Starting phenix.real_space_refine
on Thu Sep 18 04:35:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p50_17435/09_2025/8p50_17435.map"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.030
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       3      5.49       5
     Mg      1      5.21       5
     S      41      5.16       5
     C    8611      2.51       5
     N    2426      2.21       5
     O    2632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13714
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1574, 12389
          Classifications: {'peptide': 1574}
          Link IDs: {'PTRANS': 59, 'TRANS': 1514}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1292
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 3, 'TRANS': 157}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 865
    residue:
      pdb=" N   SER A   5 " occ=0.82
      ... (4 atoms not shown)
      pdb=" OG  SER A   5 " occ=0.00
    residue:
      pdb=" N   ASP A   7 " occ=0.16
      ... (6 atoms not shown)
      pdb=" OD2 ASP A   7 " occ=0.00
    residue:
      pdb=" N   PHE A   8 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE A   8 " occ=0.00
    residue:
      pdb=" N   THR A   9 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR A   9 " occ=0.00
    residue:
      pdb=" N   LEU A  11 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A  11 " occ=0.61
    residue:
      pdb=" N   ASN A  13 " occ=0.05
      ... (6 atoms not shown)
      pdb=" ND2 ASN A  13 " occ=0.19
    residue:
      pdb=" N   THR A  14 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR A  14 " occ=0.00
    residue:
      pdb=" N   ILE A  16 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD1 ILE A  16 " occ=0.90
    residue:
      pdb=" N   ASP A  17 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  17 " occ=0.00
    residue:
      pdb=" N   GLY A  18 " occ=0.31
      ... (2 atoms not shown)
      pdb=" O   GLY A  18 " occ=0.39
    residue:
      pdb=" N   GLN A  19 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  19 " occ=0.00
    residue:
      pdb=" N   ILE A  20 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD1 ILE A  20 " occ=0.00
    ... (remaining 853 not shown)
  Time building chain proxies: 3.09, per 1000 atoms: 0.23
  Number of scatterers: 13714
  At special positions: 0
  Unit cell: (99.9, 111.6, 150.3, 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      41     16.00
     P       3     15.00
     Mg      1     11.99
     O    2632      8.00
     N    2426      7.00
     C    8611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.16
  Conformation dependent library (CDL) restraints added in 682.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3242

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 12 sheets defined
      54.6% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 35 through 55
      removed outlier: 3.521A  pdb=" N   ASP A  39 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 64
      removed outlier: 3.526A  pdb=" N   GLN A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 86
    Processing helix  chain 'A' and resid 93 through 132
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 147 through 170
      removed outlier: 4.436A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 202
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 4.581A  pdb=" N   ALA A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   ALA A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 234
    Processing helix  chain 'A' and resid 283 through 291
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 4.120A  pdb=" N   ARG A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 321
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 378 through 390
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 418 through 425
    Processing helix  chain 'A' and resid 465 through 489
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 517
      removed outlier: 3.900A  pdb=" N   ARG A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.629A  pdb=" N   VAL A 524 " --> pdb=" O   THR A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 561 through 573
    Processing helix  chain 'A' and resid 574 through 576
      No H-bonds generated for 'chain 'A' and resid 574 through 576'
    Processing helix  chain 'A' and resid 577 through 583
      removed outlier: 3.925A  pdb=" N   VAL A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLN A 583 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 577 through 583'
    Processing helix  chain 'A' and resid 586 through 589
    Processing helix  chain 'A' and resid 590 through 598
    Processing helix  chain 'A' and resid 598 through 623
      removed outlier: 4.351A  pdb=" N   GLU A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ALA A 612 " --> pdb=" O   ARG A 608 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU A 613 " --> pdb=" O   ALA A 609 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR A 614 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 654 through 658
    Processing helix  chain 'A' and resid 659 through 664
      removed outlier: 3.568A  pdb=" N   ASP A 662 " --> pdb=" O   GLU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 674
    Processing helix  chain 'A' and resid 675 through 698
      removed outlier: 4.074A  pdb=" N   LEU A 686 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS A 688 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
      Proline residue:  A 692  - end of helix
      removed outlier: 3.921A  pdb=" N   SER A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 731
    Processing helix  chain 'A' and resid 735 through 740
      removed outlier: 3.542A  pdb=" N   ARG A 740 " --> pdb=" O   GLN A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 756
    Processing helix  chain 'A' and resid 763 through 773
    Processing helix  chain 'A' and resid 781 through 789
    Processing helix  chain 'A' and resid 790 through 795
    Processing helix  chain 'A' and resid 800 through 818
    Processing helix  chain 'A' and resid 823 through 834
      removed outlier: 5.029A  pdb=" N   VAL A 829 " --> pdb=" O   GLU A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 857
      removed outlier: 3.714A  pdb=" N   GLU A 855 " --> pdb=" O   LYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 878
      removed outlier: 3.812A  pdb=" N   ARG A 872 " --> pdb=" O   GLY A 868 " (cutoff:3.500A)
      Proline residue:  A 875  - end of helix
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 902 through 906
