Starting phenix.real_space_refine
on Sat Oct 11 06:47:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p51_17436/10_2025/8p51_17436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p51_17436/10_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_17436/10_2025/8p51_17436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p51_17436/10_2025/8p51_17436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p51_17436/10_2025/8p51_17436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p51_17436/10_2025/8p51_17436.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.038
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.84, per 1000 atoms: 0.23
  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: 0.83
  Conformation dependent library (CDL) restraints added in 431.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.62
  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: 2.81

  Time building geometry restraints manager: 1.10 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:             2.110
  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:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.500
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (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
 ARG   0.022   0.003   ARG A 817 
 TYR   0.026   0.005   TYR A 820 
 PHE   0.022   0.002   PHE A  30 
 TRP   0.033   0.003   TRP A1251 
 HIS   0.008   0.002   HIS A1370 

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

*********************** 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  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1509
  time to fit residues: 25.8998
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  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 785 GLN
A 862 GLN
A1052 ASN
A1446 HIS
A1486 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.080656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.054138 restraints weight = 56081.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.056161 restraints weight = 28770.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.057462 restraints weight = 19772.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.058196 restraints weight = 15907.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.058673 restraints weight = 14030.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      109 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       98 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12618  Z= 0.150
  Angle     :  0.673   8.894  17080  Z= 0.354
  Chirality :  0.041   0.161   1893
  Planarity :  0.005   0.036   2259
  Dihedral  :  5.723  21.931   1737
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  4.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.21), residues: 1570
  helix:  0.71 (0.18), residues: 806
  sheet: -0.33 (0.38), residues: 163
  loop : -0.47 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1392 
 TYR   0.021   0.002   TYR A1046 
 PHE   0.018   0.001   PHE A 395 
 TRP   0.009   0.002   TRP A 605 
 HIS   0.007   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12618)
  covalent geometry    : angle       0.67267 (17080)
  hydrogen bonds       : bond        0.05109 (  671)
  hydrogen bonds       : angle       5.13126 ( 2019)

*********************** 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
  85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9808 (tt) cc_final: 0.9453 (mp)
REVERT: A  233 MET cc_start: 0.8966 (mmm) cc_final: 0.8740 (mmm)
REVERT: A  265 LEU cc_start: 0.9203 (mp) cc_final: 0.8913 (pp)
REVERT: A  437 MET cc_start: 0.8522 (tmm) cc_final: 0.7851 (ttm)
REVERT: A 1062 MET cc_start: 0.8971 (mtt) cc_final: 0.8635 (mpp)
REVERT: A 1176 ILE cc_start: 0.9718 (pt) cc_final: 0.9426 (mm)
REVERT: A 1215 ASP cc_start: 0.8716 (t0) cc_final: 0.8472 (m-30)
REVERT: A 1392 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8115 (mtp85)
  outliers start: 10
  outliers final: 5
  residues processed: 84
  average time/residue: 0.1213
  time to fit residues: 14.9970
Evaluate side-chains
  65 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  753 SER
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 57 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 142 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 130 optimal weight:    5.9990
   chunk 151 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 39 optimal weight:   30.0000
   chunk 52 optimal weight:    0.0040
   chunk 60 optimal weight:    9.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
A 862 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.077604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.050431 restraints weight = 55409.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.052254 restraints weight = 28601.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.053495 restraints weight = 19819.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.054189 restraints weight = 15989.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.054648 restraints weight = 14146.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       98 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      103 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12618  Z= 0.124
  Angle     :  0.592   7.977  17080  Z= 0.308
  Chirality :  0.039   0.181   1893
  Planarity :  0.004   0.042   2259
  Dihedral  :  5.032  21.830   1737
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.12 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.95 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.22), residues: 1570
  helix:  1.31 (0.19), residues: 804
  sheet: -0.20 (0.39), residues: 162
  loop : -0.35 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 125 
 TYR   0.015   0.001   TYR A1046 
 PHE   0.015   0.001   PHE A 395 
 TRP   0.009   0.001   TRP A 605 
 HIS   0.008   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12618)
  covalent geometry    : angle       0.59153 (17080)
  hydrogen bonds       : bond        0.04210 (  671)
  hydrogen bonds       : angle       4.65688 ( 2019)

