Starting phenix.real_space_refine
on Thu Sep 18 03:05:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ye6_39190/09_2025/8ye6_39190.map"
  }
  resolution = 2.95
  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=   0.135
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      92      5.49       5
     S      26      5.16       5
     C    8275      2.51       5
     N    2378      2.21       5
     O    2832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 13603
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 727
          Classifications: {'peptide': 88}
          Link IDs: {'TRANS': 87}
    Chain: "A"
      Number of atoms: 10903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1359, 10903
          Classifications: {'peptide': 1359}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 35, 'TRANS': 1323}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 220
          Unresolved non-hydrogen angles: 246
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "C"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1973
          Classifications: {'RNA': 92}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 14, 'rna3p': 77}
  Time building chain proxies: 3.39, per 1000 atoms: 0.25
  Number of scatterers: 13603
  At special positions: 0
  Unit cell: (91.5705, 118.503, 128.199, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      26     16.00
     P      92     15.00
     O    2832      8.00
     N    2378      7.00
     C    8275      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: 1.08
  Conformation dependent library (CDL) restraints added in 550.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2758

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 11 sheets defined
      52.7% alpha, 7.5% beta
      17 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 24 through 34
    Processing helix  chain 'B' and resid 46 through 68
      removed outlier: 3.923A  pdb=" N   LYS B  65 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLU B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 92
      removed outlier: 3.992A  pdb=" N   LYS B  92 " --> pdb=" O   LYS B  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 5.198A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 3.516A  pdb=" N   GLU A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 4.000A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.820A  pdb=" N   ASP A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.951A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 286 through 306
      removed outlier: 3.857A  pdb=" N   LYS A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.671A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      removed outlier: 3.749A  pdb=" N   PHE A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
      Proline residue:  A 378  - end of helix
      removed outlier: 3.523A  pdb=" N   LYS A 382 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 394
      removed outlier: 3.598A  pdb=" N   LEU A 390 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.615A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE A 410 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 410'
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.194A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.901A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 3.977A  pdb=" N   LEU A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 608
      removed outlier: 3.622A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.716A  pdb=" N   LEU A 616 " --> pdb=" O   ASN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 636
    Processing helix  chain 'A' and resid 637 through 638
      No H-bonds generated for 'chain 'A' and resid 637 through 638'
    Processing helix  chain 'A' and resid 639 through 643
    Processing helix  chain 'A' and resid 645 through 652
    Processing helix  chain 'A' and resid 664 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 693 through 698
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 727
      removed outlier: 3.682A  pdb=" N   LEU A 727 " --> pdb=" O   HIS A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 775 through 792
      removed outlier: 3.920A  pdb=" N   GLU A 779 " --> pdb=" O   LYS A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
      removed outlier: 3.984A  pdb=" N   GLU A 798 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 832 through 836
      removed outlier: 3.673A  pdb=" N   TYR A 836 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 4.131A  pdb=" N   ARG A 864 " --> pdb=" O   ASP A 861 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLY A 865 " --> pdb=" O   LYS A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 879
    Processing helix  chain 'A' and resid 879 through 889
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 909 through 922
      removed outlier: 3.944A  pdb=" N   VAL A 922 " --> pdb=" O   LYS A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 981 through 1001
      removed outlier: 3.582A  pdb=" N   ALA A 987 " --> pdb=" O   HIS A 983 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 995 " --> pdb=" O   ALA A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1087
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.586A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1184
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 3.600A  pdb=" N   LEU A1194 " --> pdb=" O   LYS A1191 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE A1195 " --> pdb=" O   LYS A1192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1191 through 1195'
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1261
    Processing helix  chain 'A' and resid 1264 through 1280
    Processing helix  chain 'A' and resid 1283 through 1296
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 4.091A  pdb=" N   GLU A1307 " --> pdb=" O   ARG A1303 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.568A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11
      removed outlier: 3.513A  pdb=" N   ILE A  21 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ILE A  48 " --> pdb=" O   ASN A1093 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   VAL A1095 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ALA A  50 " --> pdb=" O   VAL A1095 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 10.172A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509
      removed outlier: 5.260A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530
    Processing sheet with id=AA5, first strand: chain 'A' and resid 758 through 761
    Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1063 through 1065
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1157 through 1167
      removed outlier: 5.831A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1325

    507 hydrogen bonds defined for protein.