    Processing helix  chain 'A' and resid 930 through 937
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 949 through 953
    Processing helix  chain 'A' and resid 985 through 988
    Processing helix  chain 'A' and resid 1052 through 1056
    Processing helix  chain 'A' and resid 1065 through 1070
      removed outlier: 3.922A  pdb=" N   TYR A1069 " --> pdb=" O   ASP A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1152
      removed outlier: 3.811A  pdb=" N   GLN A1133 " --> pdb=" O   ARG A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1173 through 1175
      No H-bonds generated for 'chain 'A' and resid 1173 through 1175'
    Processing helix  chain 'A' and resid 1176 through 1209
      removed outlier: 4.003A  pdb=" N   GLN A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A1197 " --> pdb=" O   ASP A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1259
      removed outlier: 3.621A  pdb=" N   LYS A1222 " --> pdb=" O   ASN A1218 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR A1237 " --> pdb=" O   ALA A1233 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL A1238 " --> pdb=" O   GLN A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1263
    Processing helix  chain 'A' and resid 1281 through 1289
    Processing helix  chain 'A' and resid 1299 through 1308
    Processing helix  chain 'A' and resid 1321 through 1332
    Processing helix  chain 'A' and resid 1335 through 1358
    Processing helix  chain 'A' and resid 1361 through 1374
      removed outlier: 4.282A  pdb=" N   PHE A1365 " --> pdb=" O   GLN A1361 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER A1366 " --> pdb=" O   THR A1362 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU A1367 " --> pdb=" O   ALA A1363 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A1373 " --> pdb=" O   PHE A1369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1429
      removed outlier: 3.737A  pdb=" N   ARG A1402 " --> pdb=" O   TYR A1398 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL A1406 " --> pdb=" O   ARG A1402 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   GLU A1413 " --> pdb=" O   ALA A1409 " (cutoff:3.500A)
      removed outlier: 8.373A  pdb=" N   ALA A1414 " --> pdb=" O   SER A1410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1443
    Processing helix  chain 'A' and resid 1448 through 1454
      removed outlier: 3.715A  pdb=" N   VAL A1452 " --> pdb=" O   ASN A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1473
    Processing helix  chain 'A' and resid 1515 through 1528
    Processing helix  chain 'A' and resid 1531 through 1536
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 3.857A  pdb=" N   ALA A1558 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1576 through 1589
    Processing helix  chain 'B' and resid 29 through 40
    Processing helix  chain 'B' and resid 71 through 82
      Proline residue:  B  76  - end of helix
      removed outlier: 4.115A  pdb=" N   ARG B  79 " --> pdb=" O   PRO B  76 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE B  82 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 112
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 144 through 148
    Processing helix  chain 'B' and resid 165 through 178
    Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 339
      removed outlier: 3.584A  pdb=" N   GLY A 360 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339
      removed outlier: 3.584A  pdb=" N   GLY A 360 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   VAL A 363 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE A 240 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261
    Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454
    Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722
    Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948
      removed outlier: 5.792A  pdb=" N   THR A 946 " --> pdb=" O   TYR A 974 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A 976 " --> pdb=" O   THR A 946 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   SER A 948 " --> pdb=" O   LEU A 976 " (cutoff:3.500A)
      removed outlier: 8.671A  pdb=" N   TYR A 978 " --> pdb=" O   SER A 948 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 963 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 962 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 993 " --> pdb=" O   GLY A 962 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948
      removed outlier: 5.792A  pdb=" N   THR A 946 " --> pdb=" O   TYR A 974 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A 976 " --> pdb=" O   THR A 946 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   SER A 948 " --> pdb=" O   LEU A 976 " (cutoff:3.500A)
      removed outlier: 8.671A  pdb=" N   TYR A 978 " --> pdb=" O   SER A 948 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 963 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 962 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 993 " --> pdb=" O   GLY A 962 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014
      removed outlier: 3.834A  pdb=" N   ALA A1009 " --> pdb=" O   HIS A1047 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A1033 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   SER A1037 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   VAL A1060 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1377 through 1379
      removed outlier: 3.509A  pdb=" N   SER A1477 " --> pdb=" O   SER A1492 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1461 through 1462
    Processing sheet with id=AB3, first strand: chain 'B' and resid 51 through 58
      removed outlier: 6.739A  pdb=" N   ILE B  20 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL B  68 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   MET B  22 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ARG B  19 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   ILE B  89 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B  21 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   VAL B  91 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B  23 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   ASP B  93 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   LEU B  88 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   PHE B 124 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE B  90 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASN B 126 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL B  92 " --> pdb=" O   ASN B 126 " (cutoff:3.500A)

    750 hydrogen bonds defined for protein.
