Starting phenix.real_space_refine
on Mon May 12 13:52:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pmd_17759/05_2025/8pmd_17759.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      52      5.16       5
     C    5651      2.51       5
     N    1497      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8844
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1129, 8778
          Classifications: {'peptide': 1129}
          Link IDs: {'PTRANS': 31, 'TRANS': 1097}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 66
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'undetermined': 4, 'water': 2}
          Link IDs: {None: 5}
  Time building chain proxies: 6.20, per 1000 atoms: 0.70
  Number of scatterers: 8844
  At special positions: 0
  Unit cell: (89.1, 79.2, 148.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      52     16.00
     P       6     15.00
     Mg      2     11.99
     O    1636      8.00
     N    1497      7.00
     C    5651      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: 2.23
  Conformation dependent library (CDL) restraints added in 985.4 milliseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      68.9% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 3.690A  pdb=" N   LEU A  50 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 100
      removed outlier: 4.312A  pdb=" N   GLN A  76 " --> pdb=" O   HIS A  72 " (cutoff:3.500A)
      Proline residue:  A  77  - end of helix
      removed outlier: 4.260A  pdb=" N   GLU A  96 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A  97 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 185
    Processing helix  chain 'A' and resid 186 through 193
    Processing helix  chain 'A' and resid 194 through 214
      removed outlier: 4.949A  pdb=" N   ILE A 206 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASN A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 213 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 237
      removed outlier: 4.304A  pdb=" N   GLY A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 287
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 287 through 294
    Processing helix  chain 'A' and resid 296 through 344
      removed outlier: 3.904A  pdb=" N   ASN A 307 " --> pdb=" O   ARG A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 376
    Processing helix  chain 'A' and resid 376 through 398
      removed outlier: 3.533A  pdb=" N   LEU A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   SER A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 469
      removed outlier: 3.719A  pdb=" N   ALA A 464 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN A 469 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 490 through 496
    Processing helix  chain 'A' and resid 511 through 518
    Processing helix  chain 'A' and resid 524 through 535
    Processing helix  chain 'A' and resid 537 through 543
    Processing helix  chain 'A' and resid 553 through 557
    Processing helix  chain 'A' and resid 560 through 574
    Processing helix  chain 'A' and resid 590 through 605
    Processing helix  chain 'A' and resid 616 through 621
      removed outlier: 3.568A  pdb=" N   VAL A 620 " --> pdb=" O   ARG A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 748
    Processing helix  chain 'A' and resid 751 through 781
      removed outlier: 4.402A  pdb=" N   THR A 769 " --> pdb=" O   ASN A 765 " (cutoff:3.500A)
      Proline residue:  A 770  - end of helix
      removed outlier: 3.670A  pdb=" N   GLY A 781 " --> pdb=" O   SER A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 841
      removed outlier: 3.788A  pdb=" N   PHE A 811 " --> pdb=" O   CYS A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 848
      removed outlier: 3.505A  pdb=" N   PHE A 847 " --> pdb=" O   ASP A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 873
      removed outlier: 4.211A  pdb=" N   ALA A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ALA A 871 " --> pdb=" O   GLN A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 895
    Processing helix  chain 'A' and resid 897 through 906
      removed outlier: 3.625A  pdb=" N   SER A 901 " --> pdb=" O   SER A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 946
      removed outlier: 3.846A  pdb=" N   LEU A 911 " --> pdb=" O   PHE A 907 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG A 928 " --> pdb=" O   GLY A 924 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLN A 931 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASN A 946 " --> pdb=" O   GLU A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 954
    Processing helix  chain 'A' and resid 955 through 968
      removed outlier: 3.994A  pdb=" N   PHE A 959 " --> pdb=" O   LYS A 955 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE A 960 " --> pdb=" O   GLU A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 1010
      removed outlier: 4.416A  pdb=" N   LYS A 972 " --> pdb=" O   GLU A 968 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   THR A 973 " --> pdb=" O   LYS A 969 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ASN A 979 " --> pdb=" O   ILE A 975 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A 980 " --> pdb=" O   GLN A 976 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 993 " --> pdb=" O   GLN A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1028
    Processing helix  chain 'A' and resid 1029 through 1033