    1488 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      84 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2570
        1.32 -     1.45: 3897
        1.45 -     1.57: 7351
        1.57 -     1.70: 176
        1.70 -     1.83: 49
  Bond restraints: 14043
  Sorted by residual:
  bond pdb=" CB  GLN A  83 "
       pdb=" CG  GLN A  83 "
    ideal  model  delta    sigma   weight residual
    1.520  1.438  0.082 3.00e-02 1.11e+03 7.45e+00
  bond pdb=" CD  LYS A1124 "
       pdb=" CE  LYS A1124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.78e+00
  bond pdb=" CG  ARG A  74 "
       pdb=" CD  ARG A  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.76e+00
  bond pdb=" CZ  ARG A  78 "
       pdb=" NH2 ARG A  78 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.32e+00
  bond pdb=" CB  GLU A  84 "
       pdb=" CG  GLU A  84 "
    ideal  model  delta    sigma   weight residual
    1.520  1.445  0.075 3.00e-02 1.11e+03 6.24e+00
  ... (remaining 14038 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 19024
        3.28 -     6.56: 321
        6.56 -     9.84: 33
        9.84 -    13.13: 4
       13.13 -    16.41: 1
  Bond angle restraints: 19383
  Sorted by residual:
  angle pdb=" CA  LEU A 419 "
        pdb=" CB  LEU A 419 "
        pdb=" CG  LEU A 419 "
      ideal   model   delta    sigma   weight residual
     116.30  132.71  -16.41 3.50e+00 8.16e-02 2.20e+01
  angle pdb=" CA  GLU A 102 "
        pdb=" CB  GLU A 102 "
        pdb=" CG  GLU A 102 "
      ideal   model   delta    sigma   weight residual
     114.10  123.28   -9.18 2.00e+00 2.50e-01 2.11e+01
  angle pdb=" C3'   A C  28 "
        pdb=" O3'   A C  28 "
        pdb=" P     G C  29 "
      ideal   model   delta    sigma   weight residual
     120.20  126.98   -6.78 1.50e+00 4.44e-01 2.04e+01
  angle pdb=" CG  ARG A  70 "
        pdb=" CD  ARG A  70 "
        pdb=" NE  ARG A  70 "
      ideal   model   delta    sigma   weight residual
     112.00  121.86   -9.86 2.20e+00 2.07e-01 2.01e+01
  angle pdb=" C3'   A C   9 "
        pdb=" O3'   A C   9 "
        pdb=" P     A C  10 "
      ideal   model   delta    sigma   weight residual
     120.20  126.92   -6.72 1.50e+00 4.44e-01 2.01e+01
  ... (remaining 19378 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.40: 8317
       32.40 -    64.79: 276
       64.79 -    97.19: 27
       97.19 -   129.58: 3
      129.58 -   161.98: 4
  Dihedral angle restraints: 8627
    sinusoidal: 4368
      harmonic: 4259
  Sorted by residual:
  dihedral pdb=" O4'   U C  24 "
           pdb=" C1'   U C  24 "
           pdb=" N1    U C  24 "
           pdb=" C2    U C  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    1.98 -161.98     1      1.50e+01 4.44e-03 8.32e+01
  dihedral pdb=" O4'   U C  90 "
           pdb=" C1'   U C  90 "
           pdb=" N1    U C  90 "
           pdb=" C2    U C  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   18.37 -146.37     1      1.70e+01 3.46e-03 6.09e+01
  dihedral pdb=" CA  LEU A   9 "
           pdb=" C   LEU A   9 "
           pdb=" N   ASP A  10 "
           pdb=" CA  ASP A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 8624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1818
       0.073 -    0.146: 367
       0.146 -    0.218: 42
       0.218 -    0.291: 7
       0.291 -    0.364: 4
  Chirality restraints: 2238
  Sorted by residual:
  chirality pdb=" C3'   G C  92 "
            pdb=" C4'   G C  92 "
            pdb=" O3'   G C  92 "
            pdb=" C2'   G C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.11   -0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" C3'   A C  28 "
            pdb=" C4'   A C  28 "
            pdb=" O3'   A C  28 "
            pdb=" C2'   A C  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.39   -0.36 2.00e-01 2.50e+01 3.21e+00
  chirality pdb=" CG  LEU A 419 "
            pdb=" CB  LEU A 419 "
            pdb=" CD1 LEU A 419 "
            pdb=" CD2 LEU A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 2235 not shown)

  Planarity restraints: 2145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  86 "   -0.023 2.00e-02 2.50e+03   2.99e-02 1.56e+01
        pdb=" CG  PHE A  86 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  86 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  86 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  86 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  86 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  86 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  38 "    0.021 2.00e-02 2.50e+03   1.98e-02 7.87e+00
        pdb=" CG  TYR B  38 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  38 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  38 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  38 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  38 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  38 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 450 "    0.035 2.00e-02 2.50e+03   1.89e-02 7.16e+00
        pdb=" CG  TYR A 450 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 450 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 450 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 450 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 450 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 450 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 450 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2142 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3185
        2.79 -     3.32: 11560
        3.32 -     3.84: 22725
        3.84 -     4.37: 27802
        4.37 -     4.90: 44890
  Nonbonded interactions: 110162
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 101 "
            pdb=" O2'   A C  47 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OG1 THR A 560 "
            pdb=" O   ASP A 585 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OD1 ASP A1267 "
            pdb=" OH  TYR A1294 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OE2 GLU A 762 "
