Starting phenix.real_space_refine
on Wed Mar 12 06:05:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2025/7rd7_24414.cif"
  }
  resolution = 3.08
  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=  -0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    4762      2.51       5
     N    1220      2.21       5
     O    1375      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 43 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7400
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 929, 7394
          Classifications: {'peptide': 929}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 902}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.09, per 1000 atoms: 0.69
  Number of scatterers: 7400
  At special positions: 0
  Unit cell: (74.34, 82.6, 140.42, 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      37     16.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1375      8.00
     N    1220      7.00
     C    4762      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: 1.89
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1770

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      49.2% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 161 through 167
      removed outlier: 4.054A  pdb=" N   TYR A 165 " --> pdb=" O   THR A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 194
      removed outlier: 3.571A  pdb=" N   LEU A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 209
      removed outlier: 4.290A  pdb=" N   PHE A 202 " --> pdb=" O   TYR A 198 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 250
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.564A  pdb=" N   THR A 367 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 396
      removed outlier: 3.548A  pdb=" N   ASN A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 434
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 454 through 475
      removed outlier: 3.745A  pdb=" N   SER A 458 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 496
    Processing helix  chain 'A' and resid 530 through 538
    Processing helix  chain 'A' and resid 561 through 576
    Processing helix  chain 'A' and resid 594 through 608
      removed outlier: 3.634A  pdb=" N   ILE A 598 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 671
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.666A  pdb=" N   GLU A 683 " --> pdb=" O   TRP A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 712
      removed outlier: 3.720A  pdb=" N   TYR A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 766
    Processing helix  chain 'A' and resid 777 through 788
    Processing helix  chain 'A' and resid 827 through 838
    Processing helix  chain 'A' and resid 838 through 847
      removed outlier: 3.639A  pdb=" N   PHE A 842 " --> pdb=" O   TYR A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 873
    Processing helix  chain 'A' and resid 883 through 885
      No H-bonds generated for 'chain 'A' and resid 883 through 885'
    Processing helix  chain 'A' and resid 886 through 892
    Processing helix  chain 'A' and resid 905 through 911
      removed outlier: 3.505A  pdb=" N   ALA A 910 " --> pdb=" O   GLN A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 927
      removed outlier: 4.421A  pdb=" N   GLU A 923 " --> pdb=" O   CYS A 919 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TRP A 927 " --> pdb=" O   GLU A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 961
    Processing helix  chain 'A' and resid 971 through 979
      removed outlier: 3.861A  pdb=" N   VAL A 975 " --> pdb=" O   GLY A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 990
      removed outlier: 4.155A  pdb=" N   VAL A 986 " --> pdb=" O   THR A 982 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE A 987 " --> pdb=" O   MET A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1000
      removed outlier: 3.527A  pdb=" N   THR A1000 " --> pdb=" O   GLU A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1011
      removed outlier: 3.862A  pdb=" N   LEU A1010 " --> pdb=" O   TYR A1007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1044
    Processing helix  chain 'A' and resid 1049 through 1072
      removed outlier: 3.517A  pdb=" N   ALA A1070 " --> pdb=" O   LEU A1066 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A1072 " --> pdb=" O   MET A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1093
      removed outlier: 3.882A  pdb=" N   ILE A1085 " --> pdb=" O   LEU A1081 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   THR A1087 " --> pdb=" O   THR A1083 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1138
      removed outlier: 3.895A  pdb=" N   SER A1123 " --> pdb=" O   ILE A1119 " (cutoff:3.500A)
      Proline residue:  A1126  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 157
      removed outlier: 3.678A  pdb=" N   GLY A 350 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR A 354 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR A 358 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257
    Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 279
      removed outlier: 7.573A  pdb=" N   PHE A 379 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   SER A 293 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE A 381 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASP A 287 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303
    Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 485
