Starting phenix.real_space_refine
on Thu Sep 18 03:09:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kor_62479/09_2025/9kor_62479.map"
  }
  resolution = 2.8
  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=   0.000 sd=   0.034
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: 6
    Type Number    sf(0)   Gaussians
     P     150      5.49       5
     Mg      4      5.21       5
     S      32      5.16       5
     C    7778      2.51       5
     N    2326      2.21       5
     O    2886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13176
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1229, 10004
          Classifications: {'peptide': 1229}
          Link IDs: {'PTRANS': 36, 'TRANS': 1192}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2584
          Classifications: {'RNA': 121}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 53, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 24, 'rna3p': 96}
    Chain: "C"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 84
          Classifications: {'DNA': 4}
          Link IDs: {'rna3p': 3}
    Chain: "D"
      Number of atoms: 500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 500
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.33, per 1000 atoms: 0.25
  Number of scatterers: 13176
  At special positions: 0
  Unit cell: (91.14, 112.53, 145.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P     150     15.00
     Mg      4     11.99
     O    2886      8.00
     N    2326      7.00
     C    7778      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: 1.07
  Conformation dependent library (CDL) restraints added in 499.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2350

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      53.1% alpha, 12.2% beta
      42 base pairs and 91 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 82
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 110 through 117
      removed outlier: 3.769A  pdb=" N   VAL A 113 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A 117 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 125
      removed outlier: 3.670A  pdb=" N   PHE A 121 " --> pdb=" O   GLU A 118 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   CYS A 124 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 148
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 167 through 177
      removed outlier: 3.781A  pdb=" N   GLN A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 203
    Processing helix  chain 'A' and resid 208 through 223
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 226 through 233
    Processing helix  chain 'A' and resid 235 through 248
    Processing helix  chain 'A' and resid 250 through 256
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.879A  pdb=" N   LYS A 264 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ASN A 265 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 314
    Processing helix  chain 'A' and resid 315 through 320
      removed outlier: 3.911A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 349
    Processing helix  chain 'A' and resid 350 through 362
      removed outlier: 3.529A  pdb=" N   ILE A 354 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   SER A 362 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 366
    Processing helix  chain 'A' and resid 371 through 376
    Processing helix  chain 'A' and resid 381 through 391
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'A' and resid 433 through 443
    Processing helix  chain 'A' and resid 451 through 471
    Processing helix  chain 'A' and resid 473 through 478
      removed outlier: 3.551A  pdb=" N   VAL A 477 " --> pdb=" O   TRP A 474 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLU A 478 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 501
      removed outlier: 3.809A  pdb=" N   ARG A 499 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 518
    Processing helix  chain 'A' and resid 521 through 525
      removed outlier: 4.043A  pdb=" N   SER A 524 " --> pdb=" O   LYS A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 541
    Processing helix  chain 'A' and resid 543 through 558
    Processing helix  chain 'A' and resid 564 through 587
    Processing helix  chain 'A' and resid 589 through 595
      removed outlier: 3.748A  pdb=" N   LYS A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 611
      removed outlier: 3.568A  pdb=" N   LEU A 602 " --> pdb=" O   ASN A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 632
    Processing helix  chain 'A' and resid 652 through 675
      removed outlier: 4.584A  pdb=" N   LEU A 668 " --> pdb=" O   GLU A 664 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A 675 " --> pdb=" O   GLU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 901
      removed outlier: 3.530A  pdb=" N   TRP A 880 " --> pdb=" O   GLY A 876 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   GLU A 895 " --> pdb=" O   GLU A 891 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   TRP A 896 " --> pdb=" O   LEU A 892 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN A 900 " --> pdb=" O   TRP A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 919
      removed outlier: 3.726A  pdb=" N   ASP A 919 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 929
    Processing helix  chain 'A' and resid 940 through 954
      removed outlier: 4.076A  pdb=" N   HIS A 944 " --> pdb=" O   PRO A 940 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA A 945 " --> pdb=" O   ILE A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 979
    Processing helix  chain 'A' and resid 1003 through 1007
    Processing helix  chain 'A' and resid 1045 through 1054
      removed outlier: 4.080A  pdb=" N   LEU A1049 " --> pdb=" O   ASP A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1088
    Processing helix  chain 'A' and resid 1091 through 1104
    Processing helix  chain 'A' and resid 1126 through 1131
    Processing helix  chain 'A' and resid 1132 through 1135
    Processing helix  chain 'A' and resid 1143 through 1147
      removed outlier: 3.605A  pdb=" N   GLY A1147 " --> pdb=" O   ASN A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1166
      removed outlier: 3.663A  pdb=" N   GLU A1160 " --> pdb=" O   PRO A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1198
    Processing helix  chain 'A' and resid 1269 through 1272
    Processing helix  chain 'A' and resid 1325 through 1332
    Processing helix  chain 'A' and resid 1338 through 1342
    Processing helix  chain 'A' and resid 1349 through 1361
      removed outlier: 3.807A  pdb=" N   GLN A1361 " --> pdb=" O   VAL A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1368 through 1370
