Starting phenix.real_space_refine
on Thu Jun  4 10:15:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vy1_65448/06_2026/9vy1_65448.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.037
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: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    7636      2.51       5
     N    2026      2.21       5
     O    2221      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11940
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 9180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1146, 9180
          Classifications: {'peptide': 1146}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1102}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 1221
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 157, 1218
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 5, 'TRANS': 151}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 157, 1218
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 5, 'TRANS': 151}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1225
    Chain: "C"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 591
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 452
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 1, 'TRANS': 57}
    Chain: "E"
      Number of atoms: 496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 496
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 1, 'TRANS': 63}
  Time building chain proxies: 3.40, per 1000 atoms: 0.28
  Number of scatterers: 11940
  At special positions: 0
  Unit cell: (96.36, 111.252, 178.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    2221      8.00
     N    2026      7.00
     C    7636      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: 1.01
  Conformation dependent library (CDL) restraints added in 599.0 milliseconds
  

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2836

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 7 sheets defined
      62.8% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 4.016A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 59 through 77
      removed outlier: 3.559A  pdb=" N   LYS A  77 " --> pdb=" O   ASN A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 95
    Processing helix  chain 'A' and resid 103 through 135
      removed outlier: 3.773A  pdb=" N   ILE A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   HIS A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   GLN A 123 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 151
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 161 through 181
    Processing helix  chain 'A' and resid 224 through 248
      removed outlier: 3.520A  pdb=" N   ASP A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 266
    Processing helix  chain 'A' and resid 267 through 269
      No H-bonds generated for 'chain 'A' and resid 267 through 269'
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 275 through 292
      removed outlier: 3.511A  pdb=" N   VAL A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLU A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
      removed outlier: 4.070A  pdb=" N   LEU A 288 " --> pdb=" O   GLU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 302 through 319
      removed outlier: 4.039A  pdb=" N   HIS A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 339
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 3.561A  pdb=" N   SER A 351 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 353 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 375
      removed outlier: 3.921A  pdb=" N   ALA A 366 " --> pdb=" O   GLU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 402
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.524A  pdb=" N   PHE A 443 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 480
      removed outlier: 3.593A  pdb=" N   TRP A 476 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP A 477 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A 479 " --> pdb=" O   TRP A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 504
    Processing helix  chain 'A' and resid 509 through 519
      removed outlier: 3.667A  pdb=" N   VAL A 517 " --> pdb=" O   MET A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 524
      removed outlier: 3.506A  pdb=" N   LEU A 523 " --> pdb=" O   GLY A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 566
    Processing helix  chain 'A' and resid 567 through 573
    Processing helix  chain 'A' and resid 667 through 671
      removed outlier: 3.830A  pdb=" N   TRP A 671 " --> pdb=" O   CYS A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 688
      removed outlier: 5.374A  pdb=" N   ILE A 678 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   PHE A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ARG A 682 " --> pdb=" O   ILE A 678 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 683 " --> pdb=" O   PHE A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 700
    Processing helix  chain 'A' and resid 721 through 725
      removed outlier: 3.593A  pdb=" N   VAL A 725 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 763
      Proline residue:  A 753  - end of helix
    Processing helix  chain 'A' and resid 788 through 814
    Processing helix  chain 'A' and resid 849 through 853