    2136 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: 1.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4656
        1.34 -     1.46: 2462
        1.46 -     1.57: 6764
        1.57 -     1.69: 5
        1.69 -     1.81: 80
  Bond restraints: 13967
  Sorted by residual:
  bond pdb=" CD  ARG A1530 "
       pdb=" NE  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.37e+00
  bond pdb=" CA  ARG A1530 "
       pdb=" CB  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.529  1.508  0.021 1.40e-02 5.10e+03 2.19e+00
  bond pdb=" CA  GLY A 678 "
       pdb=" C   GLY A 678 "
    ideal  model  delta    sigma   weight residual
    1.517  1.502  0.015 1.08e-02 8.57e+03 1.89e+00
  bond pdb=" C   THR A 305 "
       pdb=" N   PRO A 306 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.031 2.34e-02 1.83e+03 1.78e+00
  bond pdb=" CB  GLU A 207 "
       pdb=" CG  GLU A 207 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.65e+00
  ... (remaining 13962 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17585
        1.59 -     3.18: 1122
        3.18 -     4.76: 162
        4.76 -     6.35: 36
        6.35 -     7.94: 10
  Bond angle restraints: 18915
  Sorted by residual:
  angle pdb=" C   PRO A  91 "
        pdb=" N   GLY A  92 "
        pdb=" CA  GLY A  92 "
      ideal   model   delta    sigma   weight residual
     119.92  123.41   -3.49 9.60e-01 1.09e+00 1.32e+01
  angle pdb=" N   SER A 301 "
        pdb=" CA  SER A 301 "
        pdb=" C   SER A 301 "
      ideal   model   delta    sigma   weight residual
     109.81  117.73   -7.92 2.21e+00 2.05e-01 1.28e+01
  angle pdb=" C   LYS A1357 "
        pdb=" N   VAL A1358 "
        pdb=" CA  VAL A1358 "
      ideal   model   delta    sigma   weight residual
     121.97  115.63    6.34 1.80e+00 3.09e-01 1.24e+01
  angle pdb=" C   THR B  48 "
        pdb=" N   ILE B  49 "
        pdb=" CA  ILE B  49 "
      ideal   model   delta    sigma   weight residual
     120.77  125.71   -4.94 1.46e+00 4.69e-01 1.15e+01
  angle pdb=" CA  ARG A 344 "
        pdb=" CB  ARG A 344 "
        pdb=" CG  ARG A 344 "
      ideal   model   delta    sigma   weight residual
     114.10  107.49    6.61 2.00e+00 2.50e-01 1.09e+01
  ... (remaining 18910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.87: 8291
       32.87 -    65.74: 122
       65.74 -    98.61: 31
       98.61 -   131.47: 2
      131.47 -   164.34: 3
  Dihedral angle restraints: 8449
    sinusoidal: 3411
      harmonic: 5038
  Sorted by residual:
  dihedral pdb=" O3B GTP B1001 "
           pdb=" O3A GTP B1001 "
           pdb=" PB  GTP B1001 "
           pdb=" PA  GTP B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   95.42 -164.34     1      2.00e+01 2.50e-03 4.71e+01
  dihedral pdb=" C8  GTP B1001 "
           pdb=" C1' GTP B1001 "
           pdb=" N9  GTP B1001 "
           pdb=" O4' GTP B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -55.97  160.57     1      2.00e+01 2.50e-03 4.66e+01
  dihedral pdb=" C5' GTP B1001 "
           pdb=" O5' GTP B1001 "
           pdb=" PA  GTP B1001 "
           pdb=" O3A GTP B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -63.95  133.22     1      2.00e+01 2.50e-03 4.04e+01
  ... (remaining 8446 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1360
       0.040 -    0.080: 520
       0.080 -    0.120: 181
       0.120 -    0.161: 33
       0.161 -    0.201: 6
  Chirality restraints: 2100
  Sorted by residual:
  chirality pdb=" CA  PHE A 687 "
            pdb=" N   PHE A 687 "
            pdb=" C   PHE A 687 "
            pdb=" CB  PHE A 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE A 359 "
            pdb=" CA  ILE A 359 "
            pdb=" CG1 ILE A 359 "
            pdb=" CG2 ILE A 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  VAL A 217 "
            pdb=" N   VAL A 217 "
            pdb=" C   VAL A 217 "
            pdb=" CB  VAL A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 2097 not shown)

  Planarity restraints: 2487
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1405 "    0.019 2.00e-02 2.50e+03   3.87e-02 1.50e+01
        pdb=" C   THR A1405 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   THR A1405 "    0.025 2.00e-02 2.50e+03
        pdb=" N   VAL A1406 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1408 "   -0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   LEU A1408 "    0.063 2.00e-02 2.50e+03
        pdb=" O   LEU A1408 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ALA A1409 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 677 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   GLU A 677 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLU A 677 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A 678 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2484 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 98
        2.50 -     3.10: 10878
        3.10 -     3.70: 20823
        3.70 -     4.30: 29463
        4.30 -     4.90: 47286
  Nonbonded interactions: 108548
  Sorted by model distance:
  nonbonded pdb=" O2B GTP B1001 "
            pdb="MG    MG B1002 "
     model   vdw
     1.901 2.170
  nonbonded pdb=" O3G GTP B1001 "
            pdb="MG    MG B1002 "
     model   vdw
     2.002 2.170
  nonbonded pdb=" OG1 THR B  31 "
            pdb=" OG1 THR B  48 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O1A GTP B1001 "
            pdb="MG    MG B1002 "
     model   vdw
     2.103 2.170
  nonbonded pdb=" OD1 ASP A1318 "
            pdb=" NH1 ARG A1345 "
     model   vdw
     2.148 3.120
  ... (remaining 108543 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.40
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:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     14.190
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0320
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      :  0.008   0.851  13968  Z= 0.753
  Angle     :  0.875   7.940  18915  Z= 0.499
  Chirality :  0.048   0.201   2100
  Planarity :  0.009   0.097   2487