      No H-bonds generated for 'chain 'A' and resid 1368 through 1370'
    Processing helix  chain 'A' and resid 1392 through 1410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 904 through 910
      removed outlier: 6.040A  pdb=" N   ASP A 684 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ASP A 907 " --> pdb=" O   ASP A 684 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   VAL A 686 " --> pdb=" O   ASP A 907 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   TYR A 909 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   LEU A 688 " --> pdb=" O   TYR A 909 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ALA A  35 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   VAL A  37 " --> pdb=" O   ILE A 991 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   ILE A1376 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   GLN A1372 " --> pdb=" O   CYS A1387 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   CYS A1387 " --> pdb=" O   GLN A1372 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS A1383 " --> pdb=" O   ILE A1376 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   LEU A1378 " --> pdb=" O   THR A1381 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   THR A1381 " --> pdb=" O   LEU A1378 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 904 through 910
      removed outlier: 6.040A  pdb=" N   ASP A 684 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ASP A 907 " --> pdb=" O   ASP A 684 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   VAL A 686 " --> pdb=" O   ASP A 907 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   TYR A 909 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   LEU A 688 " --> pdb=" O   TYR A 909 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ALA A  35 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   VAL A  37 " --> pdb=" O   ILE A 991 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   ILE A1376 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1215 through 1218
      removed outlier: 6.247A  pdb=" N   ASN A1110 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
      removed outlier: 8.640A  pdb=" N   ILE A1014 " --> pdb=" O   ASN A1110 " (cutoff:3.500A)
      removed outlier: 13.699A  pdb=" N   SER A1112 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
      removed outlier: 18.546A  pdb=" N   GLU A1012 " --> pdb=" O   SER A1112 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   MET A1243 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   GLY A1013 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A1241 " --> pdb=" O   GLY A1013 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   PHE A1015 " --> pdb=" O   TYR A1239 " (cutoff:3.500A)
      removed outlier: 9.182A  pdb=" N   TYR A1239 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 12.817A  pdb=" N   GLU A1017 " --> pdb=" O   ASP A1237 " (cutoff:3.500A)
      removed outlier: 14.857A  pdb=" N   ASP A1237 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1043
      removed outlier: 4.240A  pdb=" N   CYS A1029 " --> pdb=" O   VAL A1043 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1117 through 1118
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1137 through 1141
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1266 through 1267
      removed outlier: 7.850A  pdb=" N   LEU A1266 " --> pdb=" O   LYS A1250 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      104 hydrogen bonds
      188 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      91 stacking parallelities
  Total time for adding SS restraints: 3.67

  Time building geometry restraints manager: 1.45 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: 2157
        1.33 -     1.45: 4248
        1.45 -     1.57: 6980
        1.57 -     1.69: 298
        1.69 -     1.81: 50
  Bond restraints: 13733
  Sorted by residual:
  bond pdb=" CB  PRO A  28 "
       pdb=" CG  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.585 -0.093 5.00e-02 4.00e+02 3.44e+00
  bond pdb=" C1'  DC D  13 "
       pdb=" N1   DC D  13 "
    ideal  model  delta    sigma   weight residual
    1.490  1.528 -0.038 3.00e-02 1.11e+03 1.57e+00
  bond pdb=" C2   DC D  21 "
       pdb=" O2   DC D  21 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 2.00e-02 2.50e+03 1.53e+00
  bond pdb=" C3'   U B  58 "
       pdb=" O3'   U B  58 "
    ideal  model  delta    sigma   weight residual
    1.427  1.445 -0.018 1.50e-02 4.44e+03 1.39e+00
  bond pdb=" CG  PRO A  28 "
       pdb=" CD  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.503  1.543 -0.040 3.40e-02 8.65e+02 1.36e+00
  ... (remaining 13728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 18996
        2.31 -     4.63: 212
        4.63 -     6.94: 31
        6.94 -     9.26: 1
        9.26 -    11.57: 2
  Bond angle restraints: 19242
  Sorted by residual:
  angle pdb=" C2'   A B  32 "
        pdb=" C1'   A B  32 "
        pdb=" N9    A B  32 "
      ideal   model   delta    sigma   weight residual
     114.00  121.00   -7.00 1.50e+00 4.44e-01 2.18e+01
  angle pdb=" O4'   A B  32 "
        pdb=" C1'   A B  32 "
        pdb=" N9    A B  32 "
      ideal   model   delta    sigma   weight residual
     108.20  113.77   -5.57 1.50e+00 4.44e-01 1.38e+01
  angle pdb=" CA  LEU A 513 "
        pdb=" CB  LEU A 513 "
        pdb=" CG  LEU A 513 "
      ideal   model   delta    sigma   weight residual
     116.30  127.87  -11.57 3.50e+00 8.16e-02 1.09e+01
  angle pdb=" OP1   U B  47 "
        pdb=" P     U B  47 "
        pdb=" OP2   U B  47 "
      ideal   model   delta    sigma   weight residual
     119.60  109.80    9.80 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" CA  PRO A  28 "
        pdb=" N   PRO A  28 "
        pdb=" CD  PRO A  28 "
      ideal   model   delta    sigma   weight residual
     112.00  107.44    4.56 1.40e+00 5.10e-01 1.06e+01
  ... (remaining 19237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.99: 7844
       35.99 -    71.97: 478
       71.97 -   107.96: 49
      107.96 -   143.94: 1
      143.94 -   179.93: 17
  Dihedral angle restraints: 8389
    sinusoidal: 4766
      harmonic: 3623
  Sorted by residual:
  dihedral pdb=" O4'   U B  64 "
           pdb=" C1'   U B  64 "
           pdb=" N1    U B  64 "
           pdb=" C2    U B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   19.93 -179.93     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U B  26 "
           pdb=" C1'   U B  26 "
           pdb=" N1    U B  26 "
           pdb=" C2    U B  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   21.31  178.69     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   C B  17 "
