Starting phenix.real_space_refine
on Wed Mar  4 15:53:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s4x_24838/03_2026/7s4x_24838.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.015
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     161      5.49       5
     Mg      5      5.21       5
     S      23      5.16       5
     C    8614      2.51       5
     N    2546      2.21       5
     O    3142      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14491
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 11090
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1354, 11079
          Classifications: {'peptide': 1354}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 1318}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 1354, 11079
          Classifications: {'peptide': 1354}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 1318}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 11262
    Chain: "B"
      Number of atoms: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2103
          Classifications: {'RNA': 98}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
    Chain: "C"
      Number of atoms: 325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 325
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "c"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 405
          Classifications: {'DNA': 20}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 556
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      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: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  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: 5.29, per 1000 atoms: 0.37
  Number of scatterers: 14491
  At special positions: 0
  Unit cell: (89.1, 134.46, 131.22, 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      23     16.00
     P     161     15.00
     Mg      5     11.99
     O    3142      8.00
     N    2546      7.00
     C    8614      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: 1.40
  Conformation dependent library (CDL) restraints added in 882.7 milliseconds
  

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 9 sheets defined
      55.4% alpha, 8.2% beta
      56 base pairs and 90 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.799A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 4.049A  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 145
      removed outlier: 3.707A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 214
    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: 3.726A  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
      removed outlier: 3.586A  pdb=" N   ALA A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 291
    Processing helix  chain 'A' and resid 292 through 306
      removed outlier: 5.047A  pdb=" N   ASP A 298 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 343 through 352
      removed outlier: 4.576A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    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
      removed outlier: 3.529A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.013A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.035A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.745A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASN A 436 " --> pdb=" O   PHE A 432 " (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: 3.698A  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 567
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.966A  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 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 654
      removed outlier: 3.613A  pdb=" N   ARG A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    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 697
    Processing helix  chain 'A' and resid 703 through 711
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 731 through 751
      removed outlier: 4.067A  pdb=" N   LYS A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
      removed outlier: 4.285A  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
    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 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 860 through 866
    Processing helix  chain 'A' and resid 872 through 889
      removed outlier: 5.319A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.506A  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: 3.741A  pdb=" N   GLY A 906 " --> pdb=" O   ALA A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.525A  pdb=" N   LYS A 913 " --> pdb=" O   SER A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 4.175A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL A 922 " --> pdb=" O   LYS A 918 " (cutoff:3.500A)
      removed outlier: 3.655A  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 980 through 1001
      removed outlier: 4.390A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
    Processing helix  chain 'A' and resid 1017 through 1021
    Processing helix  chain 'A' and resid 1030 through 1042
    Processing helix  chain 'A' and resid 1043 through 1047
      removed outlier: 3.522A  pdb=" N   PHE A1046 " --> pdb=" O   MET A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1087
      removed outlier: 3.898A  pdb=" N   ALA A1081 " --> pdb=" O   GLY A1077 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.672A  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
      removed outlier: 3.505A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1317
      removed outlier: 3.908A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A1312 " --> pdb=" O   ASN A1308 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   THR A1314 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LEU A1315 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 7.185A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 8.715A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.644A  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: 9.943A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA4, first strand: chain 'A' and resid 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: 6.596A  pdb=" N   GLU A1064 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.503A  pdb=" N   LYS A1151 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326

    503 hydrogen bonds defined for protein.
