Starting phenix.real_space_refine
on Wed Jul 30 15:15:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p51_17436/07_2025/8p51_17436.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    7779      2.51       5
     N    2197      2.21       5
     O    2378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12389
  Number of models: 1
  Model: ""
    Number of chains: 1
    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
  Residues with excluded nonbonded symmetry interactions: 16
    residue:
      pdb=" N   ILE A 931 " occ=0.37
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 931 " occ=0.00
    residue:
      pdb=" N   ALA A 949 " occ=0.94
      ... (3 atoms not shown)
      pdb=" CB  ALA A 949 " occ=0.21
    residue:
      pdb=" N   GLY A 972 " occ=0.51
      ... (2 atoms not shown)
      pdb=" O   GLY A 972 " occ=0.33
    residue:
      pdb=" N   ALA A 983 " occ=0.68
      ... (3 atoms not shown)
      pdb=" CB  ALA A 983 " occ=0.95
    residue:
      pdb=" N   SER A 987 " occ=0.90
      ... (4 atoms not shown)
      pdb=" OG  SER A 987 " occ=0.67
    residue:
      pdb=" N   ALA A 993 " occ=0.18
      ... (3 atoms not shown)
      pdb=" CB  ALA A 993 " occ=0.18
    residue:
      pdb=" N   ALA A1040 " occ=0.80
      ... (3 atoms not shown)
      pdb=" CB  ALA A1040 " occ=0.98
    residue:
      pdb=" N   GLN A1100 " occ=0.81
      ... (7 atoms not shown)
      pdb=" NE2 GLN A1100 " occ=0.23
    residue:
      pdb=" N   GLY A1103 " occ=0.91
      ... (2 atoms not shown)
      pdb=" O   GLY A1103 " occ=0.48
    residue:
      pdb=" N   ASP A1113 " occ=0.69
      ... (6 atoms not shown)
      pdb=" OD2 ASP A1113 " occ=0.64
    residue:
      pdb=" N   GLN A1120 " occ=0.79
      ... (7 atoms not shown)
      pdb=" NE2 GLN A1120 " occ=0.78
    residue:
      pdb=" N   SER A1160 " occ=0.14
      ... (4 atoms not shown)
      pdb=" OG  SER A1160 " occ=0.65
    ... (remaining 4 not shown)
  Time building chain proxies: 7.16, per 1000 atoms: 0.58
  Number of scatterers: 12389
  At special positions: 0
  Unit cell: (103.5, 116.1, 148.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    2378      8.00
     N    2197      7.00
     C    7779      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2942

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 11 sheets defined
      56.3% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 35 through 55
    Processing helix  chain 'A' and resid 55 through 64
      removed outlier: 3.536A  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: 4.413A  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: 4.640A  pdb=" N   ALA A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ALA A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 4.122A  pdb=" N   ARG A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.529A  pdb=" N   TYR A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 4.093A  pdb=" N   VAL A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    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
      removed outlier: 3.816A  pdb=" N   SER A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 517
      removed outlier: 3.808A  pdb=" N   ARG A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.523A  pdb=" N   ARG A 567 " --> pdb=" O   PRO A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 577
      removed outlier: 6.218A  pdb=" N   ALA A 577 " --> pdb=" O   LYS A 574 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 574 through 577'
    Processing helix  chain 'A' and resid 578 through 583
      removed outlier: 4.157A  pdb=" N   LEU A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A 583 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 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: 4.244A  pdb=" N   GLU A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ALA A 612 " --> pdb=" O   ARG A 608 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   GLU A 613 " --> pdb=" O   ALA A 609 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR A 614 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 615 " --> pdb=" O   GLU A 611 " (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
    Processing helix  chain 'A' and resid 665 through 674
      removed outlier: 3.544A  pdb=" N   LEU A 674 " --> pdb=" O   GLU A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 698
      removed outlier: 3.948A  pdb=" N   LEU A 686 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS A 688 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
      Proline residue:  A 692  - end of helix
