Starting phenix.real_space_refine
on Wed Mar  4 08:10:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o0y_0584/03_2026/6o0y_0584.cif"
  }
  resolution = 3.37
  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=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     P     149      5.49       5
     S      15      5.16       5
     C    7059      2.51       5
     N    2092      2.21       5
     O    2513      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11828
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1146, 8669
          Classifications: {'peptide': 1146}
          Incomplete info: {'truncation_to_alanine': 158}
          Link IDs: {'PTRANS': 29, 'TRANS': 1116}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 761
          Unresolved non-hydrogen angles: 916
          Unresolved non-hydrogen dihedrals: 609
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ASP:plan': 37, 'GLU:plan': 63, 'ARG:plan': 19, 'GLN:plan1': 10, 'ASN:plan1': 9, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 490
    Chain: "B"
      Number of atoms: 2104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2104
          Classifications: {'RNA': 98}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
    Chain: "C"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 261
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 331
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 463
          Classifications: {'DNA': 23}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 22}
  Time building chain proxies: 2.84, per 1000 atoms: 0.24
  Number of scatterers: 11828
  At special positions: 0
  Unit cell: (137.104, 126.236, 88.616, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P     149     15.00
     O    2513      8.00
     N    2092      7.00
     C    7059      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: 1.10
  Conformation dependent library (CDL) restraints added in 470.1 milliseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2182

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 7 sheets defined
      51.7% alpha, 7.6% beta
      52 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 92
      removed outlier: 3.720A  pdb=" N   ARG A  70 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG A  71 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TYR A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 4.005A  pdb=" N   GLU A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 145
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.590A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 352
      removed outlier: 3.737A  pdb=" N   ILE A 350 " --> pdb=" O   LYS A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.600A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.756A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.411A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.943A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
      removed outlier: 3.527A  pdb=" N   ILE A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.779A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 567
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 631 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
      removed outlier: 3.559A  pdb=" N   LYS A 652 " --> pdb=" O   MET A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.520A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.530A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 776
    Processing helix  chain 'A' and resid 779 through 791
      removed outlier: 4.053A  pdb=" N   ARG A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A 785 " --> pdb=" O   MET A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 3.983A  pdb=" N   GLU A 798 " --> pdb=" O   ILE A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 817
      removed outlier: 3.755A  pdb=" N   LEU A 813 " --> pdb=" O   GLU A 809 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR A 814 " --> pdb=" O   LYS A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 866
      removed outlier: 3.649A  pdb=" N   ASN A 863 " --> pdb=" O   ARG A 859 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LYS A 866 " --> pdb=" O   LYS A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 889
      removed outlier: 6.169A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN A 888 " --> pdb=" O   ARG A 884 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ALA A 889 " --> pdb=" O   GLN A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 902 through 905
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 4.035A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG A 925 " --> pdb=" O   LEU A 921 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 970
      removed outlier: 3.647A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1000
    Processing helix  chain 'A' and resid 1080 through 1087
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 4.102A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
      removed outlier: 3.632A  pdb=" N   PHE A1181 " --> pdb=" O   ASN A1177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 3.836A  pdb=" N   ILE A1195 " --> pdb=" O   LYS A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1240
      removed outlier: 3.508A  pdb=" N   VAL A1233 " --> pdb=" O   PRO A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1252 through 1261
    Processing helix  chain 'A' and resid 1263 through 1278
      removed outlier: 3.825A  pdb=" N   ASP A1267 " --> pdb=" O   LYS A1263 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   PHE A1276 " --> pdb=" O   GLN A1272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1296
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.808A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1317
      removed outlier: 4.072A  pdb=" N   ASN A1317 " --> pdb=" O   THR A1314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1314 through 1317'
    Processing helix  chain 'A' and resid 1341 through 1344
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 4.459A  pdb=" N   GLU A 762 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   ILE A  11 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.827A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530
      removed outlier: 3.694A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167
      removed outlier: 3.545A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325

    392 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      130 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 3.04