           pdb=" C1'   C B  17 "
           pdb=" N1    C B  17 "
           pdb=" C2    C B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   23.45  176.55     1      1.50e+01 4.44e-03 8.53e+01
  ... (remaining 8386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 2162
       0.094 -    0.188: 68
       0.188 -    0.281: 6
       0.281 -    0.375: 0
       0.375 -    0.469: 1
  Chirality restraints: 2237
  Sorted by residual:
  chirality pdb=" C1'   A B  32 "
            pdb=" O4'   A B  32 "
            pdb=" C2'   A B  32 "
            pdb=" N9    A B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.97    0.47 2.00e-01 2.50e+01 5.50e+00
  chirality pdb=" C1'   A B  42 "
            pdb=" O4'   A B  42 "
            pdb=" C2'   A B  42 "
            pdb=" N9    A B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.17    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CG  LEU A 513 "
            pdb=" CB  LEU A 513 "
            pdb=" CD1 LEU A 513 "
            pdb=" CD2 LEU A 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 2234 not shown)

  Planarity restraints: 1913
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  27 "   -0.079 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO A  28 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC D  21 "    0.007 2.00e-02 2.50e+03   2.81e-02 1.78e+01
        pdb=" N1   DC D  21 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DC D  21 "   -0.071 2.00e-02 2.50e+03
        pdb=" O2   DC D  21 "    0.043 2.00e-02 2.50e+03
        pdb=" N3   DC D  21 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC D  21 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC D  21 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DC D  21 "    0.011 2.00e-02 2.50e+03
        pdb=" C6   DC D  21 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  32 "    0.048 2.00e-02 2.50e+03   2.33e-02 1.49e+01
        pdb=" N9    A B  32 "   -0.059 2.00e-02 2.50e+03
        pdb=" C8    A B  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A B  32 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A B  32 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    A B  32 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A B  32 "    0.010 2.00e-02 2.50e+03
        pdb=" N1    A B  32 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A B  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    A B  32 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A B  32 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1910 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 444
        2.67 -     3.23: 12515
        3.23 -     3.79: 22957
        3.79 -     4.34: 31004
        4.34 -     4.90: 47206
  Nonbonded interactions: 114126
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 100 "
            pdb=" OP1   G B  19 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" O   LEU A 411 "
            pdb=" OH  TYR A 463 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OE1 GLN A1294 "
            pdb=" OH  TYR A1296 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" NZ  LYS A 492 "
            pdb=" OP1   C B   8 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OG  SER A 618 "
            pdb=" OP2   C B   7 "
     model   vdw
     2.215 3.040
  ... (remaining 114121 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=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:             4.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.310
  Find NCS groups from input model:        0.140
  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:6.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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      :  0.003   0.093  13733  Z= 0.127
  Angle     :  0.611  11.573  19242  Z= 0.320
  Chirality :  0.039   0.469   2237
  Planarity :  0.005   0.119   1913
  Dihedral  : 21.623 179.928   6039
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.29 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 16.30 %
    Favored  : 82.79 %
  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 aren not related in a simple way.
  whole:  0.11 (0.25), residues: 1225
  helix:  0.99 (0.22), residues: 571
  sheet:  0.37 (0.48), residues: 128
  loop : -1.00 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 104 
 TYR   0.024   0.001   TYR A1194 
 PHE   0.017   0.001   PHE A1356 
 TRP   0.029   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (13733)
  covalent geometry    : angle       0.61148 (19242)
  hydrogen bonds       : bond        0.13747 (  582)
  hydrogen bonds       : angle       5.64170 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 TYR cc_start: 0.7875 (m-10) cc_final: 0.7671 (m-10)
REVERT: A  292 GLN cc_start: 0.7609 (tm-30) cc_final: 0.6959 (tp40)
REVERT: A  461 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6136 (mt0)
REVERT: A  467 ASP cc_start: 0.7031 (t0) cc_final: 0.6788 (t70)
REVERT: A  482 MET cc_start: 0.8343 (mtp) cc_final: 0.8136 (mtp)
REVERT: A  486 ASP cc_start: 0.7967 (m-30) cc_final: 0.7638 (t0)
REVERT: A  987 GLU cc_start: 0.6174 (pt0) cc_final: 0.5854 (tp30)
REVERT: A  994 LYS cc_start: 0.7840 (pttm) cc_final: 0.7438 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7554 (ptpt) cc_final: 0.7267 (pttt)
REVERT: A 1121 ASN cc_start: 0.7639 (t0) cc_final: 0.7191 (t0)
REVERT: A 1122 ARG cc_start: 0.7337 (mmm160) cc_final: 0.6400 (mtp180)
REVERT: A 1186 THR cc_start: 0.6104 (m) cc_final: 0.5877 (m)
REVERT: A 1246 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7312 (t0)
REVERT: A 1257 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7206 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7498 (mmmt)
REVERT: A 1347 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7073 (tppt)
  outliers start: 10
  outliers final: 6
  residues processed: 91
  average time/residue: 0.5938
  time to fit residues: 59.7064
Evaluate side-chains
  89 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  650 PHE
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0030
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A1294 GLN
A1323 GLN
A1406 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.233714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.189085 restraints weight = 13492.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 1.70
r_work: 0.4028 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3913 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090  13733  Z= 0.264
  Angle     :  0.721   8.197  19242  Z= 0.374
  Chirality :  0.046   0.519   2237
  Planarity :  0.006   0.120   1913
  Dihedral  : 23.284 179.625   3518
