Starting phenix.real_space_refine
on Sat Aug 23 12:31:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yot_33986/08_2025/7yot_33986.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    7714      2.51       5
     N    2126      2.21       5
     O    2266      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12182
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 376
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 51, 371
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 2, 'TRANS': 48}
      Conformer: "B"
        Number of residues, atoms: 51, 371
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 2, 'TRANS': 48}
          bond proxies already assigned to first conformer: 367
    Chain: "C"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 303
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 1, 'TRANS': 40}
    Chain: "B"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 244
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "E"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 849
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 11, 'TRANS': 103}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1309, 10410
          Classifications: {'peptide': 1309}
          Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1251}
          Chain breaks: 7
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA D 301 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA D 301 " occ=0.50
  Time building chain proxies: 3.71, per 1000 atoms: 0.30
  Number of scatterers: 12182
  At special positions: 0
  Unit cell: (102.96, 112.32, 111.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    2266      8.00
     N    2126      7.00
     C    7714      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1112 " - pdb=" SG  CYS A1350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1157 " - pdb=" SG  CYS A1160 " distance=2.03

  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: 0.80
  Conformation dependent library (CDL) restraints added in 448.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2962

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 7 sheets defined
      54.4% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'D' and resid 262 through 281
      removed outlier: 3.535A  pdb=" N   ALA D 278 " --> pdb=" O   ALA D 274 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 296 through 303
      removed outlier: 3.667A  pdb=" N   ARG D 300 " --> pdb=" O   LEU D 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 286
      removed outlier: 3.713A  pdb=" N   THR C 271 " --> pdb=" O   GLN C 267 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL C 275 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET C 276 " --> pdb=" O   SER C 272 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU C 277 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   MET C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 291
    Processing helix  chain 'C' and resid 298 through 305
    Processing helix  chain 'B' and resid 269 through 280
      removed outlier: 3.842A  pdb=" N   VAL B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 300
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.898A  pdb=" N   ALA E 278 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN E 279 " --> pdb=" O   MET E 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 275 through 279'
    Processing helix  chain 'E' and resid 296 through 302
    Processing helix  chain 'E' and resid 337 through 342
    Processing helix  chain 'E' and resid 352 through 366
      removed outlier: 3.586A  pdb=" N   VAL E 359 " --> pdb=" O   GLU E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 369 through 379
    Processing helix  chain 'E' and resid 389 through 397
    Processing helix  chain 'A' and resid 9 through 13
      removed outlier: 3.514A  pdb=" N   GLN A  12 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ILE A  13 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 9 through 13'
    Processing helix  chain 'A' and resid 25 through 35
      removed outlier: 3.934A  pdb=" N   LEU A  29 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 4.067A  pdb=" N   ASP A  45 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 63 through 80
      removed outlier: 4.001A  pdb=" N   MET A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN A  78 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR A  79 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 100
      removed outlier: 3.540A  pdb=" N   GLY A 100 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 141
      removed outlier: 3.509A  pdb=" N   ASN A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LYS A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ARG A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ILE A 113 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LYS A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   GLU A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      Proline residue:  A 127  - end of helix
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 169 through 192
      removed outlier: 3.970A  pdb=" N   THR A 192 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 254
      removed outlier: 3.540A  pdb=" N   VAL A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU A 235 " --> pdb=" O   GLN A 231 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 279
      removed outlier: 3.646A  pdb=" N   ALA A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLU A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LYS A 263 " --> pdb=" O   CYS A 259 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 271 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASP A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 4.023A  pdb=" N   LEU A 288 " --> pdb=" O   ASP A 284 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   MET A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLY A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 296 " --> pdb=" O   PHE A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
    Processing helix  chain 'A' and resid 327 through 342
    Processing helix  chain 'A' and resid 346 through 352
      removed outlier: 3.732A  pdb=" N   ALA A 351 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 356
      removed outlier: 3.642A  pdb=" N   LEU A 356 " --> pdb=" O   MET A 353 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 353 through 356'
    Processing helix  chain 'A' and resid 366 through 379
      removed outlier: 4.153A  pdb=" N   GLN A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 408
    Processing helix  chain 'A' and resid 416 through 420
      removed outlier: 4.053A  pdb=" N   ILE A 420 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 432