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1912
        1.33 -     1.44: 3845
        1.44 -     1.56: 6290
        1.56 -     1.68: 294
        1.68 -     1.80: 28
  Bond restraints: 12369
  Sorted by residual:
  bond pdb=" C3'  DC C   1 "
       pdb=" O3'  DC C   1 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" C3'   A B  38 "
       pdb=" O3'   A B  38 "
    ideal  model  delta    sigma   weight residual
    1.417  1.436 -0.019 1.50e-02 4.44e+03 1.67e+00
  bond pdb=" C3'   A B   8 "
       pdb=" O3'   A B   8 "
    ideal  model  delta    sigma   weight residual
    1.417  1.436 -0.019 1.50e-02 4.44e+03 1.64e+00
  bond pdb=" O5'  DT c  21 "
       pdb=" C5'  DT c  21 "
    ideal  model  delta    sigma   weight residual
    1.423  1.385  0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" CB  ILE A 733 "
       pdb=" CG2 ILE A 733 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.58e+00
  ... (remaining 12364 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 17050
        2.10 -     4.19: 337
        4.19 -     6.29: 39
        6.29 -     8.38: 13
        8.38 -    10.48: 1
  Bond angle restraints: 17440
  Sorted by residual:
  angle pdb=" O3'   A B  42 "
        pdb=" C3'   A B  42 "
        pdb=" C2'   A B  42 "
      ideal   model   delta    sigma   weight residual
     113.70  119.97   -6.27 1.50e+00 4.44e-01 1.75e+01
  angle pdb=" C3'   A B   8 "
        pdb=" O3'   A B   8 "
        pdb=" P     A B   9 "
      ideal   model   delta    sigma   weight residual
     120.20  126.00   -5.80 1.50e+00 4.44e-01 1.49e+01
  angle pdb=" C3'   A B  38 "
        pdb=" O3'   A B  38 "
        pdb=" P     G B  39 "
      ideal   model   delta    sigma   weight residual
     120.20  125.78   -5.58 1.50e+00 4.44e-01 1.39e+01
  angle pdb=" O3'   A B  38 "
        pdb=" C3'   A B  38 "
        pdb=" C2'   A B  38 "
      ideal   model   delta    sigma   weight residual
     113.70  119.06   -5.36 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" C3'   A B  42 "
        pdb=" O3'   A B  42 "
        pdb=" P     G B  43 "
      ideal   model   delta    sigma   weight residual
     120.20  125.54   -5.34 1.50e+00 4.44e-01 1.27e+01
  ... (remaining 17435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.17: 6817
       31.17 -    62.34: 437
       62.34 -    93.51: 82
       93.51 -   124.68: 0
      124.68 -   155.86: 5
  Dihedral angle restraints: 7341
    sinusoidal: 3972
      harmonic: 3369
  Sorted by residual:
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   57.44  142.56     1      1.50e+01 4.44e-03 7.65e+01
  dihedral pdb=" O4'   U B  97 "
           pdb=" C1'   U B  97 "
           pdb=" N1    U B  97 "
           pdb=" C2    U B  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -73.39  -86.61     1      1.50e+01 4.44e-03 4.01e+01
  dihedral pdb=" CA  ASN A 612 "
           pdb=" C   ASN A 612 "
           pdb=" N   GLU A 613 "
           pdb=" CA  GLU A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.40  -24.60     0      5.00e+00 4.00e-02 2.42e+01
  ... (remaining 7338 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1810
       0.067 -    0.133: 246
       0.133 -    0.200: 28
       0.200 -    0.266: 4
       0.266 -    0.333: 3
  Chirality restraints: 2091
  Sorted by residual:
  chirality pdb=" C3'   A B  42 "
            pdb=" C4'   A B  42 "
            pdb=" O3'   A B  42 "
            pdb=" C2'   A B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" C3'   A B   8 "
            pdb=" C4'   A B   8 "
            pdb=" O3'   A B   8 "
            pdb=" C2'   A B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.42e+00
  ... (remaining 2088 not shown)