*********************** 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
  78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8762 (tt0) cc_final: 0.8561 (tt0)
REVERT: A   59 LEU cc_start: 0.9275 (tp) cc_final: 0.8932 (tt)
REVERT: A   66 MET cc_start: 0.7019 (ppp) cc_final: 0.6369 (ppp)
REVERT: A  230 LEU cc_start: 0.9679 (mt) cc_final: 0.9478 (pp)
REVERT: A  233 MET cc_start: 0.8909 (mmm) cc_final: 0.8653 (mmm)
REVERT: A  242 MET cc_start: 0.8714 (tmm) cc_final: 0.8350 (tpt)
REVERT: A  265 LEU cc_start: 0.9228 (mp) cc_final: 0.8879 (pp)
REVERT: A 1062 MET cc_start: 0.8949 (mtt) cc_final: 0.8569 (mpp)
REVERT: A 1176 ILE cc_start: 0.9737 (pt) cc_final: 0.9388 (mm)
REVERT: A 1215 ASP cc_start: 0.8903 (t0) cc_final: 0.8568 (m-30)
REVERT: A 1392 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8171 (mtp85)
REVERT: A 1488 MET cc_start: 0.8826 (mtm) cc_final: 0.8480 (mtp)
  outliers start: 9
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1015
  time to fit residues: 11.7061
Evaluate side-chains
  66 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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 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 62 optimal weight:    0.0040
   chunk 147 optimal weight:    0.0040
   chunk 141 optimal weight:    4.9990
   chunk 132 optimal weight:    5.9990
   chunk 21 optimal weight:   40.0000
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0010
   chunk 28 optimal weight:    5.9990
   chunk 155 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.3610

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

Flipped N/Q/H residues before XYZ refinement:
A 509 GLN
A1130 ASN
A1252 GLN
A1535 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.078153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.051561 restraints weight = 53556.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.053418 restraints weight = 27133.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.054641 restraints weight = 18562.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.055375 restraints weight = 14855.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.055733 restraints weight = 13083.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      103 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      109 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12618  Z= 0.100
  Angle     :  0.553   9.237  17080  Z= 0.285
  Chirality :  0.038   0.177   1893
  Planarity :  0.004   0.044   2259
  Dihedral  :  4.618  21.273   1737
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.36 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.33 %
    Favored  : 92.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.22), residues: 1570
  helix:  1.57 (0.19), residues: 799
  sheet: -0.05 (0.39), residues: 158
  loop : -0.27 (0.27), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.015   0.001   TYR A1046 
 PHE   0.014   0.001   PHE A 395 
 TRP   0.009   0.001   TRP A 605 
 HIS   0.008   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 (12618)
  covalent geometry    : angle       0.55335 (17080)
  hydrogen bonds       : bond        0.03654 (  671)
  hydrogen bonds       : angle       4.38228 ( 2019)

*********************** 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
  82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.9324 (tpp) cc_final: 0.9078 (tpp)
REVERT: A  166 LEU cc_start: 0.9795 (tt) cc_final: 0.9431 (mp)
REVERT: A  233 MET cc_start: 0.8969 (mmm) cc_final: 0.8637 (mmm)
REVERT: A  265 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8855 (pp)
REVERT: A 1062 MET cc_start: 0.8974 (mtt) cc_final: 0.8606 (mpp)
REVERT: A 1176 ILE cc_start: 0.9726 (pt) cc_final: 0.9406 (mm)
REVERT: A 1222 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9165 (mttt)
REVERT: A 1392 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8330 (mtp85)
REVERT: A 1478 MET cc_start: 0.8664 (mmm) cc_final: 0.8274 (mmt)
REVERT: A 1488 MET cc_start: 0.8868 (mtm) cc_final: 0.8517 (mtp)
  outliers start: 11
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1104
  time to fit residues: 12.9073
Evaluate side-chains
  70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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  739 TYR
Chi-restraints excluded: chain A residue  877 ILE
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 115 optimal weight:    0.0170
   chunk 83 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.9422