    1447 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      139 hydrogen bonds
      270 hydrogen bond angles
      0 basepair planarities
      56 basepair parallelities
      90 stacking parallelities
  Total time for adding SS restraints: 3.61

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2929
        1.33 -     1.45: 4075
        1.45 -     1.57: 7714
        1.57 -     1.69: 317
        1.69 -     1.81: 44
  Bond restraints: 15079
  Sorted by residual:
  bond pdb=" CA  ARG A 976 "
       pdb=" C   ARG A 976 "
    ideal  model  delta    sigma   weight residual
    1.522  1.484  0.039 1.38e-02 5.25e+03 7.79e+00
  bond pdb=" C3'  DG C   8 "
       pdb=" O3'  DG C   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.95e+00
  bond pdb=" CB  THR A 740 "
       pdb=" CG2 THR A 740 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.94e+00
  bond pdb=" CG  LEU A1312 "
       pdb=" CD1 LEU A1312 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.92e+00
  bond pdb=" CA  SER A1136 "
       pdb=" C   SER A1136 "
    ideal  model  delta    sigma   weight residual
    1.531  1.522  0.009 7.40e-03 1.83e+04 1.62e+00
  ... (remaining 15074 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 20439
        1.53 -     3.07: 521
        3.07 -     4.60: 66
        4.60 -     6.14: 14
        6.14 -     7.67: 4
  Bond angle restraints: 21044
  Sorted by residual:
  angle pdb=" N   VAL A1018 "
        pdb=" CA  VAL A1018 "
        pdb=" C   VAL A1018 "
      ideal   model   delta    sigma   weight residual
     112.50  106.96    5.54 1.39e+00 5.18e-01 1.59e+01
  angle pdb=" C   TYR A1326 "
        pdb=" N   PHE A1327 "
        pdb=" CA  PHE A1327 "
      ideal   model   delta    sigma   weight residual
     121.54  128.60   -7.06 1.91e+00 2.74e-01 1.37e+01
  angle pdb=" N   CYS A 574 "
        pdb=" CA  CYS A 574 "
        pdb=" C   CYS A 574 "
      ideal   model   delta    sigma   weight residual
     109.96  115.20   -5.24 1.49e+00 4.50e-01 1.24e+01
  angle pdb=" N   ILE A 312 "
        pdb=" CA  ILE A 312 "
        pdb=" C   ILE A 312 "
      ideal   model   delta    sigma   weight residual
     112.80  109.26    3.54 1.15e+00 7.56e-01 9.46e+00
  angle pdb=" N   LEU A 258 "
        pdb=" CA  LEU A 258 "
        pdb=" C   LEU A 258 "
      ideal   model   delta    sigma   weight residual
     113.43  109.56    3.87 1.26e+00 6.30e-01 9.44e+00
  ... (remaining 21039 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.91: 8512
       33.91 -    67.81: 542
       67.81 -   101.72: 45
      101.72 -   135.62: 0
      135.62 -   169.53: 5
  Dihedral angle restraints: 9104
    sinusoidal: 5117
      harmonic: 3987
  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
    -160.00    9.53 -169.53     1      1.50e+01 4.44e-03 8.46e+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   32.57  167.43     1      1.50e+01 4.44e-03 8.43e+01
  dihedral pdb=" CA  ARG A1122 "
           pdb=" C   ARG A1122 "
           pdb=" N   LYS A1123 "
           pdb=" CA  LYS A1123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.17   21.83     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 9101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1765
       0.040 -    0.081: 506
       0.081 -    0.121: 121
       0.121 -    0.161: 15
       0.161 -    0.202: 3
  Chirality restraints: 2410
  Sorted by residual:
  chirality pdb=" C3'   A B   8 "
            pdb=" C4'   A B   8 "
            pdb=" O3'   A B   8 "
            pdb=" C2'   A B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.28   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  ILE A 122 "
            pdb=" CA  ILE A 122 "
            pdb=" CG1 ILE A 122 "
            pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.49e-01
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 6.93e-01
  ... (remaining 2407 not shown)

  Planarity restraints: 2107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  75 "   -0.023 2.00e-02 2.50e+03   1.10e-02 3.33e+00
        pdb=" N9    A B  75 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    A B  75 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B  75 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B  75 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  75 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B  75 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B  75 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A B  75 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B  75 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A B  75 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  42 "   -0.023 2.00e-02 2.50e+03   1.04e-02 2.98e+00
        pdb=" N9    A B  42 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A B  42 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B  42 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A B  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B  42 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A B  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A B  42 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B  42 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A B  42 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  54 "    0.022 2.00e-02 2.50e+03   9.52e-03 2.72e+00
        pdb=" N9    G B  54 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8    G B  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  54 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G B  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G B  54 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G B  54 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B  54 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2104 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 76
        2.48 -     3.09: 9975
        3.09 -     3.69: 23748
        3.69 -     4.30: 36736
        4.30 -     4.90: 56487
  Nonbonded interactions: 127022
  Sorted by model distance:
  nonbonded pdb=" OP1  DC D  34 "
            pdb="MG    MG A1402 "
     model   vdw
     1.878 2.170
  nonbonded pdb=" OE1 GLU A 762 "
            pdb="MG    MG A1401 "
     model   vdw
     1.915 2.170
  nonbonded pdb=" OD2 ASP A  10 "
            pdb="MG    MG A1402 "
     model   vdw
     1.956 2.170
  nonbonded pdb=" OD1 ASP A  10 "
            pdb="MG    MG A1401 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" ND1 HIS A 983 "
            pdb="MG    MG A1402 "
     model   vdw
     2.091 2.250
  ... (remaining 127017 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.990
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     19.250
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:7.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
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      :  0.006   0.055  15079  Z= 0.257
  Angle     :  0.598   7.670  21044  Z= 0.341
  Chirality :  0.041   0.202   2410
  Planarity :  0.003   0.038   2107
  Dihedral  : 19.275 169.530   6524
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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 are not related in a simple way.