      removed outlier: 4.145A  pdb=" N   GLY A1032 " --> pdb=" O   THR A1029 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ARG A1033 " --> pdb=" O   ALA A1030 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1029 through 1033'
    Processing helix  chain 'A' and resid 1037 through 1056
      removed outlier: 3.615A  pdb=" N   ALA A1042 " --> pdb=" O   THR A1038 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   LYS A1043 " --> pdb=" O   PRO A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1127
      removed outlier: 3.556A  pdb=" N   ILE A1123 " --> pdb=" O   LYS A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1148 through 1155
      removed outlier: 3.835A  pdb=" N   ASN A1155 " --> pdb=" O   PHE A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1176
    Processing helix  chain 'A' and resid 1184 through 1195
      removed outlier: 3.543A  pdb=" N   VAL A1188 " --> pdb=" O   PRO A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1203
    Processing helix  chain 'A' and resid 1213 through 1217
    Processing helix  chain 'A' and resid 1220 through 1234
    Processing helix  chain 'A' and resid 1256 through 1266
    Processing helix  chain 'A' and resid 1299 through 1307
      removed outlier: 3.597A  pdb=" N   LYS A1307 " --> pdb=" O   LEU A1303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1308 through 1316
    Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441
      removed outlier: 5.267A  pdb=" N   VAL A 425 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 441
      removed outlier: 5.267A  pdb=" N   VAL A 425 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   PHE A 422 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   THR A 480 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   ASN A 424 " --> pdb=" O   MET A 478 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   MET A 478 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 501
      removed outlier: 6.169A  pdb=" N   GLY A 499 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ASP A 583 " --> pdb=" O   GLY A 499 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 501 " --> pdb=" O   ASP A 583 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 580 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   VAL A 613 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU A 582 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   MET A 450 " --> pdb=" O   THR A 625 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   ILE A 627 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ALA A 452 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   PHE A 629 " --> pdb=" O   ALA A 452 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL A 454 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1102 through 1103
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1083 through 1086
      removed outlier: 8.029A  pdb=" N   PHE A1085 " --> pdb=" O   ASN A1097 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   ASN A1097 " --> pdb=" O   PHE A1085 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159
      removed outlier: 6.390A  pdb=" N   GLY A1157 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ASP A1243 " --> pdb=" O   GLY A1157 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A1159 " --> pdb=" O   ASP A1243 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   LEU A1109 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   THR A1108 " --> pdb=" O   ILE A1285 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ALA A1287 " --> pdb=" O   THR A1108 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ALA A1110 " --> pdb=" O   ALA A1287 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET A1289 " --> pdb=" O   ALA A1110 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   VAL A1112 " --> pdb=" O   MET A1289 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A1296 " --> pdb=" O   VAL A1288 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ALA A1290 " --> pdb=" O   VAL A1294 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   VAL A1294 " --> pdb=" O   ALA A1290 " (cutoff:3.500A)

    585 hydrogen bonds defined for protein.
    1713 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: 3.47

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1440
        1.32 -     1.44: 2403
        1.44 -     1.56: 5073
        1.56 -     1.69: 10
        1.69 -     1.81: 85
  Bond restraints: 9011
  Sorted by residual:
  bond pdb=" C   PHE A1111 "
       pdb=" O   PHE A1111 "
    ideal  model  delta    sigma   weight residual
    1.236  1.192  0.044 1.22e-02 6.72e+03 1.31e+01
  bond pdb=" C   LYS A 930 "
       pdb=" N   GLN A 931 "
    ideal  model  delta    sigma   weight residual
    1.335  1.297  0.037 1.36e-02 5.41e+03 7.58e+00
  bond pdb=" C   ALA A 773 "
       pdb=" N   PHE A 774 "
    ideal  model  delta    sigma   weight residual
    1.334  1.298  0.037 1.33e-02 5.65e+03 7.54e+00
  bond pdb=" N   ILE A1273 "
       pdb=" CA  ILE A1273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.20e-02 6.94e+03 7.00e+00
  bond pdb=" C   GLU A 504 "
       pdb=" N   PRO A 505 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.034 1.30e-02 5.92e+03 6.81e+00
  ... (remaining 9006 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 11636
        1.34 -     2.68: 420
        2.68 -     4.02: 88
        4.02 -     5.36: 31
        5.36 -     6.70: 14
  Bond angle restraints: 12189
  Sorted by residual:
  angle pdb=" N   LEU A 332 "
        pdb=" CA  LEU A 332 "
        pdb=" C   LEU A 332 "
      ideal   model   delta    sigma   weight residual
     111.03  104.70    6.33 1.11e+00 8.12e-01 3.26e+01
  angle pdb=" CA  ILE A 416 "
        pdb=" C   ILE A 416 "
        pdb=" O   ILE A 416 "
      ideal   model   delta    sigma   weight residual
     121.23  115.36    5.87 1.07e+00 8.73e-01 3.01e+01
  angle pdb=" CA  PHE A  70 "
        pdb=" C   PHE A  70 "
        pdb=" O   PHE A  70 "
      ideal   model   delta    sigma   weight residual
     120.55  115.55    5.00 1.06e+00 8.90e-01 2.22e+01
  angle pdb=" CA  TYR A 145 "
        pdb=" C   TYR A 145 "
        pdb=" N   ALA A 146 "
      ideal   model   delta    sigma   weight residual
     117.63  122.64   -5.01 1.25e+00 6.40e-01 1.61e+01
  angle pdb=" CA  ILE A 416 "
        pdb=" C   ILE A 416 "
        pdb=" N   LYS A 417 "
      ideal   model   delta    sigma   weight residual
     116.10  120.87   -4.77 1.20e+00 6.94e-01 1.58e+01
  ... (remaining 12184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 4544
       17.11 -    34.21: 561
       34.21 -    51.32: 224
       51.32 -    68.42: 43
       68.42 -    85.53: 17
  Dihedral angle restraints: 5389
    sinusoidal: 2153
      harmonic: 3236
  Sorted by residual:
  dihedral pdb=" CA  ASP A 404 "
           pdb=" CB  ASP A 404 "
           pdb=" CG  ASP A 404 "
           pdb=" OD1 ASP A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.80   59.80     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CG  ARG A 575 "
           pdb=" CD  ARG A 575 "
           pdb=" NE  ARG A 575 "
           pdb=" CZ  ARG A 575 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.34   44.34     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CG  ARG A 487 "
           pdb=" CD  ARG A 487 "
           pdb=" NE  ARG A 487 "
           pdb=" CZ  ARG A 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.92  -41.92     2      1.50e+01 4.44e-03 9.52e+00
  ... (remaining 5386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1095
       0.051 -    0.102: 234
       0.102 -    0.153: 48
       0.153 -    0.204: 4
       0.204 -    0.255: 1
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  ILE A 416 "
            pdb=" N   ILE A 416 "
            pdb=" C   ILE A 416 "
            pdb=" CB  ILE A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  LEU A 332 "
            pdb=" N   LEU A 332 "
            pdb=" C   LEU A 332 "
            pdb=" CB  LEU A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CG  LEU A 827 "
            pdb=" CB  LEU A 827 "
            pdb=" CD1 LEU A 827 "
            pdb=" CD2 LEU A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.77e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 416 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.94e+00
        pdb=" C   ILE A 416 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ILE A 416 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A 417 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 332 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.98e+00
        pdb=" C   LEU A 332 "    0.049 2.00e-02 2.50e+03
        pdb=" O   LEU A 332 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A 333 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 216 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   GLN A 216 "    0.046 2.00e-02 2.50e+03
        pdb=" O   GLN A 216 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 217 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.06: 7
        2.06 -     2.77: 1751
        2.77 -     3.48: 13046
        3.48 -     4.19: 20598
        4.19 -     4.90: 37436
  Nonbonded interactions: 72838
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A1127 "
            pdb=" CD1 ILE A1158 "
     model   vdw
     1.353 3.460
  nonbonded pdb="MG    MG A1503 "
            pdb=" O   HOH A1601 "
     model   vdw
     1.962 2.170
  nonbonded pdb=" OE1 GLN A1161 "
            pdb="MG    MG A1503 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" OG  SER A1120 "
            pdb="MG    MG A1503 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" O3G ATP A1502 "
            pdb="MG    MG A1504 "
     model   vdw
     2.027 2.170
  ... (remaining 72833 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.93
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.290
  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:          0.000
  Check model and map are aligned:         0.290
  Set scattering table:                    0.000
  Process input model:                     23.940
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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   0.044   9011  Z= 0.210
  Angle     :  0.658   6.699  12189  Z= 0.384
  Chirality :  0.044   0.255   1382
  Planarity :  0.004   0.054   1544
  Dihedral  : 18.209  85.530   3309
  Min Nonbonded Distance : 1.353

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 28.83 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.24), residues: 1117
  helix:  1.42 (0.18), residues: 736
  sheet:  0.56 (0.54), residues: 77
  loop : -0.94 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1071 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.018   0.002   PHE A 747 
 TYR   0.025   0.002   TYR A 337 
 ARG   0.009   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11521 (  582)
  hydrogen bonds       : angle       4.80207 ( 1713)