  Planarity restraints: 1656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 622 "   -0.015 2.00e-02 2.50e+03   3.06e-02 9.35e+00
        pdb=" C   THR A 622 "    0.053 2.00e-02 2.50e+03
        pdb=" O   THR A 622 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 623 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 617 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.74e+00
        pdb=" C   GLU A 617 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   GLU A 617 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A 618 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 619 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   ILE A 619 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ILE A 619 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 620 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1653 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3093
        2.80 -     3.32: 9597
        3.32 -     3.85: 20409
        3.85 -     4.37: 22751
        4.37 -     4.90: 35911
  Nonbonded interactions: 91761
  Sorted by model distance:
  nonbonded pdb=" O2   DC C   1 "
            pdb=" N2   DG D  40 "
     model   vdw
     2.272 2.496
  nonbonded pdb=" O   TYR A 521 "
            pdb=" OG1 THR A 525 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER A 512 "
            pdb=" OE2 GLU A 617 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   TYR A  25 "
            pdb=" OH  TYR A 988 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OH  TYR A 373 "
            pdb=" O   LEU A 398 "
     model   vdw
     2.352 3.040
  ... (remaining 91756 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.590
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
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   0.047  12369  Z= 0.257
  Angle     :  0.737  10.478  17440  Z= 0.406
  Chirality :  0.048   0.333   2091
  Planarity :  0.005   0.055   1656
  Dihedral  : 19.216 155.856   5159
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.94 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.11 (0.19), residues: 1136
  helix: -2.75 (0.15), residues: 537
  sheet: -1.14 (0.48), residues: 117
  loop : -3.01 (0.22), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  71 
 TYR   0.014   0.002   TYR A 155 
 PHE   0.015   0.001   PHE A1327 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (12369)
  covalent geometry    : angle       0.73667 (17440)
  hydrogen bonds       : bond        0.15367 (  522)
  hydrogen bonds       : angle       6.25252 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  465 MET cc_start: 0.8497 (tmm) cc_final: 0.8126 (tmm)
REVERT: A  733 ILE cc_start: 0.8269 (pt) cc_final: 0.8044 (mm)
REVERT: A  746 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8535 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 75
  average time/residue: 0.1119
  time to fit residues: 12.3629
Evaluate side-chains
  52 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue 1190 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A 113 HIS
A 402 GLN
A 899 ASN
A1177 ASN
A1252 ASN
A1295 ASN
A1308 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.077175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.056397 restraints weight = 38947.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.98
r_work: 0.2705 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12369  Z= 0.152
  Angle     :  0.515   7.300  17440  Z= 0.287
  Chirality :  0.037   0.225   2091
  Planarity :  0.003   0.041   1656
  Dihedral  : 20.018 160.684   3268
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.29 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.35 (0.22), residues: 1136
  helix: -0.90 (0.20), residues: 558
  sheet: -0.76 (0.49), residues: 114
  loop : -2.54 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1333 
 TYR   0.020   0.001   TYR A 594 
 PHE   0.013   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12369)
  covalent geometry    : angle       0.51547 (17440)
  hydrogen bonds       : bond        0.05072 (  522)
  hydrogen bonds       : angle       4.27302 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8286 (pt) cc_final: 0.8059 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0942
  time to fit residues: 9.0083
Evaluate side-chains
  55 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0370
   chunk 95 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0870
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.2038

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

Flipped N/Q/H residues before XYZ refinement:
A 817 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.078479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.057715 restraints weight = 39238.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.99
r_work: 0.2741 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12369  Z= 0.112
  Angle     :  0.469   7.669  17440  Z= 0.258
  Chirality :  0.036   0.213   2091
  Planarity :  0.003   0.031   1656
  Dihedral  : 19.831 155.674   3268
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.65 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.33 (0.24), residues: 1136
  helix:  0.13 (0.22), residues: 559
  sheet: -0.59 (0.48), residues: 114
  loop : -2.24 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1333 
 TYR   0.017   0.001   TYR A 594 
 PHE   0.010   0.001   PHE A 432 
 TRP   0.006   0.000   TRP A 476 
 HIS   0.002   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (12369)
  covalent geometry    : angle       0.46880 (17440)
  hydrogen bonds       : bond        0.04097 (  522)
  hydrogen bonds       : angle       3.75975 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8225 (pt) cc_final: 0.7962 (mm)
  outliers start: 12
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0861
  time to fit residues: 9.1604
Evaluate side-chains
  59 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 117 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 107 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 35 optimal weight:    0.0670
   overall best weight:    3.1724