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.078808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.052920 restraints weight = 53157.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.054784 restraints weight = 26714.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.056011 restraints weight = 18226.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.056688 restraints weight = 14581.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.057157 restraints weight = 12859.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      109 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      114 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12618  Z= 0.106
  Angle     :  0.544  13.210  17080  Z= 0.277
  Chirality :  0.038   0.174   1893
  Planarity :  0.004   0.045   2259
  Dihedral  :  4.379  21.752   1737
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.42 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.45 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.22), residues: 1570
  helix:  1.75 (0.19), residues: 799
  sheet: -0.05 (0.38), residues: 162
  loop : -0.20 (0.27), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.014   0.001   TYR A1046 
 PHE   0.016   0.001   PHE A 395 
 TRP   0.009   0.001   TRP A1090 
 HIS   0.009   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (12618)
  covalent geometry    : angle       0.54435 (17080)
  hydrogen bonds       : bond        0.03509 (  671)
  hydrogen bonds       : angle       4.27241 ( 2019)

*********************** 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
  75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9788 (tt) cc_final: 0.9446 (mp)
REVERT: A  233 MET cc_start: 0.8994 (mmm) cc_final: 0.8631 (mmm)
REVERT: A  265 LEU cc_start: 0.9167 (mp) cc_final: 0.8834 (pp)
REVERT: A 1176 ILE cc_start: 0.9711 (pt) cc_final: 0.9396 (mm)
REVERT: A 1222 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9115 (mttt)
REVERT: A 1392 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8148 (mtp85)
REVERT: A 1488 MET cc_start: 0.8843 (mtm) cc_final: 0.8563 (mtp)
  outliers start: 14
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1064
  time to fit residues: 11.6177
Evaluate side-chains
  70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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  224 LEU
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue 1203 LYS
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 55 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 149 optimal weight:    5.9990
   chunk 128 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 52 optimal weight:    0.4980
   chunk 147 optimal weight:   10.0000
   chunk 127 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0370
   overall best weight:    0.6660

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.078970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.053160 restraints weight = 52880.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.055059 restraints weight = 26503.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.056293 restraints weight = 17998.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.056954 restraints weight = 14370.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.057179 restraints weight = 12672.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      114 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      116 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12618  Z= 0.096
  Angle     :  0.540  11.051  17080  Z= 0.272
  Chirality :  0.038   0.174   1893
  Planarity :  0.004   0.045   2259
  Dihedral  :  4.259  20.975   1737
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.68 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  7.68 %
    Favored  : 91.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.22), residues: 1570
  helix:  1.83 (0.19), residues: 801
  sheet: -0.00 (0.39), residues: 162
  loop : -0.13 (0.27), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.014   0.001   TYR A1046 
 PHE   0.010   0.001   PHE A 480 
 TRP   0.008   0.001   TRP A 124 
 HIS   0.008   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (12618)
  covalent geometry    : angle       0.53983 (17080)
  hydrogen bonds       : bond        0.03374 (  671)
  hydrogen bonds       : angle       4.22381 ( 2019)

*********************** 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
  76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9777 (tt) cc_final: 0.9430 (mp)
REVERT: A  233 MET cc_start: 0.8882 (mmm) cc_final: 0.8474 (mmm)
REVERT: A  265 LEU cc_start: 0.9180 (mp) cc_final: 0.8845 (pp)
REVERT: A 1176 ILE cc_start: 0.9713 (pt) cc_final: 0.9401 (mm)
REVERT: A 1203 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9358 (tppp)
REVERT: A 1222 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9109 (mttt)
REVERT: A 1392 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8175 (mtp85)
REVERT: A 1478 MET cc_start: 0.8682 (mmm) cc_final: 0.8270 (mmt)
REVERT: A 1488 MET cc_start: 0.8849 (mtm) cc_final: 0.8545 (mtp)
  outliers start: 15
  outliers final: 7
  residues processed: 71
  average time/residue: 0.1038
  time to fit residues: 11.4032
Evaluate side-chains
  69 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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  224 LEU
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  877 ILE
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 107 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 153 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 144 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 664 GLN
A1196 GLN
A1535 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.077730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.051077 restraints weight = 54180.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.052918 restraints weight = 27648.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.054091 restraints weight = 19125.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.054783 restraints weight = 15469.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.055156 restraints weight = 13694.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      116 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      117 |
|-----------------------------------------------------------------------------|
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3246

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= 0.154
  Angle     :  0.569  10.712  17080  Z= 0.288
  Chirality :  0.039   0.169   1893
  Planarity :  0.004   0.045   2259
  Dihedral  :  4.278  21.336   1737
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.93 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  7.53 %
    Favored  : 91.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.22), residues: 1570
  helix:  1.92 (0.19), residues: 793
  sheet: -0.02 (0.40), residues: 160
  loop : -0.16 (0.27), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.016   0.001   TYR A1046 
 PHE   0.023   0.001   PHE A 277 
 TRP   0.009   0.002   TRP A1251 
 HIS   0.006   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12618)
  covalent geometry    : angle       0.56917 (17080)
  hydrogen bonds       : bond        0.03654 (  671)
  hydrogen bonds       : angle       4.30516 ( 2019)