  covalent geometry    : bond        0.00381 ( 9011)
  covalent geometry    : angle       0.65822 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 0.882 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 207
  average time/residue: 1.0546
  time to fit residues: 234.3490
Evaluate side-chains
  187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  776 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 84 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
A 372 ASN
A 598 GLN
** A 989 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 = 0.3655 r_free = 0.3655 target = 0.147728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.136514 restraints weight = 10743.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.07
r_work: 0.3463 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3365
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      317 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      326 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9011  Z= 0.152
  Angle     :  0.562   7.463  12189  Z= 0.306
  Chirality :  0.042   0.142   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.773  87.124   1285
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 25.83 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.24), residues: 1117
  helix:  1.63 (0.19), residues: 744
  sheet:  0.53 (0.53), residues: 77
  loop : -0.92 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.023   0.001   PHE A 383 
 TYR   0.021   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06709 (  582)
  hydrogen bonds       : angle       4.26278 ( 1713)
  covalent geometry    : bond        0.00308 ( 9011)
  covalent geometry    : angle       0.56173 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 203
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8009 (mt)
REVERT: A  181 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7234 (mmm160)
REVERT: A  268 ASP cc_start: 0.8146 (t0) cc_final: 0.7879 (t0)
REVERT: A  428 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.6782 (p90)
REVERT: A  573 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: A  611 ILE cc_start: 0.8803 (mt) cc_final: 0.8519 (tt)
REVERT: A  956 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7331 (mm-30)
REVERT: A 1220 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7905 (p)
REVERT: A 1238 LYS cc_start: 0.7546 (mtpm) cc_final: 0.7289 (ttmt)
  outliers start: 56
  outliers final: 24
  residues processed: 234
  average time/residue: 1.0907
  time to fit residues: 273.7097
Evaluate side-chains
  222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  776 PHE
Chi-restraints excluded: chain A residue  813 GLN
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1072 ASP
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1220 SER
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 372 ASN
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.148323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.136402 restraints weight = 10717.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.08
r_work: 0.3460 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      326 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      337 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9011  Z= 0.144
  Angle     :  0.542   7.361  12189  Z= 0.293
  Chirality :  0.041   0.138   1382
  Planarity :  0.004   0.053   1544
  Dihedral  :  8.563  82.337   1285
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 26.15 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1117
  helix:  1.71 (0.19), residues: 744
  sheet:  0.52 (0.52), residues: 77
  loop : -0.93 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1071 
 HIS   0.004   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 540 
 TYR   0.023   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A1265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06419 (  582)
  hydrogen bonds       : angle       4.15031 ( 1713)
  covalent geometry    : bond        0.00294 ( 9011)
  covalent geometry    : angle       0.54227 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 198
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8081 (mt)
REVERT: A  181 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7179 (mmm160)
REVERT: A  254 ILE cc_start: 0.7504 (mm) cc_final: 0.7170 (tp)
REVERT: A  268 ASP cc_start: 0.8170 (t0) cc_final: 0.7911 (t0)
REVERT: A  428 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6853 (p90)
REVERT: A  573 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7856 (mp)
REVERT: A  591 ASN cc_start: 0.7675 (m-40) cc_final: 0.7441 (m110)
REVERT: A  611 ILE cc_start: 0.8821 (mt) cc_final: 0.8568 (tt)
REVERT: A  956 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7277 (mm-30)
  outliers start: 53
  outliers final: 21
  residues processed: 226
  average time/residue: 1.1244
  time to fit residues: 271.9455
Evaluate side-chains
  210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  270 GLU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  776 PHE
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 108 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0010
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1124 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.149226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.137152 restraints weight = 10591.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.08