      removed outlier: 6.785A  pdb=" N   GLY A 896 " --> pdb=" O   PHE A 913 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   ILE A 915 " --> pdb=" O   GLY A 896 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   GLY A 898 " --> pdb=" O   ILE A 915 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 877 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   VAL A 897 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   CYS A 879 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   ILE A 899 " --> pdb=" O   CYS A 879 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   GLY A 881 " --> pdb=" O   ILE A 899 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU A 500 " --> pdb=" O   TRP A 771 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU A 773 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   SER A 502 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ILE A 770 " --> pdb=" O   VAL A 852 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ALA A 854 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   MET A 772 " --> pdb=" O   ALA A 854 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 523 through 526
      removed outlier: 6.311A  pdb=" N   MET A 513 " --> pdb=" O   LYS A 751 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS A 751 " --> pdb=" O   MET A 513 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LEU A 515 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   GLU A 749 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   LEU A 742 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ARG A 699 " --> pdb=" O   LEU A 742 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY A 744 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 748 " --> pdb=" O   ARG A 693 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 659 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   GLY A 648 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   VAL A 637 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ILE A 650 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   HIS A 623 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 622 " --> pdb=" O   PHE A 612 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 582

    368 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2340
        1.34 -     1.46: 1548
        1.46 -     1.58: 3592
        1.58 -     1.70: 0
        1.70 -     1.81: 61
  Bond restraints: 7541
  Sorted by residual:
  bond pdb=" F1  ALF A1201 "
       pdb="AL   ALF A1201 "
    ideal  model  delta    sigma   weight residual
    1.684  1.782 -0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" F3  ALF A1201 "
       pdb="AL   ALF A1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.782 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" F4  ALF A1201 "
       pdb="AL   ALF A1201 "
    ideal  model  delta    sigma   weight residual
    1.686  1.782 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" F2  ALF A1201 "
       pdb="AL   ALF A1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.778 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" N   PRO A 285 "
       pdb=" CD  PRO A 285 "
    ideal  model  delta    sigma   weight residual
    1.473  1.443  0.030 1.40e-02 5.10e+03 4.49e+00
  ... (remaining 7536 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.16: 10219
       14.16 -    28.32: 4
       28.32 -    42.49: 0
       42.49 -    56.65: 0
       56.65 -    70.81: 2
  Bond angle restraints: 10225
  Sorted by residual:
  angle pdb=" F1  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F2  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     108.68  179.49  -70.81 3.00e+00 1.11e-01 5.57e+02
  angle pdb=" F3  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F4  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.63  178.84  -69.21 3.00e+00 1.11e-01 5.32e+02
  angle pdb=" F2  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F4  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     110.21   89.14   21.07 3.00e+00 1.11e-01 4.93e+01
  angle pdb=" F1  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F3  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.69   89.92   19.77 3.00e+00 1.11e-01 4.34e+01
  angle pdb=" F2  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F3  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.59   90.28   19.31 3.00e+00 1.11e-01 4.14e+01
  ... (remaining 10220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4104
       17.74 -    35.47: 343
       35.47 -    53.20: 58
       53.20 -    70.94: 11
       70.94 -    88.67: 9
  Dihedral angle restraints: 4525
    sinusoidal: 1792
      harmonic: 2733
  Sorted by residual:
  dihedral pdb=" CA  TRP A 369 "
           pdb=" C   TRP A 369 "
           pdb=" N   ALA A 370 "
           pdb=" CA  ALA A 370 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  THR A 582 "
           pdb=" C   THR A 582 "
           pdb=" N   PHE A 583 "
           pdb=" CA  PHE A 583 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  THR A 979 "
           pdb=" C   THR A 979 "
           pdb=" N   CYS A 980 "
           pdb=" CA  CYS A 980 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 751
       0.039 -    0.077: 330
       0.077 -    0.116: 104
       0.116 -    0.155: 21
       0.155 -    0.193: 5
  Chirality restraints: 1211
  Sorted by residual:
  chirality pdb=" CA  GLU A 237 "
            pdb=" N   GLU A 237 "
            pdb=" C   GLU A 237 "
            pdb=" CB  GLU A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.34e-01
  chirality pdb=" CB  ILE A 334 "
            pdb=" CA  ILE A 334 "
            pdb=" CG1 ILE A 334 "
            pdb=" CG2 ILE A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.05e-01
