Starting phenix.real_space_refine
on Sat Oct 11 10:46:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzz_41775/10_2025/8tzz_41775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzz_41775/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzz_41775/10_2025/8tzz_41775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzz_41775/10_2025/8tzz_41775.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzz_41775/10_2025/8tzz_41775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzz_41775/10_2025/8tzz_41775.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.21, per 1000 atoms: 0.37
  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: 1.33
  Conformation dependent library (CDL) restraints added in 876.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.92
  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: 3.35

  Time building geometry restraints manager: 1.69 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:             4.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.500
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.410
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (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
 ARG   0.018   0.001   ARG A1078 
 TYR   0.026   0.003   TYR A1326 
 PHE   0.018   0.002   PHE A 643 
 TRP   0.011   0.002   TRP A1136 
 HIS   0.009   0.002   HIS A 328 

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

*********************** 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  : 0.483 
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: 0.6146 (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)
REVERT: A 1303 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7576 (ttp80)
  outliers start: 8
  outliers final: 1
  residues processed: 99
  average time/residue: 0.1531
  time to fit residues: 21.4894
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  : 0.394 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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**
** A1261 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 = 0.3656 r_free = 0.3656 target = 0.106277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.079770 restraints weight = 60312.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.081205 restraints weight = 29624.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.082052 restraints weight = 19677.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.082281 restraints weight = 16208.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.082507 restraints weight = 14983.977|
|-----------------------------------------------------------------------------|
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 = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14560  Z= 0.155
  Angle     :  0.604   6.878  20271  Z= 0.322
  Chirality :  0.041   0.200   2322
  Planarity :  0.004   0.052   2066
  Dihedral  : 20.082 169.344   3432
  Min Nonbonded Distance : 1.336

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  3.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.22), residues: 1331
  helix:  0.50 (0.20), residues: 643
  sheet:  0.01 (0.49), residues: 122
  loop : -0.64 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 864 
 TYR   0.022   0.001   TYR A1326 
 PHE   0.026   0.001   PHE A1045 
 TRP   0.008   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (14560)
  covalent geometry    : angle       0.60378 (20271)
  hydrogen bonds       : bond        0.05407 (  602)
  hydrogen bonds       : angle       5.02396 ( 1629)

*********************** 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: 9
    poor density    : 73
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  919 ARG cc_start: 0.8480 (ttp-170) cc_final: 0.8196 (ttp80)
  outliers start: 9
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1453
  time to fit residues: 16.7016
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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 68 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 114 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 140 optimal weight:    9.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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**
** A1261 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 = 0.3641 r_free = 0.3641 target = 0.105192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.078848 restraints weight = 58109.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.080198 restraints weight = 28917.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.081265 restraints weight = 18769.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.081469 restraints weight = 15759.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.081715 restraints weight = 15032.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    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 = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14560  Z= 0.181
  Angle     :  0.576   6.879  20271  Z= 0.307
  Chirality :  0.040   0.206   2322
  Planarity :  0.004   0.050   2066
  Dihedral  : 19.872 167.815   3430
  Min Nonbonded Distance : 1.165

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.15 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.23), residues: 1331
  helix:  0.61 (0.20), residues: 646
  sheet:  0.21 (0.51), residues: 112
  loop : -0.62 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1078 
 TYR   0.017   0.001   TYR A1326 
 PHE   0.023   0.002   PHE A1045 
 TRP   0.006   0.001   TRP A1136 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (14560)
  covalent geometry    : angle       0.57590 (20271)
  hydrogen bonds       : bond        0.04798 (  602)
  hydrogen bonds       : angle       4.80864 ( 1629)

*********************** 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
  71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.515 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1527
  time to fit residues: 14.9731
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  : 0.458 
-------------------------------------------------------------------------------
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 77 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0970
   chunk 123 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 135 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 126 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.107384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.080814 restraints weight = 53679.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.083186 restraints weight = 26906.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.083660 restraints weight = 16549.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.083970 restraints weight = 14364.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.084134 restraints weight = 13279.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    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 = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14560  Z= 0.120
  Angle     :  0.518   6.376  20271  Z= 0.278
  Chirality :  0.038   0.210   2322
  Planarity :  0.003   0.045   2066
  Dihedral  : 19.601 165.983   3430
  Min Nonbonded Distance : 1.155

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.98 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.23), residues: 1331
  helix:  0.87 (0.20), residues: 653
  sheet:  0.20 (0.50), residues: 117
  loop : -0.47 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 215 
 TYR   0.012   0.001   TYR A1326 
 PHE   0.021   0.001   PHE A1045 
 TRP   0.006   0.001   TRP A1136 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14560)
  covalent geometry    : angle       0.51775 (20271)
  hydrogen bonds       : bond        0.04211 (  602)
  hydrogen bonds       : angle       4.55262 ( 1629)

