Starting phenix.real_space_refine
on Mon Jun  9 22:12:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hw2_35049/06_2025/8hw2_35049.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.059
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      57      5.16       5
     C    7063      2.51       5
     N    1812      2.21       5
     O    1921      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10853
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1375, 10789
          Classifications: {'peptide': 1375}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 61, 'TRANS': 1313}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'U38': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.40, per 1000 atoms: 0.59
  Number of scatterers: 10853
  At special positions: 0
  Unit cell: (78.11, 109.14, 149.8, 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      57     16.00
     O    1921      8.00
     N    1812      7.00
     C    7063      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.63
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 5 sheets defined
      63.7% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 4.392A  pdb=" N   LEU A  37 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 59
      removed outlier: 3.716A  pdb=" N   ILE A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TRP A  46 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
      removed outlier: 4.167A  pdb=" N   TYR A  55 " --> pdb=" O   CYS A  51 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A  56 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   HIS A  59 " --> pdb=" O   TYR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 94
      removed outlier: 3.658A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLY A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY A  94 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 106
      removed outlier: 4.218A  pdb=" N   PHE A 106 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 127
      removed outlier: 3.697A  pdb=" N   VAL A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LEU A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 156
      removed outlier: 3.800A  pdb=" N   VAL A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      Proline residue:  A 151  - end of helix
    Processing helix  chain 'A' and resid 167 through 189
    Processing helix  chain 'A' and resid 220 through 222
      No H-bonds generated for 'chain 'A' and resid 220 through 222'
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 236 through 240
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 298 through 305
      removed outlier: 3.761A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 5.766A  pdb=" N   SER A 309 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 326
      removed outlier: 3.915A  pdb=" N   PHE A 326 " --> pdb=" O   ASP A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 4.350A  pdb=" N   SER A 333 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 362
      removed outlier: 4.013A  pdb=" N   GLY A 349 " --> pdb=" O   PRO A 345 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 386
      removed outlier: 3.789A  pdb=" N   THR A 377 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY A 378 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 394
      removed outlier: 3.911A  pdb=" N   ARG A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS A 392 " --> pdb=" O   VAL A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 404
      removed outlier: 3.584A  pdb=" N   LYS A 401 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 412
    Processing helix  chain 'A' and resid 423 through 428
      removed outlier: 3.881A  pdb=" N   ASN A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 436
      removed outlier: 3.960A  pdb=" N   SER A 432 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      Proline residue:  A 434  - end of helix
    Processing helix  chain 'A' and resid 440 through 448
      removed outlier: 3.696A  pdb=" N   LEU A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 472
      removed outlier: 3.667A  pdb=" N   MET A 459 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
      Proline residue:  A 464  - end of helix
      removed outlier: 4.649A  pdb=" N   VAL A 469 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ALA A 470 " --> pdb=" O   ASN A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 477
    Processing helix  chain 'A' and resid 481 through 496
    Processing helix  chain 'A' and resid 497 through 504
      removed outlier: 3.704A  pdb=" N   TYR A 504 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 526
      removed outlier: 3.700A  pdb=" N   PHE A 510 " --> pdb=" O   TRP A 506 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE A 517 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 528
      No H-bonds generated for 'chain 'A' and resid 527 through 528'
    Processing helix  chain 'A' and resid 529 through 533
      removed outlier: 3.583A  pdb=" N   THR A 533 " --> pdb=" O   TYR A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 556
      removed outlier: 3.693A  pdb=" N   THR A 538 " --> pdb=" O   THR A 534 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TRP A 539 " --> pdb=" O   THR A 535 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
    Processing helix  chain 'A' and resid 564 through 579
      removed outlier: 4.909A  pdb=" N   VAL A 570 " --> pdb=" O   GLU A 566 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN A 576 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 584
      removed outlier: 3.584A  pdb=" N   ASN A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   MET A 584 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 579 through 584'
    Processing helix  chain 'A' and resid 584 through 606
      removed outlier: 3.575A  pdb=" N   LEU A 588 " --> pdb=" O   MET A 584 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR A 593 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   SER A 598 " --> pdb=" O   GLN A 594 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 675
      removed outlier: 4.142A  pdb=" N   VAL A 671 " --> pdb=" O   LYS A 667 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   SER A 672 " --> pdb=" O   SER A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 711
    Processing helix  chain 'A' and resid 716 through 727
    Processing helix  chain 'A' and resid 729 through 734
    Processing helix  chain 'A' and resid 738 through 742
    Processing helix  chain 'A' and resid 752 through 767
      removed outlier: 4.285A  pdb=" N   ARG A 758 " --> pdb=" O   GLY A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 793
      removed outlier: 3.975A  pdb=" N   HIS A 788 " --> pdb=" O   HIS A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 842