    Processing helix  chain 'A' and resid 863 through 881
      removed outlier: 3.569A  pdb=" N   ALA A 867 " --> pdb=" O   GLU A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 906
    Processing helix  chain 'A' and resid 913 through 922
      Proline residue:  A 919  - end of helix
    Processing helix  chain 'A' and resid 924 through 933
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 945 through 949
    Processing helix  chain 'A' and resid 955 through 971
    Processing helix  chain 'A' and resid 975 through 981
      removed outlier: 4.455A  pdb=" N   HIS A 979 " --> pdb=" O   GLU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 997
    Processing helix  chain 'A' and resid 1008 through 1024
      removed outlier: 3.596A  pdb=" N   SER A1024 " --> pdb=" O   TYR A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1031
    Processing helix  chain 'A' and resid 1038 through 1050
    Processing helix  chain 'A' and resid 1056 through 1066
    Processing helix  chain 'A' and resid 1067 through 1079
    Processing helix  chain 'A' and resid 1082 through 1092
    Processing helix  chain 'A' and resid 1096 through 1105
    Processing helix  chain 'A' and resid 1105 through 1118
    Processing helix  chain 'A' and resid 1132 through 1145
    Processing helix  chain 'A' and resid 1145 through 1150
    Processing helix  chain 'A' and resid 1161 through 1166
      removed outlier: 3.521A  pdb=" N   SER A1165 " --> pdb=" O   ASP A1161 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET A1166 " --> pdb=" O   ILE A1162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1161 through 1166'
    Processing helix  chain 'A' and resid 1307 through 1311
      removed outlier: 3.604A  pdb=" N   THR A1311 " --> pdb=" O   ALA A1308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1330 through 1348
    Processing helix  chain 'B' and resid 318 through 369
    Processing helix  chain 'B' and resid 458 through 471
      removed outlier: 4.324A  pdb=" N   ASN B 462 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 486
      removed outlier: 3.882A  pdb=" N   ASP B 479 " --> pdb=" O   THR B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 490 through 508
    Processing helix  chain 'C' and resid 318 through 374
      removed outlier: 3.747A  pdb=" N   THR C 362 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 371
      removed outlier: 4.301A  pdb=" N   ILE D 370 " --> pdb=" O   HIS D 366 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 318 through 368
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.208A  pdb=" N   ARG A  83 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   TYR A 222 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   TYR A 219 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381
      removed outlier: 7.626A  pdb=" N   ALA E 373 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE B 398 " --> pdb=" O   ALA E 373 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.672A  pdb=" N   LYS A 447 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549
      removed outlier: 5.041A  pdb=" N   LEU A 530 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 771
      removed outlier: 3.831A  pdb=" N   ARG A 765 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 832
      removed outlier: 4.341A  pdb=" N   ILE A 836 " --> pdb=" O   VAL A 843 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1167 through 1169

    726 hydrogen bonds defined for protein.
    2073 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.16

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3839
        1.34 -     1.46: 2258
        1.46 -     1.58: 5978
        1.58 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 12168
  Sorted by residual:
  bond pdb=" C   GLU A 284 "
       pdb=" N   PRO A 285 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.027 1.23e-02 6.61e+03 4.70e+00
  bond pdb=" C   TRP A 856 "
       pdb=" N   SER A 857 "
    ideal  model  delta    sigma   weight residual
    1.325  1.337 -0.013 1.14e-02 7.69e+03 1.21e+00
  bond pdb=" N   ASP A 509 "
       pdb=" CA  ASP A 509 "
    ideal  model  delta    sigma   weight residual
    1.457  1.441  0.015 1.41e-02 5.03e+03 1.20e+00
  bond pdb=" CA  ASP D 328 "
       pdb=" CB  ASP D 328 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.68e-02 3.54e+03 1.13e+00
  bond pdb=" C   ILE A 752 "
       pdb=" N   PRO A 753 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.28e-02 6.10e+03 1.09e+00
  ... (remaining 12163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 16096
        1.82 -     3.63: 311
        3.63 -     5.45: 26
        5.45 -     7.27: 11
        7.27 -     9.08: 1
  Bond angle restraints: 16445
  Sorted by residual:
  angle pdb=" N   ILE E 318 "
        pdb=" CA  ILE E 318 "
        pdb=" C   ILE E 318 "
      ideal   model   delta    sigma   weight residual
     113.53  109.35    4.18 9.80e-01 1.04e+00 1.82e+01
  angle pdb=" C   SER A 857 "
        pdb=" CA  SER A 857 "
        pdb=" CB  SER A 857 "
      ideal   model   delta    sigma   weight residual
     115.79  110.76    5.03 1.19e+00 7.06e-01 1.79e+01
  angle pdb=" C   ASP D 327 "
        pdb=" N   ASP D 328 "
        pdb=" CA  ASP D 328 "
      ideal   model   delta    sigma   weight residual
     121.14  115.12    6.02 1.75e+00 3.27e-01 1.18e+01
