Starting phenix.real_space_refine
on Thu Mar 13 16:30:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pmd_17759/03_2025/8pmd_17759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pmd_17759/03_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_17759/03_2025/8pmd_17759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pmd_17759/03_2025/8pmd_17759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pmd_17759/03_2025/8pmd_17759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pmd_17759/03_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-5624/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: 5.71, per 1000 atoms: 0.65
  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.02
  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: 3.11

  Time building geometry restraints manager: 2.76 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.070
-------------------------------------------------------------------------------
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= 0.249
  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 

*********************** 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  : 0.956 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 207
  average time/residue: 1.1654
  time to fit residues: 259.2554
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  : 0.866 
-------------------------------------------------------------------------------
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 = 0.136513 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: 2.90 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    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:      327 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
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= 0.201
  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 

*********************** 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  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8004 (mt)
REVERT: A  181 ARG cc_start: 0.7966 (mpt180) cc_final: 0.7232 (mmm160)
REVERT: A  268 ASP cc_start: 0.8153 (t0) cc_final: 0.7884 (t0)
REVERT: A  428 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.6779 (p90)
REVERT: A  611 ILE cc_start: 0.8799 (mt) cc_final: 0.8521 (tt)
REVERT: A  956 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7326 (mm-30)
REVERT: A 1238 LYS cc_start: 0.7553 (mtpm) cc_final: 0.7293 (ttmt)
  outliers start: 56
  outliers final: 24
  residues processed: 234
  average time/residue: 1.1417
  time to fit residues: 286.0509
Evaluate side-chains
  220 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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  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 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:    0.3980
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0050
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3678 r_free = 0.3678 target = 0.149799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.137836 restraints weight = 10678.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.09
r_work: 0.3475 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      327 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      342 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9011  Z= 0.171
  Angle     :  0.533   7.854  12189  Z= 0.288
  Chirality :  0.041   0.138   1382
  Planarity :  0.003   0.053   1544
  Dihedral  :  8.476  81.112   1285
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 26.58 %
    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:  1.49 (0.24), residues: 1117
  helix:  1.77 (0.19), residues: 744
  sheet:  0.58 (0.52), residues: 77
  loop : -0.91 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1071 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 811 
 TYR   0.024   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A1265 

*********************** 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
  253 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 204
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.7455 (mm) cc_final: 0.7142 (tp)
REVERT: A  268 ASP cc_start: 0.8154 (t0) cc_final: 0.7899 (t0)
REVERT: A  428 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.6845 (p90)
REVERT: A  591 ASN cc_start: 0.7653 (m-40) cc_final: 0.7414 (m110)
REVERT: A  611 ILE cc_start: 0.8819 (mt) cc_final: 0.8572 (tt)
REVERT: A  956 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7253 (mm-30)
  outliers start: 49
  outliers final: 16
  residues processed: 231
  average time/residue: 1.2117
  time to fit residues: 299.8973
Evaluate side-chains
  201 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  320 ILE
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  550 THR
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  625 THR
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 1122 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 105 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.150026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.137860 restraints weight = 10576.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.09
r_work: 0.3476 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      342 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1310

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= 0.178
  Angle     :  0.529   6.463  12189  Z= 0.287
  Chirality :  0.041   0.138   1382
  Planarity :  0.003   0.053   1544
  Dihedral  :  8.264  76.668   1285
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 26.58 %
    Favored  : 68.27 %
  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:  1.53 (0.24), residues: 1117
  helix:  1.82 (0.19), residues: 740
  sheet:  0.57 (0.52), residues: 78
  loop : -0.90 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.017   0.001   PHE A  70 
 TYR   0.023   0.001   TYR A 337 
 ARG   0.004   0.000   ARG A1221 

