Starting phenix.real_space_refine
on Fri May 16 06:52:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8srs_40740/05_2025/8srs_40740.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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     148      5.49       5
     Mg      4      5.21       5
     S      22      5.16       5
     C    8450      2.51       5
     N    2489      2.21       5
     O    3035      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14148
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 11002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1341, 11002
          Classifications: {'peptide': 1341}
          Link IDs: {'PTRANS': 36, 'TRANS': 1304}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2100
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
    Chain: "C"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 268
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 388
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 385
          Classifications: {'DNA': 19}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 18}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 10.50, per 1000 atoms: 0.74
  Number of scatterers: 14148
  At special positions: 0
  Unit cell: (87.486, 124.98, 121.647, 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     148     15.00
     Mg      4     11.99
     O    3035      8.00
     N    2489      7.00
     C    8450      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: 4.05
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2554

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 10 sheets defined
      53.8% alpha, 9.8% beta
      54 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 5.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 5.059A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.809A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 215
      removed outlier: 4.336A  pdb=" N   ALA A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 4.854A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 3.680A  pdb=" N   LEU A 275 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP A 276 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 306
    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: 3.574A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.168A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.758A  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 483 through 494
      removed outlier: 3.746A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 3.688A  pdb=" N   TYR A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.580A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.600A  pdb=" N   LEU A 616 " --> pdb=" O   ASN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 4.252A  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 699
    Processing helix  chain 'A' and resid 703 through 712
      removed outlier: 3.582A  pdb=" N   ASP A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 3.661A  pdb=" N   ASN A 726 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 751
      removed outlier: 4.217A  pdb=" N   LYS A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 776
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 3.554A  pdb=" N   ARG A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 829 through 833
      removed outlier: 3.505A  pdb=" N   ARG A 832 " --> pdb=" O   ASP A 829 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 829 through 833'
    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 859 through 866
    Processing helix  chain 'A' and resid 872 through 888
      removed outlier: 5.544A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.663A  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
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.571A  pdb=" N   ALA A 914 " --> pdb=" O   GLU A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 3.794A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 970
      removed outlier: 3.548A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 1001
      removed outlier: 4.584A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 3.663A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1043
      removed outlier: 4.309A  pdb=" N   MET A1043 " --> pdb=" O   TYR A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1047
    Processing helix  chain 'A' and resid 1077 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1185
    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 1312
    Processing helix  chain 'A' and resid 1313 through 1315
      No H-bonds generated for 'chain 'A' and resid 1313 through 1315'
    Processing helix  chain 'A' and resid 1340 through 1344
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 6.255A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   LEU A 958 " --> pdb=" O   ILE A 759 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE A 761 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.548A  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: 10.011A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   GLN A1219 " --> pdb=" O   ALA A1215 " (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 837 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: 3.817A  pdb=" N   TRP A1074 " --> pdb=" O   GLU A1064 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.599A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325