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.04 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 13.50 %
    Favored  : 82.79 %
  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 aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1225
  helix:  1.00 (0.22), residues: 570
  sheet:  0.52 (0.49), residues: 111
  loop : -0.98 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1211 
 TYR   0.013   0.002   TYR A 257 
 PHE   0.019   0.002   PHE A  66 
 TRP   0.016   0.002   TRP A 355 
 HIS   0.008   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (13733)
  covalent geometry    : angle       0.72096 (19242)
  hydrogen bonds       : bond        0.05686 (  582)
  hydrogen bonds       : angle       4.64324 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 86
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 LYS cc_start: 0.7713 (tmtm) cc_final: 0.7098 (mmtt)
REVERT: A  292 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7032 (tp40)
REVERT: A  381 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7366 (mtt-85)
REVERT: A  461 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6271 (tp-100)
REVERT: A  467 ASP cc_start: 0.7233 (t0) cc_final: 0.6986 (t70)
REVERT: A  482 MET cc_start: 0.8408 (mtp) cc_final: 0.8110 (mtm)
REVERT: A  483 GLU cc_start: 0.7941 (tt0) cc_final: 0.7264 (pt0)
REVERT: A  655 ARG cc_start: 0.7260 (ttt-90) cc_final: 0.5624 (ttp-110)
REVERT: A  987 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5668 (tp30)
REVERT: A  994 LYS cc_start: 0.8110 (pttm) cc_final: 0.7654 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7855 (ptpt) cc_final: 0.7351 (pttt)
REVERT: A 1121 ASN cc_start: 0.7738 (t0) cc_final: 0.7297 (t0)
REVERT: A 1177 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7538 (mttm)
REVERT: A 1186 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6145 (m)
REVERT: A 1195 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6731 (m-30)
REVERT: A 1246 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7370 (t0)
REVERT: A 1257 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7267 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7934 (ptpt) cc_final: 0.7514 (mmmt)
REVERT: A 1347 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7181 (tppt)
  outliers start: 41
  outliers final: 9
  residues processed: 120
  average time/residue: 0.6663
  time to fit residues: 87.5022
Evaluate side-chains
  97 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  883 LYS
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1177 LYS
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1195 ASP
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 131 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.8760

-------------------------------------------------------------------------------
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 = 0.4692 r_free = 0.4692 target = 0.237034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.193211 restraints weight = 13586.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 1.71
r_work: 0.4073 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  13733  Z= 0.165
  Angle     :  0.625   7.528  19242  Z= 0.326
  Chirality :  0.041   0.461   2237
  Planarity :  0.005   0.120   1913
  Dihedral  : 23.277 179.807   3514
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.31 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.04 %
    Favored  : 81.43 %
  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 aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1225
  helix:  1.24 (0.22), residues: 564
  sheet:  0.43 (0.49), residues: 111
  loop : -0.91 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1211 
 TYR   0.012   0.001   TYR A1194 
 PHE   0.017   0.001   PHE A 242 
 TRP   0.017   0.002   TRP A 355 
 HIS   0.004   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13733)
  covalent geometry    : angle       0.62483 (19242)
  hydrogen bonds       : bond        0.05056 (  582)
  hydrogen bonds       : angle       4.35824 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 89
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8200 (mmm) cc_final: 0.7840 (mmp)
REVERT: A  288 LYS cc_start: 0.7592 (tmtm) cc_final: 0.7035 (mmtt)
REVERT: A  292 GLN cc_start: 0.7789 (tm-30) cc_final: 0.6990 (tp40)
REVERT: A  381 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7893 (mtt-85)
REVERT: A  461 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6217 (tp-100)
REVERT: A  467 ASP cc_start: 0.7182 (t0) cc_final: 0.6911 (t70)
REVERT: A  482 MET cc_start: 0.8303 (mtp) cc_final: 0.8034 (mtm)
REVERT: A  655 ARG cc_start: 0.7130 (ttt-90) cc_final: 0.5641 (ttp-110)
REVERT: A  987 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5592 (tp30)
REVERT: A  994 LYS cc_start: 0.8035 (pttm) cc_final: 0.7555 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7313 (pttt)
REVERT: A 1121 ASN cc_start: 0.7758 (t0) cc_final: 0.7203 (t0)
REVERT: A 1122 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6419 (mtp180)
REVERT: A 1186 THR cc_start: 0.6404 (OUTLIER) cc_final: 0.6128 (m)
REVERT: A 1195 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6696 (m-30)
REVERT: A 1246 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7331 (t0)
REVERT: A 1257 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7276 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7932 (ptpt) cc_final: 0.7449 (tptm)
REVERT: A 1347 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7131 (tppt)
  outliers start: 39
  outliers final: 16
  residues processed: 119
  average time/residue: 0.6466
  time to fit residues: 84.6003
Evaluate side-chains
  101 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  650 PHE
Chi-restraints excluded: chain A residue  883 LYS
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1195 ASP
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 125 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 126 optimal weight:    7.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 408 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.230825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.186056 restraints weight = 13419.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.73
r_work: 0.3988 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3871 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086  13733  Z= 0.305
  Angle     :  0.749   8.275  19242  Z= 0.386
  Chirality :  0.048   0.524   2237
  Planarity :  0.006   0.120   1913
  Dihedral  : 23.432 179.999   3514
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.04 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 15.67 %
    Favored  : 79.71 %
  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 aren not related in a simple way.