*********************** 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
  241 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 193
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.7920 (mpt180) cc_final: 0.7149 (mmm160)
REVERT: A  268 ASP cc_start: 0.8126 (t0) cc_final: 0.7876 (t0)
REVERT: A  428 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.6871 (p90)
REVERT: A  591 ASN cc_start: 0.7612 (m-40) cc_final: 0.7380 (m110)
REVERT: A  611 ILE cc_start: 0.8822 (mt) cc_final: 0.8591 (tt)
REVERT: A  956 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7264 (mm-30)
REVERT: A 1226 ARG cc_start: 0.8487 (mtp180) cc_final: 0.8222 (mtm-85)
REVERT: A 1296 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7175 (mt-10)
  outliers start: 48
  outliers final: 20
  residues processed: 224
  average time/residue: 1.3042
  time to fit residues: 314.0055
Evaluate side-chains
  210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 187
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
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  245 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  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  609 THR
Chi-restraints excluded: chain A residue  625 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 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 109 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 361 GLN
A 466 GLN
** A 813 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.144750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.132590 restraints weight = 10632.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.08
r_work: 0.3414 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      338 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9011  Z= 0.312
  Angle     :  0.624   9.182  12189  Z= 0.339
  Chirality :  0.045   0.139   1382
  Planarity :  0.004   0.051   1544
  Dihedral  :  8.591  87.391   1283
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 26.47 %
    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:  1.02 (0.24), residues: 1117
  helix:  1.42 (0.18), residues: 740
  sheet:  0.34 (0.50), residues: 78
  loop : -1.06 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 163 
 HIS   0.004   0.001   HIS A 428 
 PHE   0.022   0.002   PHE A 774 
 TYR   0.021   0.002   TYR A 337 
 ARG   0.007   0.001   ARG A 184 

*********************** 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
  255 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 200
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8080 (mt)
REVERT: A  186 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7500 (pm20)
REVERT: A  268 ASP cc_start: 0.8183 (t0) cc_final: 0.7891 (t0)
REVERT: A  342 TRP cc_start: 0.6445 (t60) cc_final: 0.5846 (t-100)
REVERT: A  428 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.6932 (p-80)
REVERT: A  465 LEU cc_start: 0.8420 (mt) cc_final: 0.7835 (tp)
REVERT: A  573 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: A  591 ASN cc_start: 0.7752 (m-40) cc_final: 0.7527 (m110)
REVERT: A  850 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7892 (mt)
REVERT: A  956 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7330 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7205 (mt-10)
  outliers start: 55
  outliers final: 22
  residues processed: 232
  average time/residue: 1.1125
  time to fit residues: 277.6733
Evaluate side-chains
  218 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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  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  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  831 LEU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  940 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 1164 VAL
Chi-restraints excluded: chain A residue 1296 GLU
Chi-restraints excluded: chain A residue 1316 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 97 optimal weight:    0.2980
   chunk 56 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 361 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**
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.147971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.135915 restraints weight = 10531.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.08
r_work: 0.3452 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      338 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1426

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= 0.185
  Angle     :  0.554   6.484  12189  Z= 0.302
  Chirality :  0.042   0.185   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  8.179  76.795   1283
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 28.30 %
    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:  1.35 (0.24), residues: 1117
  helix:  1.67 (0.19), residues: 742
  sheet:  0.58 (0.51), residues: 78
  loop : -0.99 (0.31), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1071 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.022   0.001   PHE A 774 
 TYR   0.021   0.001   TYR A 337 
 ARG   0.006   0.000   ARG A 184 

*********************** 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
  237 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 195
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.7932 (mpt180) cc_final: 0.7226 (mmm160)
REVERT: A  186 GLU cc_start: 0.7538 (pt0) cc_final: 0.7253 (pm20)
REVERT: A  268 ASP cc_start: 0.8117 (t0) cc_final: 0.7865 (t0)
REVERT: A  269 TYR cc_start: 0.7295 (m-10) cc_final: 0.7093 (m-10)
REVERT: A  300 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7981 (mm-30)
REVERT: A  428 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.6881 (p90)
REVERT: A  591 ASN cc_start: 0.7625 (m-40) cc_final: 0.7388 (m110)
REVERT: A  956 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7264 (mm-30)
REVERT: A 1226 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8226 (mtm-85)
REVERT: A 1296 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7173 (mt-10)
  outliers start: 42
  outliers final: 18
  residues processed: 218
  average time/residue: 1.1399
  time to fit residues: 265.6991
Evaluate side-chains
  206 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  479 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  899 LYS
Chi-restraints excluded: chain A residue  930 LYS
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
Chi-restraints excluded: chain A residue 1296 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.0040
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.2796