      removed outlier: 3.650A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    505 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      133 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 7.55

  Time building geometry restraints manager: 4.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3071
        1.33 -     1.45: 3756
        1.45 -     1.57: 7547
        1.57 -     1.69: 297
        1.69 -     1.81: 42
  Bond restraints: 14713
  Sorted by residual:
  bond pdb=" CB  PHE A 185 "
       pdb=" CG  PHE A 185 "
    ideal  model  delta    sigma   weight residual
    1.502  1.548 -0.046 2.30e-02 1.89e+03 4.01e+00
  bond pdb=" CB  LYS A 948 "
       pdb=" CG  LYS A 948 "
    ideal  model  delta    sigma   weight residual
    1.520  1.580 -0.060 3.00e-02 1.11e+03 3.99e+00
  bond pdb=" CG  LYS A 948 "
       pdb=" CD  LYS A 948 "
    ideal  model  delta    sigma   weight residual
    1.520  1.578 -0.058 3.00e-02 1.11e+03 3.78e+00
  bond pdb=" CB  LYS A1155 "
       pdb=" CG  LYS A1155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.32e+00
  bond pdb=" CB  GLU A1253 "
       pdb=" CG  GLU A1253 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.13e+00
  ... (remaining 14708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 20172
        2.69 -     5.39: 248
        5.39 -     8.08: 56
        8.08 -    10.77: 14
       10.77 -    13.46: 4
  Bond angle restraints: 20494
  Sorted by residual:
  angle pdb=" CB  LYS A 948 "
        pdb=" CG  LYS A 948 "
        pdb=" CD  LYS A 948 "
      ideal   model   delta    sigma   weight residual
     111.30  124.76  -13.46 2.30e+00 1.89e-01 3.43e+01
  angle pdb=" CA  LYS A1155 "
        pdb=" CB  LYS A1155 "
        pdb=" CG  LYS A1155 "
      ideal   model   delta    sigma   weight residual
     114.10  124.15  -10.05 2.00e+00 2.50e-01 2.52e+01
  angle pdb=" CA  GLN A1254 "
        pdb=" CB  GLN A1254 "
        pdb=" CG  GLN A1254 "
      ideal   model   delta    sigma   weight residual
     114.10  123.58   -9.48 2.00e+00 2.50e-01 2.25e+01
  angle pdb=" CA  LYS A 183 "
        pdb=" CB  LYS A 183 "
        pdb=" CG  LYS A 183 "
      ideal   model   delta    sigma   weight residual
     114.10  123.56   -9.46 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CB  LYS A1151 "
        pdb=" CG  LYS A1151 "
        pdb=" CD  LYS A1151 "
      ideal   model   delta    sigma   weight residual
     111.30  122.09  -10.79 2.30e+00 1.89e-01 2.20e+01
  ... (remaining 20489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.82: 8100
       29.82 -    59.64: 711
       59.64 -    89.46: 103
       89.46 -   119.29: 1
      119.29 -   149.11: 2
  Dihedral angle restraints: 8917
    sinusoidal: 4973
      harmonic: 3944
  Sorted by residual:
  dihedral pdb=" CA  GLN A1261 "
           pdb=" C   GLN A1261 "
           pdb=" N   HIS A1262 "
           pdb=" CA  HIS A1262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.25   29.75     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  GLU A 505 "
           pdb=" C   GLU A 505 "
           pdb=" N   LYS A 506 "
           pdb=" CA  LYS A 506 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.65  -19.35     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" C4'  DT D  17 "
           pdb=" C3'  DT D  17 "
           pdb=" O3'  DT D  17 "
           pdb=" P    DG D  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.89  149.11     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 8914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1873
       0.052 -    0.103: 376
       0.103 -    0.155: 77
       0.155 -    0.206: 14
       0.206 -    0.257: 5
  Chirality restraints: 2345
  Sorted by residual:
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" C1'   A B   8 "
            pdb=" O4'   A B   8 "
            pdb=" C2'   A B   8 "
            pdb=" N9    A B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.21    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  GLU A 630 "
            pdb=" N   GLU A 630 "
            pdb=" C   GLU A 630 "
            pdb=" CB  GLU A 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 2342 not shown)

  Planarity restraints: 2076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1298 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   ARG A1298 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ARG A1298 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP A1299 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 653 "   -0.286 9.50e-02 1.11e+02   1.29e-01 1.06e+01
        pdb=" NE  ARG A 653 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 653 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 653 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 653 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1297 "   -0.025 2.00e-02 2.50e+03   2.60e-02 1.01e+01
        pdb=" CG  HIS A1297 "    0.056 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1297 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1297 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1297 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1297 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2073 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 146
        2.60 -     3.18: 11005
        3.18 -     3.75: 23987
        3.75 -     4.33: 33112
        4.33 -     4.90: 50694
  Nonbonded interactions: 118944
  Sorted by model distance:
  nonbonded pdb=" OP2  DC D  34 "
            pdb="MG    MG A1402 "
     model   vdw
     2.029 2.170
  nonbonded pdb=" OP1  DC D  34 "
            pdb="MG    MG A1401 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" OE2 GLU A 762 "
            pdb="MG    MG A1401 "
     model   vdw
     2.081 2.170
  nonbonded pdb=" OD1 ASP A 839 "
            pdb="MG    MG A1403 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" OD1 ASP A  10 "
            pdb="MG    MG A1401 "
     model   vdw
     2.100 2.170
  ... (remaining 118939 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.970
  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:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     41.840
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
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      :  0.004   0.060  14713  Z= 0.186
  Angle     :  0.830  13.463  20494  Z= 0.429
  Chirality :  0.045   0.257   2345
  Planarity :  0.006   0.129   2076
  Dihedral  : 19.788 149.107   6363
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 23.66 %
    Favored  : 75.77 %
  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: -1.01 (0.21), residues: 1333
  helix: -0.63 (0.18), residues: 637
  sheet: -0.34 (0.49), residues: 120
  loop : -0.59 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1136 
 HIS   0.028   0.002   HIS A1297 
 PHE   0.028   0.002   PHE A1327 
 TYR   0.016   0.002   TYR A   5 
 ARG   0.014   0.001   ARG A 884 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14710 (  626)
  hydrogen bonds       : angle       6.04717 ( 1726)
  covalent geometry    : bond        0.00416 (14713)
  covalent geometry    : angle       0.83036 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.364 
Fit side-chains
REVERT: A 1254 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (tm-30)
  outliers start: 7
  outliers final: 1
  residues processed: 62
  average time/residue: 1.2431
  time to fit residues: 86.1137
Evaluate side-chains
  55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0470
   chunk 59 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 132 optimal weight:    0.0670
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3496 r_free = 0.3496 target = 0.099602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.067581 restraints weight = 26835.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.35
r_work: 0.2780 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14713  Z= 0.144
  Angle     :  0.533   9.263  20494  Z= 0.288
  Chirality :  0.038   0.195   2345
  Planarity :  0.004   0.049   2076
  Dihedral  : 19.284 153.978   3492
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.94 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.22), residues: 1333
  helix:  0.53 (0.20), residues: 648
  sheet: -0.34 (0.49), residues: 120
  loop : -0.40 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A1297 
 PHE   0.015   0.001   PHE A1327 
 TYR   0.011   0.001   TYR A 362 
 ARG   0.007   0.001   ARG A 653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  626)
  hydrogen bonds       : angle       4.52202 ( 1726)
  covalent geometry    : bond        0.00318 (14713)
  covalent geometry    : angle       0.53255 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 1.627 
Fit side-chains
REVERT: A  618 ASP cc_start: 0.8923 (t0) cc_final: 0.8659 (t0)
REVERT: A  627 GLU cc_start: 0.7417 (pm20) cc_final: 0.7204 (pt0)
REVERT: A  664 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8393 (tpp80)
REVERT: A  802 GLU cc_start: 0.8786 (pt0) cc_final: 0.8476 (pt0)
REVERT: A 1268 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8434 (mt-10)
REVERT: A 1297 HIS cc_start: 0.7875 (m170) cc_final: 0.7381 (m170)
  outliers start: 27
  outliers final: 6
  residues processed: 85
  average time/residue: 1.5297
  time to fit residues: 142.5843
Evaluate side-chains
  57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1188 LYS
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 137 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.096506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.064241 restraints weight = 26947.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.35
r_work: 0.2705 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14713  Z= 0.173
  Angle     :  0.525   9.433  20494  Z= 0.284
  Chirality :  0.039   0.179   2345
  Planarity :  0.004   0.045   2076
  Dihedral  : 19.236 153.631   3487
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.44 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.26 (0.23), residues: 1333
  helix:  0.80 (0.20), residues: 653
  sheet: -0.25 (0.48), residues: 120
  loop : -0.36 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A1297 
 PHE   0.012   0.001   PHE A1327 
 TYR   0.014   0.001   TYR A1242 
 ARG   0.006   0.001   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  626)
  hydrogen bonds       : angle       4.31209 ( 1726)
  covalent geometry    : bond        0.00391 (14713)
  covalent geometry    : angle       0.52526 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 57
  time to evaluate  : 1.481 
Fit side-chains
REVERT: A  434 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8715 (ttmm)
REVERT: A  436 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7710 (p0)
REVERT: A  523 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8440 (tt0)
REVERT: A  548 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8862 (pt)