  Dihedral  : 14.212 164.342   5207
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.18), residues: 1729
  helix: -1.36 (0.15), residues: 817
  sheet: -0.48 (0.33), residues: 196
  loop : -1.31 (0.22), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG A1208 
 TYR   0.029   0.005   TYR A 820 
 PHE   0.033   0.003   PHE A 823 
 TRP   0.049   0.003   TRP A 556 
 HIS   0.015   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (13967)
  covalent geometry    : angle       0.87521 (18915)
  hydrogen bonds       : bond        0.17081 (  720)
  hydrogen bonds       : angle       6.96115 ( 2136)
  Misc. bond           : bond        0.85150 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.5491 (mt) cc_final: -0.6056 (mt)
REVERT: A   56 LEU cc_start: 0.6403 (tp) cc_final: 0.6096 (tp)
REVERT: A  233 MET cc_start: 0.3090 (mtt) cc_final: 0.2830 (mmm)
REVERT: A  421 GLU cc_start: 0.3242 (tp30) cc_final: 0.1670 (mt-10)
REVERT: A  437 MET cc_start: 0.7694 (ttt) cc_final: 0.7283 (tmm)
REVERT: A  519 ILE cc_start: 0.0065 (mt) cc_final: -0.2672 (mm)
REVERT: A  541 ASN cc_start: 0.4731 (t0) cc_final: 0.4304 (t0)
REVERT: A  544 LYS cc_start: 0.4106 (mttt) cc_final: 0.3823 (mttt)
REVERT: A  555 VAL cc_start: 0.1530 (t) cc_final: 0.1303 (p)
REVERT: A  780 ILE cc_start: 0.1706 (mt) cc_final: -0.0004 (mm)
REVERT: A  954 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7467 (ttt180)
REVERT: A 1210 ASN cc_start: 0.7834 (m-40) cc_final: 0.6916 (t0)
REVERT: A 1245 VAL cc_start: 0.7177 (m) cc_final: 0.5161 (m)
REVERT: A 1404 MET cc_start: -0.2311 (tpp) cc_final: -0.3653 (tpp)
REVERT: A 1513 PHE cc_start: -0.3203 (m-80) cc_final: -0.3444 (m-80)
REVERT: B  113 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9123 (tp30)
REVERT: B  146 HIS cc_start: 0.7079 (m-70) cc_final: 0.6575 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 311
  average time/residue: 0.1380
  time to fit residues: 59.4703
Evaluate side-chains
  178 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0170
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    1.9990
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 432 GLN
A 549 GLN
A 756 GLN
A1142 HIS
A1526 HIS
B  52 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.274078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5161 r_free = 0.5161 target = 0.230787 restraints weight = 99413.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5192 r_free = 0.5192 target = 0.233742 restraints weight = 85490.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.5192 r_free = 0.5192 target = 0.233747 restraints weight = 73811.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5192 r_free = 0.5192 target = 0.233747 restraints weight = 73731.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5192 r_free = 0.5192 target = 0.233747 restraints weight = 73729.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4884 r_free = 0.4884    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     5831 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4509 r_free = 0.4509    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     7427 |
|-----------------------------------------------------------------------------|
r_final: 0.4509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0334
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13968  Z= 0.200
  Angle     :  0.720   8.785  18915  Z= 0.387
  Chirality :  0.044   0.177   2100
  Planarity :  0.005   0.103   2487
  Dihedral  :  9.452 157.388   1926
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.91 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.20), residues: 1729
  helix:  0.40 (0.17), residues: 828
  sheet: -0.69 (0.34), residues: 201
  loop : -0.47 (0.25), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1278 
 TYR   0.018   0.002   TYR A1046 
 PHE   0.017   0.002   PHE A 827 
 TRP   0.027   0.002   TRP A 556 
 HIS   0.011   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (13967)
  covalent geometry    : angle       0.72022 (18915)
  hydrogen bonds       : bond        0.05233 (  720)
  hydrogen bonds       : angle       5.50272 ( 2136)
  Misc. bond           : bond        0.00059 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.6430 (tp) cc_final: 0.5955 (mt)
REVERT: A   89 ASP cc_start: 0.6629 (p0) cc_final: 0.5509 (p0)
REVERT: A  314 THR cc_start: 0.3918 (p) cc_final: 0.3537 (p)
REVERT: A  432 GLN cc_start: 0.0319 (OUTLIER) cc_final: -0.0686 (pm20)
REVERT: A  602 TYR cc_start: -0.5215 (t80) cc_final: -0.5727 (t80)
REVERT: A 1224 LEU cc_start: 0.3058 (mp) cc_final: 0.2410 (tt)
REVERT: B   85 THR cc_start: -0.0842 (p) cc_final: -0.1060 (t)
REVERT: B  107 LEU cc_start: 0.8038 (mt) cc_final: 0.7723 (mt)
REVERT: B  108 MET cc_start: 0.9093 (ppp) cc_final: 0.8873 (ppp)
REVERT: B  109 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8477 (ptt-90)
REVERT: B  110 MET cc_start: 0.3574 (mmt) cc_final: 0.3323 (mmt)
REVERT: B  146 HIS cc_start: 0.6752 (m-70) cc_final: 0.6336 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1343
  time to fit residues: 41.0512
Evaluate side-chains
  142 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 153 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 110 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 101 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 163 optimal weight:   10.0000
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 583 GLN
A1515 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.199182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.177661 restraints weight = 78741.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.179176 restraints weight = 65675.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.180539 restraints weight = 57001.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.181674 restraints weight = 50348.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.182600 restraints weight = 45444.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4810 r_free = 0.4810    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     7427 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4624 r_free = 0.4624    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8153 |