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 721 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.076206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.055357 restraints weight = 39630.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.96
r_work: 0.2685 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12369  Z= 0.211
  Angle     :  0.534   7.274  17440  Z= 0.289
  Chirality :  0.038   0.221   2091
  Planarity :  0.003   0.030   1656
  Dihedral  : 19.894 159.118   3267
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.14 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.94 (0.24), residues: 1136
  helix:  0.54 (0.22), residues: 563
  sheet: -0.38 (0.49), residues: 105
  loop : -2.16 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1333 
 TYR   0.013   0.001   TYR A 594 
 PHE   0.016   0.001   PHE A1258 
 TRP   0.008   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (12369)
  covalent geometry    : angle       0.53435 (17440)
  hydrogen bonds       : bond        0.04917 (  522)
  hydrogen bonds       : angle       3.82675 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8241 (pt) cc_final: 0.7939 (mm)
  outliers start: 16
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0868
  time to fit residues: 8.4586
Evaluate side-chains
  61 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 117 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 62 optimal weight:   30.0000
   chunk 25 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.057147 restraints weight = 39483.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.98
r_work: 0.2728 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12369  Z= 0.123
  Angle     :  0.476   7.814  17440  Z= 0.259
  Chirality :  0.036   0.212   2091
  Planarity :  0.002   0.028   1656
  Dihedral  : 19.796 156.453   3267
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.75 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.56 (0.25), residues: 1136
  helix:  0.87 (0.23), residues: 562
  sheet: -0.40 (0.48), residues: 114
  loop : -1.97 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1333 
 TYR   0.013   0.001   TYR A 594 
 PHE   0.010   0.001   PHE A 432 
 TRP   0.006   0.001   TRP A 476 
 HIS   0.002   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (12369)
  covalent geometry    : angle       0.47583 (17440)
  hydrogen bonds       : bond        0.04141 (  522)
  hydrogen bonds       : angle       3.61191 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8218 (pt) cc_final: 0.7927 (mm)
REVERT: A 1089 MET cc_start: 0.9055 (mtm) cc_final: 0.8844 (mtp)
REVERT: A 1266 LEU cc_start: 0.8827 (tt) cc_final: 0.8540 (mp)
  outliers start: 16
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0891
  time to fit residues: 9.2485
Evaluate side-chains
  63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 96 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.076825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.056059 restraints weight = 39459.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 2.96
r_work: 0.2702 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12369  Z= 0.181
  Angle     :  0.513  12.974  17440  Z= 0.276
  Chirality :  0.037   0.215   2091
  Planarity :  0.003   0.029   1656
  Dihedral  : 19.825 158.179   3267
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.13 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.45 (0.25), residues: 1136
  helix:  0.94 (0.23), residues: 564
  sheet: -0.24 (0.49), residues: 105
  loop : -1.90 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  71 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.011   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12369)
  covalent geometry    : angle       0.51286 (17440)
  hydrogen bonds       : bond        0.04538 (  522)
  hydrogen bonds       : angle       3.68456 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8213 (pt) cc_final: 0.7923 (mm)
REVERT: A 1089 MET cc_start: 0.9095 (mtm) cc_final: 0.8828 (mtp)
  outliers start: 16
  outliers final: 12
  residues processed: 61
  average time/residue: 0.0716
  time to fit residues: 7.0845
Evaluate side-chains
  61 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 86 optimal weight:    0.1980
   chunk 97 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 34 optimal weight:    0.3980
   chunk 123 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.077132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.056364 restraints weight = 39334.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 2.96
r_work: 0.2711 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12369  Z= 0.153
  Angle     :  0.510  14.256  17440  Z= 0.272
  Chirality :  0.037   0.214   2091
  Planarity :  0.003   0.028   1656
  Dihedral  : 19.817 157.838   3267
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.37 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1136
  helix:  1.03 (0.23), residues: 563
  sheet: -0.24 (0.48), residues: 114
  loop : -1.82 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1333 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.010   0.001   PHE A 432 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.002   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (12369)
  covalent geometry    : angle       0.50984 (17440)
  hydrogen bonds       : bond        0.04418 (  522)
  hydrogen bonds       : angle       3.65771 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8202 (pt) cc_final: 0.7906 (mm)
REVERT: A  746 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8837 (tm-30)
REVERT: A 1089 MET cc_start: 0.9095 (mtm) cc_final: 0.8822 (mtp)
REVERT: A 1266 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8569 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 62
  average time/residue: 0.0916
  time to fit residues: 8.9457
Evaluate side-chains
  63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 96 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 39 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    1.8588