  angle pdb=" C   HIS D 326 "
        pdb=" N   ASP D 327 "
        pdb=" CA  ASP D 327 "
      ideal   model   delta    sigma   weight residual
     121.14  115.45    5.69 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" CA  GLU A 858 "
        pdb=" CB  GLU A 858 "
        pdb=" CG  GLU A 858 "
      ideal   model   delta    sigma   weight residual
     114.10  120.32   -6.22 2.00e+00 2.50e-01 9.68e+00
  ... (remaining 16440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.27: 6681
       13.27 -    26.54: 534
       26.54 -    39.81: 136
       39.81 -    53.08: 13
       53.08 -    66.35: 5
  Dihedral angle restraints: 7369
    sinusoidal: 2980
      harmonic: 4389
  Sorted by residual:
  dihedral pdb=" CA  PHE A  57 "
           pdb=" C   PHE A  57 "
           pdb=" N   SER A  58 "
           pdb=" CA  SER A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.61  -19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  PHE E 377 "
           pdb=" C   PHE E 377 "
           pdb=" N   GLY E 378 "
           pdb=" CA  GLY E 378 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  LEU B 406 "
           pdb=" C   LEU B 406 "
           pdb=" N   ALA B 407 "
           pdb=" CA  ALA B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 7366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1217
       0.037 -    0.074: 521
       0.074 -    0.111: 123
       0.111 -    0.148: 27
       0.148 -    0.185: 5
  Chirality restraints: 1893
  Sorted by residual:
  chirality pdb=" CA  ASP D 328 "
            pdb=" N   ASP D 328 "
            pdb=" C   ASP D 328 "
            pdb=" CB  ASP D 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality pdb=" CA  ASP B 328 "
            pdb=" N   ASP B 328 "
            pdb=" C   ASP B 328 "
            pdb=" CB  ASP B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CB  ILE A1068 "
            pdb=" CA  ILE A1068 "
            pdb=" CG1 ILE A1068 "
            pdb=" CG2 ILE A1068 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.54e-01
  ... (remaining 1890 not shown)

  Planarity restraints: 2067
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 856 "    0.011 2.00e-02 2.50e+03   1.59e-02 6.29e+00
        pdb=" CG  TRP A 856 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 856 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 856 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 856 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 856 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 856 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 856 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 856 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 856 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 374 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.50e+00
        pdb=" N   PRO D 375 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D 375 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 375 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 453 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.76e+00
        pdb=" N   PRO B 454 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 454 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 454 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2064 not shown)

  Histogram of nonbonded interaction distances:
        2.60 -     3.06: 7948
        3.06 -     3.52: 12417
        3.52 -     3.98: 19365
        3.98 -     4.44: 23671
        4.44 -     4.90: 35326
  Nonbonded interactions: 98727
  Sorted by model distance:
  nonbonded pdb=" N   VAL A1006 "
            pdb=" N   GLN A1007 "
     model   vdw
     2.604 2.560
  nonbonded pdb=" N   VAL A 861 "
            pdb=" O   VAL A 861 "
     model   vdw
     2.609 2.496
  nonbonded pdb=" O   ASP D 327 "
            pdb=" CA  ASP D 328 "
     model   vdw
     2.616 2.776
  nonbonded pdb=" N   ILE C 381 "
            pdb=" N   LYS C 382 "
     model   vdw
     2.619 2.560
  nonbonded pdb=" O   ASP B 327 "
            pdb=" CA  ASP B 328 "
     model   vdw
     2.624 2.776
  ... (remaining 98722 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 317 through 375)
}

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=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.420
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12168  Z= 0.167
  Angle     :  0.606   9.084  16445  Z= 0.332
  Chirality :  0.043   0.185   1893
  Planarity :  0.005   0.053   2067
  Dihedral  : 10.218  66.352   4533
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.69 (0.21), residues: 1477
  helix:  1.17 (0.17), residues: 862
  sheet:  1.41 (0.59), residues: 81
  loop : -0.82 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 885 
 TYR   0.012   0.001   TYR A 991 
 PHE   0.022   0.002   PHE A 304 
 TRP   0.041   0.002   TRP A 856 
 HIS   0.007   0.001   HIS C 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.17 (12168)
  covalent geometry    : angle       0.60551 /  0.33 (16445)
  hydrogen bonds       : bond        0.14202 /  9.59 (  726)
  hydrogen bonds       : angle       5.30110 /  3.82 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 351
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7355 (tp40) cc_final: 0.7106 (tp-100)
REVERT: A   74 SER cc_start: 0.8864 (t) cc_final: 0.8632 (m)