  whole: -0.19 (0.24), residues: 1225
  helix:  0.83 (0.22), residues: 561
  sheet:  0.50 (0.49), residues: 107
  loop : -1.25 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 252 
 TYR   0.020   0.002   TYR A 257 
 PHE   0.021   0.002   PHE A  66 
 TRP   0.018   0.002   TRP A 355 
 HIS   0.008   0.002   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 (13733)
  covalent geometry    : angle       0.74943 (19242)
  hydrogen bonds       : bond        0.06011 (  582)
  hydrogen bonds       : angle       4.71587 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 81
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8328 (mmm) cc_final: 0.8089 (mmp)
REVERT: A  288 LYS cc_start: 0.7763 (tmtm) cc_final: 0.7181 (mtmm)
REVERT: A  292 GLN cc_start: 0.7854 (tm-30) cc_final: 0.6978 (tp40)
REVERT: A  457 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5662 (t0)
REVERT: A  461 GLN cc_start: 0.6765 (mm-40) cc_final: 0.6248 (tp-100)
REVERT: A  482 MET cc_start: 0.8383 (mtp) cc_final: 0.8125 (mtm)
REVERT: A  655 ARG cc_start: 0.7232 (ttt-90) cc_final: 0.5796 (ttp-110)
REVERT: A  984 MET cc_start: 0.4862 (mpp) cc_final: 0.4494 (mpp)
REVERT: A  987 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5696 (tp30)
REVERT: A  994 LYS cc_start: 0.8269 (pttm) cc_final: 0.7799 (ptmm)
REVERT: A 1010 MET cc_start: 0.8060 (mpt) cc_final: 0.7844 (mpt)
REVERT: A 1044 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7403 (pttt)
REVERT: A 1122 ARG cc_start: 0.7329 (mmm160) cc_final: 0.6446 (mtp180)
REVERT: A 1186 THR cc_start: 0.6415 (OUTLIER) cc_final: 0.6111 (m)
REVERT: A 1246 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7150 (t70)
REVERT: A 1257 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7401 (mtmt)
REVERT: A 1285 LYS cc_start: 0.8017 (ptpt) cc_final: 0.7529 (tptm)
REVERT: A 1347 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7113 (tppt)
  outliers start: 51
  outliers final: 19
  residues processed: 124
  average time/residue: 0.6245
  time to fit residues: 85.0962
Evaluate side-chains
  96 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  883 LYS
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 134 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0570
   chunk 133 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 299 ASN
A 607 ASN
A1121 ASN
A1144 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.236947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.193310 restraints weight = 13577.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 1.62
r_work: 0.4074 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  13733  Z= 0.151
  Angle     :  0.618   7.423  19242  Z= 0.323
  Chirality :  0.040   0.449   2237
  Planarity :  0.005   0.120   1913
  Dihedral  : 23.346 179.769   3514
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.31 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 16.30 %
    Favored  : 78.99 %
  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 aren not related in a simple way.
  whole:  0.18 (0.24), residues: 1225
  helix:  1.17 (0.22), residues: 564
  sheet:  0.74 (0.54), residues: 91
  loop : -1.07 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1211 
 TYR   0.016   0.001   TYR A1194 
 PHE   0.018   0.001   PHE A 242 
 TRP   0.014   0.002   TRP A 355 
 HIS   0.004   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (13733)
  covalent geometry    : angle       0.61808 (19242)
  hydrogen bonds       : bond        0.05031 (  582)
  hydrogen bonds       : angle       4.35085 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 90
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8273 (mmm) cc_final: 0.7964 (mmp)
REVERT: A  288 LYS cc_start: 0.7543 (tmtm) cc_final: 0.7054 (mtmm)
REVERT: A  292 GLN cc_start: 0.7784 (tm-30) cc_final: 0.6981 (tp40)
REVERT: A  384 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6985 (ttp-170)
REVERT: A  451 HIS cc_start: 0.3377 (OUTLIER) cc_final: 0.0332 (m-70)
REVERT: A  457 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5266 (t0)
REVERT: A  461 GLN cc_start: 0.6731 (mm-40) cc_final: 0.6152 (tp-100)
REVERT: A  482 MET cc_start: 0.8260 (mtp) cc_final: 0.8019 (mtm)
REVERT: A  491 MET cc_start: 0.7037 (ptm) cc_final: 0.6786 (ptm)
REVERT: A  655 ARG cc_start: 0.7133 (ttt-90) cc_final: 0.5656 (ttp-110)
REVERT: A  668 LEU cc_start: 0.7843 (mt) cc_final: 0.7266 (pp)
REVERT: A  900 ASN cc_start: 0.5062 (OUTLIER) cc_final: 0.4439 (p0)
REVERT: A  987 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5540 (tp30)
REVERT: A  994 LYS cc_start: 0.8092 (pttm) cc_final: 0.7615 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7877 (ptpt) cc_final: 0.7376 (pttt)
REVERT: A 1045 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7410 (t0)
REVERT: A 1121 ASN cc_start: 0.7712 (t0) cc_final: 0.7161 (t0)
REVERT: A 1122 ARG cc_start: 0.7277 (mmm160) cc_final: 0.6427 (mtp180)
REVERT: A 1186 THR cc_start: 0.6365 (m) cc_final: 0.5804 (m)
REVERT: A 1195 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6746 (m-30)
REVERT: A 1246 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (t70)
REVERT: A 1257 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7326 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7492 (tptm)
REVERT: A 1288 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.5450 (tm-30)
REVERT: A 1347 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7067 (tppt)
  outliers start: 52
  outliers final: 17
  residues processed: 133
  average time/residue: 0.5940
  time to fit residues: 87.0417
Evaluate side-chains
  108 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1176 ASP
Chi-restraints excluded: chain A residue 1195 ASP
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1253 VAL
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 90 optimal weight:    0.1980
   chunk 82 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.234401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.190883 restraints weight = 13433.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 1.60
r_work: 0.4048 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3934 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13733  Z= 0.199
  Angle     :  0.653   7.585  19242  Z= 0.338
  Chirality :  0.042   0.462   2237
  Planarity :  0.005   0.120   1913
  Dihedral  : 23.348 179.766   3514
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.88 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 17.48 %
    Favored  : 78.26 %
  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 aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1225
  helix:  1.16 (0.22), residues: 562
