERT: B 1007 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8864 (p)
REVERT: C    9 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7004 (mp0)
REVERT: C   12 ASP cc_start: 0.8432 (t0) cc_final: 0.8219 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 66
  average time/residue: 0.6018
  time to fit residues: 41.5695
Evaluate side-chains
  63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1012 THR
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.090009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.067869 restraints weight = 21846.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 3.69
r_work: 0.2778 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6203  Z= 0.167
  Angle     :  0.571   6.248   8422  Z= 0.302
  Chirality :  0.046   0.155    890
  Planarity :  0.005   0.051   1090
  Dihedral  : 10.718 128.872   1021
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.28 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.32), residues: 724
  helix:  1.23 (0.56), residues: 88
  sheet:  0.43 (0.27), residues: 358
  loop : -0.39 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.007   0.001   PHE B1106 
 TRP   0.009   0.001   TRP A 444 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6199)
  covalent geometry    : angle       0.57147 ( 8422)
  hydrogen bonds       : bond        0.03559 (  314)
  hydrogen bonds       : angle       5.16885 (  899)
  Misc. bond           : bond        0.00085 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.8362 (mp-120) cc_final: 0.8158 (pm20)
REVERT: A  499 MET cc_start: 0.8313 (mpp) cc_final: 0.8066 (pmm)
REVERT: B 1007 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8871 (p)
REVERT: C    9 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7001 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 60
  average time/residue: 0.6231
  time to fit residues: 39.0936
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1012 THR
Chi-restraints excluded: chain B residue 1020 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.090729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.068503 restraints weight = 21261.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 3.77
r_work: 0.2831 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6203  Z= 0.139
  Angle     :  0.564   5.969   8422  Z= 0.299
  Chirality :  0.045   0.154    890
  Planarity :  0.005   0.050   1090
  Dihedral  : 10.729 127.141   1021
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.06 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.32), residues: 724
  helix:  1.55 (0.58), residues: 82
  sheet:  0.47 (0.27), residues: 357
  loop : -0.44 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.031   0.001   PHE A 754 
 TRP   0.007   0.001   TRP A 444 
 HIS   0.005   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6199)
  covalent geometry    : angle       0.56368 ( 8422)
  hydrogen bonds       : bond        0.03368 (  314)
  hydrogen bonds       : angle       5.11216 (  899)
  Misc. bond           : bond        0.00099 (    4)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  499 MET cc_start: 0.8311 (mpp) cc_final: 0.8078 (pmm)
REVERT: B 1007 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8877 (p)
REVERT: B 1122 MET cc_start: 0.8565 (ttm) cc_final: 0.8333 (ttm)
REVERT: C    9 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7011 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 58
  average time/residue: 0.6087
  time to fit residues: 36.9812
Evaluate side-chains
  59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1011 SER
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue    9 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.090469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.067485 restraints weight = 33328.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 4.36
r_work: 0.2757 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6203  Z= 0.153
  Angle     :  0.571   6.083   8422  Z= 0.302
  Chirality :  0.045   0.154    890
  Planarity :  0.005   0.050   1090
  Dihedral  : 10.753 126.994   1021
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.22 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.32), residues: 724
  helix:  1.60 (0.59), residues: 82
  sheet:  0.46 (0.27), residues: 357
  loop : -0.42 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.007   0.001   PHE B1106 
 TRP   0.008   0.001   TRP A 444 
 HIS   0.005   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6199)
  covalent geometry    : angle       0.57052 ( 8422)
  hydrogen bonds       : bond        0.03449 (  314)
  hydrogen bonds       : angle       5.12144 (  899)
  Misc. bond           : bond        0.00099 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2219.67 seconds
wall clock time: 38 minutes 36.79 seconds (2316.79 seconds total)