      removed outlier: 3.753A  pdb=" N   ALA A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 443
    Processing helix  chain 'A' and resid 443 through 448
    Processing helix  chain 'A' and resid 479 through 484
      removed outlier: 3.752A  pdb=" N   PHE A 484 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 489
      removed outlier: 3.526A  pdb=" N   LEU A 489 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 3.533A  pdb=" N   ASN A 496 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A 497 " --> pdb=" O   LYS A 494 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 493 through 497'
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 517 through 522
    Processing helix  chain 'A' and resid 523 through 525
      No H-bonds generated for 'chain 'A' and resid 523 through 525'
    Processing helix  chain 'A' and resid 558 through 576
    Processing helix  chain 'A' and resid 577 through 581
    Processing helix  chain 'A' and resid 599 through 603
      removed outlier: 3.561A  pdb=" N   LEU A 602 " --> pdb=" O   MET A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 649
      removed outlier: 3.951A  pdb=" N   TRP A 649 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 666
      removed outlier: 5.485A  pdb=" N   LEU A 656 " --> pdb=" O   GLN A 652 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   PHE A 657 " --> pdb=" O   THR A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 681
      removed outlier: 3.908A  pdb=" N   LEU A 676 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP A 680 " --> pdb=" O   LEU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 721 through 739
      removed outlier: 3.568A  pdb=" N   TRP A 725 " --> pdb=" O   CYS A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 791
    Processing helix  chain 'A' and resid 823 through 829
      removed outlier: 3.643A  pdb=" N   ASN A 827 " --> pdb=" O   GLN A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 859
      removed outlier: 3.681A  pdb=" N   SER A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 881
    Processing helix  chain 'A' and resid 901 through 911
    Processing helix  chain 'A' and resid 922 through 926
    Processing helix  chain 'A' and resid 933 through 948
    Processing helix  chain 'A' and resid 952 through 961
      removed outlier: 4.394A  pdb=" N   MET A 956 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   THR A 957 " --> pdb=" O   PRO A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 975
    Processing helix  chain 'A' and resid 986 through 1000
      removed outlier: 3.580A  pdb=" N   PHE A1000 " --> pdb=" O   GLN A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1029
    Processing helix  chain 'A' and resid 1034 through 1045
    Processing helix  chain 'A' and resid 1045 through 1055
    Processing helix  chain 'A' and resid 1060 through 1071
    Processing helix  chain 'A' and resid 1075 through 1083
    Processing helix  chain 'A' and resid 1083 through 1096
    Processing helix  chain 'A' and resid 1112 through 1125
    Processing helix  chain 'A' and resid 1125 through 1130
    Processing helix  chain 'A' and resid 1141 through 1146
      removed outlier: 3.513A  pdb=" N   VAL A1146 " --> pdb=" O   THR A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1212 through 1230
      removed outlier: 3.585A  pdb=" N   TYR A1229 " --> pdb=" O   LEU A1225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1244
    Processing helix  chain 'A' and resid 1251 through 1256
      removed outlier: 3.809A  pdb=" N   ARG A1255 " --> pdb=" O   SER A1251 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU A1256 " --> pdb=" O   GLU A1252 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1251 through 1256'
    Processing helix  chain 'A' and resid 1287 through 1291
      removed outlier: 3.647A  pdb=" N   VAL A1291 " --> pdb=" O   SER A1288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1327
      removed outlier: 3.506A  pdb=" N   LEU A1327 " --> pdb=" O   LEU A1323 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 308 through 310
      removed outlier: 6.493A  pdb=" N   LYS B 284 " --> pdb=" O   LEU E 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.623A  pdb=" N   GLY A 207 " --> pdb=" O   HIS A 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556
      removed outlier: 4.825A  pdb=" N   VAL A 538 " --> pdb=" O   THR A 682 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 684 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 748
      removed outlier: 4.338A  pdb=" N   ARG A 743 " --> pdb=" O   THR A 758 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ASN A 795 " --> pdb=" O   GLN A 643 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 748
      removed outlier: 4.338A  pdb=" N   ARG A 743 " --> pdb=" O   THR A 758 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 810
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1292 through 1294
      removed outlier: 3.541A  pdb=" N   THR A1168 " --> pdb=" O   LEU A1343 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A1339 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)

    568 hydrogen bonds defined for protein.
    1621 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3015
        1.33 -     1.45: 2500
        1.45 -     1.58: 6782
        1.58 -     1.70: 0
        1.70 -     1.82: 123
  Bond restraints: 12420
  Sorted by residual:
  bond pdb=" CG1 ILE A 117 "
       pdb=" CD1 ILE A 117 "
    ideal  model  delta    sigma   weight residual
    1.513  1.394  0.119 3.90e-02 6.57e+02 9.32e+00
  bond pdb=" CG  LEU A 647 "
       pdb=" CD1 LEU A 647 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.18e+00
  bond pdb=" CB  VAL A 748 "
       pdb=" CG1 VAL A 748 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.62e+00
  bond pdb=" CG1 ILE A 267 "
       pdb=" CD1 ILE A 267 "
    ideal  model  delta    sigma   weight residual
    1.513  1.422  0.091 3.90e-02 6.57e+02 5.41e+00
  bond pdb=" CB  PRO A  92 "
       pdb=" CG  PRO A  92 "
    ideal  model  delta    sigma   weight residual
    1.506  1.419  0.087 3.90e-02 6.57e+02 4.97e+00
  ... (remaining 12415 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 16548
        3.30 -     6.61: 235
        6.61 -     9.91: 28
        9.91 -    13.21: 4
       13.21 -    16.52: 3
  Bond angle restraints: 16818
  Sorted by residual:
  angle pdb=" C   ASP A 706 "
        pdb=" N   ASP A 707 "
        pdb=" CA  ASP A 707 "
      ideal   model   delta    sigma   weight residual
     121.54  131.27   -9.73 1.91e+00 2.74e-01 2.60e+01
  angle pdb=" CA  LEU A1008 "
        pdb=" CB  LEU A1008 "
        pdb=" CG  LEU A1008 "
      ideal   model   delta    sigma   weight residual