REVERT: A  618 ASP cc_start: 0.8911 (t0) cc_final: 0.8671 (t0)
REVERT: A  652 LYS cc_start: 0.8595 (pttt) cc_final: 0.8350 (ptmm)
REVERT: A  664 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (tpp80)
REVERT: A  837 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8277 (t0)
REVERT: A 1257 LEU cc_start: 0.8398 (mt) cc_final: 0.8186 (mm)
  outliers start: 34
  outliers final: 11
  residues processed: 83
  average time/residue: 1.4525
  time to fit residues: 132.4614
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1188 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 137 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0770
   chunk 75 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
A1297 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.062207 restraints weight = 26675.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 2.25
r_work: 0.2673 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14713  Z= 0.227
  Angle     :  0.548   9.358  20494  Z= 0.293
  Chirality :  0.040   0.176   2345
  Planarity :  0.004   0.046   2076
  Dihedral  : 19.271 154.400   3487
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.03 %
    Favored  : 78.16 %
  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:  0.29 (0.23), residues: 1333
  helix:  0.87 (0.20), residues: 651
  sheet: -0.30 (0.47), residues: 120
  loop : -0.39 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1136 
 HIS   0.006   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A 164 
 TYR   0.013   0.001   TYR A 362 
 ARG   0.006   0.000   ARG A1303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04332 (  626)
  hydrogen bonds       : angle       4.31976 ( 1726)
  covalent geometry    : bond        0.00518 (14713)
  covalent geometry    : angle       0.54818 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 52
  time to evaluate  : 1.512 
Fit side-chains
REVERT: A  434 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8734 (ttmm)
REVERT: A  523 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8461 (tt0)
REVERT: A  548 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8905 (pt)
REVERT: A  618 ASP cc_start: 0.8906 (t0) cc_final: 0.8641 (t0)
REVERT: A  652 LYS cc_start: 0.8643 (pttt) cc_final: 0.8378 (ptmm)
REVERT: A  879 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7078 (mtp)
REVERT: A 1191 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8417 (mmtm)
REVERT: A 1268 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8409 (mt-10)
  outliers start: 46
  outliers final: 10
  residues processed: 91
  average time/residue: 1.3691
  time to fit residues: 137.1581
Evaluate side-chains
  64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  879 MET
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0170
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
A 690 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.063873 restraints weight = 26633.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.26
r_work: 0.2710 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14713  Z= 0.144
  Angle     :  0.499   8.490  20494  Z= 0.268
  Chirality :  0.037   0.174   2345
  Planarity :  0.003   0.045   2076
  Dihedral  : 19.099 154.255   3487
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.78 %
    Favored  : 78.41 %
  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:  0.47 (0.23), residues: 1333
  helix:  1.06 (0.20), residues: 651
  sheet: -0.27 (0.47), residues: 120
  loop : -0.34 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 446 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.003   0.000   ARG A 864 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  626)
  hydrogen bonds       : angle       4.17728 ( 1726)
  covalent geometry    : bond        0.00322 (14713)
  covalent geometry    : angle       0.49882 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 47
  time to evaluate  : 1.374 
Fit side-chains
REVERT: A  523 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8412 (tt0)
REVERT: A  548 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8880 (pt)
REVERT: A  618 ASP cc_start: 0.8894 (t0) cc_final: 0.8632 (t0)
REVERT: A  652 LYS cc_start: 0.8582 (pttt) cc_final: 0.8303 (ptmm)
REVERT: A 1268 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8372 (mt-10)
  outliers start: 34
  outliers final: 7
  residues processed: 74
  average time/residue: 1.3000
  time to fit residues: 106.8590
Evaluate side-chains
  57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 144 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 78 optimal weight:    0.0170
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 69 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.5220

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3445 r_free = 0.3445 target = 0.096456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.064972 restraints weight = 26788.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 2.28
r_work: 0.2732 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14713  Z= 0.129
  Angle     :  0.477   8.207  20494  Z= 0.256
  Chirality :  0.037   0.174   2345
  Planarity :  0.003   0.044   2076
  Dihedral  : 18.957 154.047   3487
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.44 %
    Favored  : 78.58 %
  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:  0.69 (0.23), residues: 1333
  helix:  1.27 (0.21), residues: 650
  sheet: -0.21 (0.48), residues: 120