-------------------------------------------------------------------------------
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 361 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 = 0.3647 r_free = 0.3647 target = 0.146991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.134991 restraints weight = 10624.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.06
r_work: 0.3439 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      345 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9011  Z= 0.224
  Angle     :  0.572   6.560  12189  Z= 0.311
  Chirality :  0.043   0.166   1382
  Planarity :  0.004   0.054   1544
  Dihedral  :  8.257  81.895   1283
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.97 %
    Favored  : 67.31 %
  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:  1.23 (0.24), residues: 1117
  helix:  1.57 (0.18), residues: 742
  sheet:  0.58 (0.51), residues: 78
  loop : -1.02 (0.31), residues: 297

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   0.028   0.002   PHE A  70 
 TYR   0.019   0.001   TYR A 145 
 ARG   0.008   0.000   ARG A 184 

*********************** 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
  236 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.7947 (mpt180) cc_final: 0.7215 (mmm160)
REVERT: A  186 GLU cc_start: 0.7605 (pt0) cc_final: 0.7313 (pm20)
REVERT: A  197 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7479 (tm-30)
REVERT: A  268 ASP cc_start: 0.8162 (t0) cc_final: 0.7898 (t0)
REVERT: A  269 TYR cc_start: 0.7291 (m-10) cc_final: 0.7057 (m-10)
REVERT: A  300 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: A  342 TRP cc_start: 0.6315 (t60) cc_final: 0.5755 (t-100)
REVERT: A  428 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.6815 (p-80)
REVERT: A  438 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8037 (tt)
REVERT: A  573 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7877 (mp)
REVERT: A  591 ASN cc_start: 0.7649 (m-40) cc_final: 0.7412 (m110)
REVERT: A  956 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7278 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7207 (mt-10)
  outliers start: 44
  outliers final: 21
  residues processed: 219
  average time/residue: 1.1260
  time to fit residues: 264.0919
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  : 0.883 
-------------------------------------------------------------------------------
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  479 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  930 LYS
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 109 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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**
A1124 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.148727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.136675 restraints weight = 10701.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.09
r_work: 0.3461 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
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:      345 |
|-----------------------------------------------------------------------------|
|-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:      346 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1612

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= 0.188
  Angle     :  0.564   6.519  12189  Z= 0.304
  Chirality :  0.042   0.169   1382
  Planarity :  0.004   0.054   1544
  Dihedral  :  8.109  82.183   1283
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.30 %
    Favored  : 67.52 %
  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:  1.38 (0.24), residues: 1117
  helix:  1.70 (0.19), residues: 742
  sheet:  0.59 (0.52), residues: 78
  loop : -0.97 (0.32), residues: 297

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   0.026   0.001   PHE A 774 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.006   0.000   ARG A 184 

*********************** 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: 39
    poor density    : 187
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7498 (pt0) cc_final: 0.7171 (pm20)
REVERT: A  268 ASP cc_start: 0.8137 (t0) cc_final: 0.7866 (t0)
REVERT: A  269 TYR cc_start: 0.7258 (m-10) cc_final: 0.7037 (m-10)
REVERT: A  342 TRP cc_start: 0.6255 (t60) cc_final: 0.5713 (t-100)
REVERT: A  428 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.6791 (p90)
REVERT: A  438 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8044 (tt)
REVERT: A  591 ASN cc_start: 0.7598 (m-40) cc_final: 0.7364 (m110)
REVERT: A  956 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7273 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8183 (mm-30)
REVERT: A 1296 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7192 (mt-10)
  outliers start: 39
  outliers final: 22
  residues processed: 215
  average time/residue: 1.0993
  time to fit residues: 253.4656
Evaluate side-chains
  212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  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  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  609 THR
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  899 LYS
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 361 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 = 0.3629 r_free = 0.3629 target = 0.145351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.133133 restraints weight = 10722.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.09
r_work: 0.3419 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      346 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9011  Z= 0.281
  Angle     :  0.643  11.311  12189  Z= 0.344
  Chirality :  0.045   0.155   1382
  Planarity :  0.004   0.053   1544
  Dihedral  :  8.441  87.321   1283
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 28.30 %
    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:  1.07 (0.24), residues: 1117
  helix:  1.43 (0.18), residues: 743
  sheet:  0.69 (0.53), residues: 77
  loop : -1.06 (0.31), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 428 
 PHE   0.027   0.002   PHE A 774 
 TYR   0.019   0.002   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