|-----------------------------------------------------------------------------|
r_final: 0.4624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0036
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13968  Z= 0.173
  Angle     :  0.654   7.218  18915  Z= 0.345
  Chirality :  0.042   0.209   2100
  Planarity :  0.005   0.074   2487
  Dihedral  :  8.969 155.985   1926
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.91 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.20), residues: 1729
  helix:  0.87 (0.18), residues: 823
  sheet: -0.59 (0.36), residues: 188
  loop : -0.29 (0.25), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 487 
 TYR   0.016   0.002   TYR A1230 
 PHE   0.017   0.002   PHE A 887 
 TRP   0.019   0.002   TRP A 556 
 HIS   0.008   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (13967)
  covalent geometry    : angle       0.65439 (18915)
  hydrogen bonds       : bond        0.04444 (  720)
  hydrogen bonds       : angle       5.12059 ( 2136)
  Misc. bond           : bond        0.00016 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 174
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.7371 (mt) cc_final: -0.7737 (mt)
REVERT: A   56 LEU cc_start: 0.6688 (tp) cc_final: 0.6288 (mt)
REVERT: A   89 ASP cc_start: 0.7353 (p0) cc_final: 0.6586 (p0)
REVERT: A  432 GLN cc_start: 0.0939 (OUTLIER) cc_final: -0.0065 (pm20)
REVERT: A  452 MET cc_start: 0.6297 (mmp) cc_final: 0.6004 (tpp)
REVERT: A 1398 TYR cc_start: 0.4082 (m-80) cc_final: 0.2894 (m-10)
REVERT: A 1489 MET cc_start: 0.0187 (tmm) cc_final: -0.0448 (tmm)
REVERT: A 1570 ASP cc_start: -0.0403 (m-30) cc_final: -0.0695 (m-30)
REVERT: B  173 LEU cc_start: 0.6281 (tp) cc_final: 0.6000 (mt)
  outliers start: 4
  outliers final: 1
  residues processed: 178
  average time/residue: 0.1293
  time to fit residues: 33.1217
Evaluate side-chains
  133 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 102 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 508 GLN
A 543 ASN
** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5037 r_free = 0.5037 target = 0.209968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.187805 restraints weight = 64788.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.189287 restraints weight = 54958.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.190447 restraints weight = 48220.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.191018 restraints weight = 43179.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.191719 restraints weight = 40119.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4852 r_free = 0.4852    target_work(ls_wunit_k1) = 0.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8153 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4803 r_free = 0.4803    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8437 |
|-----------------------------------------------------------------------------|
r_final: 0.4803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0031
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13968  Z= 0.193
  Angle     :  0.643   7.848  18915  Z= 0.341
  Chirality :  0.042   0.222   2100
  Planarity :  0.005   0.066   2487
  Dihedral  :  8.805 156.183   1926
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.52 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.20), residues: 1729
  helix:  0.87 (0.18), residues: 830
  sheet: -0.59 (0.36), residues: 193
  loop : -0.36 (0.25), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1351 
 TYR   0.025   0.002   TYR A 433 
 PHE   0.020   0.002   PHE A1513 
 TRP   0.019   0.002   TRP A 556 
 HIS   0.009   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (13967)
  covalent geometry    : angle       0.64272 (18915)
  hydrogen bonds       : bond        0.04250 (  720)
  hydrogen bonds       : angle       5.07538 ( 2136)
  Misc. bond           : bond        0.00111 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.5677 (tp) cc_final: 0.4896 (mt)
REVERT: A   89 ASP cc_start: 0.7974 (p0) cc_final: 0.7422 (p0)
REVERT: A  432 GLN cc_start: 0.0095 (OUTLIER) cc_final: -0.0393 (pm20)
REVERT: A  452 MET cc_start: 0.6154 (mmp) cc_final: 0.5861 (tpp)
REVERT: A  769 MET cc_start: -0.5845 (tmm) cc_final: -0.6286 (ttt)
REVERT: A 1398 TYR cc_start: 0.2133 (m-80) cc_final: 0.1699 (m-10)
REVERT: A 1489 MET cc_start: -0.0395 (tmm) cc_final: -0.1465 (tpt)
REVERT: B   81 TYR cc_start: 0.6483 (m-80) cc_final: 0.6177 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1346
  time to fit residues: 32.2045
Evaluate side-chains
  126 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 144 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 127 optimal weight:    0.0470
   chunk 101 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    0.9884

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 508 GLN
A 583 GLN
A 981 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5090 r_free = 0.5090 target = 0.216973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.194419 restraints weight = 58858.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.195823 restraints weight = 50017.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.196622 restraints weight = 43795.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.197848 restraints weight = 39795.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.198314 restraints weight = 36285.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4908 r_free = 0.4908    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8437 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4896 r_free = 0.4896    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8503 |
|-----------------------------------------------------------------------------|
r_final: 0.4896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0021
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13968  Z= 0.111