     116.30  132.82  -16.52 3.50e+00 8.16e-02 2.23e+01
  angle pdb=" CA  LEU E 286 "
        pdb=" CB  LEU E 286 "
        pdb=" CG  LEU E 286 "
      ideal   model   delta    sigma   weight residual
     116.30  132.35  -16.05 3.50e+00 8.16e-02 2.10e+01
  angle pdb=" C   ASN A 463 "
        pdb=" N   LEU A 464 "
        pdb=" CA  LEU A 464 "
      ideal   model   delta    sigma   weight residual
     121.54  129.74   -8.20 1.91e+00 2.74e-01 1.84e+01
  angle pdb=" N   ILE A 792 "
        pdb=" CA  ILE A 792 "
        pdb=" C   ILE A 792 "
      ideal   model   delta    sigma   weight residual
     112.29  108.60    3.69 9.40e-01 1.13e+00 1.54e+01
  ... (remaining 16813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.58: 7151
       15.58 -    31.16: 329
       31.16 -    46.74: 93
       46.74 -    62.32: 6
       62.32 -    77.90: 11
  Dihedral angle restraints: 7590
    sinusoidal: 3048
      harmonic: 4542
  Sorted by residual:
  dihedral pdb=" CB  CYS A1157 "
           pdb=" SG  CYS A1157 "
           pdb=" SG  CYS A1160 "
           pdb=" CB  CYS A1160 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.90  -77.90     1      1.00e+01 1.00e-02 7.59e+01
  dihedral pdb=" CA  ASN A 705 "
           pdb=" C   ASN A 705 "
           pdb=" N   ASP A 706 "
           pdb=" CA  ASP A 706 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  THR A 526 "
           pdb=" C   THR A 526 "
           pdb=" N   THR A 527 "
           pdb=" CA  THR A 527 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.27   25.73     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 7587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1322
       0.056 -    0.112: 503
       0.112 -    0.168: 103
       0.168 -    0.223: 6
       0.223 -    0.279: 5
  Chirality restraints: 1939
  Sorted by residual:
  chirality pdb=" CB  VAL A1037 "
            pdb=" CA  VAL A1037 "
            pdb=" CG1 VAL A1037 "
            pdb=" CG2 VAL A1037 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CB  VAL E 335 "
            pdb=" CA  VAL E 335 "
            pdb=" CG1 VAL E 335 "
            pdb=" CG2 VAL E 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CG  LEU A 489 "
            pdb=" CB  LEU A 489 "
            pdb=" CD1 LEU A 489 "
            pdb=" CD2 LEU A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 1936 not shown)

  Planarity restraints: 2144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  33 "   -0.021 2.00e-02 2.50e+03   2.46e-02 1.51e+01
        pdb=" CG  TRP A  33 "    0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  33 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  33 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  33 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  33 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  33 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  33 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  33 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  33 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 395 "   -0.021 2.00e-02 2.50e+03   2.87e-02 1.45e+01
        pdb=" CG  PHE A 395 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 395 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 395 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 395 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 395 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 395 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 265 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   ASP A 265 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASP A 265 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASP A 266 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2141 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3199
        2.80 -     3.33: 10898
        3.33 -     3.85: 20215
        3.85 -     4.38: 24316
        4.38 -     4.90: 41786
  Nonbonded interactions: 100414
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1108 "
            pdb=" OD1 ASP A1110 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER A 167 "
            pdb=" OD1 ASP A 245 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" NH1 ARG A 319 "
            pdb=" OD1 ASP A 332 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" OG  SER E 385 "
            pdb=" O   GLU E 387 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   LEU A1145 "
            pdb=" OG  SER A1348 "
     model   vdw
     2.342 3.040
  ... (remaining 100409 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.620
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.010
  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:8.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
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      :  0.009   0.119  12422  Z= 0.344
  Angle     :  1.031  16.518  16822  Z= 0.530
  Chirality :  0.059   0.279   1939
  Planarity :  0.008   0.065   2144
  Dihedral  : 10.474  76.529   4622
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  2.93 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.17), residues: 1526
  helix: -2.58 (0.13), residues: 762
  sheet: -0.81 (0.57), residues: 85
  loop : -2.29 (0.20), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 150 
 TYR   0.035   0.003   TYR A 868 
 PHE   0.061   0.004   PHE A 395 
 TRP   0.065   0.004   TRP A  33 
 HIS   0.013   0.003   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00882 (12420)
  covalent geometry    : angle       1.02998 (16818)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       2.99483 (    4)
  hydrogen bonds       : bond        0.15583 (  553)
  hydrogen bonds       : angle       6.57375 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 292
  time to evaluate  : 0.511 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7974 (mttt) cc_final: 0.7302 (mmtt)
REVERT: B  287 ASP cc_start: 0.8159 (t70) cc_final: 0.7806 (t70)
REVERT: E  325 GLU cc_start: 0.7978 (pt0) cc_final: 0.7560 (pt0)
REVERT: E  378 SER cc_start: 0.8341 (m) cc_final: 0.8133 (m)
REVERT: A   96 GLU cc_start: 0.7669 (tt0) cc_final: 0.7425 (tt0)
REVERT: A  137 LYS cc_start: 0.8114 (tttt) cc_final: 0.7753 (ttmm)
REVERT: A  769 SER cc_start: 0.8767 (m) cc_final: 0.8404 (p)
REVERT: A  956 MET cc_start: 0.8831 (tpt) cc_final: 0.8541 (tpp)
REVERT: A  989 ILE cc_start: 0.8716 (mt) cc_final: 0.8489 (mp)
REVERT: A  997 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7125 (mtm110)
REVERT: A 1087 MET cc_start: 0.8719 (mtp) cc_final: 0.8472 (mtm)
REVERT: A 1174 SER cc_start: 0.8638 (t) cc_final: 0.8201 (t)
REVERT: A 1222 SER cc_start: 0.8583 (m) cc_final: 0.8367 (p)
REVERT: A 1340 THR cc_start: 0.7360 (p) cc_final: 0.6961 (m)
  outliers start: 9
  outliers final: 3