REVERT: A  323 THR cc_start: 0.8879 (p) cc_final: 0.8575 (p)
REVERT: A  524 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8801 (mtmp)
REVERT: A  540 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8409 (mmmm)
REVERT: A  765 ARG cc_start: 0.8247 (mtt180) cc_final: 0.8039 (ttm110)
REVERT: A  859 THR cc_start: 0.8764 (p) cc_final: 0.8554 (t)
REVERT: A  997 ASP cc_start: 0.8034 (t0) cc_final: 0.7638 (t0)
REVERT: A 1013 LEU cc_start: 0.8370 (tp) cc_final: 0.8119 (tm)
REVERT: A 1054 ILE cc_start: 0.9151 (mt) cc_final: 0.8938 (mp)
REVERT: A 1062 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7502 (mm-30)
REVERT: A 1078 MET cc_start: 0.7722 (tpt) cc_final: 0.7300 (tpt)
REVERT: A 1090 MET cc_start: 0.6668 (ttm) cc_final: 0.6464 (ttm)
REVERT: A 1124 CYS cc_start: 0.8131 (t) cc_final: 0.7450 (t)
REVERT: A 1127 ILE cc_start: 0.8607 (mm) cc_final: 0.8248 (mp)
REVERT: A 1148 LEU cc_start: 0.8906 (tp) cc_final: 0.8647 (tt)
REVERT: A 1338 LEU cc_start: 0.8645 (mt) cc_final: 0.8416 (mm)
REVERT: B  359 SER cc_start: 0.8759 (m) cc_final: 0.8454 (p)
REVERT: B  458 GLU cc_start: 0.8148 (mp0) cc_final: 0.7687 (mp0)
  outliers start: 0
  outliers final: 1
  residues processed: 351
  average time/residue: 0.6743
  time to fit residues: 254.4553
Evaluate side-chains
  286 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  363 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.0770
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0970
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0060
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.3552

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

Flipped N/Q/H residues before XYZ refinement:
A 344 HIS
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN
A 566 ASN
A 909 ASN
A1105 ASN
** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 GLN
B 366 HIS
B 462 ASN
B 477 HIS
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.120128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.099986 restraints weight = 29379.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.55
r_work: 0.3437 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12168  Z= 0.116
  Angle     :  0.528  12.437  16445  Z= 0.272
  Chirality :  0.040   0.145   1893
  Planarity :  0.004   0.043   2067
  Dihedral  :  3.870  20.495   1624
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.52 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.65 (0.22), residues: 1477
  helix:  2.05 (0.18), residues: 864
  sheet:  1.05 (0.56), residues: 91
  loop : -0.53 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1052 
 TYR   0.013   0.001   TYR A 942 
 PHE   0.026   0.001   PHE A 546 
 TRP   0.012   0.001   TRP A1189 
 HIS   0.004   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 (12168)
  covalent geometry    : angle       0.52843 /  0.27 (16445)
  hydrogen bonds       : bond        0.04349 /  2.87 (  726)
  hydrogen bonds       : angle       4.03503 /  2.88 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 293
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 THR cc_start: 0.8823 (p) cc_final: 0.8532 (p)
REVERT: A  342 ASP cc_start: 0.8166 (t0) cc_final: 0.7727 (p0)
REVERT: A  491 ARG cc_start: 0.8302 (ttm170) cc_final: 0.8081 (mtp85)
REVERT: A  496 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7854 (ptp-170)
REVERT: A  997 ASP cc_start: 0.7866 (t0) cc_final: 0.7455 (t0)
REVERT: A 1062 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7433 (mm-30)
REVERT: A 1090 MET cc_start: 0.6632 (ttm) cc_final: 0.6406 (ttm)
REVERT: A 1127 ILE cc_start: 0.8601 (mm) cc_final: 0.8384 (mp)
REVERT: B  458 GLU cc_start: 0.8044 (mp0) cc_final: 0.7661 (mp0)
REVERT: E  350 LYS cc_start: 0.8845 (tppp) cc_final: 0.8627 (tmmt)
  outliers start: 25
  outliers final: 9
  residues processed: 303
  average time/residue: 0.6682
  time to fit residues: 217.6448
Evaluate side-chains
  286 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 277
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue 1099 VAL
Chi-restraints excluded: chain A residue 1316 ASP
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 121 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 ASN
A 519 ASN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
B 366 HIS
B 477 HIS
E 356 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.116656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097962 restraints weight = 19829.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.97
r_work: 0.3433 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12168  Z= 0.188
  Angle     :  0.551   9.320  16445  Z= 0.286
  Chirality :  0.042   0.175   1893
  Planarity :  0.004   0.038   2067
  Dihedral  :  3.873  17.857   1622
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.39 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.83 (0.22), residues: 1477
  helix:  2.28 (0.18), residues: 861
  sheet:  0.62 (0.54), residues: 101
  loop : -0.52 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1019 
 TYR   0.013   0.001   TYR A 999 
 PHE   0.030   0.002   PHE A 546 
 TRP   0.010   0.001   TRP A 856 
 HIS   0.010   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.19 (12168)
  covalent geometry    : angle       0.55084 /  0.29 (16445)
  hydrogen bonds       : bond        0.04660 /  3.04 (  726)
