Starting phenix.real_space_refine
on Thu Jun 12 14:15:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzz_41775/06_2025/8tzz_41775.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     144      5.49       5
     Mg      5      5.21       5
     S      22      5.16       5
     C    8375      2.51       5
     N    2458      2.21       5
     O    3008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14012
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 10962
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1336, 10951
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 35, 'TRANS': 1300}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 1336, 10951
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 35, 'TRANS': 1300}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 11134
    Chain: "B"
      Number of atoms: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2103
          Classifications: {'RNA': 98}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 10, 'rna3p': 87}
    Chain: "C"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 328
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "c"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 341
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "D"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 268
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "c"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 783 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 783 " occ=0.50
  Time building chain proxies: 14.39, per 1000 atoms: 1.03
  Number of scatterers: 14012
  At special positions: 0
  Unit cell: (87.465, 129.115, 120.785, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P     144     15.00
     Mg      5     11.99
     O    3008      8.00
     N    2458      7.00
     C    8375      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: 3.32
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2548

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 8 sheets defined
      55.5% alpha, 7.9% beta
      49 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 5.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.055A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 144
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 175 through 179
      removed outlier: 3.613A  pdb=" N   ASN A 178 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.953A  pdb=" N   GLN A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 238 through 244
      removed outlier: 3.847A  pdb=" N   ALA A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 290 through 306
      removed outlier: 4.414A  pdb=" N   LYS A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    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
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.524A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 410 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.038A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.863A  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 494
      removed outlier: 3.593A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 553
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.589A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.965A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 711
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 732 through 751
      removed outlier: 4.059A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 777
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 3.751A  pdb=" N   GLY A 787 " --> pdb=" O  AARG A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 804 through 807
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 829 through 834
      removed outlier: 5.608A  pdb=" N   SER A 834 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 853
      No H-bonds generated for 'chain 'A' and resid 851 through 853'
    Processing helix  chain 'A' and resid 860 through 866
    Processing helix  chain 'A' and resid 872 through 889
      removed outlier: 5.191A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 902 through 906
      removed outlier: 3.797A  pdb=" N   GLY A 906 " --> pdb=" O   ALA A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 4.143A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL A 922 " --> pdb=" O   LYS A 918 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 981 through 1001
    Processing helix  chain 'A' and resid 1002 through 1005
      removed outlier: 3.682A  pdb=" N   GLU A1005 " --> pdb=" O   PRO A1002 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1002 through 1005'
    Processing helix  chain 'A' and resid 1033 through 1042
      removed outlier: 3.604A  pdb=" N   ILE A1042 " --> pdb=" O   PHE A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1046
      removed outlier: 3.526A  pdb=" N   PHE A1046 " --> pdb=" O   MET A1043 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1043 through 1046'
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.721A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  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 1240
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1310
    Processing helix  chain 'A' and resid 1312 through 1317
      removed outlier: 4.026A  pdb=" N   THR A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.672A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (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 954 through 959
      removed outlier: 7.313A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 8.898A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   LEU A   9 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 4.685A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065
      removed outlier: 4.233A  pdb=" N   TRP A1074 " --> pdb=" O   GLU A1064 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 5.369A  pdb=" N   LYS A1156 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLU A1150 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325

    487 hydrogen bonds defined for protein.
    1411 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      115 hydrogen bonds
      218 hydrogen bond angles
      0 basepair planarities
      49 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 7.46