  sheet:  0.50 (0.49), residues: 107
  loop : -1.19 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1198 
 TYR   0.015   0.002   TYR A1194 
 PHE   0.019   0.002   PHE A 242 
 TRP   0.017   0.002   TRP A 355 
 HIS   0.006   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (13733)
  covalent geometry    : angle       0.65251 (19242)
  hydrogen bonds       : bond        0.05218 (  582)
  hydrogen bonds       : angle       4.39226 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 82
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8274 (mmm) cc_final: 0.7976 (mmp)
REVERT: A  288 LYS cc_start: 0.7557 (tmtm) cc_final: 0.7082 (mtmm)
REVERT: A  292 GLN cc_start: 0.7807 (tm-30) cc_final: 0.6977 (tp40)
REVERT: A  451 HIS cc_start: 0.3682 (OUTLIER) cc_final: 0.0579 (m-70)
REVERT: A  457 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.5372 (t0)
REVERT: A  461 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6110 (tp-100)
REVERT: A  482 MET cc_start: 0.8335 (mtp) cc_final: 0.8084 (mtm)
REVERT: A  655 ARG cc_start: 0.7092 (ttt-90) cc_final: 0.5628 (ttp-110)
REVERT: A  668 LEU cc_start: 0.7781 (mt) cc_final: 0.7221 (pp)
REVERT: A  961 ILE cc_start: 0.2280 (OUTLIER) cc_final: 0.1932 (mt)
REVERT: A  984 MET cc_start: 0.4658 (mpp) cc_final: 0.4282 (mpp)
REVERT: A  987 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5538 (tp30)
REVERT: A  994 LYS cc_start: 0.8118 (pttm) cc_final: 0.7645 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7376 (pttt)
REVERT: A 1045 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7440 (t0)
REVERT: A 1122 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6404 (mtp180)
REVERT: A 1186 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6093 (m)
REVERT: A 1246 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7259 (t70)
REVERT: A 1257 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7287 (mtmt)
REVERT: A 1285 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7535 (tptm)
REVERT: A 1288 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.5400 (tm-30)
REVERT: A 1347 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7090 (tppt)
  outliers start: 47
  outliers final: 21
  residues processed: 121
  average time/residue: 0.5772
  time to fit residues: 77.2835
Evaluate side-chains
  110 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  980 ILE
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Chi-restraints excluded: chain A residue 1377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 114 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A1121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.235417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.191832 restraints weight = 13421.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 1.58
r_work: 0.4065 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3951 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13733  Z= 0.181
  Angle     :  0.637   7.449  19242  Z= 0.331
  Chirality :  0.041   0.449   2237
  Planarity :  0.005   0.120   1913
  Dihedral  : 23.343 179.766   3514
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.22 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.48 %
    Favored  : 77.90 %
  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 aren not related in a simple way.
  whole:  0.18 (0.24), residues: 1225
  helix:  1.22 (0.22), residues: 563
  sheet:  0.67 (0.50), residues: 101
  loop : -1.14 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1198 
 TYR   0.017   0.002   TYR A1194 
 PHE   0.019   0.001   PHE A 242 
 TRP   0.017   0.002   TRP A 355 
 HIS   0.005   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (13733)
  covalent geometry    : angle       0.63685 (19242)
  hydrogen bonds       : bond        0.05057 (  582)
  hydrogen bonds       : angle       4.34660 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   11 MET cc_start: 0.7354 (mmm) cc_final: 0.6581 (mtp)
REVERT: A   50 MET cc_start: 0.8230 (mmm) cc_final: 0.7958 (mmp)
REVERT: A  288 LYS cc_start: 0.7519 (tmtm) cc_final: 0.7115 (mtmm)
REVERT: A  292 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7004 (tp40)
REVERT: A  451 HIS cc_start: 0.3578 (OUTLIER) cc_final: 0.0556 (m-70)
REVERT: A  457 ASP cc_start: 0.5574 (OUTLIER) cc_final: 0.5276 (t0)
REVERT: A  461 GLN cc_start: 0.6696 (mm-40) cc_final: 0.6112 (tp-100)
REVERT: A  482 MET cc_start: 0.8330 (mtp) cc_final: 0.8051 (mtm)
REVERT: A  491 MET cc_start: 0.7101 (ptm) cc_final: 0.6850 (ptm)
REVERT: A  655 ARG cc_start: 0.7054 (ttt-90) cc_final: 0.5634 (ttp-110)
REVERT: A  668 LEU cc_start: 0.7772 (mt) cc_final: 0.7236 (pp)
REVERT: A  984 MET cc_start: 0.4511 (mpp) cc_final: 0.4135 (mpp)
REVERT: A  987 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5495 (tp30)
REVERT: A  994 LYS cc_start: 0.8132 (pttm) cc_final: 0.7652 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7371 (pttt)
REVERT: A 1045 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.6988 (t0)
REVERT: A 1121 ASN cc_start: 0.7600 (t0) cc_final: 0.7168 (t0)
REVERT: A 1122 ARG cc_start: 0.7207 (mmm160) cc_final: 0.6354 (mtp180)
REVERT: A 1195 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6686 (m-30)
REVERT: A 1246 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7206 (t70)
REVERT: A 1257 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7276 (mtmt)
REVERT: A 1285 LYS cc_start: 0.8015 (ptpt) cc_final: 0.7543 (tptm)
REVERT: A 1288 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.5363 (tm-30)
REVERT: A 1347 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7084 (tppt)
  outliers start: 40
  outliers final: 23
  residues processed: 111
  average time/residue: 0.5889
  time to fit residues: 72.2738
Evaluate side-chains
  111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  980 ILE
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1195 ASP
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1253 VAL
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 680 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.231218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.186687 restraints weight = 13267.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 1.61
r_work: 0.4018 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  13733  Z= 0.278
  Angle     :  0.722   7.907  19242  Z= 0.372
  Chirality :  0.046   0.487   2237
  Planarity :  0.005   0.120   1913
  Dihedral  : 23.424 179.662   3514
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.20 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.12 %
    Favored  : 77.54 %
  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 aren not related in a simple way.