  residues processed: 299
  average time/residue: 0.5526
  time to fit residues: 178.3034
Evaluate side-chains
  195 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue 1037 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    9.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 268 GLN
E 306 HIS
E 369 HIS
A  54 GLN
A  78 GLN
** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
A 336 HIS
A 348 ASN
A 463 ASN
A 478 ASN
A 487 ASN
A 565 GLN
A 575 GLN
A 648 ASN
A 652 GLN
A 662 ASN
A 669 HIS
A 827 ASN
A 906 HIS
A 922 GLN
A 974 ASN
A1088 HIS
A1235 ASN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.133923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.100712 restraints weight = 28500.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.78
r_work: 0.2816 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12422  Z= 0.104
  Angle     :  0.540   9.709  16822  Z= 0.274
  Chirality :  0.041   0.153   1939
  Planarity :  0.005   0.043   2144
  Dihedral  :  4.995  48.774   1669
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  :  9.74 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.20), residues: 1526
  helix: -0.36 (0.18), residues: 741
  sheet: -0.57 (0.59), residues: 81
  loop : -1.50 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 319 
 TYR   0.013   0.001   TYR A 977 
 PHE   0.017   0.001   PHE A 395 
 TRP   0.018   0.002   TRP A  33 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (12420)
  covalent geometry    : angle       0.53859 (16818)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       2.11406 (    4)
  hydrogen bonds       : bond        0.03520 (  553)
  hydrogen bonds       : angle       4.15819 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 217
  time to evaluate  : 0.335 
Fit side-chains
REVERT: D  282 MET cc_start: 0.8430 (mtm) cc_final: 0.8190 (mtp)
REVERT: D  304 LYS cc_start: 0.7466 (mttt) cc_final: 0.6668 (mmtt)
REVERT: B  276 MET cc_start: 0.7283 (mmm) cc_final: 0.7052 (mmm)
REVERT: B  282 MET cc_start: 0.7310 (mmt) cc_final: 0.6954 (mmt)
REVERT: B  287 ASP cc_start: 0.8314 (t70) cc_final: 0.7942 (t70)
REVERT: B  300 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8479 (mtm-85)
REVERT: E  284 LYS cc_start: 0.8310 (tppp) cc_final: 0.8050 (tppp)
REVERT: E  325 GLU cc_start: 0.8191 (pt0) cc_final: 0.7855 (pt0)
REVERT: A  137 LYS cc_start: 0.7932 (tttt) cc_final: 0.7600 (ttmm)
REVERT: A  277 ASP cc_start: 0.8430 (p0) cc_final: 0.8201 (p0)
REVERT: A  475 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7882 (p90)
REVERT: A  520 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8027 (ttpp)
REVERT: A  702 LYS cc_start: 0.8840 (mttt) cc_final: 0.8629 (mttm)
REVERT: A  760 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6812 (mt-10)
REVERT: A  769 SER cc_start: 0.8701 (m) cc_final: 0.8472 (p)
REVERT: A  776 GLU cc_start: 0.8263 (tt0) cc_final: 0.7713 (mm-30)
REVERT: A  896 GLN cc_start: 0.7307 (mp10) cc_final: 0.6554 (mm110)
REVERT: A  914 GLN cc_start: 0.8834 (mp10) cc_final: 0.7913 (mm-40)
REVERT: A  956 MET cc_start: 0.8860 (tpt) cc_final: 0.8561 (tpp)
REVERT: A  961 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (p)
REVERT: A  989 ILE cc_start: 0.8602 (mt) cc_final: 0.8350 (mp)
REVERT: A  997 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7324 (mtm110)
REVERT: A 1019 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8404 (mt-10)
REVERT: A 1052 GLN cc_start: 0.8651 (tt0) cc_final: 0.8197 (mt0)
REVERT: A 1090 MET cc_start: 0.8757 (mmm) cc_final: 0.8522 (tpt)
REVERT: A 1111 MET cc_start: 0.8252 (mtt) cc_final: 0.7855 (mtp)
REVERT: A 1123 ARG cc_start: 0.8885 (ttt-90) cc_final: 0.8599 (ttt-90)
REVERT: A 1334 LYS cc_start: 0.7487 (mttt) cc_final: 0.6665 (mptt)
REVERT: A 1340 THR cc_start: 0.7505 (p) cc_final: 0.7222 (m)
REVERT: A 1370 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7574 (ptt-90)
  outliers start: 43
  outliers final: 21
  residues processed: 244
  average time/residue: 0.5113
  time to fit residues: 135.5799
Evaluate side-chains
  208 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  760 GLU
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  961 THR
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain A residue 1096 VAL
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1150 ILE
Chi-restraints excluded: chain A residue 1183 SER
Chi-restraints excluded: chain A residue 1331 THR
Chi-restraints excluded: chain A residue 1365 VAL
Chi-restraints excluded: chain A residue 1370 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 140 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 119 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  54 GLN
A  78 GLN
A 120 HIS
A 183 GLN
A 463 ASN
A 487 ASN
A1171 HIS
A1314 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.129748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.094881 restraints weight = 25246.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.49
r_work: 0.2772 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12422  Z= 0.161
  Angle     :  0.571  11.205  16822  Z= 0.285
  Chirality :  0.043   0.161   1939
  Planarity :  0.004   0.044   2144
  Dihedral  :  4.937  57.566   1669
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 12.09 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.21), residues: 1526
  helix:  0.27 (0.19), residues: 748
  sheet: -0.34 (0.60), residues: 83
  loop : -1.17 (0.23), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 319 
 TYR   0.016   0.001   TYR A 977 
 PHE   0.025   0.002   PHE A 395 
 TRP   0.020   0.002   TRP A  33 
 HIS   0.007   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (12420)
  covalent geometry    : angle       0.57056 (16818)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       1.95195 (    4)
  hydrogen bonds       : bond        0.03829 (  553)
  hydrogen bonds       : angle       3.95270 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 191
  time to evaluate  : 0.442 
Fit side-chains
REVERT: D  282 MET cc_start: 0.8329 (mtm) cc_final: 0.8117 (mtp)
REVERT: D  304 LYS cc_start: 0.7703 (mttt) cc_final: 0.7140 (mptt)
REVERT: B  282 MET cc_start: 0.7125 (mmt) cc_final: 0.6305 (mmt)
REVERT: B  287 ASP cc_start: 0.8243 (t70) cc_final: 0.7953 (t70)
REVERT: E  325 GLU cc_start: 0.8278 (pt0) cc_final: 0.7904 (pt0)
REVERT: A  137 LYS cc_start: 0.7925 (tttt) cc_final: 0.7545 (ttmm)
REVERT: A  173 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8941 (ttpt)
REVERT: A  377 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7424 (mp10)
REVERT: A  520 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8138 (ttpp)
REVERT: A  702 LYS cc_start: 0.8931 (mttt) cc_final: 0.8717 (mttm)
REVERT: A  776 GLU cc_start: 0.8242 (tt0) cc_final: 0.7749 (mm-30)
