Starting phenix.real_space_refine
on Thu Mar 14 16:30:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/03_2024/8fzq_29637_updated.pdb"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      46      5.16       5
     C    6017      2.51       5
     N    1530      2.21       5
     O    1643      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  391": "OE1" <-> "OE2"
    Residue "A PHE  587": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  625": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9244
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1156, 9244
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'peptide': 1152, 'undetermined': 4}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 27, 'TRANS': 1124, None: 4}
            Not linked:
              pdbres="SER A1435 "
              pdbres=" MG A1501 "
            Not linked:
              pdbres=" MG A1501 "
              pdbres=" MG A1502 "
            Not linked:
              pdbres=" MG A1502 "
              pdbres="ATP A1503 "
            Not linked:
              pdbres="ATP A1503 "
              pdbres="ATP A1504 "
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'UNK:plan-1': 19}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 5.30, per 1000 atoms: 0.57
  Number of scatterers: 9244
  At special positions: 0
  Unit cell: (108.15, 117.42, 111.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      46     16.00
     P       6     15.00
     Mg      2     11.99
     O    1643      8.00
     N    1530      7.00
     C    6017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.71
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      63.9% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 16
    Processing helix  chain 'A' and resid 21 through 29
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 46 through 63
      removed outlier: 3.654A  pdb=" N   GLU A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 109
      removed outlier: 3.770A  pdb=" N   ARG A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ARG A  80 " --> pdb=" O   CYS A  76 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      Proline residue:  A  99  - end of helix
    Processing helix  chain 'A' and resid 117 through 165
      removed outlier: 3.538A  pdb=" N   GLY A 126 " --> pdb=" O   TYR A 122 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 170 through 172
      No H-bonds generated for 'chain 'A' and resid 170 through 172'
    Processing helix  chain 'A' and resid 177 through 185
    Processing helix  chain 'A' and resid 190 through 214
      removed outlier: 4.481A  pdb=" N   LEU A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ALA A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU A 197 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   PHE A 200 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TRP A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE A 203 " --> pdb=" O   HIS A 199 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA A 204 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      Proline residue:  A 205  - end of helix
    Processing helix  chain 'A' and resid 223 through 275
      removed outlier: 3.714A  pdb=" N   ILE A 231 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG A 242 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 248 " --> pdb=" O   MET A 245 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASP A 249 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 252 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY A 253 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE A 255 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 258 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL A 260 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 266 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLU A 267 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   GLN A 270 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 326
      removed outlier: 3.834A  pdb=" N   LYS A 294 " --> pdb=" O   GLN A 290 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLY A 314 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER A 321 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 333 through 351
      removed outlier: 3.920A  pdb=" N   VAL A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 375
    Processing helix  chain 'A' and resid 388 through 390
      No H-bonds generated for 'chain 'A' and resid 388 through 390'
    Processing helix  chain 'A' and resid 403 through 406
      No H-bonds generated for 'chain 'A' and resid 403 through 406'
    Processing helix  chain 'A' and resid 464 through 472
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 514 through 524
    Processing helix  chain 'A' and resid 527 through 532
      removed outlier: 4.062A  pdb=" N   LYS A 532 " --> pdb=" O   GLU A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 563