  chirality pdb=" CB  VAL A 229 "
            pdb=" CA  VAL A 229 "
            pdb=" CG1 VAL A 229 "
            pdb=" CG2 VAL A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.00e-01
  ... (remaining 1208 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 158 "    0.074 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO A 159 "   -0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO A 159 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 159 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 360 "   -0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO A 361 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 858 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO A 859 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 859 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 859 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 55
        2.50 -     3.10: 5214
        3.10 -     3.70: 11428
        3.70 -     4.30: 16551
        4.30 -     4.90: 27644
  Nonbonded interactions: 60892
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1102 "
            pdb=" OD1 ASP A1103 "
     model   vdw
     1.902 3.040
  nonbonded pdb=" O   ASP A 882 "
            pdb="MG    MG A1202 "
     model   vdw
     2.128 2.170
  nonbonded pdb=" OD1 ASN A 885 "
            pdb="MG    MG A1202 "
     model   vdw
     2.130 2.170
  nonbonded pdb=" O   ASP A1100 "
            pdb=" OD1 ASP A1100 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" OG  SER A 594 "
            pdb=" OD1 ASP A 596 "
     model   vdw
     2.241 3.040
  ... (remaining 60887 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 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:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.920
  Find NCS groups from input model:        0.080
  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:3.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
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   0.098   7541  Z= 0.287
  Angle     :  1.331  70.809  10225  Z= 0.564
  Chirality :  0.048   0.193   1211
  Planarity :  0.005   0.112   1267
  Dihedral  : 13.974  88.675   2755
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.27), residues: 919
  helix: -0.41 (0.24), residues: 419
  sheet: -1.74 (0.42), residues: 150
  loop : -1.72 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 660 
 HIS   0.008   0.001   HIS A 945 
 PHE   0.014   0.002   PHE A 843 
 TYR   0.025   0.002   TYR A 198 
 ARG   0.017   0.001   ARG A 567 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A  516 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8193 (ttpp)
REVERT: A  795 GLN cc_start: 0.8370 (tt0) cc_final: 0.7985 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1709
  time to fit residues: 27.1124
Evaluate side-chains
  92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 591 GLN
A 945 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.185199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.149362 restraints weight = 7781.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.98
r_work: 0.3820 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7541  Z= 0.210
  Angle     :  0.903  31.154  10225  Z= 0.393
  Chirality :  0.043   0.144   1211
  Planarity :  0.005   0.071   1267
  Dihedral  :  5.063  23.610   1004
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  8.81 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.28), residues: 919
  helix: -0.00 (0.25), residues: 427
  sheet: -1.65 (0.41), residues: 148
  loop : -1.73 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 369 
 HIS   0.007   0.001   HIS A 945 
 PHE   0.032   0.001   PHE A 202 
 TYR   0.023   0.002   TYR A 707 
 ARG   0.004   0.001   ARG A 389 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  362 LEU cc_start: 0.6443 (mt) cc_final: 0.6025 (mt)
REVERT: A  795 GLN cc_start: 0.8630 (tt0) cc_final: 0.8293 (tt0)
REVERT: A 1079 THR cc_start: 0.7838 (t) cc_final: 0.7449 (m)
  outliers start: 3
  outliers final: 3
  residues processed: 104
  average time/residue: 0.1719
  time to fit residues: 25.6730
Evaluate side-chains
  95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  990 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0970
   chunk 38 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.185687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.150381 restraints weight = 7826.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.91
r_work: 0.3827 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.179
  Angle     :  0.874  31.698  10225  Z= 0.375
  Chirality :  0.042   0.139   1211
  Planarity :  0.004   0.054   1267
  Dihedral  :  4.833  23.071   1004
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.49 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.28), residues: 919
  helix:  0.26 (0.25), residues: 427
  sheet: -1.60 (0.41), residues: 148
  loop : -1.67 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 577 
 PHE   0.025   0.001   PHE A 202 
 TYR   0.022   0.001   TYR A 707 
 ARG   0.003   0.000   ARG A 389 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  795 GLN cc_start: 0.8599 (tt0) cc_final: 0.8252 (tt0)
REVERT: A 1079 THR cc_start: 0.7875 (t) cc_final: 0.7514 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1810
  time to fit residues: 28.1302
Evaluate side-chains
  98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  990 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0670