      removed outlier: 3.571A  pdb=" N   PHE A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 4.029A  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: 3.573A  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: 4.915A  pdb=" N   VAL A 829 " --> pdb=" O   GLU A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 857
      removed outlier: 3.673A  pdb=" N   GLU A 855 " --> pdb=" O   LYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 878
      removed outlier: 3.922A  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: 3.908A  pdb=" N   TYR A1069 " --> pdb=" O   ASP A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1152
      removed outlier: 3.953A  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: 3.624A  pdb=" N   ILE A1190 " --> pdb=" O   VAL A1186 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASP A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLN A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A1197 " --> pdb=" O   ASP A1193 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A1200 " --> pdb=" O   GLN A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1259
      removed outlier: 4.129A  pdb=" N   ILE A1217 " --> pdb=" O   ARG A1213 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLN A1219 " --> pdb=" O   ASP A1215 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   GLN A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A1221 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR A1231 " --> pdb=" O   THR A1227 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   THR A1237 " --> pdb=" O   ALA A1233 " (cutoff:3.500A)
      removed outlier: 5.155A  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 1298 through 1308
      removed outlier: 4.304A  pdb=" N   SER A1302 " --> pdb=" O   GLY A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1331
    Processing helix  chain 'A' and resid 1335 through 1358
    Processing helix  chain 'A' and resid 1361 through 1373
      removed outlier: 3.852A  pdb=" N   PHE A1365 " --> pdb=" O   GLN A1361 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER A1366 " --> pdb=" O   THR A1362 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLU A1367 " --> pdb=" O   ALA A1363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1396
      removed outlier: 3.950A  pdb=" N   GLY A1395 " --> pdb=" O   ASP A1391 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ARG A1396 " --> pdb=" O   ARG A1392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1391 through 1396'
    Processing helix  chain 'A' and resid 1396 through 1429
      removed outlier: 3.759A  pdb=" N   ARG A1402 " --> pdb=" O   TYR A1398 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL A1406 " --> pdb=" O   ARG A1402 " (cutoff:3.500A)
      removed outlier: 8.600A  pdb=" N   GLU A1413 " --> pdb=" O   ALA A1409 " (cutoff:3.500A)
      removed outlier: 8.279A  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 1453
    Processing helix  chain 'A' and resid 1463 through 1473
    Processing helix  chain 'A' and resid 1515 through 1528
      removed outlier: 3.529A  pdb=" N   GLN A1525 " --> pdb=" O   ARG A1521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1531 through 1536
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 3.765A  pdb=" N   ALA A1558 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1576 through 1589
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236
      removed outlier: 7.640A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 241 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 236 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 363 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339
      removed outlier: 5.357A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 363 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 307 " --> pdb=" O   ILE A 398 " (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: 6.729A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.469A  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: 6.729A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.469A  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: 6.609A  pdb=" N   SER A1037 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL A1060 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1376 through 1379
      removed outlier: 4.286A  pdb=" N   PHE A1376 " --> pdb=" O   ALA A1512 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1462
      removed outlier: 5.020A  pdb=" N   GLY A1459 " --> pdb=" O   LEU A1549 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A1549 " --> pdb=" O   GLY A1459 " (cutoff:3.500A)

    703 hydrogen bonds defined for protein.