    Processing helix  chain 'A' and resid 580 through 590
      removed outlier: 3.748A  pdb=" N   PHE A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 588 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 630 through 633
      No H-bonds generated for 'chain 'A' and resid 630 through 633'
    Processing helix  chain 'A' and resid 756 through 766
      removed outlier: 4.666A  pdb=" N   UNK A 761 " --> pdb=" O   UNK A 757 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   UNK A 762 " --> pdb=" O   UNK A 758 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   UNK A 765 " --> pdb=" O   UNK A 761 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   UNK A 766 " --> pdb=" O   UNK A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 853
    Processing helix  chain 'A' and resid 857 through 882
    Processing helix  chain 'A' and resid 917 through 921
    Processing helix  chain 'A' and resid 923 through 926
      No H-bonds generated for 'chain 'A' and resid 923 through 926'
    Processing helix  chain 'A' and resid 935 through 956
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 969 through 984
      removed outlier: 3.635A  pdb=" N   ARG A 975 " --> pdb=" O   GLY A 971 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE A 976 " --> pdb=" O   ILE A 972 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   ILE A 980 " --> pdb=" O   PHE A 976 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ALA A 981 " --> pdb=" O   SER A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 1011
      removed outlier: 3.538A  pdb=" N   VAL A1001 " --> pdb=" O   LEU A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1046
      removed outlier: 3.734A  pdb=" N   VAL A1017 " --> pdb=" O   PRO A1013 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
      Proline residue:  A1021  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN A1035 " --> pdb=" O   ALA A1031 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   THR A1036 " --> pdb=" O   TYR A1032 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN A1039 " --> pdb=" O   GLN A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1060
    Processing helix  chain 'A' and resid 1062 through 1068
    Processing helix  chain 'A' and resid 1071 through 1120
      removed outlier: 3.523A  pdb=" N   LEU A1084 " --> pdb=" O   LYS A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1168
      removed outlier: 3.617A  pdb=" N   ILE A1139 " --> pdb=" O   LEU A1135 " (cutoff:3.500A)
      removed outlier: 5.489A  pdb=" N   MET A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   SER A1141 " --> pdb=" O   MET A1137 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   THR A1142 " --> pdb=" O   ASN A1138 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TRP A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP A1154 " --> pdb=" O   SER A1150 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   SER A1159 " --> pdb=" O   SER A1155 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   VAL A1160 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ARG A1162 " --> pdb=" O   ARG A1158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1257
    Processing helix  chain 'A' and resid 1279 through 1285
    Processing helix  chain 'A' and resid 1300 through 1304
    Processing helix  chain 'A' and resid 1312 through 1322
    Processing helix  chain 'A' and resid 1325 through 1330
    Processing helix  chain 'A' and resid 1348 through 1361
    Processing helix  chain 'A' and resid 1378 through 1391
    Processing helix  chain 'A' and resid 1405 through 1409
      removed outlier: 3.759A  pdb=" N   LEU A1408 " --> pdb=" O   GLU A1405 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A1409 " --> pdb=" O   ALA A1406 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1405 through 1409'
    Processing helix  chain 'A' and resid 1430 through 1433
      No H-bonds generated for 'chain 'A' and resid 1430 through 1433'
    Processing sheet with id=  A, first strand: chain 'A' and resid 392 through 394
      removed outlier: 3.665A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 446 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 600 through 603
      removed outlier: 6.823A  pdb=" N   LYS A 615 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   ALA A 457 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE A 626 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   HIS A 620 " --> pdb=" O   SER A 624 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   SER A 624 " --> pdb=" O   HIS A 620 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 489 through 491
    Processing sheet with id=  D, first strand: chain 'A' and resid 1262 through 1264