*********************** 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: 37
    poor density    : 195
  time to evaluate  : 1.244 
Fit side-chains
REVERT: A  268 ASP cc_start: 0.8196 (t0) cc_final: 0.7904 (t0)
REVERT: A  269 TYR cc_start: 0.7322 (m-10) cc_final: 0.7028 (m-10)
REVERT: A  342 TRP cc_start: 0.6374 (t60) cc_final: 0.6001 (t60)
REVERT: A  428 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6854 (p-80)
REVERT: A  438 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8123 (tt)
REVERT: A  591 ASN cc_start: 0.7695 (m-40) cc_final: 0.7467 (m110)
REVERT: A  935 MET cc_start: 0.8500 (tpp) cc_final: 0.8152 (tpp)
REVERT: A  956 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7327 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8202 (mm-30)
REVERT: A 1221 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7672 (mmp80)
REVERT: A 1296 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7206 (mt-10)
  outliers start: 37
  outliers final: 24
  residues processed: 219
  average time/residue: 1.3748
  time to fit residues: 324.2825
Evaluate side-chains
  211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
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  227 THR
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  438 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  541 ILE
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    0.0770
   chunk 77 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0070
   chunk 21 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 109 optimal weight:    0.4980
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 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 = 0.3685 r_free = 0.3685 target = 0.150250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.138223 restraints weight = 10525.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.07
r_work: 0.3483 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      346 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1816

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= 0.179
  Angle     :  0.599  10.623  12189  Z= 0.316
  Chirality :  0.041   0.169   1382
  Planarity :  0.004   0.055   1544
  Dihedral  :  7.947  81.970   1283
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 30.33 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1117
  helix:  1.75 (0.19), residues: 742
  sheet:  0.68 (0.53), residues: 78
  loop : -0.91 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.027   0.001   PHE A 774 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 184 

********************** 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
  222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A  197 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7434 (tm-30)
REVERT: A  268 ASP cc_start: 0.8142 (t0) cc_final: 0.7874 (t0)
REVERT: A  269 TYR cc_start: 0.7225 (m-10) cc_final: 0.6998 (m-10)
REVERT: A  300 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7870 (mm-30)
REVERT: A  342 TRP cc_start: 0.6232 (t60) cc_final: 0.5869 (t60)
REVERT: A  428 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6776 (p90)
REVERT: A  438 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8016 (tt)
REVERT: A  591 ASN cc_start: 0.7545 (m-40) cc_final: 0.7325 (m110)
REVERT: A  935 MET cc_start: 0.8460 (tpp) cc_final: 0.8093 (tpp)
REVERT: A  956 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7251 (mm-30)
REVERT: A 1209 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: A 1284 ASP cc_start: 0.8572 (m-30) cc_final: 0.7876 (m-30)
REVERT: A 1296 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7140 (mt-10)
  outliers start: 27
  outliers final: 15
  residues processed: 211
  average time/residue: 1.0901
  time to fit residues: 247.2755
Evaluate side-chains
  203 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  336 CYS
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  609 THR
Chi-restraints excluded: chain A residue  625 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 361 GLN
A 598 GLN
** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1300 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.148089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.135966 restraints weight = 10608.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.08
r_work: 0.3450 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      346 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      350 |
|-----------------------------------------------------------------------------|
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9011  Z= 0.229
  Angle     :  0.640  10.549  12189  Z= 0.338
  Chirality :  0.043   0.156   1382
  Planarity :  0.004   0.054   1544
  Dihedral  :  8.064  83.875   1283
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 31.51 %
    Favored  : 65.81 %
  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:  1.35 (0.24), residues: 1117
  helix:  1.67 (0.19), residues: 741
  sheet:  0.66 (0.53), residues: 78
  loop : -0.97 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.033   0.002   PHE A  70 
 TYR   0.019   0.001   TYR A 337 
 ARG   0.005   0.000   ARG A 830 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7289.24 seconds
wall clock time: 126 minutes 56.77 seconds (7616.77 seconds total)