    2019 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: 5.71

  Time building geometry restraints manager: 3.35 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: 4230
        1.34 -     1.46: 2258
        1.46 -     1.57: 6061
        1.57 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 12618
  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 2.53e+00
  bond pdb=" CD  ARG A1209 "
       pdb=" NE  ARG A1209 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.45e+00
  bond pdb=" CA  ARG A1530 "
       pdb=" CB  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.529  1.507  0.022 1.40e-02 5.10e+03 2.38e+00
  bond pdb=" C   TYR A1398 "
       pdb=" N   PRO A1399 "
    ideal  model  delta    sigma   weight residual
    1.336  1.319  0.017 1.20e-02 6.94e+03 2.05e+00
  bond pdb=" CB  TRP A 805 "
       pdb=" CG  TRP A 805 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.01e+00
  ... (remaining 12613 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 15635
        1.37 -     2.75: 1166
        2.75 -     4.12: 219
        4.12 -     5.49: 48
        5.49 -     6.87: 12
  Bond angle restraints: 17080
  Sorted by residual:
  angle pdb=" N   VAL A 969 "
        pdb=" CA  VAL A 969 "
        pdb=" C   VAL A 969 "
      ideal   model   delta    sigma   weight residual
     113.71  109.85    3.86 9.50e-01 1.11e+00 1.65e+01
  angle pdb=" C   GLU A1206 "
        pdb=" N   ASN A1207 "
        pdb=" CA  ASN A1207 "
      ideal   model   delta    sigma   weight residual
     121.52  115.83    5.69 1.84e+00 2.95e-01 9.56e+00
  angle pdb=" CA  ARG A1214 "
        pdb=" CB  ARG A1214 "
        pdb=" CG  ARG A1214 "
      ideal   model   delta    sigma   weight residual
     114.10  120.09   -5.99 2.00e+00 2.50e-01 8.97e+00
  angle pdb=" N   SER A 301 "
        pdb=" CA  SER A 301 "
        pdb=" C   SER A 301 "
      ideal   model   delta    sigma   weight residual
     109.81  115.95   -6.14 2.21e+00 2.05e-01 7.71e+00
  angle pdb=" CA  GLN A  65 "
        pdb=" CB  GLN A  65 "
        pdb=" CG  GLN A  65 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.59e+00
  ... (remaining 17075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7066
       17.95 -    35.89: 471
       35.89 -    53.84: 63
       53.84 -    71.79: 36
       71.79 -    89.74: 15
  Dihedral angle restraints: 7651
    sinusoidal: 3078
      harmonic: 4573
  Sorted by residual:
  dihedral pdb=" CA  PRO A1014 "
           pdb=" C   PRO A1014 "
           pdb=" N   LYS A1015 "
           pdb=" CA  LYS A1015 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ASN A 984 "
           pdb=" C   ASN A 984 "
           pdb=" N   ASP A 985 "
           pdb=" CA  ASP A 985 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  SER A 394 "
           pdb=" C   SER A 394 "
           pdb=" N   PHE A 395 "
           pdb=" CA  PHE A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.77   28.23     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 7648 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1373
       0.050 -    0.100: 423
       0.100 -    0.149: 91
       0.149 -    0.199: 5
       0.199 -    0.249: 1
  Chirality restraints: 1893
  Sorted by residual:
  chirality pdb=" CA  ARG A1209 "
            pdb=" N   ARG A1209 "
            pdb=" C   ARG A1209 "
            pdb=" CB  ARG A1209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LYS A1357 "
            pdb=" N   LYS A1357 "
            pdb=" C   LYS A1357 "
            pdb=" CB  LYS A1357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.59e-01
  chirality pdb=" CA  PHE A 827 "
            pdb=" N   PHE A 827 "
            pdb=" C   PHE A 827 "
            pdb=" CB  PHE A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.39e-01
  ... (remaining 1890 not shown)

  Planarity restraints: 2259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1578 "   -0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   SER A1578 "    0.067 2.00e-02 2.50e+03
        pdb=" O   SER A1578 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER A1579 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1408 "   -0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   LEU A1408 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LEU A1408 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A1409 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1405 "    0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   THR A1405 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   THR A1405 "    0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A1406 "    0.020 2.00e-02 2.50e+03
  ... (remaining 2256 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 215
        2.67 -     3.23: 12886
        3.23 -     3.79: 18643
        3.79 -     4.34: 25100
        4.34 -     4.90: 40789
  Nonbonded interactions: 97633
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 144 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OG  SER A1054 "