      removed outlier: 4.542A  pdb=" N   ASN A1262 " --> pdb=" O   LYS A1218 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LYS A1218 " --> pdb=" O   ASN A1262 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR A1216 " --> pdb=" O   GLU A1264 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A1230 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ALA A1217 " --> pdb=" O   GLU A1228 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   GLU A1228 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 1397 through 1400
      removed outlier: 6.959A  pdb=" N   GLN A1412 " --> pdb=" O   GLY A1241 " (cutoff:3.500A)
      removed outlier: 8.322A  pdb=" N   LEU A1243 " --> pdb=" O   GLN A1412 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LEU A1414 " --> pdb=" O   LEU A1243 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1326 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: 2.92

  Time building geometry restraints manager: 4.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2877
        1.34 -     1.46: 2110
        1.46 -     1.58: 4362
        1.58 -     1.69: 10
        1.69 -     1.81: 77
  Bond restraints: 9436
  Sorted by residual:
  bond pdb=" C   ALA A1081 "
       pdb=" O   ALA A1081 "
    ideal  model  delta    sigma   weight residual
    1.237  1.247 -0.010 1.19e-02 7.06e+03 7.62e-01
  bond pdb=" CA  ILE A 328 "
       pdb=" C   ILE A 328 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.27e-02 6.20e+03 7.22e-01
  bond pdb=" CB  MET A 265 "
       pdb=" CG  MET A 265 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 6.68e-01
  bond pdb=" CA  HIS A 139 "
       pdb=" C   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 1.23e-02 6.61e+03 6.04e-01
  bond pdb=" N   GLN A 493 "
       pdb=" CA  GLN A 493 "
    ideal  model  delta    sigma   weight residual
    1.459  1.450  0.009 1.19e-02 7.06e+03 5.94e-01
  ... (remaining 9431 not shown)

  Histogram of bond angle deviations from ideal:
       98.93 -   107.13: 210
      107.13 -   115.33: 5844
      115.33 -   123.52: 6486
      123.52 -   131.72: 204
      131.72 -   139.92: 27
  Bond angle restraints: 12771
  Sorted by residual:
  angle pdb=" N   GLN A 493 "
        pdb=" CA  GLN A 493 "
        pdb=" C   GLN A 493 "
      ideal   model   delta    sigma   weight residual
     111.07  105.15    5.92 1.07e+00 8.73e-01 3.06e+01
  angle pdb=" C   ARG A1048 "
        pdb=" N   SER A1049 "
        pdb=" CA  SER A1049 "
      ideal   model   delta    sigma   weight residual
     120.06  123.71   -3.65 1.19e+00 7.06e-01 9.38e+00
  angle pdb=" C   THR A 388 "
        pdb=" N   THR A 389 "
        pdb=" CA  THR A 389 "
      ideal   model   delta    sigma   weight residual
     121.54  127.01   -5.47 1.91e+00 2.74e-01 8.21e+00
  angle pdb=" CA  LEU A 327 "
        pdb=" CB  LEU A 327 "
        pdb=" CG  LEU A 327 "
      ideal   model   delta    sigma   weight residual
     116.30  126.08   -9.78 3.50e+00 8.16e-02 7.81e+00
  angle pdb=" N   LEU A1335 "
        pdb=" CA  LEU A1335 "
        pdb=" CB  LEU A1335 "
      ideal   model   delta    sigma   weight residual
     113.65  109.82    3.83 1.47e+00 4.63e-01 6.79e+00
  ... (remaining 12766 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 4957
       17.67 -    35.35: 529
       35.35 -    53.02: 111
       53.02 -    70.69: 29
       70.69 -    88.37: 7
  Dihedral angle restraints: 5633
    sinusoidal: 2287
      harmonic: 3346
  Sorted by residual:
  dihedral pdb=" CA  LEU A 387 "
           pdb=" C   LEU A 387 "
           pdb=" N   THR A 388 "
           pdb=" CA  THR A 388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  CYS A 590 "
           pdb=" C   CYS A 590 "
           pdb=" N   VAL A 591 "
           pdb=" CA  VAL A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.68  -16.32     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  CYS A  76 "
           pdb=" C   CYS A  76 "
           pdb=" N   PHE A  77 "
           pdb=" CA  PHE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.18  -15.82     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 5630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 974
       0.032 -    0.063: 356
       0.063 -    0.095: 99
       0.095 -    0.127: 44
       0.127 -    0.159: 5
  Chirality restraints: 1478
  Sorted by residual:
  chirality pdb=" CA  GLN A 493 "
            pdb=" N   GLN A 493 "
            pdb=" C   GLN A 493 "
            pdb=" CB  GLN A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CA  LEU A 323 "
            pdb=" N   LEU A 323 "
            pdb=" C   LEU A 323 "
            pdb=" CB  LEU A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 1475 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1274 "    0.017 2.00e-02 2.50e+03   1.33e-02 4.44e+00