            pdb=" OG  SER A 960 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   GLN A 817 "
            pdb=" OH  TYR A 882 "
     model   vdw
     2.308 3.040
  ... (remaining 110157 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:             1.050
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.950
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
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      :  0.010   0.105  14043  Z= 0.441
  Angle     :  1.070  16.407  19383  Z= 0.556
  Chirality :  0.060   0.364   2238
  Planarity :  0.006   0.059   2145
  Dihedral  : 15.480 161.978   5869
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.36 %
    Favored  : 96.48 %
  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: -4.09 (0.17), residues: 1437
  helix: -3.06 (0.13), residues: 720
  sheet: -1.80 (0.38), residues: 133
  loop : -2.23 (0.21), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG A  71 
 TYR   0.049   0.005   TYR B  38 
 PHE   0.066   0.005   PHE A  86 
 TRP   0.027   0.005   TRP A 476 
 HIS   0.016   0.003   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.01024 (14043)
  covalent geometry    : angle       1.07046 (19383)
  hydrogen bonds       : bond        0.16111 (  549)
  hydrogen bonds       : angle       8.25927 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 295
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.8389 (mttt) cc_final: 0.7966 (mtmt)
REVERT: A  224 ASN cc_start: 0.6807 (m-40) cc_final: 0.6490 (m110)
REVERT: A  234 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7740 (tttm)
REVERT: A  255 ASN cc_start: 0.7166 (m110) cc_final: 0.6966 (m110)
REVERT: A  268 LYS cc_start: 0.7770 (tppp) cc_final: 0.7256 (tttt)
REVERT: A  350 ILE cc_start: 0.8228 (mt) cc_final: 0.7970 (mm)
REVERT: A  395 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7270 (ttp80)
REVERT: A  406 ASP cc_start: 0.7592 (m-30) cc_final: 0.6975 (t0)
REVERT: A  428 ASP cc_start: 0.7713 (m-30) cc_final: 0.7452 (t0)
REVERT: A  556 ASN cc_start: 0.7374 (m-40) cc_final: 0.7153 (t0)
REVERT: A  596 ASP cc_start: 0.7926 (m-30) cc_final: 0.7668 (m-30)
REVERT: A  661 ARG cc_start: 0.7355 (ptp90) cc_final: 0.7124 (ptp-170)
REVERT: A  694 MET cc_start: 0.7894 (mmm) cc_final: 0.6960 (mmt)
REVERT: A  703 THR cc_start: 0.8828 (m) cc_final: 0.8555 (p)
REVERT: A 1003 LYS cc_start: 0.8090 (mttt) cc_final: 0.7833 (mtmm)
REVERT: A 1039 TYR cc_start: 0.8211 (m-80) cc_final: 0.7939 (m-80)
REVERT: A 1059 LYS cc_start: 0.7710 (mttp) cc_final: 0.7271 (mttm)
REVERT: A 1286 ASN cc_start: 0.7616 (m-40) cc_final: 0.7355 (m-40)
REVERT: A 1300 LYS cc_start: 0.6638 (mmmm) cc_final: 0.6407 (mtpt)
REVERT: A 1364 GLN cc_start: 0.7748 (mt0) cc_final: 0.7307 (tm130)
  outliers start: 2
  outliers final: 0
  residues processed: 296
  average time/residue: 0.7282
  time to fit residues: 231.7733
Evaluate side-chains
  181 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  14 HIS
A 194 GLN
A 277 ASN
A 501 ASN
A 522 ASN
A 844 GLN
A 920 GLN
A 971 GLN
A1241 HIS
A1262 HIS
A1297 HIS
A1311 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.196981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.152926 restraints weight = 14568.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.20
r_work: 0.3155 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14043  Z= 0.135
  Angle     :  0.578  10.688  19383  Z= 0.309
  Chirality :  0.041   0.231   2238
  Planarity :  0.004   0.039   2145
  Dihedral  : 17.924 155.495   2968
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.23 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.02 (0.19), residues: 1437
  helix: -0.98 (0.17), residues: 731
  sheet: -1.09 (0.41), residues: 124
  loop : -1.72 (0.22), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 655 
 TYR   0.019   0.001   TYR A 450 
 PHE   0.016   0.002   PHE A  86 
 TRP   0.007   0.001   TRP A1074 
 HIS   0.006   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (14043)
  covalent geometry    : angle       0.57788 (19383)
  hydrogen bonds       : bond        0.04742 (  549)
  hydrogen bonds       : angle       4.94495 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8004 (mp10)
REVERT: A    4 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8410 (mmpt)
REVERT: A   26 LYS cc_start: 0.8633 (mttt) cc_final: 0.8358 (mtmt)
REVERT: A  211 ILE cc_start: 0.8904 (mt) cc_final: 0.8693 (mp)
REVERT: A  224 ASN cc_start: 0.6856 (m-40) cc_final: 0.6486 (m110)
REVERT: A  234 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7847 (tttt)
REVERT: A  255 ASN cc_start: 0.7223 (m110) cc_final: 0.7010 (m110)
REVERT: A  268 LYS cc_start: 0.7797 (tppp) cc_final: 0.7450 (ttmm)
REVERT: A  364 ASP cc_start: 0.7548 (m-30) cc_final: 0.7314 (m-30)
REVERT: A  395 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7190 (ttp80)
REVERT: A  406 ASP cc_start: 0.8146 (m-30) cc_final: 0.7534 (t0)
REVERT: A  428 ASP cc_start: 0.8168 (m-30) cc_final: 0.7716 (t0)
REVERT: A  502 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8441 (tt)
REVERT: A  556 ASN cc_start: 0.7758 (m-40) cc_final: 0.7386 (t0)
REVERT: A  596 ASP cc_start: 0.8022 (m-30) cc_final: 0.7785 (m-30)
REVERT: A  599 LYS cc_start: 0.7649 (ttmp) cc_final: 0.6612 (ttpp)
REVERT: A  613 GLU cc_start: 0.7952 (tp30) cc_final: 0.7688 (tp30)
REVERT: A  661 ARG cc_start: 0.8012 (ptp90) cc_final: 0.7767 (ptp-170)
REVERT: A  694 MET cc_start: 0.8227 (mmm) cc_final: 0.7870 (mmp)
REVERT: A  952 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7226 (pt0)
REVERT: A  961 LYS cc_start: 0.7347 (mmtt) cc_final: 0.7048 (mmtt)
REVERT: A 1018 VAL cc_start: 0.7679 (t) cc_final: 0.7375 (t)
REVERT: A 1039 TYR cc_start: 0.8173 (m-80) cc_final: 0.7790 (m-80)
REVERT: A 1286 ASN cc_start: 0.7872 (m-40) cc_final: 0.7529 (m-40)
REVERT: A 1307 GLU cc_start: 0.7032 (tp30) cc_final: 0.6821 (tp30)
REVERT: A 1364 GLN cc_start: 0.8043 (mt0) cc_final: 0.7332 (tm130)
  outliers start: 36
  outliers final: 7
  residues processed: 209
  average time/residue: 0.5808
  time to fit residues: 132.2802
Evaluate side-chains