            pdb=" OD2 ASP A1065 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OH  TYR A1137 "
            pdb=" OE2 GLU A1241 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER A 500 "
            pdb=" OE1 GLU A 502 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OD1 ASN A  13 "
            pdb=" NH1 ARG A  37 "
     model   vdw
     2.257 3.120
  ... (remaining 97628 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.97
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  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:          0.490
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     31.340
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
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      :  0.006   0.044  12618  Z= 0.289
  Angle     :  0.827   6.865  17080  Z= 0.472
  Chirality :  0.048   0.249   1893
  Planarity :  0.009   0.101   2259
  Dihedral  : 13.504  89.737   4709
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.19), residues: 1570
  helix: -1.25 (0.16), residues: 786
  sheet: -0.49 (0.38), residues: 160
  loop : -1.33 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A1251 
 HIS   0.008   0.002   HIS A1370 
 PHE   0.022   0.002   PHE A  30 
 TYR   0.026   0.005   TYR A 820 
 ARG   0.022   0.003   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16011 (  671)
  hydrogen bonds       : angle       7.02184 ( 2019)
  covalent geometry    : bond        0.00637 (12618)
  covalent geometry    : angle       0.82672 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.3407
  time to fit residues: 58.6745
Evaluate side-chains
  62 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 80 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 123 optimal weight:    9.9990
   chunk 47 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 142 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A  52 GLN
A 288 GLN
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 862 GLN
A1052 ASN
A1446 HIS
A1486 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.080979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054576 restraints weight = 55587.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.056584 restraints weight = 28491.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.057899 restraints weight = 19594.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      109 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       99 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12618  Z= 0.151
  Angle     :  0.658   8.935  17080  Z= 0.345
  Chirality :  0.041   0.156   1893
  Planarity :  0.005   0.037   2259
  Dihedral  :  5.642  21.240   1737
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.89 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.21), residues: 1570
  helix:  0.73 (0.18), residues: 807
  sheet: -0.26 (0.39), residues: 162
  loop : -0.43 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 605 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.018   0.001   PHE A 395 
 TYR   0.020   0.002   TYR A1046 
 ARG   0.008   0.001   ARG A1584 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05017 (  671)
  hydrogen bonds       : angle       5.03050 ( 2019)
  covalent geometry    : bond        0.00282 (12618)
  covalent geometry    : angle       0.65840 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9804 (tt) cc_final: 0.9444 (mp)
REVERT: A  233 MET cc_start: 0.8841 (mmm) cc_final: 0.8627 (mmm)
REVERT: A  265 LEU cc_start: 0.9201 (mp) cc_final: 0.8909 (pp)
REVERT: A 1062 MET cc_start: 0.8995 (mtt) cc_final: 0.8654 (mpp)
REVERT: A 1176 ILE cc_start: 0.9720 (pt) cc_final: 0.9425 (mm)
REVERT: A 1215 ASP cc_start: 0.8787 (t0) cc_final: 0.8542 (m-30)
REVERT: A 1222 LYS cc_start: 0.9376 (mmtt) cc_final: 0.9107 (mttp)
REVERT: A 1392 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8110 (mtp85)
  outliers start: 9
  outliers final: 4
  residues processed: 86
  average time/residue: 0.2905
  time to fit residues: 36.5269
Evaluate side-chains
  63 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 149 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 142 optimal weight:    0.8980
   chunk 138 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 140 optimal weight:    3.9990
   overall best weight:    2.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.075960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.049295 restraints weight = 54474.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.051086 restraints weight = 28041.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.052201 restraints weight = 19427.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       99 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       98 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12618  Z= 0.197
  Angle     :  0.645  10.637  17080  Z= 0.335
  Chirality :  0.041   0.215   1893
  Planarity :  0.004   0.041   2259