  whole:  0.02 (0.22), residues: 1351
  helix:  0.57 (0.20), residues: 646
  sheet: -0.55 (0.46), residues: 117
  loop : -0.37 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1019 
 TYR   0.016   0.002   TYR A1265 
 PHE   0.021   0.002   PHE A1327 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (15079)
  covalent geometry    : angle       0.59769 (21044)
  hydrogen bonds       : bond        0.14069 (  642)
  hydrogen bonds       : angle       5.95173 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.498 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.8820
  time to fit residues: 69.2588
Evaluate side-chains
  52 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.101876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.066627 restraints weight = 47205.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.68
r_work: 0.2791 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.0923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  15079  Z= 0.146
  Angle     :  0.546   7.599  21044  Z= 0.292
  Chirality :  0.038   0.193   2410
  Planarity :  0.003   0.041   2107
  Dihedral  : 20.797 171.871   3634
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.86 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.23), residues: 1351
  helix:  1.04 (0.20), residues: 645
  sheet: -0.79 (0.42), residues: 120
  loop : -0.16 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 653 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.017   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 840 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (15079)
  covalent geometry    : angle       0.54558 (21044)
  hydrogen bonds       : bond        0.03960 (  642)
  hydrogen bonds       : angle       4.69290 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  905 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7449 (ptp90)
REVERT: A 1271 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7569 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 66
  average time/residue: 0.9562
  time to fit residues: 67.6399
Evaluate side-chains
  57 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 105 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0060
   chunk 31 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 844 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.067633 restraints weight = 40194.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.49
r_work: 0.2815 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15079  Z= 0.136
  Angle     :  0.517   7.244  21044  Z= 0.278
  Chirality :  0.037   0.178   2410
  Planarity :  0.003   0.043   2107
  Dihedral  : 20.637 172.800   3634
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.58 %
    Favored  : 93.84 %
  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 are not related in a simple way.
  whole:  0.71 (0.23), residues: 1351
  helix:  1.30 (0.20), residues: 646
  sheet: -0.74 (0.42), residues: 133
  loop : -0.05 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1058 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.018   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (15079)
  covalent geometry    : angle       0.51680 (21044)
  hydrogen bonds       : bond        0.03526 (  642)
  hydrogen bonds       : angle       4.45330 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: A  674 GLN cc_start: 0.8819 (tp40) cc_final: 0.8429 (mm110)
REVERT: A  905 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7419 (ptp90)
REVERT: A 1019 ARG cc_start: 0.7276 (mmm160) cc_final: 0.7060 (mmm160)
REVERT: A 1271 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7609 (tp30)
REVERT: A 1275 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7181 (mm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 66
  average time/residue: 0.9248
  time to fit residues: 65.5350
Evaluate side-chains
  61 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 111 optimal weight:    0.1980
   chunk 90 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   overall best weight:    2.2388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.099511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.063766 restraints weight = 49110.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.73
r_work: 0.2722 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083  15079  Z= 0.286
  Angle     :  0.590   7.339  21044  Z= 0.313
  Chirality :  0.042   0.211   2410
  Planarity :  0.004   0.047   2107
  Dihedral  : 20.735 168.713   3634
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  6.81 %
    Favored  : 92.28 %
  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 are not related in a simple way.