  167 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  952 GLU
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  14 HIS
A  88 ASN
A 277 ASN
A 511 HIS
A 844 GLN
** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1286 ASN
A1311 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.148399 restraints weight = 14647.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.11
r_work: 0.3100 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  14043  Z= 0.211
  Angle     :  0.613  11.729  19383  Z= 0.322
  Chirality :  0.043   0.232   2238
  Planarity :  0.004   0.040   2145
  Dihedral  : 17.783 157.365   2968
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 12.23 %
    Favored  : 84.49 %
  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: -1.29 (0.21), residues: 1437
  helix: -0.24 (0.19), residues: 736
  sheet: -1.09 (0.41), residues: 126
  loop : -1.50 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 139 
 TYR   0.026   0.002   TYR A 450 
 PHE   0.019   0.002   PHE A1327 
 TRP   0.007   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (14043)
  covalent geometry    : angle       0.61286 (19383)
  hydrogen bonds       : bond        0.05307 (  549)
  hydrogen bonds       : angle       4.68942 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8035 (mp10)
REVERT: B   84 ASN cc_start: 0.8019 (m-40) cc_final: 0.7768 (m-40)
REVERT: A    1 MET cc_start: 0.1637 (tpp) cc_final: 0.1125 (ttt)
REVERT: A   26 LYS cc_start: 0.8665 (mttt) cc_final: 0.8401 (mtmt)
REVERT: A  211 ILE cc_start: 0.8807 (mt) cc_final: 0.8568 (mp)
REVERT: A  224 ASN cc_start: 0.6773 (m-40) cc_final: 0.6413 (m110)
REVERT: A  234 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7796 (tttt)
REVERT: A  235 ASN cc_start: 0.7975 (t0) cc_final: 0.7486 (t0)
REVERT: A  255 ASN cc_start: 0.7152 (m110) cc_final: 0.6934 (m110)
REVERT: A  268 LYS cc_start: 0.7806 (tppp) cc_final: 0.7507 (ttmm)
REVERT: A  349 GLU cc_start: 0.8238 (tp30) cc_final: 0.7574 (tp30)
REVERT: A  397 ASP cc_start: 0.7045 (t70) cc_final: 0.6436 (t0)
REVERT: A  406 ASP cc_start: 0.8202 (m-30) cc_final: 0.7634 (t0)
REVERT: A  428 ASP cc_start: 0.8200 (m-30) cc_final: 0.7694 (t0)
REVERT: A  556 ASN cc_start: 0.7694 (m-40) cc_final: 0.7347 (t0)
REVERT: A  596 ASP cc_start: 0.7977 (m-30) cc_final: 0.7611 (m-30)
REVERT: A  613 GLU cc_start: 0.7867 (tp30) cc_final: 0.7491 (tp30)
REVERT: A  661 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7778 (ptp-170)
REVERT: A  694 MET cc_start: 0.8243 (mmm) cc_final: 0.7882 (mmp)
REVERT: A  703 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8497 (p)
REVERT: A  961 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6762 (mmtt)
REVERT: A 1039 TYR cc_start: 0.8157 (m-80) cc_final: 0.7747 (m-80)
REVERT: A 1296 LYS cc_start: 0.7454 (mtmt) cc_final: 0.7121 (mtmt)
REVERT: A 1307 GLU cc_start: 0.7097 (tp30) cc_final: 0.6831 (tp30)
REVERT: A 1333 ARG cc_start: 0.7565 (mtm110) cc_final: 0.6914 (ppp80)
REVERT: A 1344 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7451 (p0)
REVERT: A 1364 GLN cc_start: 0.7888 (mt0) cc_final: 0.7359 (tm130)
  outliers start: 41
  outliers final: 12
  residues processed: 194
  average time/residue: 0.6398
  time to fit residues: 134.8677
Evaluate side-chains
  166 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 ASN
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1344 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 55 optimal weight:    0.6980
   chunk 98 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 698 HIS
A 844 GLN
A 971 GLN
A 985 HIS
A1252 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.199060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.157812 restraints weight = 14566.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.04
r_work: 0.3185 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14043  Z= 0.105
  Angle     :  0.504   8.620  19383  Z= 0.268
  Chirality :  0.039   0.226   2238
  Planarity :  0.003   0.039   2145
  Dihedral  : 17.456 153.610   2968
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.51 %
    Favored  : 83.29 %
  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: -0.56 (0.21), residues: 1437
  helix:  0.40 (0.19), residues: 742
  sheet: -0.68 (0.43), residues: 124
  loop : -1.26 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 653 
 TYR   0.012   0.001   TYR A 450 
 PHE   0.012   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (14043)
  covalent geometry    : angle       0.50358 (19383)
  hydrogen bonds       : bond        0.03670 (  549)
  hydrogen bonds       : angle       4.21882 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7981 (m-40) cc_final: 0.7729 (m-40)
REVERT: A    1 MET cc_start: 0.1817 (tpp) cc_final: 0.1579 (ttt)
REVERT: A    4 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8433 (mptt)
REVERT: A   26 LYS cc_start: 0.8650 (mttt) cc_final: 0.8358 (mtmt)
REVERT: A   70 ARG cc_start: 0.8657 (ptp-170) cc_final: 0.8293 (mtm180)
REVERT: A  202 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8100 (t0)
REVERT: A  224 ASN cc_start: 0.6823 (m-40) cc_final: 0.6474 (m110)
REVERT: A  234 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7824 (tttt)
REVERT: A  235 ASN cc_start: 0.7809 (t0) cc_final: 0.7357 (t0)
REVERT: A  255 ASN cc_start: 0.7263 (m110) cc_final: 0.7014 (m110)
REVERT: A  364 ASP cc_start: 0.7518 (m-30) cc_final: 0.7213 (m-30)
REVERT: A  397 ASP cc_start: 0.7131 (t70) cc_final: 0.6573 (t0)
REVERT: A  406 ASP cc_start: 0.8061 (m-30) cc_final: 0.7523 (t0)
REVERT: A  419 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8512 (tp)
REVERT: A  428 ASP cc_start: 0.8132 (m-30) cc_final: 0.7714 (t0)
REVERT: A  556 ASN cc_start: 0.7694 (m-40) cc_final: 0.7278 (t0)
REVERT: A  596 ASP cc_start: 0.7888 (m-30) cc_final: 0.7616 (m-30)
REVERT: A  613 GLU cc_start: 0.7973 (tp30) cc_final: 0.7645 (tp30)
REVERT: A  661 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7853 (ptp-170)
REVERT: A  694 MET cc_start: 0.8163 (mmm) cc_final: 0.7653 (mmp)
REVERT: A  703 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8388 (p)