  Angle     :  0.577   9.213  18915  Z= 0.299
  Chirality :  0.040   0.168   2100
  Planarity :  0.004   0.058   2487
  Dihedral  :  8.534 152.862   1926
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.35 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.36 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.21), residues: 1729
  helix:  1.16 (0.18), residues: 829
  sheet: -0.45 (0.35), residues: 192
  loop : -0.28 (0.25), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1351 
 TYR   0.017   0.001   TYR A 433 
 PHE   0.036   0.001   PHE A1424 
 TRP   0.016   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (13967)
  covalent geometry    : angle       0.57672 (18915)
  hydrogen bonds       : bond        0.03760 (  720)
  hydrogen bonds       : angle       4.72937 ( 2136)
  Misc. bond           : bond        0.00059 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.6877 (mt) cc_final: -0.7439 (mt)
REVERT: A   56 LEU cc_start: 0.5852 (tp) cc_final: 0.5013 (mt)
REVERT: A  432 GLN cc_start: 0.0542 (OUTLIER) cc_final: 0.0088 (pm20)
REVERT: A  452 MET cc_start: 0.6040 (mmp) cc_final: 0.5774 (tpp)
REVERT: A  873 VAL cc_start: -0.2267 (t) cc_final: -0.3185 (t)
REVERT: A 1489 MET cc_start: -0.0503 (tmm) cc_final: -0.1408 (tpt)
  outliers start: 3
  outliers final: 1
  residues processed: 177
  average time/residue: 0.1266
  time to fit residues: 32.0072
Evaluate side-chains
  133 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 129 optimal weight:    0.0050
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0670
   chunk 88 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.8138

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 583 GLN
A1100 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5108 r_free = 0.5108 target = 0.220321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.196314 restraints weight = 57291.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.197210 restraints weight = 49105.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.198588 restraints weight = 44002.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.199027 restraints weight = 39890.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4978 r_free = 0.4978 target = 0.200010 restraints weight = 37461.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4913 r_free = 0.4913    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8503 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4915 r_free = 0.4915    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8512 |
|-----------------------------------------------------------------------------|
r_final: 0.4915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0009
moved from start:          0.4681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13968  Z= 0.127
  Angle     :  0.586  10.142  18915  Z= 0.304
  Chirality :  0.040   0.176   2100
  Planarity :  0.004   0.050   2487
  Dihedral  :  8.381 160.325   1926
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.88 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.50 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.21), residues: 1729
  helix:  1.25 (0.18), residues: 822
  sheet: -0.37 (0.36), residues: 200
  loop : -0.29 (0.25), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1240 
 TYR   0.021   0.001   TYR A1398 
 PHE   0.012   0.001   PHE A1043 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.009   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (13967)
  covalent geometry    : angle       0.58558 (18915)
  hydrogen bonds       : bond        0.03753 (  720)
  hydrogen bonds       : angle       4.69828 ( 2136)
  Misc. bond           : bond        0.00085 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.5803 (tp) cc_final: 0.5041 (mt)
REVERT: A   87 MET cc_start: 0.6009 (mtt) cc_final: 0.5780 (ttm)
REVERT: A  432 GLN cc_start: 0.0567 (OUTLIER) cc_final: 0.0087 (pm20)
REVERT: A  452 MET cc_start: 0.6101 (mmp) cc_final: 0.5839 (tpp)
REVERT: A  769 MET cc_start: -0.5481 (tmm) cc_final: -0.5948 (ttt)
REVERT: A  873 VAL cc_start: -0.0918 (t) cc_final: -0.2142 (t)
REVERT: A 1424 PHE cc_start: 0.5788 (m-10) cc_final: 0.4235 (m-10)
REVERT: A 1489 MET cc_start: -0.1014 (tmm) cc_final: -0.1809 (tmm)
REVERT: B   81 TYR cc_start: 0.6232 (m-10) cc_final: 0.5148 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1205
  time to fit residues: 29.1422
Evaluate side-chains
  124 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 169 optimal weight:   30.0000
   chunk 41 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 131 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0970
   chunk 75 optimal weight:    0.0970
   chunk 16 optimal weight:    6.9990
   chunk 171 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.5376

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 583 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5114 r_free = 0.5114 target = 0.220184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4963 r_free = 0.4963 target = 0.196111 restraints weight = 55217.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.197348 restraints weight = 47734.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.198047 restraints weight = 42490.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4975 r_free = 0.4975 target = 0.199184 restraints weight = 38951.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.199798 restraints weight = 36016.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4912 r_free = 0.4912    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8512 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4912 r_free = 0.4912    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8513 |
|-----------------------------------------------------------------------------|
r_final: 0.4912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0050
moved from start:          0.4881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13968  Z= 0.105
  Angle     :  0.581  11.311  18915  Z= 0.294
  Chirality :  0.040   0.183   2100
  Planarity :  0.004   0.049   2487