        pdb=" CG  TRP A1274 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1274 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1274 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1274 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1274 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1274 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1274 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1274 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1049 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A1050 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A1050 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1050 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  98 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A  99 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  99 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  99 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 69
        2.58 -     3.16: 7787
        3.16 -     3.74: 14729
        3.74 -     4.32: 18338
        4.32 -     4.90: 30635
  Nonbonded interactions: 71558
  Sorted by model distance:
  nonbonded pdb="MG    MG A1502 "
            pdb=" O2B ATP A1504 "
     model   vdw
     1.999 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O2B ATP A1503 "
     model   vdw
     2.003 2.170
  nonbonded pdb="MG    MG A1502 "
            pdb=" O3G ATP A1504 "
     model   vdw
     2.043 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O3B ATP A1503 "
     model   vdw
     2.062 2.170
  nonbonded pdb=" OG  SER A1251 "
            pdb="MG    MG A1502 "
     model   vdw
     2.137 2.170
  ... (remaining 71553 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          12.230
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     27.490
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
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      :  0.002   0.026   9436  Z= 0.143
  Angle     :  0.529   9.779  12771  Z= 0.275
  Chirality :  0.039   0.159   1478
  Planarity :  0.003   0.044   1560
  Dihedral  : 15.435  88.368   3469
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.26), residues: 1121
  helix:  1.60 (0.20), residues: 743
  sheet: -0.26 (0.66), residues: 65
  loop : -1.42 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A 609 
 PHE   0.024   0.001   PHE A 587 
 TYR   0.011   0.001   TYR A 304 
 ARG   0.002   0.000   ARG A 975 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 GLN cc_start: 0.5535 (mp10) cc_final: 0.5065 (pp30)
REVERT: A 1354 MET cc_start: 0.8421 (tpp) cc_final: 0.8190 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 204
  average time/residue: 0.1644
  time to fit residues: 50.0692
Evaluate side-chains
  105 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0020
   chunk 104 optimal weight:   20.0000
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 HIS
A1088 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9436  Z= 0.183
  Angle     :  0.538   6.309  12771  Z= 0.275
  Chirality :  0.039   0.143   1478
  Planarity :  0.004   0.044   1560
  Dihedral  :  7.880  84.432   1306
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1121
  helix:  1.30 (0.20), residues: 743
  sheet: -0.12 (0.62), residues: 71
  loop : -1.38 (0.31), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1274 
 HIS   0.002   0.000   HIS A 949 
 PHE   0.018   0.001   PHE A 131 
 TYR   0.010   0.001   TYR A 304 
 ARG   0.002   0.000   ARG A  75 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ARG cc_start: 0.5024 (ptp90) cc_final: 0.4511 (tpt170)
REVERT: A  525 GLN cc_start: 0.5383 (mp10) cc_final: 0.5021 (pp30)
REVERT: A  602 LEU cc_start: 0.7984 (tp) cc_final: 0.7518 (mp)
REVERT: A 1160 VAL cc_start: 0.8573 (p) cc_final: 0.8070 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1664
  time to fit residues: 35.3240
Evaluate side-chains
  88 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0980
   chunk 93 optimal weight:    7.9990
   chunk 103 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9436  Z= 0.216
  Angle     :  0.570   9.487  12771  Z= 0.293
  Chirality :  0.040   0.191   1478
  Planarity :  0.004   0.043   1560
  Dihedral  :  7.279  83.090   1306
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1121
  helix:  1.14 (0.20), residues: 726
  sheet: -0.25 (0.60), residues: 71
  loop : -1.20 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 202 
 HIS   0.003   0.001   HIS A 147 
 PHE   0.025   0.002   PHE A 131 
 TYR   0.018   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A1158 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ARG cc_start: 0.5668 (ptp90) cc_final: 0.5004 (tpt90)
REVERT: A  304 TYR cc_start: 0.7912 (t80) cc_final: 0.7420 (t80)
REVERT: A  321 SER cc_start: 0.8962 (m) cc_final: 0.8699 (p)
REVERT: A  525 GLN cc_start: 0.5355 (mt0) cc_final: 0.4831 (mp10)
REVERT: A  602 LEU cc_start: 0.8213 (tp) cc_final: 0.7675 (mp)
REVERT: A 1105 MET cc_start: 0.7981 (mtt) cc_final: 0.7761 (mtt)
REVERT: A 1354 MET cc_start: 0.7837 (tpt) cc_final: 0.7517 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1748