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 85 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.187491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.152337 restraints weight = 7803.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.91
r_work: 0.3852 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7541  Z= 0.155
  Angle     :  0.860  31.670  10225  Z= 0.365
  Chirality :  0.041   0.141   1211
  Planarity :  0.004   0.041   1267
  Dihedral  :  4.680  21.659   1004
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.82 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.28), residues: 919
  helix:  0.44 (0.25), residues: 428
  sheet: -1.70 (0.40), residues: 156
  loop : -1.60 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 369 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.031   0.001   PHE A 202 
 TYR   0.020   0.001   TYR A1101 
 ARG   0.004   0.000   ARG A 699 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7470 (mp)
REVERT: A  795 GLN cc_start: 0.8567 (tt0) cc_final: 0.8254 (tt0)
REVERT: A 1079 THR cc_start: 0.7852 (t) cc_final: 0.7475 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 105
  average time/residue: 0.1460
  time to fit residues: 22.7606
Evaluate side-chains
  99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue 1068 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 591 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.175825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.139557 restraints weight = 8017.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.99
r_work: 0.3701 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   7541  Z= 0.436
  Angle     :  0.992  31.462  10225  Z= 0.445
  Chirality :  0.049   0.174   1211
  Planarity :  0.005   0.042   1267
  Dihedral  :  5.358  28.291   1004
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.94 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.27), residues: 919
  helix: -0.30 (0.24), residues: 430
  sheet: -1.93 (0.39), residues: 158
  loop : -1.64 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 660 
 HIS   0.008   0.001   HIS A 945 
 PHE   0.024   0.002   PHE A 843 
 TYR   0.021   0.002   TYR A 707 
 ARG   0.005   0.001   ARG A 946 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7635 (mp)
REVERT: A  690 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7950 (mm-30)
REVERT: A  795 GLN cc_start: 0.8646 (tt0) cc_final: 0.8410 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1743
  time to fit residues: 27.5763
Evaluate side-chains
  101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  488 SER
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  990 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0270
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 591 GLN
A 891 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.183881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.148503 restraints weight = 7832.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 1.95
r_work: 0.3813 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3675 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.177
  Angle     :  0.876  32.126  10225  Z= 0.377
  Chirality :  0.042   0.161   1211
  Planarity :  0.004   0.042   1267
  Dihedral  :  4.932  23.427   1004
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.08 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.28), residues: 919
  helix:  0.22 (0.25), residues: 430
  sheet: -1.74 (0.40), residues: 155
  loop : -1.61 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 577 
 PHE   0.034   0.001   PHE A 202 
 TYR   0.017   0.001   TYR A 707 
 ARG   0.004   0.000   ARG A 652 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7429 (mp)
REVERT: A  690 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: A  795 GLN cc_start: 0.8619 (tt0) cc_final: 0.8331 (tt0)
  outliers start: 9
  outliers final: 7
  residues processed: 102
  average time/residue: 0.1549
  time to fit residues: 23.0033
Evaluate side-chains
  95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 90 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.183039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146812 restraints weight = 7882.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 2.01
r_work: 0.3799 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.196
  Angle     :  0.880  31.884  10225  Z= 0.378
  Chirality :  0.042   0.157   1211
  Planarity :  0.004   0.042   1267
  Dihedral  :  4.813  24.050   1004
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.48 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 919
  helix:  0.30 (0.25), residues: 430
  sheet: -1.70 (0.40), residues: 155
  loop : -1.55 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 577 
 PHE   0.030   0.001   PHE A 202 
 TYR   0.014   0.001   TYR A 165 
 ARG   0.004   0.000   ARG A 699 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7521 (mp)
REVERT: A  568 ASP cc_start: 0.7711 (t0) cc_final: 0.7332 (t0)
REVERT: A  690 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7804 (mm-30)
REVERT: A  795 GLN cc_start: 0.8621 (tt0) cc_final: 0.8336 (tt0)
REVERT: A  939 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7174 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1549
  time to fit residues: 24.4558
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 63 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 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 = 0.4304 r_free = 0.4304 target = 0.184596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.148505 restraints weight = 7893.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.02
r_work: 0.3813 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.181