  Dihedral  :  8.190 175.472   1926
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.30 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.68 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.21), residues: 1729
  helix:  1.34 (0.18), residues: 822
  sheet: -0.20 (0.37), residues: 194
  loop : -0.27 (0.25), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A1240 
 TYR   0.013   0.001   TYR A1046 
 PHE   0.015   0.001   PHE A 807 
 TRP   0.011   0.001   TRP B  66 
 HIS   0.008   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (13967)
  covalent geometry    : angle       0.58073 (18915)
  hydrogen bonds       : bond        0.03494 (  720)
  hydrogen bonds       : angle       4.56168 ( 2136)
  Misc. bond           : bond        0.00119 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.6672 (mt) cc_final: -0.7323 (mt)
REVERT: A   56 LEU cc_start: 0.5557 (tp) cc_final: 0.4724 (mt)
REVERT: A   87 MET cc_start: 0.6179 (mtt) cc_final: 0.5904 (ttm)
REVERT: A  432 GLN cc_start: 0.0516 (OUTLIER) cc_final: -0.0113 (pm20)
REVERT: A  452 MET cc_start: 0.6211 (mmp) cc_final: 0.5987 (tpp)
REVERT: A  873 VAL cc_start: -0.1538 (t) cc_final: -0.2754 (t)
REVERT: A 1489 MET cc_start: -0.1169 (tmm) cc_final: -0.1794 (tpt)
REVERT: B   81 TYR cc_start: 0.6161 (m-10) cc_final: 0.5568 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1198
  time to fit residues: 29.2230
Evaluate side-chains
  134 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 169 optimal weight:    9.9990
   chunk 112 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 146 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 148 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 62 optimal weight:    0.2980
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A 432 GLN
A 583 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5169 r_free = 0.5169 target = 0.259011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.5071 r_free = 0.5071 target = 0.239894 restraints weight = 94457.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.231333 restraints weight = 68577.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.232399 restraints weight = 56990.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.5047 r_free = 0.5047 target = 0.233018 restraints weight = 47747.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5048 r_free = 0.5048 target = 0.233353 restraints weight = 42570.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4926 r_free = 0.4926    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8513 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4924 r_free = 0.4924    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
r_final: 0.4924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0149
moved from start:          0.5072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13968  Z= 0.121
  Angle     :  0.589  12.777  18915  Z= 0.300
  Chirality :  0.040   0.227   2100
  Planarity :  0.004   0.049   2487
  Dihedral  :  7.947 171.707   1926
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.95 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.21), residues: 1729
  helix:  1.33 (0.18), residues: 826
  sheet: -0.32 (0.36), residues: 201
  loop : -0.23 (0.25), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1240 
 TYR   0.021   0.001   TYR A 290 
 PHE   0.014   0.001   PHE A 807 
 TRP   0.026   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (13967)
  covalent geometry    : angle       0.58928 (18915)
  hydrogen bonds       : bond        0.03490 (  720)
  hydrogen bonds       : angle       4.59285 ( 2136)
  Misc. bond           : bond        0.00136 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.6056 (tp) cc_final: 0.5409 (mt)
REVERT: A   87 MET cc_start: 0.6907 (mtt) cc_final: 0.6551 (ttm)
REVERT: A   89 ASP cc_start: 0.7623 (p0) cc_final: 0.6664 (p0)
REVERT: A  432 GLN cc_start: 0.1137 (OUTLIER) cc_final: 0.0291 (pm20)
REVERT: A  769 MET cc_start: -0.5276 (tmm) cc_final: -0.5691 (ttt)
REVERT: A 1489 MET cc_start: -0.0720 (tmm) cc_final: -0.1323 (tmm)
REVERT: B   81 TYR cc_start: -0.0708 (m-10) cc_final: -0.0970 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1234
  time to fit residues: 29.0946
Evaluate side-chains
  127 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 105 optimal weight:    0.0030
   chunk 104 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 164 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 119 optimal weight:    0.0870
   chunk 127 optimal weight:    0.8980
   chunk 39 optimal weight:   20.0000
   overall best weight:    0.7970

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 583 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5118 r_free = 0.5118 target = 0.220228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.196490 restraints weight = 56850.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.197825 restraints weight = 49263.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.198940 restraints weight = 44139.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.199371 restraints weight = 39935.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.200269 restraints weight = 37581.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4921 r_free = 0.4921    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4921 r_free = 0.4921    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
r_final: 0.4921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0000
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13968  Z= 0.104
  Angle     :  0.588  13.403  18915  Z= 0.297
  Chirality :  0.041   0.188   2100
  Planarity :  0.004   0.049   2487
  Dihedral  :  7.661 162.047   1926
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.41 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.21), residues: 1729
  helix:  1.35 (0.18), residues: 824
  sheet: -0.23 (0.37), residues: 193
  loop : -0.26 (0.25), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1240 
 TYR   0.025   0.001   TYR A 290 
 PHE   0.013   0.001   PHE A 807 
