Starting phenix.real_space_refine
on Fri Dec  8 22:01:59 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/12_2023/8fzq_29637_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/12_2023/8fzq_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_29637/12_2023/8fzq_29637.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/12_2023/8fzq_29637.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/12_2023/8fzq_29637_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzq_29637/12_2023/8fzq_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-1.21rc1-5172/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: 5.40, per 1000 atoms: 0.58
  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: 3.42
  Conformation dependent library (CDL) restraints added in 1.7 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: 2.41
  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: 2.93

  Time building geometry restraints manager: 3.74 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:             3.410
  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:          12.520
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     27.590
  Find NCS groups from input model:        0.250
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.670
-------------------------------------------------------------------------------
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  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 204
  average time/residue: 0.1721
  time to fit residues: 52.2699
Evaluate side-chains
  104 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 1.056 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1363
  time to fit residues: 2.0982
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.0980
   chunk 67 optimal weight:    0.0020
   chunk 104 optimal weight:   20.0000
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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**
A1088 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9436  Z= 0.170
  Angle     :  0.531   6.576  12771  Z= 0.273
  Chirality :  0.039   0.146   1478
  Planarity :  0.004   0.043   1560
  Dihedral  :  7.945  78.031   1306
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  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:  0.78 (0.25), residues: 1121
  helix:  1.38 (0.20), residues: 736
  sheet: -0.11 (0.62), residues: 71
  loop : -1.37 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.001   TRP A1274 
   HIS   0.002   0.000   HIS A 139 
   PHE   0.017   0.001   PHE A 131 
   TYR   0.010   0.001   TYR A 304 
   ARG   0.002   0.000   ARG A 258 

*********************** 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
  142 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1696
  time to fit residues: 36.3205
Evaluate side-chains
  88 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.834 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2566
-------------------------------------------------------------------------------
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:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   9436  Z= 0.377
  Angle     :  0.733  10.166  12771  Z= 0.378
  Chirality :  0.045   0.197   1478
  Planarity :  0.005   0.046   1560
  Dihedral  :  7.638  64.737   1306
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.45 %
    Favored  : 93.45 %
  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: -0.12 (0.24), residues: 1121
  helix:  0.64 (0.19), residues: 720
  sheet: -0.67 (0.57), residues: 70
  loop : -1.42 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.063   0.002   TRP A 202 
   HIS   0.005   0.001   HIS A1085 
   PHE   0.023   0.002   PHE A 131 
   TYR   0.022   0.002   TYR A1032 
   ARG   0.006   0.001   ARG A1102 

*********************** 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
  109 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.095 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1779
  time to fit residues: 29.6450
Evaluate side-chains
  65 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.062 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4050
-------------------------------------------------------------------------------
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:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0050
   chunk 11 optimal weight:    0.0000
   chunk 49 optimal weight:    9.9990
   chunk 70 optimal weight:    0.8980
   chunk 104 optimal weight:    9.9990
   chunk 111 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0.7588
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9436  Z= 0.151
  Angle     :  0.527   7.405  12771  Z= 0.270
  Chirality :  0.038   0.142   1478
  Planarity :  0.003   0.046   1560
  Dihedral  :  6.799  63.480   1306
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.02 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1121
  helix:  0.96 (0.20), residues: 725
  sheet: -0.54 (0.59), residues: 71
  loop : -1.20 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP A1274 
   HIS   0.011   0.001   HIS A1079 
   PHE   0.029   0.001   PHE A 131 
   TYR   0.010   0.001   TYR A 325 
   ARG   0.009   0.000   ARG A1259 

*********************** 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
  115 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 1.063 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1746
  time to fit residues: 30.6743
Evaluate side-chains
  72 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.371 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2655
-------------------------------------------------------------------------------
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:    2.9990
   chunk 1 optimal weight:    0.0870
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0070
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7978

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 HIS
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9436  Z= 0.188
  Angle     :  0.532   7.033  12771  Z= 0.275
  Chirality :  0.039   0.144   1478
  Planarity :  0.004   0.045   1560
  Dihedral  :  6.395  62.384   1306
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  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:  0.45 (0.25), residues: 1121
  helix:  1.10 (0.20), residues: 718
  sheet: -0.50 (0.60), residues: 71
  loop : -1.20 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP A1274 
   HIS   0.011   0.001   HIS A1079 
   PHE   0.025   0.001   PHE A 131 
   TYR   0.014   0.001   TYR A 325 
   ARG   0.004   0.000   ARG A1070 

*********************** 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
  112 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.974 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1884
  time to fit residues: 31.4897
Evaluate side-chains
  69 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.080 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5308
-------------------------------------------------------------------------------
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:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 92 optimal weight:    0.1980
   chunk 51 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   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 270 GLN ** 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: 0.7627
moved from start:          0.4994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9436  Z= 0.169
  Angle     :  0.508   6.316  12771  Z= 0.261
  Chirality :  0.038   0.140   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  6.142  60.815   1306
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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:  0.50 (0.25), residues: 1121
  helix:  1.16 (0.20), residues: 718
  sheet: -0.44 (0.61), residues: 71
  loop : -1.25 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A1274 
   HIS   0.006   0.001   HIS A1079 
   PHE   0.023   0.001   PHE A 131 
   TYR   0.012   0.001   TYR A 325 
   ARG   0.004   0.000   ARG A1102 