  hydrogen bonds       : angle       3.97286 /  2.84 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 288
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 THR cc_start: 0.8966 (p) cc_final: 0.8694 (p)
REVERT: A  491 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8368 (mtp85)
REVERT: A  496 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.8017 (ptp-170)
REVERT: A  997 ASP cc_start: 0.8067 (t0) cc_final: 0.7681 (t0)
REVERT: A 1045 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8725 (tp)
REVERT: A 1062 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7669 (mm-30)
REVERT: A 1090 MET cc_start: 0.6865 (ttm) cc_final: 0.6650 (ttm)
REVERT: B  458 GLU cc_start: 0.8238 (mp0) cc_final: 0.7814 (mp0)
REVERT: E  350 LYS cc_start: 0.8959 (tppp) cc_final: 0.8731 (tppp)
  outliers start: 34
  outliers final: 21
  residues processed: 297
  average time/residue: 0.6871
  time to fit residues: 218.6960
Evaluate side-chains
  295 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 273
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain B residue  350 LYS
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  489 LYS
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  352 GLN
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 124 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 ASN
A 519 ASN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
A 952 ASN
B 366 HIS
B 477 HIS
** D 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 356 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.120621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.100808 restraints weight = 24505.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.29
r_work: 0.3421 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12168  Z= 0.140
  Angle     :  0.538   8.396  16445  Z= 0.276
  Chirality :  0.041   0.216   1893
  Planarity :  0.004   0.035   2067
  Dihedral  :  3.796  17.813   1622
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.66 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.98 (0.22), residues: 1477
  helix:  2.41 (0.18), residues: 865
  sheet:  0.61 (0.53), residues: 101
  loop : -0.48 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1019 
 TYR   0.010   0.001   TYR A 277 
 PHE   0.031   0.001   PHE A 546 
 TRP   0.009   0.001   TRP A1189 
 HIS   0.011   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 (12168)
  covalent geometry    : angle       0.53757 /  0.28 (16445)
  hydrogen bonds       : bond        0.04229 /  2.76 (  726)
  hydrogen bonds       : angle       3.84660 /  2.76 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 279
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASN cc_start: 0.6921 (p0) cc_final: 0.6682 (p0)
REVERT: A  284 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7980 (mm-30)
REVERT: A  323 THR cc_start: 0.8949 (p) cc_final: 0.8675 (p)
REVERT: A  491 ARG cc_start: 0.8626 (ttm170) cc_final: 0.8395 (mtp85)
REVERT: A  496 ARG cc_start: 0.8258 (ptp-170) cc_final: 0.7997 (ptp-170)
REVERT: A  997 ASP cc_start: 0.8123 (t0) cc_final: 0.7728 (t0)
REVERT: A 1043 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: A 1062 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7672 (mm-30)
REVERT: A 1090 MET cc_start: 0.6851 (ttm) cc_final: 0.6643 (ttm)
REVERT: A 1102 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8324 (ttt-90)
REVERT: B  458 GLU cc_start: 0.8277 (mp0) cc_final: 0.7824 (mp0)
REVERT: B  492 LYS cc_start: 0.8339 (mppt) cc_final: 0.7942 (mppt)
  outliers start: 42
  outliers final: 20
  residues processed: 293
  average time/residue: 0.7014
  time to fit residues: 220.4159
Evaluate side-chains
  295 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 274
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1102 ARG
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  489 LYS
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9990
   chunk 136 optimal weight:    6.9990
   chunk 97 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 134 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 474 ASN
A 504 ASN
A 519 ASN
A 845 GLN
A 909 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.120118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.100637 restraints weight = 22168.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.18
r_work: 0.3426 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12168  Z= 0.154
  Angle     :  0.534   9.025  16445  Z= 0.277
  Chirality :  0.041   0.274   1893
  Planarity :  0.004   0.041   2067
  Dihedral  :  3.767  17.913   1622
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.93 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.00 (0.22), residues: 1477
  helix:  2.44 (0.18), residues: 868
  sheet:  0.67 (0.53), residues: 101
  loop : -0.52 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1019 
 TYR   0.011   0.001   TYR A 277 
 PHE   0.032   0.001   PHE A 546 
 TRP   0.008   0.001   TRP A 440 
 HIS   0.012   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 (12168)
  covalent geometry    : angle       0.53371 /  0.28 (16445)
  hydrogen bonds       : bond        0.04306 /  2.81 (  726)
  hydrogen bonds       : angle       3.82090 /  2.74 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 278