  Time building geometry restraints manager: 3.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2075
        1.31 -     1.44: 4532
        1.44 -     1.56: 7627
        1.56 -     1.69: 284
        1.69 -     1.81: 42
  Bond restraints: 14560
  Sorted by residual:
  bond pdb=" CA  SER A1216 "
       pdb=" CB  SER A1216 "
    ideal  model  delta    sigma   weight residual
    1.530  1.457  0.073 1.69e-02 3.50e+03 1.87e+01
  bond pdb=" C   PRO A1137 "
       pdb=" O   PRO A1137 "
    ideal  model  delta    sigma   weight residual
    1.233  1.186  0.047 1.12e-02 7.97e+03 1.76e+01
  bond pdb=" N   LEU A1214 "
       pdb=" CA  LEU A1214 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.046 1.22e-02 6.72e+03 1.40e+01
  bond pdb=" C   PRO A1199 "
       pdb=" O   PRO A1199 "
    ideal  model  delta    sigma   weight residual
    1.235  1.192  0.043 1.30e-02 5.92e+03 1.09e+01
  bond pdb=" CA  ALA A1217 "
       pdb=" CB  ALA A1217 "
    ideal  model  delta    sigma   weight residual
    1.533  1.483  0.050 1.63e-02 3.76e+03 9.33e+00
  ... (remaining 14555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 19629
        2.13 -     4.25: 548
        4.25 -     6.38: 76
        6.38 -     8.50: 13
        8.50 -    10.63: 5
  Bond angle restraints: 20271
  Sorted by residual:
  angle pdb=" N   ALA A1217 "
        pdb=" CA  ALA A1217 "
        pdb=" C   ALA A1217 "
      ideal   model   delta    sigma   weight residual
     113.02  105.12    7.90 1.49e+00 4.50e-01 2.81e+01
  angle pdb=" O3'  DG C  17 "
        pdb=" C3'  DG C  17 "
        pdb=" C2'  DG C  17 "
      ideal   model   delta    sigma   weight residual
     111.50  103.83    7.67 1.50e+00 4.44e-01 2.61e+01
  angle pdb=" CG  MET A 383 "
        pdb=" SD  MET A 383 "
        pdb=" CE  MET A 383 "
      ideal   model   delta    sigma   weight residual
     100.90   90.65   10.25 2.20e+00 2.07e-01 2.17e+01
  angle pdb=" N   TYR A1326 "
        pdb=" CA  TYR A1326 "
        pdb=" C   TYR A1326 "
      ideal   model   delta    sigma   weight residual
     110.17  103.51    6.66 1.51e+00 4.39e-01 1.95e+01
  angle pdb=" N   GLN A 190 "
        pdb=" CA  GLN A 190 "
        pdb=" CB  GLN A 190 "
      ideal   model   delta    sigma   weight residual
     110.28  116.83   -6.55 1.55e+00 4.16e-01 1.79e+01
  ... (remaining 20266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.57: 8312
       33.57 -    67.14: 478
       67.14 -   100.70: 40
      100.70 -   134.27: 1
      134.27 -   167.84: 5
  Dihedral angle restraints: 8836
    sinusoidal: 4901
      harmonic: 3935
  Sorted by residual:
  dihedral pdb=" O4'   U B  59 "
           pdb=" C1'   U B  59 "
           pdb=" N1    U B  59 "
           pdb=" C2    U B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   32.16  167.84     1      1.50e+01 4.44e-03 8.44e+01
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   33.20  166.80     1      1.50e+01 4.44e-03 8.42e+01
  dihedral pdb=" CA  TYR A1326 "
           pdb=" C   TYR A1326 "
           pdb=" N   PHE A1327 "
           pdb=" CA  PHE A1327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.09  -26.91     0      5.00e+00 4.00e-02 2.90e+01
  ... (remaining 8833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 2152
       0.087 -    0.173: 153
       0.173 -    0.260: 13
       0.260 -    0.347: 3
       0.347 -    0.434: 1
  Chirality restraints: 2322
  Sorted by residual:
  chirality pdb=" P    DT c  23 "
            pdb=" OP1  DT c  23 "
            pdb=" OP2  DT c  23 "
            pdb=" O5'  DT c  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.78   -0.43 2.00e-01 2.50e+01 4.70e+00
  chirality pdb=" C3'  DG C  17 "
            pdb=" C4'  DG C  17 "
            pdb=" O3'  DG C  17 "
            pdb=" C2'  DG C  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.97    0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  LYS A1222 "
            pdb=" N   LYS A1222 "
            pdb=" C   LYS A1222 "
            pdb=" CB  LYS A1222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 2319 not shown)