*********************** 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
  79 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.497 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1397
  time to fit residues: 15.4505
Evaluate side-chains
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 125 optimal weight:    0.4980
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 ** 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 = 0.3672 r_free = 0.3672 target = 0.107673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.081395 restraints weight = 44695.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.083443 restraints weight = 23443.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.084709 restraints weight = 14792.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.084799 restraints weight = 12320.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.084910 restraints weight = 11683.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    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 = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14560  Z= 0.117
  Angle     :  0.500   6.150  20271  Z= 0.268
  Chirality :  0.037   0.210   2322
  Planarity :  0.003   0.045   2066
  Dihedral  : 19.421 164.201   3430
  Min Nonbonded Distance : 1.156

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.31 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.23), residues: 1331
  helix:  1.02 (0.20), residues: 649
  sheet:  0.27 (0.51), residues: 117
  loop : -0.35 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1078 
 TYR   0.014   0.001   TYR A1265 
 PHE   0.021   0.001   PHE A 606 
 TRP   0.005   0.001   TRP A1136 
 HIS   0.006   0.001   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14560)
  covalent geometry    : angle       0.50032 (20271)
  hydrogen bonds       : bond        0.04048 (  602)
  hydrogen bonds       : angle       4.44528 ( 1629)

*********************** 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
  75 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  822 MET cc_start: 0.7942 (mmm) cc_final: 0.7697 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1488
  time to fit residues: 15.4383
Evaluate side-chains
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 96 optimal weight:    0.0060
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0980
   chunk 39 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 142 optimal weight:    7.9990
   chunk 110 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 129 optimal weight:    0.0470
   overall best weight:    1.6298

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.105699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.079302 restraints weight = 51089.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.081077 restraints weight = 25228.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.082280 restraints weight = 16366.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.082369 restraints weight = 13781.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.082593 restraints weight = 13362.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    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 = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2070

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= 0.177
  Angle     :  0.551   8.550  20271  Z= 0.292
  Chirality :  0.039   0.213   2322
  Planarity :  0.004   0.067   2066
  Dihedral  : 19.466 165.632   3430
  Min Nonbonded Distance : 1.086

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.39 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.23), residues: 1331
  helix:  0.87 (0.20), residues: 661
  sheet:  0.06 (0.48), residues: 125
  loop : -0.45 (0.27), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 139 
 TYR   0.011   0.001   TYR A 988 
 PHE   0.020   0.002   PHE A1045 
 TRP   0.004   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (14560)
  covalent geometry    : angle       0.55072 (20271)
  hydrogen bonds       : bond        0.04384 (  602)
  hydrogen bonds       : angle       4.52586 ( 1629)

*********************** 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
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.487 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1521
  time to fit residues: 13.5315
Evaluate side-chains
  61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue   55 SER
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 142 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 124 optimal weight:    0.3980
   chunk 121 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0170
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    1.0822

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.106896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.080700 restraints weight = 48045.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.082087 restraints weight = 25346.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.082920 restraints weight = 17325.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083763 restraints weight = 14876.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.083885 restraints weight = 13860.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    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 = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14560  Z= 0.135
  Angle     :  0.512   8.961  20271  Z= 0.272
  Chirality :  0.037   0.211   2322
  Planarity :  0.003   0.045   2066
  Dihedral  : 19.374 165.202   3430
  Min Nonbonded Distance : 1.143

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.23), residues: 1331
  helix:  1.02 (0.20), residues: 657
  sheet:  0.16 (0.49), residues: 123
  loop : -0.35 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1078 
 TYR   0.010   0.001   TYR A 155 
 PHE   0.019   0.001   PHE A1045 
 TRP   0.006   0.001   TRP A1136 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (14560)
  covalent geometry    : angle       0.51157 (20271)
  hydrogen bonds       : bond        0.04094 (  602)
  hydrogen bonds       : angle       4.41956 ( 1629)

*********************** 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
  72 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A 1091 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8593 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 67
  average time/residue: 0.1373
  time to fit residues: 13.6271
Evaluate side-chains
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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  651 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0870
   chunk 60 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 139 optimal weight:    6.9990
   chunk 140 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0170
   chunk 62 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    2.0202

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.105076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.077932 restraints weight = 40316.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.080054 restraints weight = 24513.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.080776 restraints weight = 15422.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.081011 restraints weight = 12941.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.081113 restraints weight = 12948.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3208
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14560  Z= 0.210
  Angle     :  0.580   8.665  20271  Z= 0.304
  Chirality :  0.040   0.214   2322
  Planarity :  0.004   0.046   2066
  Dihedral  : 19.471 166.474   3430
  Min Nonbonded Distance : 1.074