REVERT: A  896 GLN cc_start: 0.7397 (mp10) cc_final: 0.6695 (mm110)
REVERT: A  956 MET cc_start: 0.8883 (tpt) cc_final: 0.8592 (tpp)
REVERT: A  989 ILE cc_start: 0.8667 (mt) cc_final: 0.8422 (mp)
REVERT: A  997 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7339 (mtm110)
REVERT: A 1025 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7131 (tm-30)
REVERT: A 1052 GLN cc_start: 0.8615 (tt0) cc_final: 0.8239 (mt0)
REVERT: A 1111 MET cc_start: 0.8294 (mtt) cc_final: 0.7961 (mtm)
REVERT: A 1123 ARG cc_start: 0.8922 (ttt-90) cc_final: 0.8544 (ttt-90)
REVERT: A 1133 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8202 (mmtp)
REVERT: A 1317 MET cc_start: 0.7895 (mtm) cc_final: 0.7653 (mtp)
REVERT: A 1340 THR cc_start: 0.7496 (p) cc_final: 0.7162 (m)
  outliers start: 55
  outliers final: 30
  residues processed: 223
  average time/residue: 0.5428
  time to fit residues: 130.9884
Evaluate side-chains
  211 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 177
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain E residue  286 LEU
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue 1025 GLU
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain A residue 1096 VAL
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1150 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1330 MET
Chi-restraints excluded: chain A residue 1331 THR
Chi-restraints excluded: chain A residue 1337 ASP
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 125 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 127 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  54 GLN
A  78 GLN
A 463 ASN
A 648 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.132751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.098939 restraints weight = 28601.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 2.72
r_work: 0.2748 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12422  Z= 0.113
  Angle     :  0.508   9.816  16822  Z= 0.257
  Chirality :  0.041   0.148   1939
  Planarity :  0.004   0.043   2144
  Dihedral  :  4.431  41.537   1668
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.07 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.22), residues: 1526
  helix:  0.74 (0.19), residues: 743
  sheet:  0.33 (0.63), residues: 72
  loop : -0.99 (0.24), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 319 
 TYR   0.011   0.001   TYR A 908 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A  33 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12420)
  covalent geometry    : angle       0.50724 (16818)
  SS BOND              : bond        0.00179 (    2)
  SS BOND              : angle       1.76635 (    4)
  hydrogen bonds       : bond        0.03244 (  553)
  hydrogen bonds       : angle       3.69807 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 178
  time to evaluate  : 0.376 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7567 (mttt) cc_final: 0.6980 (mptt)
REVERT: B  287 ASP cc_start: 0.8137 (t70) cc_final: 0.7809 (t70)
REVERT: E  325 GLU cc_start: 0.8230 (pt0) cc_final: 0.7847 (pt0)
REVERT: A  137 LYS cc_start: 0.7783 (tttt) cc_final: 0.7396 (ttmm)
REVERT: A  520 LYS cc_start: 0.8698 (ttmm) cc_final: 0.7956 (ttpp)
REVERT: A  702 LYS cc_start: 0.8826 (mttt) cc_final: 0.8599 (mttm)
REVERT: A  776 GLU cc_start: 0.8151 (tt0) cc_final: 0.7634 (mm-30)
REVERT: A  896 GLN cc_start: 0.7334 (mp10) cc_final: 0.6588 (mm110)
REVERT: A  956 MET cc_start: 0.8846 (tpt) cc_final: 0.8529 (tpp)
REVERT: A  997 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7233 (mtm110)
REVERT: A 1052 GLN cc_start: 0.8541 (tt0) cc_final: 0.8140 (mt0)
REVERT: A 1090 MET cc_start: 0.8623 (mmm) cc_final: 0.8330 (tpt)
REVERT: A 1096 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8605 (t)
REVERT: A 1111 MET cc_start: 0.8119 (mtt) cc_final: 0.7773 (mtm)
REVERT: A 1123 ARG cc_start: 0.8833 (ttt-90) cc_final: 0.8481 (ttt-90)
REVERT: A 1133 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8113 (mmtp)
REVERT: A 1317 MET cc_start: 0.7709 (mtm) cc_final: 0.7467 (mtp)
REVERT: A 1334 LYS cc_start: 0.7576 (mttt) cc_final: 0.6703 (mptt)
REVERT: A 1340 THR cc_start: 0.7406 (p) cc_final: 0.7114 (m)
  outliers start: 40
  outliers final: 21
  residues processed: 205
  average time/residue: 0.5269
  time to fit residues: 117.2927
Evaluate side-chains
  195 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain C residue  276 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1096 VAL
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1331 THR
Chi-restraints excluded: chain A residue 1337 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   chunk 143 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 99 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 463 ASN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.129034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.096258 restraints weight = 16316.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 1.87
r_work: 0.2793 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12422  Z= 0.153
  Angle     :  0.547   9.674  16822  Z= 0.274
  Chirality :  0.043   0.156   1939
  Planarity :  0.004   0.045   2144
  Dihedral  :  4.536  45.274   1668
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.99 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.22), residues: 1526
  helix:  0.81 (0.19), residues: 744
  sheet:  0.37 (0.62), residues: 72
  loop : -0.86 (0.24), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 414 
 TYR   0.014   0.001   TYR A 977 
 PHE   0.018   0.001   PHE A 395 
 TRP   0.013   0.002   TRP A 169 
 HIS   0.006   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12420)
  covalent geometry    : angle       0.54589 (16818)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       1.75811 (    4)
  hydrogen bonds       : bond        0.03657 (  553)
  hydrogen bonds       : angle       3.76418 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 176
  time to evaluate  : 0.404 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7620 (mttt) cc_final: 0.6870 (mmtt)
REVERT: B  287 ASP cc_start: 0.8246 (t70) cc_final: 0.7966 (t70)
REVERT: E  325 GLU cc_start: 0.8214 (pt0) cc_final: 0.7875 (pt0)
REVERT: A  137 LYS cc_start: 0.7869 (tttt) cc_final: 0.7487 (ttmm)
REVERT: A  173 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8861 (ttpt)
REVERT: A  377 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7733 (mp10)
REVERT: A  520 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8023 (ttpp)
REVERT: A  680 ASP cc_start: 0.8921 (t0) cc_final: 0.8665 (t0)
REVERT: A  702 LYS cc_start: 0.8841 (mttt) cc_final: 0.8610 (mttm)
REVERT: A  776 GLU cc_start: 0.8241 (tt0) cc_final: 0.7733 (mm-30)
REVERT: A  896 GLN cc_start: 0.7475 (mp10) cc_final: 0.6706 (mm110)