r_work: 0.3471 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      337 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      340 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9011  Z= 0.136
  Angle     :  0.531   6.901  12189  Z= 0.287
  Chirality :  0.041   0.138   1382
  Planarity :  0.003   0.053   1544
  Dihedral  :  8.329  78.008   1285
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.94 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1117
  helix:  1.77 (0.19), residues: 740
  sheet:  0.55 (0.52), residues: 78
  loop : -0.92 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.018   0.001   PHE A  70 
 TYR   0.023   0.001   TYR A 337 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06161 (  582)
  hydrogen bonds       : angle       4.10336 ( 1713)
  covalent geometry    : bond        0.00271 ( 9011)
  covalent geometry    : angle       0.53130 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 192
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 ASP cc_start: 0.8120 (t0) cc_final: 0.7855 (t0)
REVERT: A  428 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.6859 (p90)
REVERT: A  591 ASN cc_start: 0.7622 (m-40) cc_final: 0.7383 (m110)
REVERT: A  611 ILE cc_start: 0.8821 (mt) cc_final: 0.8597 (tt)
REVERT: A  956 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7258 (mm-30)
REVERT: A 1226 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8235 (mtm-85)
REVERT: A 1296 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7196 (mt-10)
  outliers start: 52
  outliers final: 23
  residues processed: 227
  average time/residue: 1.0210
  time to fit residues: 249.2969
Evaluate side-chains
  211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  813 GLN
Chi-restraints excluded: chain A residue  831 LEU
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 57 optimal weight:    0.2980
   chunk 109 optimal weight:    7.9990
   chunk 99 optimal weight:    0.2980
   chunk 86 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0670
   chunk 25 optimal weight:    0.4980
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
A 530 GLN
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 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 = 0.3689 r_free = 0.3689 target = 0.150651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.138685 restraints weight = 10523.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.07
r_work: 0.3489 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3388
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3388 r_free = 0.3388    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      340 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9011  Z= 0.131
  Angle     :  0.524   6.554  12189  Z= 0.283
  Chirality :  0.040   0.137   1382
  Planarity :  0.003   0.053   1544
  Dihedral  :  8.014  80.433   1283
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 26.47 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1117
  helix:  1.83 (0.19), residues: 740
  sheet:  0.65 (0.52), residues: 78
  loop : -0.91 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.022   0.001   PHE A 774 
 TYR   0.022   0.001   TYR A 337 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05919 (  582)
  hydrogen bonds       : angle       4.01545 ( 1713)
  covalent geometry    : bond        0.00257 ( 9011)
  covalent geometry    : angle       0.52368 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 197
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7149 (mmm160)
REVERT: A  268 ASP cc_start: 0.8132 (t0) cc_final: 0.7891 (t0)
REVERT: A  428 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.6854 (p90)
REVERT: A  591 ASN cc_start: 0.7573 (m-40) cc_final: 0.7343 (m110)
REVERT: A  611 ILE cc_start: 0.8829 (mt) cc_final: 0.8606 (tt)
REVERT: A  956 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7265 (mm-30)
REVERT: A 1226 ARG cc_start: 0.8475 (mtp180) cc_final: 0.8208 (mtm-85)
REVERT: A 1296 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7174 (mt-10)
  outliers start: 50
  outliers final: 16
  residues processed: 226
  average time/residue: 1.0451
  time to fit residues: 253.7931
Evaluate side-chains
  204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 96 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
A 813 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1124 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.147252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.135145 restraints weight = 10553.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.08
r_work: 0.3446 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9011  Z= 0.174
  Angle     :  0.583   7.863  12189  Z= 0.317
  Chirality :  0.043   0.182   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.266  82.547   1283
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 27.12 %
    Favored  : 67.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.24), residues: 1117
  helix:  1.62 (0.18), residues: 740
  sheet:  0.44 (0.51), residues: 78
  loop : -0.99 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 428 
 PHE   0.029   0.002   PHE A 202 
 TYR   0.021   0.002   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06680 (  582)
  hydrogen bonds       : angle       4.12213 ( 1713)
  covalent geometry    : bond        0.00374 ( 9011)
  covalent geometry    : angle       0.58299 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 192
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7239 (mmm160)