  time to fit residues: 32.8275
Evaluate side-chains
  79 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
A1088 ASN
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9436  Z= 0.285
  Angle     :  0.619   7.773  12771  Z= 0.316
  Chirality :  0.041   0.186   1478
  Planarity :  0.004   0.045   1560
  Dihedral  :  7.105  79.013   1306
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.14 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.25), residues: 1121
  helix:  0.94 (0.20), residues: 729
  sheet: -0.63 (0.58), residues: 70
  loop : -1.17 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A1274 
 HIS   0.003   0.001   HIS A 139 
 PHE   0.028   0.002   PHE A 131 
 TYR   0.018   0.002   TYR A1032 
 ARG   0.005   0.001   ARG A1158 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  150 MET cc_start: 0.8067 (tpp) cc_final: 0.7713 (tpp)
REVERT: A  602 LEU cc_start: 0.8461 (tp) cc_final: 0.7850 (mp)
REVERT: A 1354 MET cc_start: 0.8140 (tpt) cc_final: 0.7666 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1795
  time to fit residues: 30.3876
Evaluate side-chains
  64 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    0.0670
   chunk 1 optimal weight:    0.3980
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 94 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0980
   chunk 28 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0060
   overall best weight:    0.2334

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1088 ASN
A1280 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9436  Z= 0.139
  Angle     :  0.507   6.368  12771  Z= 0.260
  Chirality :  0.038   0.144   1478
  Planarity :  0.003   0.044   1560
  Dihedral  :  6.675  70.926   1306
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.42 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1121
  helix:  1.20 (0.20), residues: 721
  sheet: -0.39 (0.61), residues: 69
  loop : -1.27 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1274 
 HIS   0.012   0.001   HIS A1079 
 PHE   0.027   0.001   PHE A 131 
 TYR   0.014   0.001   TYR A 325 
 ARG   0.004   0.000   ARG A1259 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7828 (tpp) cc_final: 0.7487 (tpp)
REVERT: A  321 SER cc_start: 0.8878 (m) cc_final: 0.8593 (p)
REVERT: A  342 PHE cc_start: 0.8532 (m-10) cc_final: 0.8282 (m-10)
REVERT: A  469 MET cc_start: 0.9232 (mmt) cc_final: 0.8616 (mpp)
REVERT: A  602 LEU cc_start: 0.8372 (tp) cc_final: 0.7790 (mp)
REVERT: A 1088 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8546 (t0)
REVERT: A 1354 MET cc_start: 0.8097 (tpt) cc_final: 0.7752 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1494
  time to fit residues: 26.6561
Evaluate side-chains
  71 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0000
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
A 525 GLN
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9436  Z= 0.262
  Angle     :  0.592  10.454  12771  Z= 0.303
  Chirality :  0.040   0.165   1478
  Planarity :  0.004   0.044   1560
  Dihedral  :  6.605  59.325   1306
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.91 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1121
  helix:  1.00 (0.20), residues: 722
  sheet: -0.45 (0.62), residues: 63
  loop : -1.18 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1274 
 HIS   0.008   0.001   HIS A1079 
 PHE   0.030   0.002   PHE A 131 
 TYR   0.017   0.001   TYR A 325 
 ARG   0.005   0.001   ARG A 933 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7893 (tpp) cc_final: 0.7507 (tpp)
REVERT: A  525 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6040 (mp10)
REVERT: A  602 LEU cc_start: 0.8472 (tp) cc_final: 0.7771 (mp)
REVERT: A 1354 MET cc_start: 0.8295 (tpt) cc_final: 0.7837 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1566
  time to fit residues: 23.3928
Evaluate side-chains
  64 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 63 optimal weight:    0.2980
   chunk 81 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 68 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1088 ASN
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9436  Z= 0.166
  Angle     :  0.514   8.648  12771  Z= 0.263
  Chirality :  0.038   0.142   1478
  Planarity :  0.003   0.044   1560
  Dihedral  :  6.174  59.266   1306
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.01 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1121
  helix:  1.14 (0.20), residues: 721
  sheet: -0.53 (0.61), residues: 69
  loop : -1.21 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1274 
 HIS   0.005   0.001   HIS A1079 
 PHE   0.027   0.001   PHE A 131 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A1102 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7900 (tpp) cc_final: 0.7465 (tpp)
REVERT: A  469 MET cc_start: 0.9308 (mmt) cc_final: 0.8601 (mpp)
REVERT: A  602 LEU cc_start: 0.8475 (tp) cc_final: 0.7807 (mp)