REVERT: A  956 MET cc_start: 0.8880 (tpt) cc_final: 0.8545 (tpp)
REVERT: A  989 ILE cc_start: 0.8576 (mt) cc_final: 0.8314 (mp)
REVERT: A  997 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7313 (mtm110)
REVERT: A 1042 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8295 (ttp)
REVERT: A 1052 GLN cc_start: 0.8618 (tt0) cc_final: 0.8229 (mt0)
REVERT: A 1090 MET cc_start: 0.8717 (mmm) cc_final: 0.8421 (tpt)
REVERT: A 1111 MET cc_start: 0.8249 (mtt) cc_final: 0.7866 (mtp)
REVERT: A 1123 ARG cc_start: 0.8921 (ttt-90) cc_final: 0.8580 (ttt-90)
REVERT: A 1133 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8084 (mmtp)
REVERT: A 1249 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8413 (pp)
REVERT: A 1317 MET cc_start: 0.7829 (mtm) cc_final: 0.7575 (mtp)
REVERT: A 1340 THR cc_start: 0.7472 (p) cc_final: 0.7146 (m)
  outliers start: 47
  outliers final: 27
  residues processed: 204
  average time/residue: 0.5305
  time to fit residues: 117.0806
Evaluate side-chains
  202 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 170
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain A residue 1096 VAL
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1150 ILE
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1330 MET
Chi-restraints excluded: chain A residue 1331 THR
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 72 optimal weight:    0.2980
   chunk 67 optimal weight:    0.6980
   chunk 139 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 314 ASN
A 463 ASN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.132390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.098207 restraints weight = 27443.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.64
r_work: 0.2765 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2615 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12422  Z= 0.094
  Angle     :  0.483  11.589  16822  Z= 0.243
  Chirality :  0.040   0.145   1939
  Planarity :  0.004   0.042   2144
  Dihedral  :  4.239  41.395   1668
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.24 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.22), residues: 1526
  helix:  1.03 (0.19), residues: 754
  sheet:  0.36 (0.61), residues: 72
  loop : -0.76 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 276 
 TYR   0.011   0.001   TYR A 908 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (12420)
  covalent geometry    : angle       0.48291 (16818)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       1.61546 (    4)
  hydrogen bonds       : bond        0.02959 (  553)
  hydrogen bonds       : angle       3.55825 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.498 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7402 (mttt) cc_final: 0.6646 (mmtt)
REVERT: B  287 ASP cc_start: 0.8237 (t70) cc_final: 0.7945 (t70)
REVERT: E  325 GLU cc_start: 0.8161 (pt0) cc_final: 0.7864 (pt0)
REVERT: A  137 LYS cc_start: 0.7790 (tttt) cc_final: 0.7422 (ttmm)
REVERT: A  149 ARG cc_start: 0.7391 (mmt-90) cc_final: 0.7089 (mmt90)
REVERT: A  277 ASP cc_start: 0.8319 (p0) cc_final: 0.8108 (p0)
REVERT: A  492 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7668 (pm20)
REVERT: A  540 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7640 (m-80)
REVERT: A  543 LYS cc_start: 0.7462 (ptpt) cc_final: 0.6706 (mttt)
REVERT: A  680 ASP cc_start: 0.8983 (t0) cc_final: 0.8715 (t0)
REVERT: A  776 GLU cc_start: 0.8328 (tt0) cc_final: 0.7814 (mm-30)
REVERT: A  896 GLN cc_start: 0.7435 (mp10) cc_final: 0.6685 (mm-40)
REVERT: A  956 MET cc_start: 0.8848 (tpt) cc_final: 0.8522 (tpp)
REVERT: A 1025 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7236 (tm-30)
REVERT: A 1042 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8319 (ttp)
REVERT: A 1052 GLN cc_start: 0.8628 (tt0) cc_final: 0.8242 (mt0)
REVERT: A 1087 MET cc_start: 0.8900 (mtp) cc_final: 0.8633 (mtp)
REVERT: A 1090 MET cc_start: 0.8726 (mmm) cc_final: 0.8421 (tpt)
REVERT: A 1111 MET cc_start: 0.8169 (mtt) cc_final: 0.7759 (mtp)
REVERT: A 1133 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8166 (mmtp)
REVERT: A 1249 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8302 (pp)
REVERT: A 1334 LYS cc_start: 0.7285 (mttt) cc_final: 0.6732 (tppt)
REVERT: A 1340 THR cc_start: 0.7337 (p) cc_final: 0.7097 (m)
  outliers start: 35
  outliers final: 16
  residues processed: 195
  average time/residue: 0.5532
  time to fit residues: 116.9210
Evaluate side-chains
  191 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  540 TYR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue 1025 GLU
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 463 ASN
A 859 ASN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.128230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.094187 restraints weight = 28809.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.75
r_work: 0.2695 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2543 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2539 r_free = 0.2539    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2539 r_free = 0.2539    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12422  Z= 0.180
  Angle     :  0.567  11.777  16822  Z= 0.282
  Chirality :  0.044   0.156   1939
  Planarity :  0.004   0.043   2144
  Dihedral  :  4.541  47.814   1668
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.53 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.22), residues: 1526
  helix:  0.94 (0.19), residues: 747
  sheet:  0.39 (0.61), residues: 72
  loop : -0.75 (0.24), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1189 
 TYR   0.015   0.001   TYR A 977 
 PHE   0.018   0.002   PHE A 395 
 TRP   0.013   0.002   TRP A 169 
 HIS   0.008   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (12420)
  covalent geometry    : angle       0.56609 (16818)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       1.70381 (    4)
  hydrogen bonds       : bond        0.03798 (  553)
  hydrogen bonds       : angle       3.77800 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.357 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7436 (mttt) cc_final: 0.6644 (mmtt)
REVERT: B  287 ASP cc_start: 0.8307 (t70) cc_final: 0.8022 (t70)
REVERT: E  325 GLU cc_start: 0.8175 (pt0) cc_final: 0.7803 (pt0)
REVERT: A  137 LYS cc_start: 0.7807 (tttt) cc_final: 0.7423 (ttmm)
REVERT: A  277 ASP cc_start: 0.8425 (p0) cc_final: 0.8210 (p0)
REVERT: A  492 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7618 (pm20)
REVERT: A  520 LYS cc_start: 0.8686 (ttmm) cc_final: 0.7878 (ttpp)
REVERT: A  680 ASP cc_start: 0.9063 (t0) cc_final: 0.8796 (t0)
REVERT: A  776 GLU cc_start: 0.8277 (tt0) cc_final: 0.7741 (mm-30)
REVERT: A  826 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8395 (mtpt)