  whole:  0.54 (0.23), residues: 1351
  helix:  1.15 (0.21), residues: 647
  sheet: -0.77 (0.43), residues: 133
  loop : -0.15 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1078 
 TYR   0.017   0.002   TYR A 155 
 PHE   0.021   0.002   PHE A1327 
 TRP   0.008   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 (15079)
  covalent geometry    : angle       0.58984 (21044)
  hydrogen bonds       : bond        0.04051 (  642)
  hydrogen bonds       : angle       4.50262 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8803 (tt)
REVERT: A  190 GLN cc_start: 0.8299 (tt0) cc_final: 0.7950 (tm130)
REVERT: A  674 GLN cc_start: 0.8863 (tp40) cc_final: 0.8481 (mm110)
REVERT: A  905 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7329 (ptp90)
REVERT: A 1029 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7800 (pp)
REVERT: A 1078 ARG cc_start: 0.7739 (ptt90) cc_final: 0.7389 (ptt90)
REVERT: A 1271 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7655 (tp30)
REVERT: A 1275 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7328 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 64
  average time/residue: 0.9265
  time to fit residues: 63.4713
Evaluate side-chains
  63 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   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 240 ASN
A1261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.067419 restraints weight = 39900.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 2.47
r_work: 0.2797 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15079  Z= 0.141
  Angle     :  0.514   7.166  21044  Z= 0.276
  Chirality :  0.037   0.175   2410
  Planarity :  0.003   0.051   2107
  Dihedral  : 20.640 172.334   3634
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.39 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.23), residues: 1351
  helix:  1.35 (0.21), residues: 646
  sheet: -0.59 (0.45), residues: 125
  loop : -0.10 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 653 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.018   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15079)
  covalent geometry    : angle       0.51364 (21044)
  hydrogen bonds       : bond        0.03400 (  642)
  hydrogen bonds       : angle       4.35476 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8777 (tt)
REVERT: A  190 GLN cc_start: 0.8337 (tt0) cc_final: 0.8027 (tm-30)
REVERT: A  298 ASP cc_start: 0.7823 (m-30) cc_final: 0.7594 (m-30)
REVERT: A  674 GLN cc_start: 0.8874 (tp40) cc_final: 0.8511 (mm110)
REVERT: A  905 ARG cc_start: 0.7658 (ptp90) cc_final: 0.7249 (ptp90)
REVERT: A 1019 ARG cc_start: 0.7213 (mmm160) cc_final: 0.6973 (mmm160)
REVERT: A 1029 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7556 (pp)
REVERT: A 1078 ARG cc_start: 0.7679 (ptt90) cc_final: 0.7352 (ptt90)
REVERT: A 1271 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7506 (tp30)
REVERT: A 1275 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7028 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 0.9440
  time to fit residues: 67.9177
Evaluate side-chains
  66 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 126 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN
A1261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.099432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.063757 restraints weight = 44284.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.62
r_work: 0.2727 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082  15079  Z= 0.291
  Angle     :  0.591   7.275  21044  Z= 0.312
  Chirality :  0.042   0.208   2410
  Planarity :  0.004   0.047   2107
  Dihedral  : 20.710 168.813   3634
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  7.06 %
    Favored  : 91.46 %
  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 are not related in a simple way.