  Dihedral  :  5.128  22.018   1737
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.31 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  6.55 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.22), residues: 1570
  helix:  1.19 (0.19), residues: 804
  sheet: -0.31 (0.39), residues: 162
  loop : -0.37 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 124 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.015   0.001   PHE A 395 
 TYR   0.017   0.002   TYR A1046 
 ARG   0.010   0.001   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  671)
  hydrogen bonds       : angle       4.78615 ( 2019)
  covalent geometry    : bond        0.00433 (12618)
  covalent geometry    : angle       0.64523 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9127 (mtp) cc_final: 0.8903 (mtp)
REVERT: A  233 MET cc_start: 0.8814 (mmm) cc_final: 0.8532 (mmm)
REVERT: A  242 MET cc_start: 0.8732 (tmm) cc_final: 0.8369 (tpt)
REVERT: A  265 LEU cc_start: 0.9234 (mp) cc_final: 0.8898 (pp)
REVERT: A  308 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7143 (mmm-85)
REVERT: A 1062 MET cc_start: 0.9017 (mtt) cc_final: 0.8692 (mpp)
REVERT: A 1176 ILE cc_start: 0.9757 (pt) cc_final: 0.9415 (mm)
REVERT: A 1222 LYS cc_start: 0.9451 (mmtt) cc_final: 0.9191 (mttt)
REVERT: A 1404 MET cc_start: 0.8957 (ttm) cc_final: 0.8704 (ttm)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.2349
  time to fit residues: 26.1660
Evaluate side-chains
  64 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 30 optimal weight:   20.0000
   chunk 105 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 103 optimal weight:    9.9990
   chunk 115 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 72 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 509 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.076866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.049616 restraints weight = 54667.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.051496 restraints weight = 28139.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.052678 restraints weight = 19486.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       98 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      111 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12618  Z= 0.124
  Angle     :  0.562   9.166  17080  Z= 0.291
  Chirality :  0.039   0.167   1893
  Planarity :  0.004   0.042   2259
  Dihedral  :  4.725  21.126   1737
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.38 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.22), residues: 1570
  helix:  1.52 (0.19), residues: 796
  sheet: -0.21 (0.40), residues: 156
  loop : -0.30 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 605 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.014   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.006   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  671)
  hydrogen bonds       : angle       4.46077 ( 2019)
  covalent geometry    : bond        0.00267 (12618)
  covalent geometry    : angle       0.56224 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9288 (tp) cc_final: 0.8961 (tt)
REVERT: A  166 LEU cc_start: 0.9798 (tt) cc_final: 0.9440 (mp)
REVERT: A  233 MET cc_start: 0.8776 (mmm) cc_final: 0.8485 (mmm)
REVERT: A  265 LEU cc_start: 0.9236 (mp) cc_final: 0.8887 (pp)
REVERT: A  652 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8845 (mp)
REVERT: A 1062 MET cc_start: 0.9065 (mtt) cc_final: 0.8689 (mpp)
REVERT: A 1176 ILE cc_start: 0.9747 (pt) cc_final: 0.9422 (mm)
REVERT: A 1222 LYS cc_start: 0.9426 (mmtt) cc_final: 0.9148 (mttt)
REVERT: A 1392 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8361 (mtp85)
REVERT: A 1404 MET cc_start: 0.9065 (ttm) cc_final: 0.8809 (ttm)
REVERT: A 1478 MET cc_start: 0.8735 (mmm) cc_final: 0.8335 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.2447
  time to fit residues: 26.5048
Evaluate side-chains
  68 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 34 optimal weight:   20.0000
   chunk 82 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 150 optimal weight:    6.9990
   chunk 144 optimal weight:    8.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 664 GLN
A1130 ASN
A1252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.077559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.050810 restraints weight = 54231.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.052662 restraints weight = 27972.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.053873 restraints weight = 19327.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      111 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      114 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12618  Z= 0.140
  Angle     :  0.562   9.437  17080  Z= 0.289
  Chirality :  0.039   0.173   1893
  Planarity :  0.004   0.042   2259
  Dihedral  :  4.516  21.456   1737