*********************** 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
  81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.9777 (tt) cc_final: 0.9441 (mp)
REVERT: A  233 MET cc_start: 0.8746 (mmm) cc_final: 0.8439 (mmm)
REVERT: A  265 LEU cc_start: 0.9186 (mp) cc_final: 0.8886 (pp)
REVERT: A  769 MET cc_start: 0.8985 (ttm) cc_final: 0.8775 (mtp)
REVERT: A 1176 ILE cc_start: 0.9711 (pt) cc_final: 0.9414 (mm)
REVERT: A 1203 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9348 (tppp)
REVERT: A 1222 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9125 (mttt)
REVERT: A 1392 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8181 (mtp85)
REVERT: A 1478 MET cc_start: 0.8736 (mmm) cc_final: 0.8321 (mmt)
REVERT: A 1488 MET cc_start: 0.8830 (mtm) cc_final: 0.8566 (mtp)
  outliers start: 17
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1008
  time to fit residues: 11.7712
Evaluate side-chains
  70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
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  224 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  346 MET
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  893 THR
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 41 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 150 optimal weight:    0.4980
   chunk 114 optimal weight:   20.0000
   chunk 102 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A1535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.078462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.051840 restraints weight = 53826.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.053729 restraints weight = 27383.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.054946 restraints weight = 18785.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055633 restraints weight = 15133.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.056088 restraints weight = 13411.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      117 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      118 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12618  Z= 0.109
  Angle     :  0.570  11.280  17080  Z= 0.284
  Chirality :  0.038   0.155   1893
  Planarity :  0.003   0.044   2259
  Dihedral  :  4.230  23.377   1737
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.12 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.13 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.22), residues: 1570
  helix:  1.90 (0.19), residues: 800
  sheet: -0.15 (0.39), residues: 169
  loop : -0.09 (0.27), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1189 
 TYR   0.015   0.001   TYR A1046 
 PHE   0.015   0.001   PHE A 277 
 TRP   0.008   0.001   TRP A 124 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (12618)
  covalent geometry    : angle       0.57003 (17080)
  hydrogen bonds       : bond        0.03469 (  671)
  hydrogen bonds       : angle       4.24976 ( 2019)

*********************** 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
  74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9776 (tt) cc_final: 0.9428 (mp)
REVERT: A  233 MET cc_start: 0.8680 (mmm) cc_final: 0.8314 (mmm)
REVERT: A  265 LEU cc_start: 0.9190 (mp) cc_final: 0.8881 (pp)
REVERT: A 1203 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9350 (tppp)
REVERT: A 1222 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9123 (mttt)
REVERT: A 1392 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7931 (mtp85)
REVERT: A 1478 MET cc_start: 0.8741 (mmm) cc_final: 0.8296 (mmt)
REVERT: A 1488 MET cc_start: 0.8854 (mtm) cc_final: 0.8567 (mtp)
  outliers start: 13
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1032
  time to fit residues: 11.1741
Evaluate side-chains
  70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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  224 LEU
Chi-restraints excluded: chain A residue  346 MET
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  877 ILE
Chi-restraints excluded: chain A residue  893 THR
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 34 optimal weight:   30.0000
   chunk 151 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 156 optimal weight:    9.9990
   chunk 9 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 143 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.078366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.051653 restraints weight = 54275.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.053526 restraints weight = 27522.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.054739 restraints weight = 18895.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.055459 restraints weight = 15222.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.055886 restraints weight = 13442.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      118 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      118 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12618  Z= 0.120
  Angle     :  0.573  11.526  17080  Z= 0.284
  Chirality :  0.038   0.146   1893
  Planarity :  0.003   0.044   2259
  Dihedral  :  4.185  23.960   1737
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.93 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.51 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.22), residues: 1570
  helix:  1.93 (0.19), residues: 803
  sheet: -0.14 (0.39), residues: 169
  loop : -0.07 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.016   0.001   TYR A1046 
 PHE   0.041   0.001   PHE A 277 
 TRP   0.007   0.001   TRP A 124 
 HIS   0.007   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (12618)
  covalent geometry    : angle       0.57280 (17080)
  hydrogen bonds       : bond        0.03445 (  671)
  hydrogen bonds       : angle       4.26194 ( 2019)