REVERT: A  896 GLN cc_start: 0.7462 (mp10) cc_final: 0.6661 (mm110)
REVERT: A  956 MET cc_start: 0.8823 (tpt) cc_final: 0.8473 (tpp)
REVERT: A  989 ILE cc_start: 0.8478 (mt) cc_final: 0.8217 (mp)
REVERT: A 1042 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8363 (ttp)
REVERT: A 1052 GLN cc_start: 0.8629 (tt0) cc_final: 0.8238 (mt0)
REVERT: A 1087 MET cc_start: 0.8876 (mtp) cc_final: 0.8606 (mtp)
REVERT: A 1090 MET cc_start: 0.8722 (mmm) cc_final: 0.8452 (tpt)
REVERT: A 1111 MET cc_start: 0.8208 (mtt) cc_final: 0.7782 (mtp)
REVERT: A 1133 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8060 (mmtp)
REVERT: A 1249 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8299 (pp)
REVERT: A 1331 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8430 (t)
REVERT: A 1340 THR cc_start: 0.7521 (p) cc_final: 0.7203 (m)
  outliers start: 41
  outliers final: 21
  residues processed: 194
  average time/residue: 0.5051
  time to fit residues: 106.4870
Evaluate side-chains
  194 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1331 THR
Chi-restraints excluded: chain A residue 1337 ASP
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 112 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 126 optimal weight:    0.0070
   chunk 48 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   chunk 133 optimal weight:    0.9990
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
C 279 ASN
A  78 GLN
A 463 ASN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.131535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.097279 restraints weight = 28719.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 2.75
r_work: 0.2735 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12422  Z= 0.100
  Angle     :  0.492  10.828  16822  Z= 0.248
  Chirality :  0.040   0.143   1939
  Planarity :  0.004   0.042   2144
  Dihedral  :  4.273  43.899   1668
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.85 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.22), residues: 1526
  helix:  1.19 (0.19), residues: 747
  sheet:  0.46 (0.60), residues: 72
  loop : -0.67 (0.24), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1189 
 TYR   0.011   0.001   TYR A 908 
 PHE   0.015   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12420)
  covalent geometry    : angle       0.49159 (16818)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       1.56891 (    4)
  hydrogen bonds       : bond        0.03059 (  553)
  hydrogen bonds       : angle       3.58480 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.323 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7640 (mttt) cc_final: 0.6916 (mmtt)
REVERT: B  282 MET cc_start: 0.7123 (mmt) cc_final: 0.6864 (mmt)
REVERT: B  287 ASP cc_start: 0.8121 (t70) cc_final: 0.7860 (t70)
REVERT: E  325 GLU cc_start: 0.8194 (pt0) cc_final: 0.7872 (pt0)
REVERT: A  137 LYS cc_start: 0.7813 (tttt) cc_final: 0.7432 (ttmm)
REVERT: A  138 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7766 (tttp)
REVERT: A  149 ARG cc_start: 0.7242 (mmt-90) cc_final: 0.6897 (mmt90)
REVERT: A  277 ASP cc_start: 0.8267 (p0) cc_final: 0.7996 (p0)
REVERT: A  492 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7733 (pm20)
REVERT: A  520 LYS cc_start: 0.8691 (ttmm) cc_final: 0.7948 (ttpp)
REVERT: A  543 LYS cc_start: 0.7609 (ptpt) cc_final: 0.6934 (mttt)
REVERT: A  680 ASP cc_start: 0.8844 (t0) cc_final: 0.8576 (t0)
REVERT: A  776 GLU cc_start: 0.8210 (tt0) cc_final: 0.7709 (mm-30)
REVERT: A  826 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8264 (tttt)
REVERT: A  896 GLN cc_start: 0.7466 (mp10) cc_final: 0.6742 (mm-40)
REVERT: A  956 MET cc_start: 0.8858 (tpt) cc_final: 0.8518 (tpp)
REVERT: A 1042 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (ttp)
REVERT: A 1052 GLN cc_start: 0.8493 (tt0) cc_final: 0.8181 (mt0)
REVERT: A 1087 MET cc_start: 0.8844 (mtp) cc_final: 0.8528 (mtp)
REVERT: A 1090 MET cc_start: 0.8678 (mmm) cc_final: 0.8357 (tpt)
REVERT: A 1111 MET cc_start: 0.8094 (mtt) cc_final: 0.7733 (mtm)
REVERT: A 1133 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8080 (mmtp)
REVERT: A 1249 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8364 (pp)
REVERT: A 1334 LYS cc_start: 0.7316 (mttt) cc_final: 0.7096 (tppt)
REVERT: A 1340 THR cc_start: 0.7341 (p) cc_final: 0.7111 (m)
  outliers start: 27
  outliers final: 18
  residues processed: 192
  average time/residue: 0.5599
  time to fit residues: 116.0929
Evaluate side-chains
  192 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0670
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0970
   chunk 105 optimal weight:    2.9990
   chunk 135 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
A 749 GLN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.133061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.099177 restraints weight = 27125.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 2.65
r_work: 0.2765 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12422  Z= 0.098
  Angle     :  0.487  10.136  16822  Z= 0.245
  Chirality :  0.040   0.148   1939
  Planarity :  0.004   0.042   2144
  Dihedral  :  4.166  40.996   1668
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.00 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.22), residues: 1526
  helix:  1.28 (0.19), residues: 755
  sheet:  0.45 (0.59), residues: 72
  loop : -0.58 (0.24), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1189 
 TYR   0.010   0.001   TYR A 908 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.011   0.001   TRP A1227 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (12420)
  covalent geometry    : angle       0.48679 (16818)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       1.49773 (    4)
  hydrogen bonds       : bond        0.02984 (  553)
  hydrogen bonds       : angle       3.53129 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.431 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7565 (mttt) cc_final: 0.6824 (mmtt)
REVERT: B  282 MET cc_start: 0.7316 (mmt) cc_final: 0.7038 (mmt)
REVERT: E  325 GLU cc_start: 0.8211 (pt0) cc_final: 0.7896 (pt0)
REVERT: A  137 LYS cc_start: 0.7885 (tttt) cc_final: 0.7524 (ttmm)
REVERT: A  149 ARG cc_start: 0.7245 (mmt-90) cc_final: 0.6985 (mmt90)
REVERT: A  277 ASP cc_start: 0.8350 (p0) cc_final: 0.8120 (p0)
REVERT: A  329 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7477 (pmm-80)
REVERT: A  492 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7731 (pm20)
REVERT: A  520 LYS cc_start: 0.8740 (ttmm) cc_final: 0.7981 (ttpp)
REVERT: A  540 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7672 (m-80)
REVERT: A  543 LYS cc_start: 0.7592 (ptpt) cc_final: 0.6910 (mttt)
REVERT: A  680 ASP cc_start: 0.8985 (t0) cc_final: 0.8754 (t0)