  whole: -0.13 (0.24), residues: 1225
  helix:  0.94 (0.22), residues: 561
  sheet:  0.45 (0.49), residues: 105
  loop : -1.28 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1198 
 TYR   0.021   0.002   TYR A 257 
 PHE   0.021   0.002   PHE A  66 
 TRP   0.019   0.002   TRP A 355 
 HIS   0.007   0.002   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 (13733)
  covalent geometry    : angle       0.72156 (19242)
  hydrogen bonds       : bond        0.05704 (  582)
  hydrogen bonds       : angle       4.60001 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 78
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 LYS cc_start: 0.7632 (tmtm) cc_final: 0.7195 (mtmm)
REVERT: A  292 GLN cc_start: 0.7813 (tm-30) cc_final: 0.6971 (tp-100)
REVERT: A  317 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7761 (mp0)
REVERT: A  451 HIS cc_start: 0.3760 (OUTLIER) cc_final: 0.0609 (m-70)
REVERT: A  457 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5676 (t0)
REVERT: A  461 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6082 (tp-100)
REVERT: A  482 MET cc_start: 0.8392 (mtp) cc_final: 0.8124 (mtm)
REVERT: A  655 ARG cc_start: 0.7068 (ttt-90) cc_final: 0.5649 (ttp-110)
REVERT: A  660 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7022 (mmm-85)
REVERT: A  961 ILE cc_start: 0.2233 (OUTLIER) cc_final: 0.1887 (mt)
REVERT: A  987 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5552 (tp30)
REVERT: A  994 LYS cc_start: 0.8247 (pttm) cc_final: 0.7629 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7425 (pttt)
REVERT: A 1045 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7369 (t0)
REVERT: A 1122 ARG cc_start: 0.7215 (mmm160) cc_final: 0.6357 (mtp180)
REVERT: A 1180 ASP cc_start: 0.6142 (t0) cc_final: 0.5892 (t0)
REVERT: A 1246 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7190 (t70)
REVERT: A 1257 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7374 (mtmt)
REVERT: A 1285 LYS cc_start: 0.8051 (ptpt) cc_final: 0.7537 (tptm)
REVERT: A 1288 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.5505 (tm-30)
REVERT: A 1308 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7558 (mtpp)
REVERT: A 1347 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7029 (tppt)
  outliers start: 48
  outliers final: 23
  residues processed: 118
  average time/residue: 0.6289
  time to fit residues: 81.4596
Evaluate side-chains
  109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  660 ARG
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  980 ILE
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1308 LYS
Chi-restraints excluded: chain A residue 1319 ILE
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A1121 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.235869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.192140 restraints weight = 13534.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.4272 rms_B_bonded: 1.62
r_work: 0.4068 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3955 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13733  Z= 0.161
  Angle     :  0.632   7.344  19242  Z= 0.329
  Chirality :  0.041   0.439   2237
  Planarity :  0.005   0.119   1913
  Dihedral  : 23.384 179.781   3514
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.47 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.47 %
    Favored  : 77.17 %
  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 aren not related in a simple way.
  whole:  0.15 (0.24), residues: 1225
  helix:  1.16 (0.22), residues: 566
  sheet:  0.63 (0.50), residues: 99
  loop : -1.12 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1211 
 TYR   0.018   0.002   TYR A1194 
 PHE   0.018   0.001   PHE A 242 
 TRP   0.019   0.002   TRP A 355 
 HIS   0.004   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (13733)
  covalent geometry    : angle       0.63169 (19242)
  hydrogen bonds       : bond        0.05029 (  582)
  hydrogen bonds       : angle       4.36218 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8245 (mmm) cc_final: 0.7925 (mmp)
REVERT: A  288 LYS cc_start: 0.7488 (tmtm) cc_final: 0.7098 (mtmm)
REVERT: A  292 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7008 (tp40)
REVERT: A  451 HIS cc_start: 0.3420 (OUTLIER) cc_final: 0.0408 (m-70)
REVERT: A  457 ASP cc_start: 0.5513 (OUTLIER) cc_final: 0.5128 (t0)
REVERT: A  461 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6080 (tp-100)
REVERT: A  482 MET cc_start: 0.8309 (mtp) cc_final: 0.8021 (mtm)
REVERT: A  491 MET cc_start: 0.7139 (ptm) cc_final: 0.6882 (ptm)
REVERT: A  655 ARG cc_start: 0.7040 (ttt-90) cc_final: 0.5604 (ttp-110)
REVERT: A  668 LEU cc_start: 0.7758 (mt) cc_final: 0.7236 (pp)
REVERT: A  890 ARG cc_start: 0.7081 (mpt-90) cc_final: 0.6840 (mpt-90)
REVERT: A  984 MET cc_start: 0.4733 (mpp) cc_final: 0.4475 (mpp)
REVERT: A  987 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5484 (tp30)
REVERT: A  994 LYS cc_start: 0.8114 (pttm) cc_final: 0.7611 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7893 (ptpt) cc_final: 0.7368 (pttt)
REVERT: A 1121 ASN cc_start: 0.7581 (t0) cc_final: 0.7170 (t0)
REVERT: A 1122 ARG cc_start: 0.7210 (mmm160) cc_final: 0.6310 (mtp180)
REVERT: A 1195 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6658 (m-30)
REVERT: A 1246 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7134 (t70)
REVERT: A 1257 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7304 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7920 (ptpt) cc_final: 0.7524 (tptm)