  whole:  0.56 (0.23), residues: 1351
  helix:  1.18 (0.21), residues: 647
  sheet: -0.77 (0.43), residues: 133
  loop : -0.16 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1058 
 TYR   0.018   0.002   TYR A 155 
 PHE   0.019   0.002   PHE A1327 
 TRP   0.008   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 (15079)
  covalent geometry    : angle       0.59085 (21044)
  hydrogen bonds       : bond        0.03983 (  642)
  hydrogen bonds       : angle       4.44783 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8802 (tt)
REVERT: A  190 GLN cc_start: 0.8311 (tt0) cc_final: 0.8004 (tm-30)
REVERT: A  576 ASP cc_start: 0.8756 (m-30) cc_final: 0.8553 (m-30)
REVERT: A  627 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6900 (tp30)
REVERT: A  674 GLN cc_start: 0.8882 (tp40) cc_final: 0.8495 (mm110)
REVERT: A  781 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8663 (tpt)
REVERT: A  905 ARG cc_start: 0.7660 (ptp90) cc_final: 0.7217 (ptp90)
REVERT: A  939 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8082 (mmt)
REVERT: A 1029 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (pp)
REVERT: A 1271 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7602 (tp30)
REVERT: A 1275 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7179 (mm-30)
  outliers start: 17
  outliers final: 5
  residues processed: 67
  average time/residue: 0.9370
  time to fit residues: 67.6027
Evaluate side-chains
  68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 133 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0570
   chunk 73 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 129 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A1261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.067987 restraints weight = 38029.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.41
r_work: 0.2818 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15079  Z= 0.129
  Angle     :  0.507   7.286  21044  Z= 0.272
  Chirality :  0.037   0.173   2410
  Planarity :  0.003   0.044   2107
  Dihedral  : 20.604 172.929   3634
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.72 %
    Favored  : 91.22 %
  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 are not related in a simple way.
  whole:  0.81 (0.23), residues: 1351
  helix:  1.42 (0.21), residues: 646
  sheet: -0.64 (0.45), residues: 125
  loop : -0.10 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 653 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.017   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (15079)
  covalent geometry    : angle       0.50654 (21044)
  hydrogen bonds       : bond        0.03284 (  642)
  hydrogen bonds       : angle       4.29245 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8811 (tt)
REVERT: A  190 GLN cc_start: 0.8343 (tt0) cc_final: 0.8016 (tm-30)
REVERT: A  674 GLN cc_start: 0.8849 (tp40) cc_final: 0.8462 (mm110)
REVERT: A  837 ASP cc_start: 0.8062 (p0) cc_final: 0.7850 (p0)
REVERT: A  905 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7199 (ptp90)
REVERT: A 1029 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7501 (pp)
REVERT: A 1078 ARG cc_start: 0.7673 (ptt90) cc_final: 0.7296 (ptt90)
REVERT: A 1271 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7628 (tp30)
REVERT: A 1275 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7155 (mm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 70
  average time/residue: 0.8717
  time to fit residues: 65.5592
Evaluate side-chains
  68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  868 ASP
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0980
   chunk 67 optimal weight:    0.8980
   chunk 138 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 145 optimal weight:    2.9990
   chunk 146 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A1261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.066619 restraints weight = 40322.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 2.49
r_work: 0.2787 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15079  Z= 0.172
  Angle     :  0.523   8.232  21044  Z= 0.280
  Chirality :  0.038   0.175   2410
  Planarity :  0.004   0.082   2107
  Dihedral  : 20.585 171.563   3634
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.13 %
    Favored  : 91.05 %
  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 are not related in a simple way.
  whole:  0.79 (0.23), residues: 1351
  helix:  1.40 (0.20), residues: 646
  sheet: -0.62 (0.45), residues: 125
  loop : -0.10 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 653 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.017   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (15079)
  covalent geometry    : angle       0.52307 (21044)
  hydrogen bonds       : bond        0.03407 (  642)
  hydrogen bonds       : angle       4.29408 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8813 (tt)
REVERT: A  190 GLN cc_start: 0.8329 (tt0) cc_final: 0.8007 (tm-30)
REVERT: A  674 GLN cc_start: 0.8848 (tp40) cc_final: 0.8462 (mm110)
REVERT: A  879 MET cc_start: 0.6453 (mtt) cc_final: 0.6019 (mtt)
REVERT: A  905 ARG cc_start: 0.7618 (ptp90) cc_final: 0.7193 (ptp90)
REVERT: A 1029 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7481 (pp)
REVERT: A 1271 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7621 (tp30)
REVERT: A 1275 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7183 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 67
  average time/residue: 0.9246
  time to fit residues: 66.6732
Evaluate side-chains
  67 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  868 ASP
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 240 ASN
A1261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.101970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.066553 restraints weight = 44239.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.60
r_work: 0.2781 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15079  Z= 0.162
  Angle     :  0.518   8.665  21044  Z= 0.277
  Chirality :  0.038   0.176   2410
  Planarity :  0.003   0.047   2107
  Dihedral  : 20.578 171.425   3634
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.13 %
    Favored  : 90.97 %
  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 are not related in a simple way.