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A   59 ASN cc_start: 0.7067 (p0) cc_final: 0.6765 (p0)
REVERT: A  174 GLU cc_start: 0.8474 (tt0) cc_final: 0.8202 (tm-30)
REVERT: A  323 THR cc_start: 0.8942 (p) cc_final: 0.8674 (p)
REVERT: A  491 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8428 (mtp85)
REVERT: A  496 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.8011 (ptp-170)
REVERT: A  997 ASP cc_start: 0.8112 (t0) cc_final: 0.7691 (t0)
REVERT: A 1045 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8779 (tp)
REVERT: A 1062 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7704 (mm-30)
REVERT: A 1090 MET cc_start: 0.6855 (ttm) cc_final: 0.6653 (ttm)
REVERT: B  458 GLU cc_start: 0.8258 (mp0) cc_final: 0.7762 (mp0)
REVERT: B  492 LYS cc_start: 0.8372 (mppt) cc_final: 0.7989 (mppt)
REVERT: E  350 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8675 (tppp)
  outliers start: 44
  outliers final: 25
  residues processed: 292
  average time/residue: 0.7038
  time to fit residues: 220.4598
Evaluate side-chains
  301 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 274
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  489 LYS
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 76 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 744 GLN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
B 326 HIS
B 366 HIS
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.118533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.098879 restraints weight = 22660.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.20
r_work: 0.3436 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12168  Z= 0.129
  Angle     :  0.541  10.165  16445  Z= 0.277
  Chirality :  0.040   0.255   1893
  Planarity :  0.004   0.039   2067
  Dihedral  :  3.705  17.494   1622
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.43 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.19 (0.22), residues: 1477
  helix:  2.57 (0.18), residues: 864
  sheet:  0.73 (0.53), residues: 101
  loop : -0.39 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1019 
 TYR   0.010   0.001   TYR A 277 
 PHE   0.034   0.001   PHE A 546 
 TRP   0.009   0.001   TRP A 695 
 HIS   0.012   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (12168)
  covalent geometry    : angle       0.54111 /  0.28 (16445)
  hydrogen bonds       : bond        0.04067 /  2.66 (  726)
  hydrogen bonds       : angle       3.75367 /  2.69 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 279
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASN cc_start: 0.6898 (p0) cc_final: 0.6609 (p0)
REVERT: A  323 THR cc_start: 0.8893 (p) cc_final: 0.8619 (p)
REVERT: A  491 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8392 (mtp85)
REVERT: A  496 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.7979 (ptp-170)
REVERT: A  654 GLU cc_start: 0.7842 (pt0) cc_final: 0.7634 (pt0)
REVERT: A  997 ASP cc_start: 0.8085 (t0) cc_final: 0.7664 (t0)
REVERT: A 1045 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8760 (tp)
REVERT: A 1062 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7712 (mm-30)
REVERT: A 1102 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8394 (ttt-90)
REVERT: B  458 GLU cc_start: 0.8241 (mp0) cc_final: 0.7760 (mp0)
REVERT: E  350 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (tppp)
  outliers start: 35
  outliers final: 21
  residues processed: 290
  average time/residue: 0.6985
  time to fit residues: 217.5807
Evaluate side-chains
  297 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 273
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1102 ARG
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  489 LYS
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  345 GLU
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 138 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 504 ASN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
B 366 HIS
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.117965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.098226 restraints weight = 22735.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.22
r_work: 0.3427 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12168  Z= 0.143
  Angle     :  0.551  10.951  16445  Z= 0.283
  Chirality :  0.041   0.309   1893
  Planarity :  0.004   0.046   2067
  Dihedral  :  3.693  17.573   1622
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.80 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.24 (0.22), residues: 1477
  helix:  2.61 (0.18), residues: 863
  sheet:  0.81 (0.54), residues: 101
  loop : -0.35 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1019 
 TYR   0.010   0.001   TYR A 277 
 PHE   0.033   0.001   PHE A 546 
 TRP   0.008   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 (12168)
  covalent geometry    : angle       0.55120 /  0.28 (16445)
  hydrogen bonds       : bond        0.04140 /  2.71 (  726)
  hydrogen bonds       : angle       3.75312 /  2.69 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 277
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASN cc_start: 0.7038 (p0) cc_final: 0.6738 (p0)
REVERT: A  323 THR cc_start: 0.8912 (p) cc_final: 0.8640 (p)
REVERT: A  491 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8408 (mtp85)
REVERT: A  496 ARG cc_start: 0.8301 (ptp-170) cc_final: 0.8015 (ptp-170)