REVERT: A  757 GLU cc_start: 0.8095 (tp30) cc_final: 0.7880 (mm-30)
REVERT: A  844 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7203 (mm-40)
REVERT: A  856 VAL cc_start: 0.6847 (m) cc_final: 0.6593 (p)
REVERT: A  857 LEU cc_start: 0.8408 (tt) cc_final: 0.7396 (mt)
REVERT: A  961 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6883 (mmtt)
REVERT: A 1015 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7661 (t)
REVERT: A 1039 TYR cc_start: 0.8121 (m-80) cc_final: 0.7638 (m-80)
REVERT: A 1043 MET cc_start: 0.8329 (mmt) cc_final: 0.8015 (mmp)
REVERT: A 1146 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8258 (p)
REVERT: A 1169 MET cc_start: 0.8725 (ttp) cc_final: 0.8400 (ttm)
REVERT: A 1194 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: A 1297 HIS cc_start: 0.7146 (m170) cc_final: 0.6848 (m170)
REVERT: A 1333 ARG cc_start: 0.7587 (mtm110) cc_final: 0.6989 (ppp80)
REVERT: A 1364 GLN cc_start: 0.8009 (mt0) cc_final: 0.7620 (tm-30)
  outliers start: 40
  outliers final: 12
  residues processed: 192
  average time/residue: 0.6352
  time to fit residues: 133.4861
Evaluate side-chains
  164 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 ASN
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  844 GLN
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1191 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 131 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 88 optimal weight:    9.9990
   chunk 138 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 357 ASN
A 698 HIS
A1224 ASN
A1256 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.188968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.155167 restraints weight = 14531.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.61
r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.070  14043  Z= 0.366
  Angle     :  0.756  13.419  19383  Z= 0.389
  Chirality :  0.049   0.229   2238
  Planarity :  0.006   0.091   2145
  Dihedral  : 17.655 159.615   2968
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 13.91 %
    Favored  : 81.85 %
  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: -0.98 (0.21), residues: 1437
  helix:  0.01 (0.19), residues: 735
  sheet: -0.72 (0.45), residues: 119
  loop : -1.40 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 653 
 TYR   0.031   0.003   TYR A 450 
 PHE   0.028   0.003   PHE A1327 
 TRP   0.010   0.003   TRP A  18 
 HIS   0.012   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00855 (14043)
  covalent geometry    : angle       0.75557 (19383)
  hydrogen bonds       : bond        0.06572 (  549)
  hydrogen bonds       : angle       4.75987 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 156
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7541 (mt0)
REVERT: B   31 SER cc_start: 0.8145 (t) cc_final: 0.7779 (t)
REVERT: B   84 ASN cc_start: 0.7988 (m-40) cc_final: 0.7737 (m-40)
REVERT: A    4 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8248 (mptt)
REVERT: A   26 LYS cc_start: 0.8711 (mttt) cc_final: 0.8414 (mtmt)
REVERT: A  224 ASN cc_start: 0.6901 (m-40) cc_final: 0.6589 (m110)
REVERT: A  234 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7847 (tttt)
REVERT: A  235 ASN cc_start: 0.8078 (t0) cc_final: 0.7568 (t0)
REVERT: A  255 ASN cc_start: 0.7195 (m110) cc_final: 0.6993 (m110)
REVERT: A  294 LYS cc_start: 0.7608 (tttm) cc_final: 0.7336 (ttpp)
REVERT: A  307 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6962 (mtt180)
REVERT: A  397 ASP cc_start: 0.7217 (t70) cc_final: 0.6763 (t0)
REVERT: A  406 ASP cc_start: 0.8383 (m-30) cc_final: 0.7764 (t0)
REVERT: A  428 ASP cc_start: 0.8232 (m-30) cc_final: 0.7749 (t70)
REVERT: A  470 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: A  556 ASN cc_start: 0.7798 (m-40) cc_final: 0.7331 (t0)
REVERT: A  613 GLU cc_start: 0.7843 (tp30) cc_final: 0.7519 (tp30)
REVERT: A  661 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7779 (ptp-170)
REVERT: A  694 MET cc_start: 0.8342 (mmm) cc_final: 0.8014 (mmp)
REVERT: A  703 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8526 (p)
REVERT: A  757 GLU cc_start: 0.8260 (tp30) cc_final: 0.7938 (tp30)
REVERT: A  844 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6987 (mm-40)
REVERT: A  919 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7535 (mtp180)
REVERT: A  929 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8107 (ttpp)
REVERT: A  961 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6856 (mmtt)
REVERT: A 1015 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7890 (t)
REVERT: A 1039 TYR cc_start: 0.8209 (m-80) cc_final: 0.7703 (m-80)
REVERT: A 1296 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7354 (mtmt)
REVERT: A 1333 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7042 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7967 (mt0) cc_final: 0.7488 (tm-30)
  outliers start: 53
  outliers final: 20
  residues processed: 192
  average time/residue: 0.6945
  time to fit residues: 145.0359
Evaluate side-chains
  180 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  929 LYS
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1224 ASN
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1291 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0670
   chunk 151 optimal weight:    6.9990
   chunk 0 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 698 HIS
A 844 GLN
A1224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.196723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.151497 restraints weight = 14562.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.20
r_work: 0.3182 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14043  Z= 0.108
  Angle     :  0.523   9.178  19383  Z= 0.277
  Chirality :  0.039   0.227   2238
  Planarity :  0.003   0.050   2145
  Dihedral  : 17.286 153.549   2968
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.39 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.22), residues: 1437
  helix:  0.64 (0.20), residues: 740
  sheet: -0.64 (0.45), residues: 126
  loop : -1.13 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 653 