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.077417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.056674 restraints weight = 39216.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.96
r_work: 0.2717 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12369  Z= 0.140
  Angle     :  0.501  12.740  17440  Z= 0.268
  Chirality :  0.037   0.213   2091
  Planarity :  0.003   0.027   1656
  Dihedral  : 19.805 157.567   3267
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.13 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1136
  helix:  1.13 (0.23), residues: 563
  sheet: -0.16 (0.48), residues: 114
  loop : -1.77 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  71 
 TYR   0.015   0.001   TYR A 594 
 PHE   0.014   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12369)
  covalent geometry    : angle       0.50076 (17440)
  hydrogen bonds       : bond        0.04326 (  522)
  hydrogen bonds       : angle       3.63449 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8218 (pt) cc_final: 0.7910 (mm)
REVERT: A  746 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8817 (tm-30)
REVERT: A 1089 MET cc_start: 0.9054 (mtm) cc_final: 0.8769 (mtp)
REVERT: A 1266 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8570 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 63
  average time/residue: 0.0898
  time to fit residues: 9.1194
Evaluate side-chains
  65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 101 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0020
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.3794

-------------------------------------------------------------------------------
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 = 0.3363 r_free = 0.3363 target = 0.078361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.057642 restraints weight = 38959.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 2.96
r_work: 0.2739 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12369  Z= 0.118
  Angle     :  0.484  12.405  17440  Z= 0.259
  Chirality :  0.036   0.206   2091
  Planarity :  0.003   0.026   1656
  Dihedral  : 19.735 156.315   3267
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.75 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.06 (0.26), residues: 1136
  helix:  1.24 (0.23), residues: 562
  sheet: -0.10 (0.49), residues: 115
  loop : -1.69 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1333 
 TYR   0.015   0.001   TYR A 594 
 PHE   0.010   0.001   PHE A 432 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.002   0.000   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12369)
  covalent geometry    : angle       0.48380 (17440)
  hydrogen bonds       : bond        0.03984 (  522)
  hydrogen bonds       : angle       3.55781 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8246 (pt) cc_final: 0.7907 (mm)
REVERT: A  746 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: A 1089 MET cc_start: 0.9023 (mtm) cc_final: 0.8736 (mtp)
REVERT: A 1266 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (mp)
  outliers start: 17
  outliers final: 15
  residues processed: 64
  average time/residue: 0.0869
  time to fit residues: 8.8994
Evaluate side-chains
  66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 72 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.6026

-------------------------------------------------------------------------------
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 = 0.3327 r_free = 0.3327 target = 0.076833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.055829 restraints weight = 39212.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 3.01
r_work: 0.2681 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12369  Z= 0.177
  Angle     :  0.522  12.064  17440  Z= 0.279
  Chirality :  0.037   0.212   2091
  Planarity :  0.003   0.028   1656
  Dihedral  : 19.791 158.338   3267
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.12 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.09 (0.25), residues: 1136
  helix:  1.23 (0.23), residues: 563
  sheet:  0.07 (0.51), residues: 105
  loop : -1.74 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  71 
 TYR   0.013   0.001   TYR A 594 
 PHE   0.015   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.002   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12369)
  covalent geometry    : angle       0.52223 (17440)
  hydrogen bonds       : bond        0.04540 (  522)
  hydrogen bonds       : angle       3.65183 ( 1395)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  733 ILE cc_start: 0.8199 (pt) cc_final: 0.7893 (mm)
REVERT: A  746 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: A 1089 MET cc_start: 0.9129 (mtm) cc_final: 0.8862 (mtp)
REVERT: A 1266 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8585 (mp)
  outliers start: 16
  outliers final: 14
  residues processed: 60
  average time/residue: 0.0889
  time to fit residues: 8.5704
Evaluate side-chains
  64 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 120 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.075803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.054708 restraints weight = 39385.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 3.01
r_work: 0.2656 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
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      :  0.005   0.045  12369  Z= 0.235
  Angle     :  0.560  11.725  17440  Z= 0.299
  Chirality :  0.039   0.221   2091
  Planarity :  0.003   0.029   1656
  Dihedral  : 19.875 159.532   3267
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.99 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.19 (0.25), residues: 1136
  helix:  1.13 (0.23), residues: 563
  sheet:  0.08 (0.50), residues: 105
  loop : -1.79 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 967 
 TYR   0.013   0.001   TYR A 594 
 PHE   0.012   0.001   PHE A1327 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (12369)
  covalent geometry    : angle       0.56027 (17440)
  hydrogen bonds       : bond        0.04998 (  522)
  hydrogen bonds       : angle       3.78301 ( 1395)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2457.84 seconds
wall clock time: 42 minutes 52.41 seconds (2572.41 seconds total)