REVERT: A  654 GLU cc_start: 0.7848 (pt0) cc_final: 0.7634 (pt0)
REVERT: A  736 MET cc_start: 0.8721 (mmm) cc_final: 0.8406 (mmt)
REVERT: A  739 ILE cc_start: 0.8939 (mm) cc_final: 0.8738 (mp)
REVERT: A  997 ASP cc_start: 0.8111 (t0) cc_final: 0.7696 (t0)
REVERT: A 1062 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: B  458 GLU cc_start: 0.8293 (mp0) cc_final: 0.7815 (mp0)
REVERT: E  350 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8693 (tppp)
  outliers start: 42
  outliers final: 26
  residues processed: 289
  average time/residue: 0.7039
  time to fit residues: 218.2739
Evaluate side-chains
  301 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 274
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  666 LYS
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  989 SER
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  489 LYS
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Chi-restraints excluded: chain E residue  352 GLN
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 110 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   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  60 GLN
A 775 GLN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
A1143 HIS
B 366 HIS
E 356 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.119119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.099885 restraints weight = 19681.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.01
r_work: 0.3421 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12168  Z= 0.188
  Angle     :  0.590   9.880  16445  Z= 0.302
  Chirality :  0.043   0.339   1893
  Planarity :  0.004   0.048   2067
  Dihedral  :  3.796  18.843   1622
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.62 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.13 (0.22), residues: 1477
  helix:  2.47 (0.17), residues: 877
  sheet:  0.83 (0.54), residues: 101
  loop : -0.41 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1019 
 TYR   0.014   0.001   TYR A 991 
 PHE   0.034   0.001   PHE A 546 
 TRP   0.008   0.001   TRP A 440 
 HIS   0.014   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.19 (12168)
  covalent geometry    : angle       0.59024 /  0.30 (16445)
  hydrogen bonds       : bond        0.04448 /  2.91 (  726)
  hydrogen bonds       : angle       3.82976 /  2.74 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 282
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASN cc_start: 0.7174 (p0) cc_final: 0.6953 (p0)
REVERT: A  111 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8633 (mttt)
REVERT: A  323 THR cc_start: 0.8927 (p) cc_final: 0.8662 (p)
REVERT: A  491 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8332 (mtp85)
REVERT: A  496 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.8020 (ptp-170)
REVERT: A  654 GLU cc_start: 0.7810 (pt0) cc_final: 0.7574 (pt0)
REVERT: A  739 ILE cc_start: 0.8970 (mm) cc_final: 0.8769 (mp)
REVERT: A  997 ASP cc_start: 0.8084 (t0) cc_final: 0.7669 (t0)
REVERT: A 1102 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8395 (ttt-90)
REVERT: A 1120 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8869 (tttm)
REVERT: B  458 GLU cc_start: 0.8283 (mp0) cc_final: 0.7819 (mp0)
REVERT: E  350 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8630 (tppp)
  outliers start: 39
  outliers final: 23
  residues processed: 297
  average time/residue: 0.6973
  time to fit residues: 221.8688
Evaluate side-chains
  304 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 277
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  666 LYS
Chi-restraints excluded: chain A residue  736 MET
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  989 SER
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1102 ARG
Chi-restraints excluded: chain A residue 1120 LYS
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 130 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 775 GLN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 HIS
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.116949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.096170 restraints weight = 31191.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.68
r_work: 0.3378 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12168  Z= 0.171
  Angle     :  0.612  13.721  16445  Z= 0.310
  Chirality :  0.042   0.351   1893
  Planarity :  0.004   0.069   2067
  Dihedral  :  3.803  19.397   1622
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.12 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.10 (0.22), residues: 1477
  helix:  2.46 (0.17), residues: 875
  sheet:  0.80 (0.53), residues: 101
  loop : -0.43 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 794 
 TYR   0.013   0.001   TYR A 991 
 PHE   0.036   0.001   PHE A 546 
 TRP   0.008   0.001   TRP A 440 
 HIS   0.013   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.17 (12168)
  covalent geometry    : angle       0.61164 /  0.31 (16445)
  hydrogen bonds       : bond        0.04365 /  2.86 (  726)
  hydrogen bonds       : angle       3.81810 /  2.74 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 278
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASN cc_start: 0.6970 (p0) cc_final: 0.6720 (p0)
REVERT: A  111 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8512 (mttt)