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.12 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.76 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.22), residues: 1570
  helix:  1.66 (0.19), residues: 802
  sheet: -0.17 (0.39), residues: 157
  loop : -0.29 (0.27), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1090 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.011   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A 768 
 ARG   0.006   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  671)
  hydrogen bonds       : angle       4.37589 ( 2019)
  covalent geometry    : bond        0.00303 (12618)
  covalent geometry    : angle       0.56153 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9284 (tp) cc_final: 0.9075 (tp)
REVERT: A  166 LEU cc_start: 0.9793 (tt) cc_final: 0.9462 (mp)
REVERT: A  233 MET cc_start: 0.8814 (mmm) cc_final: 0.8499 (mmm)
REVERT: A  265 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8872 (pp)
REVERT: A  652 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8877 (mp)
REVERT: A 1062 MET cc_start: 0.9169 (mtt) cc_final: 0.8817 (mpp)
REVERT: A 1176 ILE cc_start: 0.9725 (pt) cc_final: 0.9400 (mm)
REVERT: A 1222 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9128 (mttt)
REVERT: A 1404 MET cc_start: 0.9078 (ttm) cc_final: 0.8803 (ttm)
  outliers start: 19
  outliers final: 13
  residues processed: 73
  average time/residue: 0.2307
  time to fit residues: 26.2554
Evaluate side-chains
  72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 38 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 664 GLN
A1196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.076937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.050626 restraints weight = 54065.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.052380 restraints weight = 27769.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.053552 restraints weight = 19159.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      114 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      115 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12618  Z= 0.163
  Angle     :  0.567   9.994  17080  Z= 0.290
  Chirality :  0.039   0.169   1893
  Planarity :  0.004   0.042   2259
  Dihedral  :  4.449  20.338   1737
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.18 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.81 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.22), residues: 1570
  helix:  1.72 (0.19), residues: 799
  sheet: -0.24 (0.39), residues: 160
  loop : -0.31 (0.27), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 124 
 HIS   0.007   0.001   HIS A  63 
 PHE   0.010   0.001   PHE A 497 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  671)
  hydrogen bonds       : angle       4.41760 ( 2019)
  covalent geometry    : bond        0.00358 (12618)
  covalent geometry    : angle       0.56713 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 MET cc_start: 0.8853 (mmm) cc_final: 0.8519 (mmm)
REVERT: A  265 LEU cc_start: 0.9251 (mp) cc_final: 0.8917 (pp)
REVERT: A  652 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8897 (mp)
REVERT: A 1062 MET cc_start: 0.9207 (mtt) cc_final: 0.8858 (mpp)
REVERT: A 1176 ILE cc_start: 0.9717 (pt) cc_final: 0.9399 (mm)
REVERT: A 1203 LYS cc_start: 0.9600 (OUTLIER) cc_final: 0.9344 (tppp)
REVERT: A 1222 LYS cc_start: 0.9451 (mmtt) cc_final: 0.9129 (mttt)
REVERT: A 1392 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8139 (mtp85)
REVERT: A 1404 MET cc_start: 0.9121 (ttm) cc_final: 0.8829 (ttm)
REVERT: A 1478 MET cc_start: 0.8748 (mmm) cc_final: 0.8362 (mmt)
  outliers start: 16
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2445
  time to fit residues: 26.0106
Evaluate side-chains
  67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 102 optimal weight:    0.9990
   chunk 118 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0670
   chunk 129 optimal weight:    0.0060
   chunk 96 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.5936

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.078271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.052185 restraints weight = 52882.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.054050 restraints weight = 26751.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.055245 restraints weight = 18302.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      115 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      121 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12618  Z= 0.092
  Angle     :  0.533  10.633  17080  Z= 0.269
  Chirality :  0.037   0.173   1893
  Planarity :  0.003   0.043   2259
  Dihedral  :  4.231  20.785   1737
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.74 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.79 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.22), residues: 1570
  helix:  1.83 (0.19), residues: 802
  sheet: -0.28 (0.37), residues: 171