REVERT: A 1288 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.5408 (tm-30)
REVERT: A 1347 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7087 (tppt)
  outliers start: 37
  outliers final: 21
  residues processed: 110
  average time/residue: 0.6278
  time to fit residues: 75.9697
Evaluate side-chains
  107 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1195 ASP
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    0.0670
   chunk 111 optimal weight:    0.9980
   chunk 99 optimal weight:    0.3980
   chunk 69 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 98 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.239254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.196729 restraints weight = 13555.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4313 rms_B_bonded: 1.55
r_work: 0.4112 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3999 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  13733  Z= 0.137
  Angle     :  0.606   7.036  19242  Z= 0.317
  Chirality :  0.040   0.413   2237
  Planarity :  0.005   0.119   1913
  Dihedral  : 23.326 179.969   3514
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.88 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.75 %
    Favored  : 77.26 %
  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 aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1225
  helix:  1.35 (0.22), residues: 566
  sheet:  0.69 (0.51), residues: 99
  loop : -1.03 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1211 
 TYR   0.017   0.001   TYR A1194 
 PHE   0.019   0.001   PHE A1356 
 TRP   0.024   0.002   TRP A 355 
 HIS   0.003   0.001   HIS A1083 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (13733)
  covalent geometry    : angle       0.60639 (19242)
  hydrogen bonds       : bond        0.04693 (  582)
  hydrogen bonds       : angle       4.22234 ( 1556)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.7324 (mmm) cc_final: 0.6558 (mtp)
REVERT: A   50 MET cc_start: 0.8211 (mmm) cc_final: 0.7884 (mmp)
REVERT: A  288 LYS cc_start: 0.7475 (tmtm) cc_final: 0.7068 (mtmm)
REVERT: A  292 GLN cc_start: 0.7665 (tm-30) cc_final: 0.6919 (tp-100)
REVERT: A  451 HIS cc_start: 0.3177 (OUTLIER) cc_final: 0.0246 (m-70)
REVERT: A  461 GLN cc_start: 0.6600 (mm-40) cc_final: 0.6198 (tp-100)
REVERT: A  482 MET cc_start: 0.8293 (mtp) cc_final: 0.7996 (mtm)
REVERT: A  491 MET cc_start: 0.7186 (ptm) cc_final: 0.6896 (ptm)
REVERT: A  655 ARG cc_start: 0.6965 (ttt-90) cc_final: 0.5579 (ttp-110)
REVERT: A  984 MET cc_start: 0.4999 (mpp) cc_final: 0.4785 (mpp)
REVERT: A  987 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5453 (tp30)
REVERT: A  994 LYS cc_start: 0.8065 (pttm) cc_final: 0.7583 (ptmm)
REVERT: A 1044 LYS cc_start: 0.7816 (ptpt) cc_final: 0.7357 (pttt)
REVERT: A 1121 ASN cc_start: 0.7602 (t0) cc_final: 0.7116 (t0)
REVERT: A 1122 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6303 (mtp180)
REVERT: A 1180 ASP cc_start: 0.6053 (t0) cc_final: 0.5712 (t0)
REVERT: A 1257 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7253 (mtmt)
REVERT: A 1285 LYS cc_start: 0.7900 (ptpt) cc_final: 0.7466 (tptm)
REVERT: A 1288 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.5551 (tm-30)
REVERT: A 1347 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7069 (tppt)
  outliers start: 33
  outliers final: 21
  residues processed: 110
  average time/residue: 0.5774
  time to fit residues: 70.2480
Evaluate side-chains
  102 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  451 HIS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue 1045 ASP
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 THR
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1245 ASN
Chi-restraints excluded: chain A residue 1253 VAL
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1288 GLN
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1347 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 112 optimal weight:    0.0060
   chunk 7 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0770
   chunk 59 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.2354

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

Flipped N/Q/H residues before XYZ refinement:
A1144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.239435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.196988 restraints weight = 13498.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.4319 rms_B_bonded: 1.54
r_work: 0.4115 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.151  13733  Z= 0.195
  Angle     :  0.831  59.197  19242  Z= 0.478
  Chirality :  0.047   1.267   2237
  Planarity :  0.005   0.119   1913
  Dihedral  : 23.317 179.982   3508
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.04 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.29 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  0.38 (0.25), residues: 1225
  helix:  1.37 (0.22), residues: 566
  sheet:  0.70 (0.51), residues: 99
  loop : -1.02 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 381 
 TYR   0.013   0.001   TYR A1194 
 PHE   0.019   0.001   PHE A1356 
 TRP   0.024   0.002   TRP A 355 
 HIS   0.003   0.001   HIS A1083 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (13733)
  covalent geometry    : angle       0.83085 (19242)
  hydrogen bonds       : bond        0.04681 (  582)
  hydrogen bonds       : angle       4.22230 ( 1556)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5169.34 seconds
wall clock time: 89 minutes 12.55 seconds (5352.55 seconds total)