REVERT: A  776 GLU cc_start: 0.8421 (tt0) cc_final: 0.7922 (mm-30)
REVERT: A  826 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8398 (tttt)
REVERT: A  896 GLN cc_start: 0.7445 (mp10) cc_final: 0.6681 (mm-40)
REVERT: A  956 MET cc_start: 0.8868 (tpt) cc_final: 0.8524 (tpp)
REVERT: A 1042 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8346 (ttp)
REVERT: A 1052 GLN cc_start: 0.8571 (tt0) cc_final: 0.8350 (mt0)
REVERT: A 1087 MET cc_start: 0.8929 (mtp) cc_final: 0.8615 (mtp)
REVERT: A 1090 MET cc_start: 0.8810 (mmm) cc_final: 0.8549 (tpt)
REVERT: A 1111 MET cc_start: 0.8161 (mtt) cc_final: 0.7762 (mtp)
REVERT: A 1123 ARG cc_start: 0.8841 (ttt-90) cc_final: 0.8611 (ttt-90)
REVERT: A 1133 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8097 (mmtp)
REVERT: A 1249 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8385 (pp)
REVERT: A 1334 LYS cc_start: 0.7262 (mttt) cc_final: 0.6657 (tppt)
REVERT: A 1340 THR cc_start: 0.7320 (p) cc_final: 0.7072 (m)
  outliers start: 24
  outliers final: 18
  residues processed: 188
  average time/residue: 0.5584
  time to fit residues: 113.7575
Evaluate side-chains
  192 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  540 TYR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1365 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0570
   chunk 104 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0020
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.3644

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
A 749 GLN
A 974 ASN
A1314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.133814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.098956 restraints weight = 21050.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.30
r_work: 0.2835 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12422  Z= 0.085
  Angle     :  0.480   9.771  16822  Z= 0.240
  Chirality :  0.040   0.155   1939
  Planarity :  0.004   0.042   2144
  Dihedral  :  4.044  37.684   1668
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.58 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.22), residues: 1526
  helix:  1.45 (0.20), residues: 754
  sheet:  0.58 (0.58), residues: 72
  loop : -0.52 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1189 
 TYR   0.011   0.001   TYR A 908 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.011   0.001   TRP A1227 
 HIS   0.004   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 (12420)
  covalent geometry    : angle       0.47979 (16818)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       1.48699 (    4)
  hydrogen bonds       : bond        0.02727 (  553)
  hydrogen bonds       : angle       3.45905 ( 1621)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.504 
Fit side-chains
REVERT: D  304 LYS cc_start: 0.7476 (mttt) cc_final: 0.6727 (mmtt)
REVERT: E  325 GLU cc_start: 0.8200 (pt0) cc_final: 0.7883 (pt0)
REVERT: A  137 LYS cc_start: 0.7793 (tttt) cc_final: 0.7445 (ttmm)
REVERT: A  138 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7753 (tttp)
REVERT: A  277 ASP cc_start: 0.8221 (p0) cc_final: 0.8011 (p0)
REVERT: A  319 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7883 (ttt-90)
REVERT: A  329 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7492 (pmm-80)
REVERT: A  492 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7702 (pm20)
REVERT: A  520 LYS cc_start: 0.8683 (ttmm) cc_final: 0.7918 (ttpp)
REVERT: A  540 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7616 (m-80)
REVERT: A  543 LYS cc_start: 0.7542 (ptpt) cc_final: 0.6861 (mttt)
REVERT: A  743 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7404 (mtp-110)
REVERT: A  776 GLU cc_start: 0.8337 (tt0) cc_final: 0.7824 (mm-30)
REVERT: A  844 MET cc_start: 0.8881 (ttm) cc_final: 0.8637 (mtm)
REVERT: A  873 MET cc_start: 0.9246 (mmm) cc_final: 0.9040 (mmp)
REVERT: A  896 GLN cc_start: 0.7410 (mp10) cc_final: 0.6599 (mm110)
REVERT: A  956 MET cc_start: 0.8861 (tpt) cc_final: 0.8516 (tpp)
REVERT: A 1042 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8326 (ttp)
REVERT: A 1052 GLN cc_start: 0.8524 (tt0) cc_final: 0.8241 (mt0)
REVERT: A 1087 MET cc_start: 0.8842 (mtp) cc_final: 0.8527 (mtp)
REVERT: A 1090 MET cc_start: 0.8728 (mmm) cc_final: 0.8514 (tpt)
REVERT: A 1111 MET cc_start: 0.8073 (mtt) cc_final: 0.7690 (mtp)
REVERT: A 1123 ARG cc_start: 0.8742 (ttt-90) cc_final: 0.8504 (ttt-90)
REVERT: A 1249 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8407 (pp)
REVERT: A 1340 THR cc_start: 0.7186 (p) cc_final: 0.6964 (m)
  outliers start: 21
  outliers final: 15
  residues processed: 186
  average time/residue: 0.5389
  time to fit residues: 108.4227
Evaluate side-chains
  184 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain E residue  373 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  540 TYR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  682 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue 1031 GLU
Chi-restraints excluded: chain A residue 1037 VAL
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1256 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 143 optimal weight:    7.9990
   chunk 103 optimal weight:    0.1980
   chunk 80 optimal weight:    0.0020
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 64 optimal weight:    0.1980
   chunk 11 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
E 333 GLN
A  78 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
A 749 GLN
A 974 ASN
A1034 HIS
A1314 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.134530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.099667 restraints weight = 24988.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.48
r_work: 0.2833 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12422  Z= 0.085
  Angle     :  0.475   9.423  16822  Z= 0.237
  Chirality :  0.040   0.161   1939
  Planarity :  0.004   0.041   2144
  Dihedral  :  3.991  38.093   1668
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.95 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.22), residues: 1526
  helix:  1.54 (0.20), residues: 754
  sheet:  0.60 (0.57), residues: 72
  loop : -0.45 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1189 
 TYR   0.021   0.001   TYR A 134 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.011   0.001   TRP A1227 
 HIS   0.004   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (12420)
  covalent geometry    : angle       0.47455 (16818)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       1.43476 (    4)
  hydrogen bonds       : bond        0.02701 (  553)
  hydrogen bonds       : angle       3.40405 ( 1621)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3996.98 seconds
wall clock time: 68 minutes 44.78 seconds (4124.78 seconds total)