  loop : -0.14 (0.27), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 556 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.019   0.001   PHE A 395 
 TYR   0.016   0.001   TYR A1046 
 ARG   0.006   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  671)
  hydrogen bonds       : angle       4.23206 ( 2019)
  covalent geometry    : bond        0.00186 (12618)
  covalent geometry    : angle       0.53330 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9214 (tp) cc_final: 0.8956 (tt)
REVERT: A  166 LEU cc_start: 0.9801 (tt) cc_final: 0.9442 (mt)
REVERT: A  233 MET cc_start: 0.8815 (mmm) cc_final: 0.8469 (mmm)
REVERT: A  265 LEU cc_start: 0.9214 (mp) cc_final: 0.8891 (pp)
REVERT: A 1062 MET cc_start: 0.9232 (mtt) cc_final: 0.8865 (mpp)
REVERT: A 1176 ILE cc_start: 0.9712 (pt) cc_final: 0.9433 (mm)
REVERT: A 1203 LYS cc_start: 0.9604 (OUTLIER) cc_final: 0.9346 (tppp)
REVERT: A 1222 LYS cc_start: 0.9430 (mmtt) cc_final: 0.9110 (mttt)
REVERT: A 1392 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8172 (mtp85)
REVERT: A 1478 MET cc_start: 0.8736 (mmm) cc_final: 0.8294 (mmt)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 0.2614
  time to fit residues: 26.9967
Evaluate side-chains
  69 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 132 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:   20.0000
   chunk 138 optimal weight:    1.9990
   chunk 20 optimal weight:   30.0000
   chunk 133 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 134 optimal weight:    0.7980
   chunk 110 optimal weight:    9.9990
   chunk 135 optimal weight:    0.0010
   overall best weight:    1.3590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.077774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.051462 restraints weight = 53840.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.053265 restraints weight = 27355.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.054438 restraints weight = 18814.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      121 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      123 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12618  Z= 0.119
  Angle     :  0.540  11.018  17080  Z= 0.273
  Chirality :  0.038   0.165   1893
  Planarity :  0.003   0.042   2259
  Dihedral  :  4.177  21.335   1737
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.71 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.22), residues: 1570
  helix:  1.88 (0.19), residues: 803
  sheet: -0.20 (0.38), residues: 169
  loop : -0.16 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1251 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.010   0.001   PHE A  64 
 TYR   0.014   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  671)
  hydrogen bonds       : angle       4.24406 ( 2019)
  covalent geometry    : bond        0.00258 (12618)
  covalent geometry    : angle       0.54032 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 2.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9234 (tp) cc_final: 0.8863 (tt)
REVERT: A  166 LEU cc_start: 0.9804 (tt) cc_final: 0.9459 (mp)
REVERT: A  233 MET cc_start: 0.8833 (mmm) cc_final: 0.8480 (mmm)
REVERT: A  265 LEU cc_start: 0.9224 (mp) cc_final: 0.8917 (pp)
REVERT: A  652 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8912 (mp)
REVERT: A 1062 MET cc_start: 0.9262 (mtt) cc_final: 0.8886 (mpp)
REVERT: A 1203 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9337 (tppp)
REVERT: A 1222 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9115 (mttt)
REVERT: A 1441 SER cc_start: 0.9649 (m) cc_final: 0.9432 (t)
REVERT: A 1478 MET cc_start: 0.8762 (mmm) cc_final: 0.8313 (mmt)
REVERT: A 1488 MET cc_start: 0.8949 (mpp) cc_final: 0.8514 (mpp)
  outliers start: 12
  outliers final: 5
  residues processed: 68
  average time/residue: 0.3069
  time to fit residues: 33.4464
Evaluate side-chains
  65 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 83 optimal weight:    0.0970
   chunk 155 optimal weight:    0.8980
   chunk 156 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 151 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.078321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.052360 restraints weight = 52924.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.054210 restraints weight = 26611.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.055425 restraints weight = 18140.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      123 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      125 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12618  Z= 0.096
  Angle     :  0.539  11.339  17080  Z= 0.270
  Chirality :  0.038   0.161   1893
  Planarity :  0.003   0.043   2259
  Dihedral  :  4.065  24.393   1737
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.55 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.02 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.22), residues: 1570
  helix:  1.89 (0.19), residues: 802
  sheet: -0.17 (0.38), residues: 169