*********************** 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
  71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.9782 (tt) cc_final: 0.9439 (mp)
REVERT: A  233 MET cc_start: 0.8611 (mmm) cc_final: 0.8244 (mmm)
REVERT: A  265 LEU cc_start: 0.9213 (mp) cc_final: 0.8903 (pp)
REVERT: A 1222 LYS cc_start: 0.9432 (mmtt) cc_final: 0.9119 (mttt)
REVERT: A 1392 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8200 (mtp85)
REVERT: A 1478 MET cc_start: 0.8755 (mmm) cc_final: 0.8313 (mmt)
REVERT: A 1488 MET cc_start: 0.8811 (mtm) cc_final: 0.8530 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1038
  time to fit residues: 11.1043
Evaluate side-chains
  68 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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  224 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  893 THR
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 154 optimal weight:    0.6980
   chunk 83 optimal weight:    0.2980
   chunk 18 optimal weight:    9.9990
   chunk 85 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0370
   chunk 110 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 153 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.079406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.052878 restraints weight = 53685.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.054800 restraints weight = 26970.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.056032 restraints weight = 18427.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.056721 restraints weight = 14819.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.057173 restraints weight = 13120.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      118 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      122 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12618  Z= 0.096
  Angle     :  0.589  13.898  17080  Z= 0.286
  Chirality :  0.038   0.147   1893
  Planarity :  0.003   0.044   2259
  Dihedral  :  4.130  24.233   1737
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.89 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1570
  helix:  1.98 (0.19), residues: 803
  sheet: -0.25 (0.39), residues: 171
  loop : -0.09 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1392 
 TYR   0.016   0.001   TYR A1046 
 PHE   0.023   0.001   PHE A 335 
 TRP   0.009   0.001   TRP A 556 
 HIS   0.009   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 (12618)
  covalent geometry    : angle       0.58882 (17080)
  hydrogen bonds       : bond        0.03190 (  671)
  hydrogen bonds       : angle       4.23869 ( 2019)

********************** 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
  78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.9780 (tt) cc_final: 0.9438 (mp)
REVERT: A  233 MET cc_start: 0.8305 (mmm) cc_final: 0.8077 (mmp)
REVERT: A  265 LEU cc_start: 0.9218 (mp) cc_final: 0.8893 (pp)
REVERT: A  324 TYR cc_start: 0.7813 (t80) cc_final: 0.7378 (m-80)
REVERT: A 1222 LYS cc_start: 0.9430 (mmtt) cc_final: 0.9124 (mttt)
REVERT: A 1392 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7896 (mtp85)
REVERT: A 1478 MET cc_start: 0.8745 (mmm) cc_final: 0.8281 (mmt)
REVERT: A 1488 MET cc_start: 0.8827 (mtm) cc_final: 0.8528 (mtp)
  outliers start: 11
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1062
  time to fit residues: 12.2556
Evaluate side-chains
  67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
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  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  893 THR
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 45 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 147 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.078343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.052211 restraints weight = 53029.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.054089 restraints weight = 26744.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.055213 restraints weight = 18314.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.055957 restraints weight = 14756.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.056338 restraints weight = 12973.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      122 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      124 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12618  Z= 0.132
  Angle     :  0.594  11.501  17080  Z= 0.291
  Chirality :  0.039   0.166   1893
  Planarity :  0.003   0.043   2259
  Dihedral  :  4.107  23.904   1737
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.93 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.19 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.23), residues: 1570
  helix:  2.01 (0.19), residues: 802
  sheet: -0.28 (0.39), residues: 171
  loop : -0.09 (0.28), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1189 
 TYR   0.014   0.001   TYR A1046 
 PHE   0.021   0.001   PHE A 395 
 TRP   0.010   0.002   TRP A 805 
 HIS   0.003   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (12618)
  covalent geometry    : angle       0.59351 (17080)
  hydrogen bonds       : bond        0.03377 (  671)
  hydrogen bonds       : angle       4.28314 ( 2019)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2769.77 seconds
wall clock time: 48 minutes 18.00 seconds (2898.00 seconds total)