 TRP   0.012   0.001   TRP A 556 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (13967)
  covalent geometry    : angle       0.58813 (18915)
  hydrogen bonds       : bond        0.03475 (  720)
  hydrogen bonds       : angle       4.52026 ( 2136)
  Misc. bond           : bond        0.00154 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.6676 (mt) cc_final: -0.7294 (mt)
REVERT: A   56 LEU cc_start: 0.5706 (tp) cc_final: 0.5007 (mt)
REVERT: A   87 MET cc_start: 0.5928 (mtt) cc_final: 0.5642 (ttm)
REVERT: A  432 GLN cc_start: 0.0700 (OUTLIER) cc_final: -0.0122 (pm20)
REVERT: A  486 LEU cc_start: 0.8872 (tt) cc_final: 0.8515 (tt)
REVERT: B   81 TYR cc_start: 0.6376 (m-10) cc_final: 0.5830 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1240
  time to fit residues: 30.3954
Evaluate side-chains
  127 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 125 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 148 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 155 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A 432 GLN
A 583 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5113 r_free = 0.5113 target = 0.219954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.196136 restraints weight = 55789.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.197474 restraints weight = 48454.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.198476 restraints weight = 43178.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.198863 restraints weight = 39457.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.199672 restraints weight = 37340.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4917 r_free = 0.4917    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4917 r_free = 0.4917    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
r_final: 0.4917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0010
moved from start:          0.5390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13968  Z= 0.108
  Angle     :  0.590  14.239  18915  Z= 0.302
  Chirality :  0.041   0.246   2100
  Planarity :  0.004   0.049   2487
  Dihedral  :  7.485 155.941   1926
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.53 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.21), residues: 1729
  helix:  1.34 (0.18), residues: 826
  sheet: -0.21 (0.36), residues: 198
  loop : -0.21 (0.25), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1240 
 TYR   0.027   0.001   TYR A1235 
 PHE   0.013   0.001   PHE A1308 
 TRP   0.017   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (13967)
  covalent geometry    : angle       0.58986 (18915)
  hydrogen bonds       : bond        0.03444 (  720)
  hydrogen bonds       : angle       4.54338 ( 2136)
  Misc. bond           : bond        0.00150 (    1)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: -0.6629 (mt) cc_final: -0.7004 (mt)
REVERT: A   56 LEU cc_start: 0.5797 (tp) cc_final: 0.5004 (mt)
REVERT: A   87 MET cc_start: 0.6021 (mtt) cc_final: 0.5713 (ttm)
REVERT: A  432 GLN cc_start: 0.0730 (OUTLIER) cc_final: 0.0026 (pm20)
REVERT: A  517 ASN cc_start: 0.1501 (p0) cc_final: 0.1038 (p0)
REVERT: B   81 TYR cc_start: 0.6156 (m-10) cc_final: 0.5875 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1224
  time to fit residues: 28.5578
Evaluate side-chains
  126 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0670
   chunk 100 optimal weight:    2.9990
   chunk 127 optimal weight:    7.9990
   chunk 108 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 155 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 165 optimal weight:    7.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    1.6122

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 583 GLN
B 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5161 r_free = 0.5161 target = 0.258228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5044 r_free = 0.5044 target = 0.238522 restraints weight = 94612.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5068 r_free = 0.5068 target = 0.240900 restraints weight = 68371.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5082 r_free = 0.5082 target = 0.242258 restraints weight = 52679.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5093 r_free = 0.5093 target = 0.243100 restraints weight = 43179.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 97)----------------|
| r_work = 0.5062 r_free = 0.5062 target = 0.237541 restraints weight = 36893.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4991
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4991 r_free = 0.4991    target_work(ls_wunit_k1) = 0.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4991 r_free = 0.4991    target_work(ls_wunit_k1) = 0.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     8514 |
|-----------------------------------------------------------------------------|
r_final: 0.4991
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0073
moved from start:          0.5538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13968  Z= 0.117
  Angle     :  0.587  14.191  18915  Z= 0.300
  Chirality :  0.041   0.235   2100
  Planarity :  0.004   0.049   2487
  Dihedral  :  7.394 152.318   1926
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.70 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.34 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.21), residues: 1729
  helix:  1.33 (0.18), residues: 826
  sheet: -0.20 (0.36), residues: 198
  loop : -0.22 (0.25), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1240 
 TYR   0.028   0.001   TYR A1235 
 PHE   0.011   0.001   PHE A 807 
 TRP   0.017   0.001   TRP A 556 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (13967)
  covalent geometry    : angle       0.58671 (18915)
  hydrogen bonds       : bond        0.03435 (  720)
  hydrogen bonds       : angle       4.56502 ( 2136)
  Misc. bond           : bond        0.00140 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2514.81 seconds
wall clock time: 43 minutes 27.61 seconds (2607.61 seconds total)