  Planarity restraints: 2066
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 730 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO A 731 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 731 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 731 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO A1229 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 549 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" C   VAL A 549 "    0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A 549 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASP A 550 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2063 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.13: 3
        2.13 -     2.82: 4064
        2.82 -     3.51: 19523
        3.51 -     4.21: 35299
        4.21 -     4.90: 57477
  Nonbonded interactions: 116366
  Sorted by model distance:
  nonbonded pdb="MG    MG A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     1.432 1.300
  nonbonded pdb=" OP2  DT c  23 "
            pdb="MG    MG c 101 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OP2   A B  65 "
            pdb="MG    MG B 101 "
     model   vdw
     2.013 2.170
  nonbonded pdb=" O3'  DG C  22 "
            pdb="MG    MG c 101 "
     model   vdw
     2.137 2.170
  nonbonded pdb=" OG  SER A 860 "
            pdb=" NH1 ARG A 864 "
     model   vdw
     2.138 3.120
  ... (remaining 116361 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     47.490
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
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      :  0.007   0.073  14560  Z= 0.323
  Angle     :  0.857  10.629  20271  Z= 0.494
  Chirality :  0.050   0.434   2322
  Planarity :  0.004   0.064   2066
  Dihedral  : 18.892 167.840   6288
  Min Nonbonded Distance : 1.432

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  0.25 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.22), residues: 1331
  helix:  0.01 (0.20), residues: 633
  sheet: -0.54 (0.47), residues: 128
  loop : -0.67 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1136 
 HIS   0.009   0.002   HIS A 328 
 PHE   0.018   0.002   PHE A 643 
 TYR   0.026   0.003   TYR A1326 
 ARG   0.018   0.001   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17116 (  602)
  hydrogen bonds       : angle       7.72888 ( 1629)
  covalent geometry    : bond        0.00676 (14560)
  covalent geometry    : angle       0.85674 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.330 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7358 (ttt-90)
REVERT: A  311 GLU cc_start: 0.5489 (mp0) cc_final: 0.5279 (mp0)
REVERT: A  383 MET cc_start: 0.6979 (ttt) cc_final: 0.6200 (ttt)
REVERT: A  919 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8126 (ttp80)
REVERT: A 1006 SER cc_start: 0.8563 (t) cc_final: 0.8224 (m)
  outliers start: 8
  outliers final: 1
  residues processed: 99
  average time/residue: 0.3479
  time to fit residues: 49.2194
Evaluate side-chains
  63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 1.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1332 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 109 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.106775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.080337 restraints weight = 58713.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.081790 restraints weight = 28704.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.082605 restraints weight = 19803.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14560  Z= 0.150
  Angle     :  0.597   7.306  20271  Z= 0.320
  Chirality :  0.041   0.201   2322
  Planarity :  0.004   0.051   2066
  Dihedral  : 20.076 167.975   3432
  Min Nonbonded Distance : 1.358

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.90 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.22), residues: 1331
  helix:  0.53 (0.20), residues: 643
  sheet:  0.01 (0.48), residues: 122
  loop : -0.63 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.026   0.001   PHE A1045 
 TYR   0.023   0.001   TYR A1326 
 ARG   0.006   0.001   ARG A 864 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05311 (  602)
  hydrogen bonds       : angle       5.01297 ( 1629)
  covalent geometry    : bond        0.00318 (14560)
  covalent geometry    : angle       0.59713 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 1.520 
Fit side-chains
REVERT: A  919 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.8192 (ttp80)
  outliers start: 8
  outliers final: 4
  residues processed: 80
  average time/residue: 0.2983
  time to fit residues: 35.3089
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  585 ASP
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 140 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 113 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.106381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.080002 restraints weight = 53188.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.081562 restraints weight = 26363.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.082510 restraints weight = 17660.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14560  Z= 0.146
  Angle     :  0.547   6.637  20271  Z= 0.293
  Chirality :  0.039   0.205   2322
  Planarity :  0.004   0.098   2066
  Dihedral  : 19.800 167.186   3430
  Min Nonbonded Distance : 1.232

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.73 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.23), residues: 1331
  helix:  0.67 (0.20), residues: 651
  sheet:  0.29 (0.51), residues: 112
  loop : -0.62 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1136 
 HIS   0.005   0.001   HIS A 328 
 PHE   0.022   0.001   PHE A1045 
 TYR   0.025   0.001   TYR A1201 
 ARG   0.005   0.000   ARG A1303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04594 (  602)
  hydrogen bonds       : angle       4.73221 ( 1629)
  covalent geometry    : bond        0.00321 (14560)
  covalent geometry    : angle       0.54733 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 1.515 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.2972
  time to fit residues: 32.9600
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 140 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0270
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 134 optimal weight:    4.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 341 GLN
A1262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.108778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.082474 restraints weight = 59891.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.084001 restraints weight = 28881.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.085205 restraints weight = 18190.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  14560  Z= 0.108
  Angle     :  0.500   6.151  20271  Z= 0.269
  Chirality :  0.037   0.209   2322
  Planarity :  0.003   0.047   2066
  Dihedral  : 19.485 165.286   3430
  Min Nonbonded Distance : 1.176