 TYR   0.012   0.001   TYR A 450 
 PHE   0.015   0.001   PHE A1258 
 TRP   0.008   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (14043)
  covalent geometry    : angle       0.52340 (19383)
  hydrogen bonds       : bond        0.03784 (  549)
  hydrogen bonds       : angle       4.23548 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7956 (m-40) cc_final: 0.7689 (m-40)
REVERT: A    4 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8298 (mptt)
REVERT: A   26 LYS cc_start: 0.8586 (mttt) cc_final: 0.8365 (mtmt)
REVERT: A   89 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7380 (mm-30)
REVERT: A   99 HIS cc_start: 0.7379 (m-70) cc_final: 0.7038 (m-70)
REVERT: A  224 ASN cc_start: 0.6820 (m-40) cc_final: 0.6495 (m110)
REVERT: A  234 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7912 (tttt)
REVERT: A  235 ASN cc_start: 0.7987 (t0) cc_final: 0.7507 (t0)
REVERT: A  364 ASP cc_start: 0.7505 (m-30) cc_final: 0.7219 (m-30)
REVERT: A  397 ASP cc_start: 0.6943 (t70) cc_final: 0.6504 (t0)
REVERT: A  406 ASP cc_start: 0.8102 (m-30) cc_final: 0.7648 (t0)
REVERT: A  419 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (tp)
REVERT: A  428 ASP cc_start: 0.8080 (m-30) cc_final: 0.7687 (t0)
REVERT: A  534 MET cc_start: 0.4870 (pp-130) cc_final: 0.4361 (ppp)
REVERT: A  556 ASN cc_start: 0.7722 (m-40) cc_final: 0.7311 (t0)
REVERT: A  596 ASP cc_start: 0.7798 (m-30) cc_final: 0.7507 (m-30)
REVERT: A  613 GLU cc_start: 0.7807 (tp30) cc_final: 0.7526 (tp30)
REVERT: A  694 MET cc_start: 0.8162 (mmm) cc_final: 0.7698 (mmp)
REVERT: A  703 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8483 (p)
REVERT: A  757 GLU cc_start: 0.8095 (tp30) cc_final: 0.7838 (tp30)
REVERT: A  844 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6975 (mm-40)
REVERT: A  961 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6706 (mmtt)
REVERT: A 1015 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7621 (t)
REVERT: A 1039 TYR cc_start: 0.8182 (m-80) cc_final: 0.7686 (m-80)
REVERT: A 1043 MET cc_start: 0.8360 (mmt) cc_final: 0.8080 (mmp)
REVERT: A 1063 ILE cc_start: 0.8577 (mt) cc_final: 0.8199 (tt)
REVERT: A 1169 MET cc_start: 0.8737 (ttp) cc_final: 0.8470 (ttm)
REVERT: A 1297 HIS cc_start: 0.7084 (m170) cc_final: 0.6783 (m170)
REVERT: A 1333 ARG cc_start: 0.7560 (mtm110) cc_final: 0.6908 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7943 (mt0) cc_final: 0.7544 (tm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 175
  average time/residue: 0.6658
  time to fit residues: 127.0694
Evaluate side-chains
  161 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  844 GLN
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1224 ASN
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 114 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 146 optimal weight:    6.9990
   chunk 94 optimal weight:   20.0000
   chunk 141 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 240 ASN
A 277 ASN
A 844 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.162221 restraints weight = 14409.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.38
r_work: 0.3176 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14043  Z= 0.157
  Angle     :  0.552  10.432  19383  Z= 0.291
  Chirality :  0.041   0.262   2238
  Planarity :  0.004   0.059   2145
  Dihedral  : 17.238 155.932   2968
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.31 %
    Favored  : 80.98 %
  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 (0.22), residues: 1437
  helix:  0.76 (0.20), residues: 734
  sheet: -0.53 (0.46), residues: 124
  loop : -1.03 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 653 
 TYR   0.019   0.001   TYR A 450 
 PHE   0.015   0.002   PHE A1327 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (14043)
  covalent geometry    : angle       0.55224 (19383)
  hydrogen bonds       : bond        0.04413 (  549)
  hydrogen bonds       : angle       4.25478 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7931 (m-40) cc_final: 0.7663 (m-40)
REVERT: A    4 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8275 (mptt)
REVERT: A   26 LYS cc_start: 0.8575 (mttt) cc_final: 0.8320 (mtmt)
REVERT: A   99 HIS cc_start: 0.7406 (m-70) cc_final: 0.6987 (m-70)
REVERT: A  224 ASN cc_start: 0.6832 (m-40) cc_final: 0.6512 (m110)
REVERT: A  234 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7922 (tttt)
REVERT: A  235 ASN cc_start: 0.7951 (t0) cc_final: 0.7472 (t0)
REVERT: A  338 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7305 (tp)
REVERT: A  397 ASP cc_start: 0.6929 (t70) cc_final: 0.6507 (t0)
REVERT: A  406 ASP cc_start: 0.8045 (m-30) cc_final: 0.7582 (t0)
REVERT: A  428 ASP cc_start: 0.7992 (m-30) cc_final: 0.7739 (t0)
REVERT: A  556 ASN cc_start: 0.7681 (m-40) cc_final: 0.7315 (t0)
REVERT: A  596 ASP cc_start: 0.7804 (m-30) cc_final: 0.7529 (m-30)
REVERT: A  613 GLU cc_start: 0.7718 (tp30) cc_final: 0.7369 (tp30)
REVERT: A  694 MET cc_start: 0.8115 (mmm) cc_final: 0.7647 (mmp)
REVERT: A  703 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8526 (p)
REVERT: A  757 GLU cc_start: 0.8030 (tp30) cc_final: 0.7778 (tp30)
REVERT: A  844 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7066 (mm-40)
REVERT: A  921 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6464 (mm)
REVERT: A  929 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7823 (ttpp)
REVERT: A  961 LYS cc_start: 0.7274 (mmtt) cc_final: 0.6737 (mmtt)
REVERT: A 1015 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7682 (t)
REVERT: A 1039 TYR cc_start: 0.8199 (m-80) cc_final: 0.7658 (m-80)
REVERT: A 1043 MET cc_start: 0.8385 (mmt) cc_final: 0.8101 (mmp)
REVERT: A 1063 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8143 (tt)
REVERT: A 1252 ASN cc_start: 0.7302 (t0) cc_final: 0.6883 (t0)
REVERT: A 1297 HIS cc_start: 0.7134 (m170) cc_final: 0.6923 (m170)
REVERT: A 1333 ARG cc_start: 0.7563 (mtm110) cc_final: 0.6927 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7931 (mt0) cc_final: 0.7563 (tm-30)
  outliers start: 34