  whole:  0.83 (0.23), residues: 1351
  helix:  1.44 (0.20), residues: 646
  sheet: -0.61 (0.45), residues: 125
  loop : -0.09 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1078 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.017   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (15079)
  covalent geometry    : angle       0.51768 (21044)
  hydrogen bonds       : bond        0.03366 (  642)
  hydrogen bonds       : angle       4.28730 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8818 (tt)
REVERT: A  190 GLN cc_start: 0.8333 (tt0) cc_final: 0.8012 (tm-30)
REVERT: A  674 GLN cc_start: 0.8855 (tp40) cc_final: 0.8465 (mm110)
REVERT: A  781 MET cc_start: 0.8870 (tpp) cc_final: 0.8618 (tpt)
REVERT: A  879 MET cc_start: 0.6470 (mtt) cc_final: 0.6030 (mtt)
REVERT: A  905 ARG cc_start: 0.7601 (ptp90) cc_final: 0.7173 (ptp90)
REVERT: A 1029 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7529 (pp)
REVERT: A 1271 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7661 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 68
  average time/residue: 0.9621
  time to fit residues: 69.9301
Evaluate side-chains
  66 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 146 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0070
   chunk 55 optimal weight:    4.9990
   chunk 140 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 129 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A1261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.067163 restraints weight = 46289.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.66
r_work: 0.2795 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15079  Z= 0.134
  Angle     :  0.512   8.742  21044  Z= 0.274
  Chirality :  0.037   0.175   2410
  Planarity :  0.004   0.091   2107
  Dihedral  : 20.568 172.125   3634
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.29 %
    Favored  : 91.05 %
  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 are not related in a simple way.
  whole:  0.88 (0.23), residues: 1351
  helix:  1.49 (0.21), residues: 646
  sheet: -0.52 (0.45), residues: 123
  loop : -0.10 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A 653 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.016   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (15079)
  covalent geometry    : angle       0.51246 (21044)
  hydrogen bonds       : bond        0.03267 (  642)
  hydrogen bonds       : angle       4.26277 ( 1717)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8819 (tt)
REVERT: A  190 GLN cc_start: 0.8331 (tt0) cc_final: 0.8007 (tm-30)
REVERT: A  674 GLN cc_start: 0.8848 (tp40) cc_final: 0.8461 (mm110)
REVERT: A  781 MET cc_start: 0.8856 (tpp) cc_final: 0.8610 (tpt)
REVERT: A  879 MET cc_start: 0.6504 (mtt) cc_final: 0.6085 (mtt)
REVERT: A  905 ARG cc_start: 0.7628 (ptp90) cc_final: 0.7208 (ptp90)
REVERT: A 1029 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7506 (pp)
REVERT: A 1271 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7670 (tp30)
REVERT: A 1275 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7316 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 0.9299
  time to fit residues: 64.0675
Evaluate side-chains
  65 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1029 ILE
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.102603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.067577 restraints weight = 36552.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 2.41
r_work: 0.2814 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  15079  Z= 0.142
  Angle     :  0.509   8.600  21044  Z= 0.272
  Chirality :  0.037   0.174   2410
  Planarity :  0.003   0.075   2107
  Dihedral  : 20.536 172.152   3634
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.46 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.23), residues: 1351
  helix:  1.54 (0.21), residues: 646
  sheet: -0.51 (0.45), residues: 123
  loop : -0.10 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 653 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.016   0.001   PHE A1327 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (15079)
  covalent geometry    : angle       0.50856 (21044)
  hydrogen bonds       : bond        0.03258 (  642)
  hydrogen bonds       : angle       4.23211 ( 1717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4803.19 seconds
wall clock time: 82 minutes 39.54 seconds (4959.54 seconds total)