  loop : -0.12 (0.27), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 556 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.022   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  671)
  hydrogen bonds       : angle       4.18978 ( 2019)
  covalent geometry    : bond        0.00203 (12618)
  covalent geometry    : angle       0.53866 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 3.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9187 (tp) cc_final: 0.8911 (tt)
REVERT: A  166 LEU cc_start: 0.9798 (tt) cc_final: 0.9462 (mp)
REVERT: A  233 MET cc_start: 0.8836 (mmm) cc_final: 0.8470 (mmm)
REVERT: A  265 LEU cc_start: 0.9214 (mp) cc_final: 0.8901 (pp)
REVERT: A  652 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8835 (mp)
REVERT: A 1062 MET cc_start: 0.9219 (mtt) cc_final: 0.8851 (mpp)
REVERT: A 1222 LYS cc_start: 0.9444 (mmtt) cc_final: 0.9119 (mttt)
REVERT: A 1392 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7931 (mtp85)
REVERT: A 1441 SER cc_start: 0.9608 (m) cc_final: 0.9406 (t)
REVERT: A 1478 MET cc_start: 0.8767 (mmm) cc_final: 0.8315 (mmt)
REVERT: A 1488 MET cc_start: 0.8943 (mpp) cc_final: 0.8641 (mpp)
  outliers start: 10
  outliers final: 5
  residues processed: 70
  average time/residue: 0.4592
  time to fit residues: 51.5064
Evaluate side-chains
  67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 2.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.078358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.052234 restraints weight = 53129.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.054047 restraints weight = 26873.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.055223 restraints weight = 18456.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      125 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12618  Z= 0.100
  Angle     :  0.551  11.548  17080  Z= 0.275
  Chirality :  0.038   0.158   1893
  Planarity :  0.003   0.043   2259
  Dihedral  :  4.016  23.756   1737
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.55 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.17 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.22), residues: 1570
  helix:  1.91 (0.19), residues: 802
  sheet: -0.13 (0.38), residues: 169
  loop : -0.13 (0.27), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 124 
 HIS   0.002   0.000   HIS A 821 
 PHE   0.010   0.001   PHE A 497 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  671)
  hydrogen bonds       : angle       4.16317 ( 2019)
  covalent geometry    : bond        0.00215 (12618)
  covalent geometry    : angle       0.55101 (17080)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9801 (tt) cc_final: 0.9474 (mp)
REVERT: A  233 MET cc_start: 0.8827 (mmm) cc_final: 0.8451 (mmm)
REVERT: A  265 LEU cc_start: 0.9216 (mp) cc_final: 0.8905 (pp)
REVERT: A  652 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8831 (mp)
REVERT: A 1062 MET cc_start: 0.9235 (mtt) cc_final: 0.8861 (mpp)
REVERT: A 1222 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9120 (mttt)
REVERT: A 1392 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7911 (mtp85)
REVERT: A 1441 SER cc_start: 0.9602 (m) cc_final: 0.9395 (t)
REVERT: A 1478 MET cc_start: 0.8768 (mmm) cc_final: 0.8310 (mmt)
REVERT: A 1488 MET cc_start: 0.8952 (mpp) cc_final: 0.8612 (mpp)
  outliers start: 10
  outliers final: 6
  residues processed: 70
  average time/residue: 0.3481
  time to fit residues: 36.7216
Evaluate side-chains
  70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1392 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 2 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 862 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.078590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.052760 restraints weight = 52671.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.054613 restraints weight = 26425.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.055819 restraints weight = 18038.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      125 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12618  Z= 0.097
  Angle     :  0.544  11.035  17080  Z= 0.272
  Chirality :  0.038   0.163   1893
  Planarity :  0.003   0.043   2259
  Dihedral  :  3.927  24.494   1737
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.47 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.22), residues: 1570
  helix:  1.94 (0.19), residues: 802
  sheet: -0.11 (0.38), residues: 169
  loop : -0.13 (0.27), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1090 
 HIS   0.002   0.000   HIS A 821 
 PHE   0.025   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  671)
  hydrogen bonds       : angle       4.13827 ( 2019)
  covalent geometry    : bond        0.00206 (12618)
  covalent geometry    : angle       0.54380 (17080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5140.18 seconds
wall clock time: 92 minutes 21.04 seconds (5541.04 seconds total)