REVERT: A  849 TYR cc_start: 0.8313 (m-10) cc_final: 0.7280 (m-10)
REVERT: A 1354 MET cc_start: 0.8249 (tpt) cc_final: 0.7936 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1582
  time to fit residues: 26.0004
Evaluate side-chains
  70 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.5515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9436  Z= 0.170
  Angle     :  0.529   8.664  12771  Z= 0.270
  Chirality :  0.038   0.144   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  5.965  62.839   1306
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1121
  helix:  1.20 (0.20), residues: 714
  sheet: -0.36 (0.63), residues: 63
  loop : -1.20 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 
 PHE   0.027   0.001   PHE A 131 
 TYR   0.010   0.001   TYR A 325 
 ARG   0.006   0.000   ARG A 933 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7810 (tpp) cc_final: 0.7464 (tpp)
REVERT: A  469 MET cc_start: 0.9340 (mmt) cc_final: 0.8571 (mpp)
REVERT: A  602 LEU cc_start: 0.8411 (tp) cc_final: 0.7694 (mp)
REVERT: A 1354 MET cc_start: 0.8241 (tpt) cc_final: 0.7906 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1603
  time to fit residues: 25.6221
Evaluate side-chains
  70 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 93 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0670
   chunk 67 optimal weight:    0.0980
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.2918

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.5598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9436  Z= 0.140
  Angle     :  0.514   7.498  12771  Z= 0.261
  Chirality :  0.038   0.145   1478
  Planarity :  0.004   0.045   1560
  Dihedral  :  5.792  62.437   1306
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1121
  helix:  1.27 (0.20), residues: 713
  sheet: -0.22 (0.64), residues: 63
  loop : -1.24 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A1274 
 HIS   0.006   0.001   HIS A1079 
 PHE   0.026   0.001   PHE A 131 
 TYR   0.008   0.001   TYR A 849 
 ARG   0.003   0.000   ARG A1162 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7724 (tpp) cc_final: 0.7358 (tpp)
REVERT: A  321 SER cc_start: 0.8771 (m) cc_final: 0.8487 (p)
REVERT: A  469 MET cc_start: 0.9325 (mmt) cc_final: 0.8555 (mpp)
REVERT: A  525 GLN cc_start: 0.5140 (mp10) cc_final: 0.4545 (pp30)
REVERT: A  602 LEU cc_start: 0.8422 (tp) cc_final: 0.7772 (mp)
REVERT: A 1267 ILE cc_start: 0.7693 (pt) cc_final: 0.7431 (pt)
REVERT: A 1354 MET cc_start: 0.8159 (tpt) cc_final: 0.7867 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1644
  time to fit residues: 27.4000
Evaluate side-chains
  70 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.0000
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 114 optimal weight:    0.5980
   chunk 105 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9436  Z= 0.160
  Angle     :  0.527   7.999  12771  Z= 0.266
  Chirality :  0.038   0.187   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  5.741  62.027   1306
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1121
  helix:  1.29 (0.20), residues: 708
  sheet: -0.23 (0.62), residues: 63
  loop : -1.20 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 
 PHE   0.031   0.001   PHE A 587 
 TYR   0.020   0.001   TYR A1073 
 ARG   0.003   0.000   ARG A1158 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A  150 MET cc_start: 0.7784 (tpp) cc_final: 0.7455 (tpp)
REVERT: A  321 SER cc_start: 0.8763 (m) cc_final: 0.8533 (p)
REVERT: A  469 MET cc_start: 0.9293 (mmt) cc_final: 0.8557 (mpp)
REVERT: A  525 GLN cc_start: 0.5225 (mp10) cc_final: 0.4683 (pp30)
REVERT: A  602 LEU cc_start: 0.8427 (tp) cc_final: 0.7777 (mp)
REVERT: A 1267 ILE cc_start: 0.7750 (pt) cc_final: 0.7450 (pt)
REVERT: A 1354 MET cc_start: 0.8167 (tpt) cc_final: 0.7867 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1565
  time to fit residues: 24.9040
Evaluate side-chains
  70 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.087329 restraints weight = 24273.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.087310 restraints weight = 17996.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.087768 restraints weight = 14792.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9436  Z= 0.157
  Angle     :  0.513   7.742  12771  Z= 0.261
  Chirality :  0.038   0.175   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  5.690  60.333   1306
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1121
  helix:  1.25 (0.20), residues: 711
  sheet: -0.32 (0.60), residues: 69
  loop : -1.12 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1274 
 HIS   0.005   0.001   HIS A1079 
 PHE   0.031   0.001   PHE A 131 
 TYR   0.011   0.001   TYR A 304 
 ARG   0.002   0.000   ARG A 600 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1781.62 seconds
wall clock time: 32 minutes 55.15 seconds (1975.15 seconds total)