  outliers final: 17
  residues processed: 171
  average time/residue: 0.6551
  time to fit residues: 122.1554
Evaluate side-chains
  168 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  844 GLN
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  929 LYS
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0010
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A1224 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.197377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.157090 restraints weight = 14408.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.94
r_work: 0.3204 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14043  Z= 0.107
  Angle     :  0.514  10.470  19383  Z= 0.273
  Chirality :  0.039   0.283   2238
  Planarity :  0.003   0.057   2145
  Dihedral  : 17.166 153.244   2968
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.11 %
    Favored  : 80.74 %
  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 (0.22), residues: 1437
  helix:  1.04 (0.20), residues: 734
  sheet: -0.32 (0.48), residues: 117
  loop : -0.98 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 653 
 TYR   0.014   0.001   TYR A 450 
 PHE   0.014   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (14043)
  covalent geometry    : angle       0.51442 (19383)
  hydrogen bonds       : bond        0.03634 (  549)
  hydrogen bonds       : angle       4.09380 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7999 (m-40) cc_final: 0.7726 (m-40)
REVERT: A   26 LYS cc_start: 0.8667 (mttt) cc_final: 0.8363 (mtmt)
REVERT: A   99 HIS cc_start: 0.7069 (m-70) cc_final: 0.6606 (m-70)
REVERT: A  224 ASN cc_start: 0.6811 (m-40) cc_final: 0.6492 (m110)
REVERT: A  234 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7881 (tttt)
REVERT: A  235 ASN cc_start: 0.7905 (t0) cc_final: 0.7459 (t0)
REVERT: A  338 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7275 (tp)
REVERT: A  364 ASP cc_start: 0.7416 (m-30) cc_final: 0.7063 (m-30)
REVERT: A  374 LYS cc_start: 0.6967 (mppt) cc_final: 0.6602 (pttt)
REVERT: A  397 ASP cc_start: 0.7039 (t70) cc_final: 0.6567 (t0)
REVERT: A  406 ASP cc_start: 0.8042 (m-30) cc_final: 0.7572 (t0)
REVERT: A  419 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (tp)
REVERT: A  428 ASP cc_start: 0.8033 (m-30) cc_final: 0.7779 (t0)
REVERT: A  534 MET cc_start: 0.5078 (pp-130) cc_final: 0.4791 (ppp)
REVERT: A  556 ASN cc_start: 0.7822 (m-40) cc_final: 0.7436 (t0)
REVERT: A  596 ASP cc_start: 0.7798 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  694 MET cc_start: 0.8092 (mmm) cc_final: 0.7548 (mmp)
REVERT: A  703 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8509 (p)
REVERT: A  921 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6633 (mm)
REVERT: A  961 LYS cc_start: 0.7263 (mmtt) cc_final: 0.6751 (mmtt)
REVERT: A 1039 TYR cc_start: 0.8182 (m-80) cc_final: 0.7622 (m-80)
REVERT: A 1043 MET cc_start: 0.8377 (mmt) cc_final: 0.8070 (mmp)
REVERT: A 1063 ILE cc_start: 0.8524 (mt) cc_final: 0.8143 (tt)
REVERT: A 1169 MET cc_start: 0.8728 (ttp) cc_final: 0.8476 (ttm)
REVERT: A 1252 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (t0)
REVERT: A 1297 HIS cc_start: 0.6971 (m170) cc_final: 0.6635 (m170)
REVERT: A 1333 ARG cc_start: 0.7469 (mtm110) cc_final: 0.6923 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7897 (mt0) cc_final: 0.7576 (tm-30)
  outliers start: 27
  outliers final: 14
  residues processed: 171
  average time/residue: 0.6068
  time to fit residues: 113.9616
Evaluate side-chains
  166 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1224 ASN
Chi-restraints excluded: chain A residue 1252 ASN
Chi-restraints excluded: chain A residue 1284 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 126 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 817 GLN
A 844 GLN
A1224 ASN
A1256 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.196551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.164487 restraints weight = 14503.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.31
r_work: 0.3206 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14043  Z= 0.120
  Angle     :  0.528  10.257  19383  Z= 0.279
  Chirality :  0.040   0.291   2238
  Planarity :  0.004   0.064   2145
  Dihedral  : 17.143 153.596   2968
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.51 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.26 (0.22), residues: 1437
  helix:  1.14 (0.20), residues: 734
  sheet: -0.65 (0.44), residues: 130
  loop : -0.84 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 653 
 TYR   0.015   0.001   TYR A 450 
 PHE   0.014   0.001   PHE A 539 
 TRP   0.008   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (14043)
  covalent geometry    : angle       0.52847 (19383)
  hydrogen bonds       : bond        0.03826 (  549)
  hydrogen bonds       : angle       4.08462 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7995 (m-40) cc_final: 0.7722 (m-40)
REVERT: A   26 LYS cc_start: 0.8634 (mttt) cc_final: 0.8316 (mtmt)
REVERT: A   99 HIS cc_start: 0.7023 (m-70) cc_final: 0.6551 (m-70)
REVERT: A  224 ASN cc_start: 0.6781 (m-40) cc_final: 0.6461 (m110)
REVERT: A  234 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7861 (tttt)
REVERT: A  235 ASN cc_start: 0.7880 (t0) cc_final: 0.7417 (t0)
REVERT: A  338 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7212 (tp)
REVERT: A  364 ASP cc_start: 0.7347 (m-30) cc_final: 0.6968 (m-30)
REVERT: A  374 LYS cc_start: 0.6964 (mppt) cc_final: 0.6586 (pttt)
REVERT: A  397 ASP cc_start: 0.6919 (t70) cc_final: 0.6478 (t0)
REVERT: A  406 ASP cc_start: 0.8027 (m-30) cc_final: 0.7577 (t0)
REVERT: A  419 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8486 (tp)
REVERT: A  428 ASP cc_start: 0.8101 (m-30) cc_final: 0.7801 (t0)
REVERT: A  556 ASN cc_start: 0.7805 (m-40) cc_final: 0.7454 (t0)
REVERT: A  596 ASP cc_start: 0.7835 (m-30) cc_final: 0.7552 (m-30)
REVERT: A  613 GLU cc_start: 0.7716 (tp30) cc_final: 0.7475 (tp30)
REVERT: A  694 MET cc_start: 0.8072 (mmm) cc_final: 0.7530 (mmp)
REVERT: A  703 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8464 (p)