REVERT: A  186 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7346 (pm20)
REVERT: A  268 ASP cc_start: 0.8169 (t0) cc_final: 0.7907 (t0)
REVERT: A  300 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: A  428 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.6837 (p90)
REVERT: A  591 ASN cc_start: 0.7646 (m-40) cc_final: 0.7429 (m110)
REVERT: A  790 GLU cc_start: 0.4030 (OUTLIER) cc_final: 0.3705 (pp20)
REVERT: A  956 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7337 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7212 (mt-10)
  outliers start: 48
  outliers final: 22
  residues processed: 220
  average time/residue: 1.0536
  time to fit residues: 249.0098
Evaluate side-chains
  213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 186
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 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 = 0.3654 r_free = 0.3654 target = 0.147534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.135431 restraints weight = 10636.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.08
r_work: 0.3447 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9011  Z= 0.152
  Angle     :  0.564   6.548  12189  Z= 0.306
  Chirality :  0.042   0.175   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.173  84.482   1283
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 28.08 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.24), residues: 1117
  helix:  1.66 (0.18), residues: 740
  sheet:  0.55 (0.52), residues: 78
  loop : -0.99 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.026   0.001   PHE A 202 
 TYR   0.020   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06499 (  582)
  hydrogen bonds       : angle       4.09689 ( 1713)
  covalent geometry    : bond        0.00316 ( 9011)
  covalent geometry    : angle       0.56421 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7198 (mmm160)
REVERT: A  186 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7196 (pm20)
REVERT: A  268 ASP cc_start: 0.8155 (t0) cc_final: 0.7882 (t0)
REVERT: A  269 TYR cc_start: 0.7266 (m-10) cc_final: 0.7061 (m-10)
REVERT: A  300 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7986 (mm-30)
REVERT: A  428 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.6850 (p90)
REVERT: A  591 ASN cc_start: 0.7623 (m-40) cc_final: 0.7391 (m110)
REVERT: A  956 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7297 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7197 (mt-10)
  outliers start: 42
  outliers final: 22
  residues processed: 213
  average time/residue: 1.0383
  time to fit residues: 238.4708
Evaluate side-chains
  211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 102 optimal weight:    0.1980
   chunk 70 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0470
   chunk 109 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 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 = 0.3653 r_free = 0.3653 target = 0.147418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.135317 restraints weight = 10746.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.09
r_work: 0.3444 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      340 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9011  Z= 0.158
  Angle     :  0.571   6.549  12189  Z= 0.310
  Chirality :  0.042   0.160   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.184  84.910   1283
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 28.08 %
    Favored  : 67.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.24), residues: 1117
  helix:  1.65 (0.18), residues: 740
  sheet:  0.56 (0.51), residues: 78
  loop : -1.01 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.031   0.002   PHE A  70 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06563 (  582)
  hydrogen bonds       : angle       4.11141 ( 1713)
  covalent geometry    : bond        0.00333 ( 9011)
  covalent geometry    : angle       0.57149 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  268 ASP cc_start: 0.8145 (t0) cc_final: 0.7875 (t0)
REVERT: A  269 TYR cc_start: 0.7318 (m-10) cc_final: 0.7102 (m-10)
REVERT: A  300 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8010 (mm-30)
REVERT: A  342 TRP cc_start: 0.6291 (t60) cc_final: 0.5737 (t-100)
REVERT: A  428 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.6818 (p-80)
REVERT: A  438 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8093 (tt)
REVERT: A  591 ASN cc_start: 0.7626 (m-40) cc_final: 0.7401 (m110)
REVERT: A  956 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7315 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8220 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7209 (mt-10)
  outliers start: 40
  outliers final: 22
  residues processed: 211
  average time/residue: 1.0832
  time to fit residues: 245.3959
Evaluate side-chains
  208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 182
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 83 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 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 = 0.3648 r_free = 0.3648 target = 0.146986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.134908 restraints weight = 10706.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.09
r_work: 0.3439 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      340 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      339 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9011  Z= 0.169