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.64 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.23), residues: 1331
  helix:  1.03 (0.20), residues: 649
  sheet:  0.46 (0.52), residues: 112
  loop : -0.38 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A1262 
 PHE   0.025   0.001   PHE A 606 
 TYR   0.020   0.001   TYR A1201 
 ARG   0.007   0.000   ARG A1303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  602)
  hydrogen bonds       : angle       4.47734 ( 1629)
  covalent geometry    : bond        0.00228 (14560)
  covalent geometry    : angle       0.50023 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 1.406 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 77
  average time/residue: 0.3328
  time to fit residues: 37.9418
Evaluate side-chains
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1038 PHE
Chi-restraints excluded: chain A residue 1262 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 118 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 108 optimal weight:    0.1980
   chunk 124 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0010
   chunk 52 optimal weight:    0.0470
   chunk 13 optimal weight:    1.9990
   chunk 119 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.3484

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1262 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.109562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.083590 restraints weight = 41545.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.085547 restraints weight = 22740.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.086657 restraints weight = 14774.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  14560  Z= 0.106
  Angle     :  0.489   6.783  20271  Z= 0.262
  Chirality :  0.036   0.209   2322
  Planarity :  0.003   0.063   2066
  Dihedral  : 19.344 163.864   3430
  Min Nonbonded Distance : 1.188

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.14 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1331
  helix:  1.14 (0.21), residues: 648
  sheet:  0.51 (0.52), residues: 112
  loop : -0.31 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1136 
 HIS   0.010   0.001   HIS A1262 
 PHE   0.021   0.001   PHE A 606 
 TYR   0.020   0.001   TYR A1201 
 ARG   0.008   0.000   ARG A 925 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  602)
  hydrogen bonds       : angle       4.38819 ( 1629)
  covalent geometry    : bond        0.00217 (14560)
  covalent geometry    : angle       0.48881 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.097 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 0.3118
  time to fit residues: 32.2518
Evaluate side-chains
  63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1038 PHE
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 118 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 139 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.106369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.080539 restraints weight = 35766.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.082407 restraints weight = 22645.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.082899 restraints weight = 16014.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14560  Z= 0.183
  Angle     :  0.543   6.589  20271  Z= 0.287
  Chirality :  0.039   0.211   2322
  Planarity :  0.004   0.047   2066
  Dihedral  : 19.415 165.601   3430
  Min Nonbonded Distance : 1.098

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.64 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1331
  helix:  1.01 (0.20), residues: 655
  sheet:  0.36 (0.51), residues: 114
  loop : -0.38 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 883 
 HIS   0.007   0.001   HIS A 328 
 PHE   0.020   0.002   PHE A 606 
 TYR   0.026   0.002   TYR A1201 
 ARG   0.007   0.001   ARG A 925 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  602)
  hydrogen bonds       : angle       4.47251 ( 1629)
  covalent geometry    : bond        0.00412 (14560)
  covalent geometry    : angle       0.54258 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 1.440 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.3154
  time to fit residues: 29.6289
Evaluate side-chains
  63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 81 optimal weight:    0.0870
   chunk 94 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 141 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.107981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.081841 restraints weight = 49823.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.083469 restraints weight = 26097.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.084346 restraints weight = 17303.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14560  Z= 0.111
  Angle     :  0.495   6.767  20271  Z= 0.263
  Chirality :  0.036   0.209   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.295 164.612   3430
  Min Nonbonded Distance : 1.169

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  9.22 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.23), residues: 1331
  helix:  1.23 (0.21), residues: 648
  sheet:  0.30 (0.50), residues: 120
  loop : -0.26 (0.27), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.019   0.001   PHE A 606 
 TYR   0.021   0.001   TYR A1201 
 ARG   0.008   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  602)
  hydrogen bonds       : angle       4.33559 ( 1629)
  covalent geometry    : bond        0.00239 (14560)
  covalent geometry    : angle       0.49483 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 1.241 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 63
  average time/residue: 0.2995
  time to fit residues: 27.8370
Evaluate side-chains
  60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1038 PHE
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 110 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 141 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.108016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.081636 restraints weight = 53160.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.083219 restraints weight = 26703.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.084168 restraints weight = 17661.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14560  Z= 0.121
  Angle     :  0.497   6.475  20271  Z= 0.265
  Chirality :  0.037   0.210   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.256 164.395   3430
  Min Nonbonded Distance : 1.132