  Angle     :  0.874  31.847  10225  Z= 0.374
  Chirality :  0.042   0.151   1211
  Planarity :  0.003   0.042   1267
  Dihedral  :  4.765  22.917   1004
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.08 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.28), residues: 919
  helix:  0.39 (0.25), residues: 429
  sheet: -1.68 (0.40), residues: 155
  loop : -1.54 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 369 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.031   0.001   PHE A 202 
 TYR   0.014   0.001   TYR A 707 
 ARG   0.004   0.000   ARG A 699 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.785 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: A  568 ASP cc_start: 0.7718 (t0) cc_final: 0.7340 (t0)
REVERT: A  690 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7763 (mm-30)
REVERT: A  795 GLN cc_start: 0.8630 (tt0) cc_final: 0.8337 (tt0)
REVERT: A  939 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7139 (tt)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1543
  time to fit residues: 23.5711
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 31 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0040
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0060
   overall best weight:    0.3186

-------------------------------------------------------------------------------
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 = 0.4342 r_free = 0.4342 target = 0.188190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.153173 restraints weight = 7826.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.95
r_work: 0.3866 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7541  Z= 0.147
  Angle     :  0.861  31.839  10225  Z= 0.365
  Chirality :  0.041   0.145   1211
  Planarity :  0.003   0.043   1267
  Dihedral  :  4.578  21.257   1004
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.56 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.28), residues: 919
  helix:  0.59 (0.25), residues: 428
  sheet: -1.39 (0.41), residues: 147
  loop : -1.55 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 369 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.032   0.001   PHE A 202 
 TYR   0.012   0.001   TYR A1101 
 ARG   0.005   0.000   ARG A 699 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7382 (mp)
REVERT: A  362 LEU cc_start: 0.6523 (mt) cc_final: 0.6007 (mt)
REVERT: A  568 ASP cc_start: 0.7667 (t0) cc_final: 0.7302 (t0)
REVERT: A  690 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7770 (mm-30)
REVERT: A  795 GLN cc_start: 0.8618 (tt0) cc_final: 0.8347 (tt0)
REVERT: A  939 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6941 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1606
  time to fit residues: 25.1458
Evaluate side-chains
  103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.2980
   chunk 86 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4319 r_free = 0.4319 target = 0.185958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.149913 restraints weight = 7984.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.01
r_work: 0.3830 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.175
  Angle     :  0.871  31.648  10225  Z= 0.370
  Chirality :  0.042   0.157   1211
  Planarity :  0.003   0.043   1267
  Dihedral  :  4.564  22.462   1004
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.92 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.28), residues: 919
  helix:  0.54 (0.25), residues: 429
  sheet: -1.30 (0.42), residues: 147
  loop : -1.48 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 369 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.030   0.001   PHE A 202 
 TYR   0.013   0.001   TYR A 707 
 ARG   0.005   0.000   ARG A 699 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  223 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7499 (mp)
REVERT: A  269 ASP cc_start: 0.6950 (t0) cc_final: 0.6745 (t0)
REVERT: A  362 LEU cc_start: 0.6499 (mt) cc_final: 0.5963 (mt)
REVERT: A  795 GLN cc_start: 0.8625 (tt0) cc_final: 0.8331 (tt0)
REVERT: A  939 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7115 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1714
  time to fit residues: 25.5928
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1101 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0570
   chunk 63 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.8902

-------------------------------------------------------------------------------
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 = 0.4308 r_free = 0.4308 target = 0.184524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.148763 restraints weight = 7843.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.93
r_work: 0.3818 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3681 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7541  Z= 0.201
  Angle     :  0.884  31.592  10225  Z= 0.378
  Chirality :  0.043   0.168   1211
  Planarity :  0.003   0.043   1267
  Dihedral  :  4.654  23.864   1004
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.16 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.28), residues: 919
  helix:  0.46 (0.25), residues: 429
  sheet: -1.46 (0.41), residues: 155
  loop : -1.44 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 660 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.030   0.001   PHE A 202 
 TYR   0.014   0.001   TYR A 707 
 ARG   0.004   0.000   ARG A 699 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5054.04 seconds
wall clock time: 87 minutes 4.26 seconds (5224.26 seconds total)