REVERT: A  921 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6586 (mm)
REVERT: A  961 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6826 (mmtt)
REVERT: A 1043 MET cc_start: 0.8371 (mmt) cc_final: 0.8101 (mmp)
REVERT: A 1063 ILE cc_start: 0.8519 (mt) cc_final: 0.8143 (tt)
REVERT: A 1169 MET cc_start: 0.8746 (ttp) cc_final: 0.8491 (ttm)
REVERT: A 1252 ASN cc_start: 0.7258 (t0) cc_final: 0.6797 (p0)
REVERT: A 1297 HIS cc_start: 0.6912 (m170) cc_final: 0.6573 (m170)
REVERT: A 1333 ARG cc_start: 0.7455 (mtm110) cc_final: 0.6916 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7846 (mt0) cc_final: 0.7565 (tm-30)
  outliers start: 23
  outliers final: 16
  residues processed: 159
  average time/residue: 0.6122
  time to fit residues: 106.3160
Evaluate side-chains
  164 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1224 ASN
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 96 optimal weight:    0.0470
   chunk 72 optimal weight:    0.6980
   chunk 139 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 112 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 138 optimal weight:    0.8980
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 844 GLN
A1224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.197582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158644 restraints weight = 14417.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 1.75
r_work: 0.3188 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14043  Z= 0.113
  Angle     :  0.526  11.066  19383  Z= 0.278
  Chirality :  0.039   0.287   2238
  Planarity :  0.004   0.067   2145
  Dihedral  : 17.128 152.728   2968
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.67 %
    Favored  : 80.50 %
  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 (0.22), residues: 1437
  helix:  1.21 (0.20), residues: 735
  sheet: -0.63 (0.44), residues: 130
  loop : -0.77 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 653 
 TYR   0.014   0.001   TYR A 450 
 PHE   0.014   0.001   PHE A 539 
 TRP   0.008   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (14043)
  covalent geometry    : angle       0.52645 (19383)
  hydrogen bonds       : bond        0.03669 (  549)
  hydrogen bonds       : angle       4.04666 ( 1572)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 ASN cc_start: 0.7972 (m-40) cc_final: 0.7704 (m-40)
REVERT: A   24 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: A   26 LYS cc_start: 0.8647 (mttt) cc_final: 0.8333 (mtmt)
REVERT: A   99 HIS cc_start: 0.7049 (m-70) cc_final: 0.6627 (m-70)
REVERT: A  224 ASN cc_start: 0.6818 (m-40) cc_final: 0.6501 (m110)
REVERT: A  235 ASN cc_start: 0.7908 (t0) cc_final: 0.7450 (t0)
REVERT: A  338 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7321 (tp)
REVERT: A  374 LYS cc_start: 0.6976 (mppt) cc_final: 0.6609 (pttt)
REVERT: A  397 ASP cc_start: 0.6959 (t70) cc_final: 0.6522 (t0)
REVERT: A  406 ASP cc_start: 0.8020 (m-30) cc_final: 0.7592 (t0)
REVERT: A  419 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8511 (tp)
REVERT: A  428 ASP cc_start: 0.8125 (m-30) cc_final: 0.7831 (t0)
REVERT: A  534 MET cc_start: 0.5097 (pp-130) cc_final: 0.3277 (ppp)
REVERT: A  556 ASN cc_start: 0.7875 (m-40) cc_final: 0.7527 (t0)
REVERT: A  596 ASP cc_start: 0.7857 (m-30) cc_final: 0.7615 (m-30)
REVERT: A  613 GLU cc_start: 0.7709 (tp30) cc_final: 0.7445 (tp30)
REVERT: A  694 MET cc_start: 0.8088 (mmm) cc_final: 0.7551 (mmp)
REVERT: A  703 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8480 (p)
REVERT: A  921 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6613 (mm)
REVERT: A  961 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6899 (mmtt)
REVERT: A 1039 TYR cc_start: 0.8066 (m-80) cc_final: 0.7574 (m-80)
REVERT: A 1043 MET cc_start: 0.8362 (mmt) cc_final: 0.8093 (mmp)
REVERT: A 1063 ILE cc_start: 0.8508 (mt) cc_final: 0.8129 (tt)
REVERT: A 1169 MET cc_start: 0.8785 (ttp) cc_final: 0.8522 (ttm)
REVERT: A 1252 ASN cc_start: 0.7382 (t0) cc_final: 0.6811 (p0)
REVERT: A 1297 HIS cc_start: 0.6947 (m170) cc_final: 0.6588 (m170)
REVERT: A 1333 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6924 (ppp80)
REVERT: A 1364 GLN cc_start: 0.7833 (mt0) cc_final: 0.7566 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 160
  average time/residue: 0.6185
  time to fit residues: 108.0810
Evaluate side-chains
  160 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  844 GLN
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1224 ASN
Chi-restraints excluded: chain A residue 1284 ASP
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 134 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 58 optimal weight:    0.4980
   chunk 38 optimal weight:    0.4980
   chunk 109 optimal weight:    8.9990
   chunk 133 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 844 GLN
A1224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.197588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165893 restraints weight = 14527.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 1.32
r_work: 0.3238 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14043  Z= 0.114
  Angle     :  0.522  11.042  19383  Z= 0.275
  Chirality :  0.039   0.285   2238
  Planarity :  0.004   0.067   2145
  Dihedral  : 17.119 152.600   2968
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.67 %
    Favored  : 80.42 %
  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:  0.41 (0.22), residues: 1437
  helix:  1.23 (0.20), residues: 735
  sheet: -0.53 (0.44), residues: 128
  loop : -0.74 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 653 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.016   0.001   PHE A1258 
 TRP   0.007   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (14043)
  covalent geometry    : angle       0.52167 (19383)
  hydrogen bonds       : bond        0.03672 (  549)
  hydrogen bonds       : angle       4.03418 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4407.09 seconds
wall clock time: 75 minutes 58.93 seconds (4558.93 seconds total)