  Angle     :  0.600   6.571  12189  Z= 0.323
  Chirality :  0.043   0.161   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.231  85.706   1283
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.97 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1117
  helix:  1.59 (0.18), residues: 741
  sheet:  0.50 (0.51), residues: 78
  loop : -1.00 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.027   0.002   PHE A 774 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06735 (  582)
  hydrogen bonds       : angle       4.15350 ( 1713)
  covalent geometry    : bond        0.00363 ( 9011)
  covalent geometry    : angle       0.60027 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 189
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  268 ASP cc_start: 0.8150 (t0) cc_final: 0.7872 (t0)
REVERT: A  269 TYR cc_start: 0.7303 (m-10) cc_final: 0.7051 (m-10)
REVERT: A  300 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: A  342 TRP cc_start: 0.6326 (t60) cc_final: 0.5934 (t60)
REVERT: A  428 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.6819 (p-80)
REVERT: A  438 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8081 (tt)
REVERT: A  591 ASN cc_start: 0.7648 (m-40) cc_final: 0.7406 (m110)
REVERT: A  956 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7311 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8202 (mm-30)
REVERT: A 1276 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5699 (mpp-170)
REVERT: A 1296 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7193 (mt-10)
  outliers start: 43
  outliers final: 23
  residues processed: 217
  average time/residue: 1.0440
  time to fit residues: 243.7779
Evaluate side-chains
  215 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1276 ARG
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    8.9990
   chunk 109 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.148252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.136176 restraints weight = 10572.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.09
r_work: 0.3457 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      339 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9011  Z= 0.150
  Angle     :  0.596   7.944  12189  Z= 0.318
  Chirality :  0.042   0.163   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.135  84.654   1283
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 29.58 %
    Favored  : 67.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.24), residues: 1117
  helix:  1.69 (0.19), residues: 741
  sheet:  0.61 (0.53), residues: 78
  loop : -0.99 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.036   0.002   PHE A  70 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06444 (  582)
  hydrogen bonds       : angle       4.11384 ( 1713)
  covalent geometry    : bond        0.00312 ( 9011)
  covalent geometry    : angle       0.59628 (12189)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  268 ASP cc_start: 0.8132 (t0) cc_final: 0.7860 (t0)
REVERT: A  269 TYR cc_start: 0.7285 (m-10) cc_final: 0.7050 (m-10)
REVERT: A  300 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7999 (mm-30)
REVERT: A  342 TRP cc_start: 0.6268 (t60) cc_final: 0.5891 (t60)
REVERT: A  428 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6783 (p90)
REVERT: A  438 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8064 (tt)
REVERT: A  541 ILE cc_start: 0.8407 (pt) cc_final: 0.8132 (mt)
REVERT: A  591 ASN cc_start: 0.7616 (m-40) cc_final: 0.7382 (m110)
REVERT: A  956 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7299 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8148 (mm-30)
REVERT: A 1276 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.5618 (mpp-170)
REVERT: A 1296 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7175 (mt-10)
  outliers start: 30
  outliers final: 20
  residues processed: 206
  average time/residue: 1.1020
  time to fit residues: 243.0509
Evaluate side-chains
  208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 HIS
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  956 GLU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1276 ARG
Chi-restraints excluded: chain A residue 1296 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 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 = 0.3674 r_free = 0.3674 target = 0.149104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.137003 restraints weight = 10663.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.09
r_work: 0.3466 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9011  Z= 0.144
  Angle     :  0.588   7.057  12189  Z= 0.315
  Chirality :  0.042   0.162   1382
  Planarity :  0.004   0.053   1544
  Dihedral  :  8.037  84.732   1283
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.80 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.24), residues: 1117
  helix:  1.73 (0.19), residues: 741
  sheet:  0.64 (0.53), residues: 78
  loop : -0.94 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.027   0.001   PHE A 774 
 TYR   0.020   0.001   TYR A 337 
 ARG   0.009   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06226 (  582)
  hydrogen bonds       : angle       4.08644 ( 1713)
  covalent geometry    : bond        0.00297 ( 9011)
  covalent geometry    : angle       0.58846 (12189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6820.35 seconds
wall clock time: 118 minutes 12.83 seconds (7092.83 seconds total)