  loop : -0.26 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 164 
 TYR   0.009   0.001   TYR A 155 
 ARG   0.002   0.000   ARG A 783 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03484 (  626)
  hydrogen bonds       : angle       4.05456 ( 1726)
  covalent geometry    : bond        0.00285 (14713)
  covalent geometry    : angle       0.47683 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 51
  time to evaluate  : 1.691 
Fit side-chains
REVERT: A  618 ASP cc_start: 0.8903 (t0) cc_final: 0.8641 (t0)
REVERT: A  627 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (pp20)
REVERT: A  671 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7556 (mtp85)
REVERT: A 1268 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8329 (mt-10)
  outliers start: 24
  outliers final: 7
  residues processed: 74
  average time/residue: 1.4381
  time to fit residues: 118.2915
Evaluate side-chains
  52 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0570
   chunk 37 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 143 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 141 optimal weight:    4.9990
   chunk 96 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3435 r_free = 0.3435 target = 0.095884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.064499 restraints weight = 26650.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.25
r_work: 0.2718 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14713  Z= 0.142
  Angle     :  0.487   8.644  20494  Z= 0.260
  Chirality :  0.037   0.174   2345
  Planarity :  0.003   0.045   2076
  Dihedral  : 18.940 154.082   3487
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.60 %
    Favored  : 78.33 %
  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:  0.71 (0.23), residues: 1333
  helix:  1.29 (0.21), residues: 650
  sheet: -0.18 (0.48), residues: 120
  loop : -0.26 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 164 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.005   0.000   ARG A1317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  626)
  hydrogen bonds       : angle       4.04029 ( 1726)
  covalent geometry    : bond        0.00319 (14713)
  covalent geometry    : angle       0.48712 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 46
  time to evaluate  : 1.344 
Fit side-chains
REVERT: A  434 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8621 (ttmm)
REVERT: A  523 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8409 (tt0)
REVERT: A  618 ASP cc_start: 0.8896 (t0) cc_final: 0.8641 (t0)
REVERT: A  627 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7943 (pp20)
REVERT: A  671 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7537 (mtp85)
REVERT: A 1268 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8331 (mt-10)
  outliers start: 25
  outliers final: 9
  residues processed: 67
  average time/residue: 1.3203
  time to fit residues: 98.1420
Evaluate side-chains
  56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 137 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 104 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 116 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3412 r_free = 0.3412 target = 0.094355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.062850 restraints weight = 26501.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.24
r_work: 0.2690 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2574 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14713  Z= 0.170
  Angle     :  0.498   8.770  20494  Z= 0.266
  Chirality :  0.038   0.174   2345
  Planarity :  0.003   0.046   2076
  Dihedral  : 18.951 154.244   3487
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.27 %
    Favored  : 78.41 %
  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:  0.65 (0.23), residues: 1333
  helix:  1.24 (0.21), residues: 651
  sheet: -0.18 (0.48), residues: 120
  loop : -0.29 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.008   0.001   PHE A 290 
 TYR   0.011   0.001   TYR A 155 
 ARG   0.004   0.000   ARG A1317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03821 (  626)
  hydrogen bonds       : angle       4.08966 ( 1726)
  covalent geometry    : bond        0.00386 (14713)
  covalent geometry    : angle       0.49758 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 43
  time to evaluate  : 1.451 
Fit side-chains
REVERT: A  523 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8390 (tt0)
REVERT: A  618 ASP cc_start: 0.8900 (t0) cc_final: 0.8635 (t0)
REVERT: A  646 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8591 (tptt)
REVERT: A  671 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7548 (mtp85)
REVERT: A 1068 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8611 (mp0)
REVERT: A 1268 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8361 (mt-10)
  outliers start: 28
  outliers final: 10
  residues processed: 68
  average time/residue: 1.3798
  time to fit residues: 103.9170
Evaluate side-chains
  57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1188 LYS
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0970
   chunk 58 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 135 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3413 r_free = 0.3413 target = 0.094389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.063016 restraints weight = 26485.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.23