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  9.63 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.23), residues: 1331
  helix:  0.83 (0.20), residues: 660
  sheet:  0.02 (0.49), residues: 125
  loop : -0.50 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 925 
 TYR   0.011   0.001   TYR A 136 
 PHE   0.019   0.002   PHE A1045 
 TRP   0.004   0.001   TRP A1074 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (14560)
  covalent geometry    : angle       0.58028 (20271)
  hydrogen bonds       : bond        0.04525 (  602)
  hydrogen bonds       : angle       4.55455 ( 1629)

*********************** 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
  65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A 1091 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8639 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1343
  time to fit residues: 12.2730
Evaluate side-chains
  61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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  893 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0570
   chunk 74 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 134 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 144 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 139 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   overall best weight:    2.1704

-------------------------------------------------------------------------------
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 863 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.104014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.076597 restraints weight = 68521.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.078130 restraints weight = 30063.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.079337 restraints weight = 18679.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.079614 restraints weight = 14941.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.079794 restraints weight = 14451.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14560  Z= 0.220
  Angle     :  0.598   8.453  20271  Z= 0.314
  Chirality :  0.041   0.212   2322
  Planarity :  0.004   0.048   2066
  Dihedral  : 19.601 167.942   3430
  Min Nonbonded Distance : 1.062

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.47 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.23), residues: 1331
  helix:  0.71 (0.20), residues: 657
  sheet: -0.03 (0.49), residues: 124
  loop : -0.59 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1078 
 TYR   0.012   0.002   TYR A 988 
 PHE   0.019   0.002   PHE A1045 
 TRP   0.004   0.001   TRP A  18 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (14560)
  covalent geometry    : angle       0.59829 (20271)
  hydrogen bonds       : bond        0.04716 (  602)
  hydrogen bonds       : angle       4.66913 ( 1629)

*********************** 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
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A  311 GLU cc_start: 0.5415 (mp0) cc_final: 0.5044 (mp0)
REVERT: A 1091 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8728 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1428
  time to fit residues: 13.3527
Evaluate side-chains
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue   55 SER
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  893 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.106528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.080419 restraints weight = 48693.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.082690 restraints weight = 25407.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.083612 restraints weight = 15710.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.083837 restraints weight = 13346.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.084038 restraints weight = 12691.509|
|-----------------------------------------------------------------------------|
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) = 0.084         |
| 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) = 0.084         |
| 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: 0.8167
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14560  Z= 0.128
  Angle     :  0.522   8.764  20271  Z= 0.277
  Chirality :  0.037   0.209   2322
  Planarity :  0.003   0.046   2066
  Dihedral  : 19.417 165.726   3430
  Min Nonbonded Distance : 1.145

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.63 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.23), residues: 1331
  helix:  0.95 (0.20), residues: 656
  sheet:  0.19 (0.50), residues: 122
  loop : -0.41 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1303 
 TYR   0.013   0.001   TYR A 521 
 PHE   0.017   0.001   PHE A1045 
 TRP   0.006   0.001   TRP A1074 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14560)
  covalent geometry    : angle       0.52241 (20271)
  hydrogen bonds       : bond        0.04132 (  602)
  hydrogen bonds       : angle       4.45067 ( 1629)

********************** 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
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A 1038 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7072 (t80)
REVERT: A 1091 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8647 (tm-30)
  outliers start: 9
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1344
  time to fit residues: 12.8397
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue   55 SER
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  893 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1038 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 128 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 125 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.106848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.080062 restraints weight = 68448.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.081693 restraints weight = 34512.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.082937 restraints weight = 19818.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.083204 restraints weight = 15729.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.083377 restraints weight = 14786.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    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 = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2528

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= 0.129
  Angle     :  0.516   8.688  20271  Z= 0.273
  Chirality :  0.037   0.211   2322
  Planarity :  0.003   0.045   2066
  Dihedral  : 19.366 165.143   3430
  Min Nonbonded Distance : 1.105

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.72 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.23), residues: 1331
  helix:  1.03 (0.20), residues: 660
  sheet:  0.14 (0.50), residues: 124
  loop : -0.40 (0.27), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1078 
 TYR   0.011   0.001   TYR A 521 
 PHE   0.023   0.001   PHE A 606 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (14560)
  covalent geometry    : angle       0.51640 (20271)
  hydrogen bonds       : bond        0.04059 (  602)
  hydrogen bonds       : angle       4.37901 ( 1629)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2193.76 seconds
wall clock time: 38 minutes 58.59 seconds (2338.59 seconds total)