*********************** 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
  103 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.075 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1717
  time to fit residues: 27.4642
Evaluate side-chains
  67 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.065 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4935
-------------------------------------------------------------------------------
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:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** 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: 0.7637
moved from start:          0.5196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9436  Z= 0.167
  Angle     :  0.518   9.951  12771  Z= 0.265
  Chirality :  0.038   0.138   1478
  Planarity :  0.003   0.046   1560
  Dihedral  :  5.984  59.379   1306
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  0.58 (0.25), residues: 1121
  helix:  1.22 (0.20), residues: 714
  sheet: -0.39 (0.62), residues: 71
  loop : -1.20 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP A1274 
   HIS   0.004   0.001   HIS A1079 
   PHE   0.025   0.001   PHE A 131 
   TYR   0.014   0.001   TYR A1073 
   ARG   0.003   0.000   ARG A1325 

*********************** 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
  106 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.038 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1937
  time to fit residues: 31.7237
Evaluate side-chains
  67 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.088 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5832
-------------------------------------------------------------------------------
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:    0.1980
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0030
   chunk 54 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 87 optimal weight:    0.8980
   chunk 100 optimal weight:    0.2980
   chunk 106 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** 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: 0.7606
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9436  Z= 0.135
  Angle     :  0.499   8.943  12771  Z= 0.254
  Chirality :  0.037   0.131   1478
  Planarity :  0.003   0.046   1560
  Dihedral  :  5.827  58.848   1306
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  0.58 (0.25), residues: 1121
  helix:  1.19 (0.20), residues: 726
  sheet: -0.20 (0.64), residues: 65
  loop : -1.24 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.031   0.001   TRP A1274 
   HIS   0.004   0.001   HIS A1079 
   PHE   0.023   0.001   PHE A 131 
   TYR   0.016   0.001   TYR A1073 
   ARG   0.002   0.000   ARG A1162 

*********************** 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
  112 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.968 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2292
  time to fit residues: 39.2753
Evaluate side-chains
  73 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.123 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.7606
-------------------------------------------------------------------------------
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:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 44 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 102 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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**
** 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:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9436  Z= 0.169
  Angle     :  0.522   8.894  12771  Z= 0.265
  Chirality :  0.038   0.136   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  5.798  58.290   1306
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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:  0.60 (0.25), residues: 1121
  helix:  1.19 (0.20), residues: 725
  sheet: -0.29 (0.63), residues: 70
  loop : -1.17 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.001   TRP A1274 
   HIS   0.004   0.001   HIS A1079 
   PHE   0.027   0.001   PHE A 131 
   TYR   0.011   0.001   TYR A 304 
   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
  105 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.138 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1832
  time to fit residues: 29.3560
Evaluate side-chains
  66 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.991 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5609
-------------------------------------------------------------------------------
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:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   chunk 114 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0270
   chunk 91 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.4016

-------------------------------------------------------------------------------
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**
** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9436  Z= 0.143
  Angle     :  0.552  12.342  12771  Z= 0.271
  Chirality :  0.038   0.153   1478
  Planarity :  0.003   0.045   1560
  Dihedral  :  5.717  58.358   1306
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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:  0.60 (0.25), residues: 1121
  helix:  1.18 (0.20), residues: 722
  sheet: -0.20 (0.63), residues: 70
  loop : -1.13 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.032   0.001   TRP A1274 
   HIS   0.006   0.001   HIS A1079 
   PHE   0.028   0.001   PHE A 131 
   TYR   0.013   0.001   TYR A 304 
   ARG   0.002   0.000   ARG A 560 

********************** 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
  107 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2266
  time to fit residues: 38.2433
Evaluate side-chains
  69 residues out of total 994 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.256 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6054
-------------------------------------------------------------------------------
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:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 91 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 80 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   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 270 GLN ** 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 = 0.3504 r_free = 0.3504 target = 0.100245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.087365 restraints weight = 23857.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088091 restraints weight = 17844.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.088564 restraints weight = 14135.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.5666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9436  Z= 0.171
  Angle     :  0.546  12.112  12771  Z= 0.271
  Chirality :  0.039   0.179   1478
  Planarity :  0.004   0.045   1560
  Dihedral  :  5.705  58.321   1306
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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:  0.60 (0.25), residues: 1121
  helix:  1.18 (0.20), residues: 720
  sheet: -0.15 (0.63), residues: 69
  loop : -1.14 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.028   0.001   TRP A1274 
   HIS   0.005   0.001   HIS A1079 
   PHE   0.030   0.001   PHE A 131 
   TYR   0.012   0.001   TYR A 304 
   ARG   0.003   0.000   ARG A1162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1893.36 seconds
wall clock time: 35 minutes 25.29 seconds (2125.29 seconds total)