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.97 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.23), residues: 1331
  helix:  1.26 (0.21), residues: 648
  sheet:  0.34 (0.52), residues: 114
  loop : -0.27 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 883 
 HIS   0.005   0.001   HIS A 328 
 PHE   0.018   0.001   PHE A1045 
 TYR   0.023   0.001   TYR A1201 
 ARG   0.007   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03900 (  602)
  hydrogen bonds       : angle       4.30312 ( 1629)
  covalent geometry    : bond        0.00264 (14560)
  covalent geometry    : angle       0.49681 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 1.477 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2693
  time to fit residues: 27.3954
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    0.4980
   chunk 85 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 128 optimal weight:    0.0040
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.109026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.082611 restraints weight = 47956.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.085320 restraints weight = 25334.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.085753 restraints weight = 15864.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14560  Z= 0.108
  Angle     :  0.488   7.156  20271  Z= 0.259
  Chirality :  0.036   0.209   2322
  Planarity :  0.003   0.043   2066
  Dihedral  : 19.170 163.619   3430
  Min Nonbonded Distance : 1.169

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.30 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.23), residues: 1331
  helix:  1.34 (0.21), residues: 648
  sheet:  0.37 (0.52), residues: 114
  loop : -0.24 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1136 
 HIS   0.005   0.001   HIS A 328 
 PHE   0.017   0.001   PHE A1045 
 TYR   0.021   0.001   TYR A1201 
 ARG   0.009   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  602)
  hydrogen bonds       : angle       4.23237 ( 1629)
  covalent geometry    : bond        0.00233 (14560)
  covalent geometry    : angle       0.48752 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 1.365 
Fit side-chains
REVERT: A  311 GLU cc_start: 0.5107 (mp0) cc_final: 0.4729 (mp0)
REVERT: A  921 LEU cc_start: 0.7978 (tt) cc_final: 0.7760 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2636
  time to fit residues: 27.0508
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 117 optimal weight:    0.2980
   chunk 107 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.108676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.082328 restraints weight = 53866.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.083754 restraints weight = 26607.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.084800 restraints weight = 18002.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14560  Z= 0.114
  Angle     :  0.491   6.982  20271  Z= 0.261
  Chirality :  0.036   0.208   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.157 163.613   3430
  Min Nonbonded Distance : 1.133

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.39 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.23), residues: 1331
  helix:  1.37 (0.21), residues: 648
  sheet:  0.37 (0.52), residues: 114
  loop : -0.25 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 883 
 HIS   0.006   0.001   HIS A 328 
 PHE   0.017   0.001   PHE A1045 
 TYR   0.023   0.001   TYR A1201 
 ARG   0.006   0.000   ARG A1303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  602)
  hydrogen bonds       : angle       4.21712 ( 1629)
  covalent geometry    : bond        0.00249 (14560)
  covalent geometry    : angle       0.49066 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 1.387 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2687
  time to fit residues: 26.5412
Evaluate side-chains
  62 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue 1339 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 141 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 100 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0000
   chunk 7 optimal weight:    2.9990
   chunk 142 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0980
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.6904

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.109097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.082744 restraints weight = 51030.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.084719 restraints weight = 26453.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.085544 restraints weight = 16673.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14560  Z= 0.110
  Angle     :  0.484   6.923  20271  Z= 0.258
  Chirality :  0.036   0.207   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.123 163.486   3430
  Min Nonbonded Distance : 1.151

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.22 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1331
  helix:  1.40 (0.21), residues: 655
  sheet:  0.46 (0.52), residues: 114
  loop : -0.23 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 883 
 HIS   0.006   0.001   HIS A 328 
 PHE   0.017   0.001   PHE A1045 
 TYR   0.023   0.001   TYR A1201 
 ARG   0.009   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  602)
  hydrogen bonds       : angle       4.17924 ( 1629)
  covalent geometry    : bond        0.00239 (14560)
  covalent geometry    : angle       0.48432 (20271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5003.00 seconds
wall clock time: 89 minutes 32.68 seconds (5372.68 seconds total)