r_work: 0.2690 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14713  Z= 0.173
  Angle     :  0.498   8.935  20494  Z= 0.266
  Chirality :  0.038   0.174   2345
  Planarity :  0.003   0.046   2076
  Dihedral  : 18.951 154.206   3487
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.93 %
    Favored  : 78.58 %
  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:  0.63 (0.23), residues: 1333
  helix:  1.23 (0.20), residues: 651
  sheet: -0.21 (0.48), residues: 120
  loop : -0.30 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 164 
 TYR   0.011   0.001   TYR A 155 
 ARG   0.004   0.000   ARG A1317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  626)
  hydrogen bonds       : angle       4.08970 ( 1726)
  covalent geometry    : bond        0.00391 (14713)
  covalent geometry    : angle       0.49786 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 1.704 
Fit side-chains
REVERT: A  434 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8586 (ttmm)
REVERT: A  523 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8402 (tt0)
REVERT: A  618 ASP cc_start: 0.8897 (t0) cc_final: 0.8627 (t0)
REVERT: A  646 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8590 (tptt)
REVERT: A  671 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7694 (mtp85)
REVERT: A 1068 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8590 (mp0)
REVERT: A 1268 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8353 (mt-10)
  outliers start: 18
  outliers final: 9
  residues processed: 65
  average time/residue: 1.5692
  time to fit residues: 112.0159
Evaluate side-chains
  58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1188 LYS
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 37 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0970
   chunk 50 optimal weight:    0.5980
   chunk 135 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 141 optimal weight:    4.9990
   chunk 142 optimal weight:    3.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** 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 = 0.3430 r_free = 0.3430 target = 0.095399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.064031 restraints weight = 26430.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 2.24
r_work: 0.2718 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14713  Z= 0.138
  Angle     :  0.482   9.622  20494  Z= 0.259
  Chirality :  0.037   0.174   2345
  Planarity :  0.003   0.045   2076
  Dihedral  : 18.915 154.009   3487
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.93 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.68 (0.23), residues: 1333
  helix:  1.26 (0.20), residues: 657
  sheet: -0.17 (0.48), residues: 120
  loop : -0.30 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 290 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.004   0.000   ARG A1317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  626)
  hydrogen bonds       : angle       4.03903 ( 1726)
  covalent geometry    : bond        0.00309 (14713)
  covalent geometry    : angle       0.48245 (20494)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 47
  time to evaluate  : 1.379 
Fit side-chains
REVERT: A  434 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8559 (ttmm)
REVERT: A  523 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8394 (tt0)
REVERT: A  618 ASP cc_start: 0.8905 (t0) cc_final: 0.8642 (t0)
REVERT: A  646 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8587 (tptt)
REVERT: A  671 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7612 (mtp85)
REVERT: A 1068 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8556 (mp0)
REVERT: A 1268 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8314 (mt-10)
  outliers start: 19
  outliers final: 9
  residues processed: 64
  average time/residue: 1.5201
  time to fit residues: 106.8580
Evaluate side-chains
  58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  574 CYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1116 SER
Chi-restraints excluded: chain A residue 1188 LYS
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 143 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 77 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
** 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 = 0.3430 r_free = 0.3430 target = 0.095380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.064080 restraints weight = 26613.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.25
r_work: 0.2720 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14713  Z= 0.138
  Angle     :  0.485   9.694  20494  Z= 0.259
  Chirality :  0.037   0.175   2345
  Planarity :  0.003   0.045   2076
  Dihedral  : 18.893 153.922   3487
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.18 %
    Favored  : 78.25 %
  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:  0.70 (0.23), residues: 1333
  helix:  1.29 (0.20), residues: 657
  sheet: -0.16 (0.48), residues: 120
  loop : -0.31 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 290 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.004   0.000   ARG A1317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  626)
  hydrogen bonds       : angle       4.02598 ( 1726)
  covalent geometry    : bond        0.00310 (14713)
  covalent geometry    : angle       0.48533 (20494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9303.75 seconds
wall clock time: 161 minutes 24.69 seconds (9684.69 seconds total)