REVERT: A  323 THR cc_start: 0.8872 (p) cc_final: 0.8608 (p)
REVERT: A  491 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8175 (mtp85)
REVERT: A  496 ARG cc_start: 0.8192 (ptp-170) cc_final: 0.7929 (ptp-170)
REVERT: A  654 GLU cc_start: 0.7614 (pt0) cc_final: 0.7411 (pt0)
REVERT: A  997 ASP cc_start: 0.7905 (t0) cc_final: 0.7509 (t0)
REVERT: A 1102 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8302 (ttt-90)
REVERT: B  458 GLU cc_start: 0.8131 (mp0) cc_final: 0.7684 (mp0)
REVERT: E  350 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8525 (tppp)
  outliers start: 34
  outliers final: 23
  residues processed: 290
  average time/residue: 0.7008
  time to fit residues: 217.8583
Evaluate side-chains
  300 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 274
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  666 LYS
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue  989 SER
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1102 ARG
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1158 GLU
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Chi-restraints excluded: chain E residue  368 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0060
   chunk 129 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 142 optimal weight:    1.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.120470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.099947 restraints weight = 29598.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.60
r_work: 0.3398 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12168  Z= 0.142
  Angle     :  0.629  13.420  16445  Z= 0.314
  Chirality :  0.042   0.372   1893
  Planarity :  0.004   0.085   2067
  Dihedral  :  3.753  18.721   1622
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.64 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.20 (0.22), residues: 1477
  helix:  2.56 (0.18), residues: 871
  sheet:  0.78 (0.53), residues: 101
  loop : -0.39 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 794 
 TYR   0.011   0.001   TYR A 991 
 PHE   0.038   0.001   PHE A 546 
 TRP   0.014   0.001   TRP A 695 
 HIS   0.014   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 (12168)
  covalent geometry    : angle       0.62851 /  0.31 (16445)
  hydrogen bonds       : bond        0.04166 /  2.76 (  726)
  hydrogen bonds       : angle       3.77244 /  2.71 ( 2073)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 281
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8471 (mttt)
REVERT: A  323 THR cc_start: 0.8846 (p) cc_final: 0.8568 (p)
REVERT: A  491 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8160 (mtp85)
REVERT: A  496 ARG cc_start: 0.8174 (ptp-170) cc_final: 0.7916 (ptp-170)
REVERT: A  736 MET cc_start: 0.8373 (mmm) cc_final: 0.8072 (mmm)
REVERT: A  997 ASP cc_start: 0.7869 (t0) cc_final: 0.7469 (t0)
REVERT: A 1102 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8275 (ttt-90)
REVERT: B  458 GLU cc_start: 0.8110 (mp0) cc_final: 0.7595 (mp0)
REVERT: E  350 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8560 (tppp)
  outliers start: 30
  outliers final: 21
  residues processed: 291
  average time/residue: 0.7004
  time to fit residues: 218.5562
Evaluate side-chains
  301 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 277
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  666 LYS
Chi-restraints excluded: chain A residue  781 LYS
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  989 SER
Chi-restraints excluded: chain A residue 1016 ILE
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1102 ARG
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1147 ARG
Chi-restraints excluded: chain A residue 1158 GLU
Chi-restraints excluded: chain A residue 1337 MET
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain C residue  338 SER
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain D residue  339 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  350 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 HIS
** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.119411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098664 restraints weight = 31634.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.71
r_work: 0.3378 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3378
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12168  Z= 0.168
  Angle     :  0.628  12.608  16445  Z= 0.317
  Chirality :  0.043   0.304   1893
  Planarity :  0.004   0.081   2067
  Dihedral  :  3.787  18.679   1622
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.57 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  2.14 (0.22), residues: 1477
  helix:  2.47 (0.17), residues: 875
  sheet:  0.77 (0.53), residues: 101
  loop : -0.35 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 794 
 TYR   0.010   0.001   TYR A 277 
 PHE   0.035   0.001   PHE A 546 
 TRP   0.013   0.001   TRP A 695 
 HIS   0.013   0.001   HIS A 979 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 (12168)
  covalent geometry    : angle       0.62761 /  0.32 (16445)
  hydrogen bonds       : bond        0.04308 /  2.83 (  726)
  hydrogen bonds       : angle       3.78983 /  2.72 ( 2073)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7192.34 seconds
wall clock time: 122 minutes 46.65 seconds (7366.65 seconds total)