      removed outlier: 3.952A  pdb=" N   ARG A 841 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 852
      removed outlier: 3.871A  pdb=" N   ASN A 847 " --> pdb=" O   GLY A 843 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   PHE A 848 " --> pdb=" O   SER A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 967
      removed outlier: 4.363A  pdb=" N   PHE A 959 " --> pdb=" O   GLU A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 972
    Processing helix  chain 'A' and resid 974 through 997
    Processing helix  chain 'A' and resid 998 through 1001
      removed outlier: 3.762A  pdb=" N   ALA A1001 " --> pdb=" O   ASP A 998 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 998 through 1001'
    Processing helix  chain 'A' and resid 1004 through 1006
      No H-bonds generated for 'chain 'A' and resid 1004 through 1006'
    Processing helix  chain 'A' and resid 1007 through 1020
      removed outlier: 4.083A  pdb=" N   LEU A1012 " --> pdb=" O   THR A1008 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A1013 " --> pdb=" O   SER A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1053
      removed outlier: 3.895A  pdb=" N   ALA A1032 " --> pdb=" O   LEU A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1063
      removed outlier: 4.019A  pdb=" N   PHE A1060 " --> pdb=" O   PRO A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1071
      removed outlier: 3.713A  pdb=" N   CYS A1071 " --> pdb=" O   ARG A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1082
    Processing helix  chain 'A' and resid 1083 through 1108
      removed outlier: 3.729A  pdb=" N   PHE A1095 " --> pdb=" O   LEU A1091 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR A1100 " --> pdb=" O   ASN A1096 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A1105 " --> pdb=" O   LEU A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1116 through 1151
      removed outlier: 4.592A  pdb=" N   TYR A1122 " --> pdb=" O   LEU A1118 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG A1134 " --> pdb=" O   ALA A1130 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER A1143 " --> pdb=" O   LEU A1139 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   SER A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      Proline residue:  A1146  - end of helix
    Processing helix  chain 'A' and resid 1157 through 1162
    Processing helix  chain 'A' and resid 1167 through 1169
      No H-bonds generated for 'chain 'A' and resid 1167 through 1169'
    Processing helix  chain 'A' and resid 1170 through 1183
      removed outlier: 3.877A  pdb=" N   THR A1176 " --> pdb=" O   ILE A1172 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN A1181 " --> pdb=" O   LYS A1177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1190
      removed outlier: 3.640A  pdb=" N   ILE A1189 " --> pdb=" O   CYS A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1217
      removed outlier: 4.436A  pdb=" N   VAL A1207 " --> pdb=" O   GLY A1203 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE A1213 " --> pdb=" O   PHE A1209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1221
    Processing helix  chain 'A' and resid 1222 through 1232
    Processing helix  chain 'A' and resid 1235 through 1240
      removed outlier: 3.624A  pdb=" N   ALA A1239 " --> pdb=" O   GLN A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1253
    Processing helix  chain 'A' and resid 1254 through 1263
    Processing helix  chain 'A' and resid 1274 through 1278
    Processing helix  chain 'A' and resid 1328 through 1337
      removed outlier: 3.505A  pdb=" N   MET A1332 " --> pdb=" O   GLY A1328 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A1337 " --> pdb=" O   THR A1333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1358 through 1365
      removed outlier: 3.735A  pdb=" N   GLN A1365 " --> pdb=" O   ASP A1361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1379 through 1385
      removed outlier: 3.625A  pdb=" N   ASN A1383 " --> pdb=" O   THR A1379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1402
    Processing helix  chain 'A' and resid 1404 through 1411
    Processing helix  chain 'A' and resid 1413 through 1417
    Processing helix  chain 'A' and resid 1420 through 1424
      removed outlier: 3.630A  pdb=" N   GLU A1424 " --> pdb=" O   GLU A1421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1443
      removed outlier: 3.731A  pdb=" N   ARG A1442 " --> pdb=" O   ARG A1438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1457 through 1472
      removed outlier: 3.959A  pdb=" N   LEU A1463 " --> pdb=" O   GLU A1459 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A1472 " --> pdb=" O   ILE A1468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1514
      removed outlier: 3.775A  pdb=" N   ALA A1512 " --> pdb=" O   ALA A1508 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG A1514 " --> pdb=" O   LEU A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1524
    Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 647
      removed outlier: 5.492A  pdb=" N   HIS A 645 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE A 634 " --> pdb=" O   HIS A 645 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 642 through 647
      removed outlier: 5.492A  pdb=" N   HIS A 645 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE A 634 " --> pdb=" O   HIS A 645 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 628 " --> pdb=" O   HIS A 686 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLY A 632 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   GLU A 682 " --> pdb=" O   GLY A 632 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   PHE A 634 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LYS A 680 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 692 through 694
      removed outlier: 6.032A  pdb=" N   PHE A 772 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL A 808 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU A 774 " --> pdb=" O   VAL A 808 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL A 657 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 823 " --> pdb=" O   GLU A 831 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLU A 831 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ALA A 825 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   VAL A 829 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1304 through 1309
      removed outlier: 3.624A  pdb=" N   ASP A1308 " --> pdb=" O   TYR A1294 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   TYR A1294 " --> pdb=" O   ASP A1308 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   PHE A1291 " --> pdb=" O   ARG A1348 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ARG A1348 " --> pdb=" O   PHE A1291 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   ASN A1293 " --> pdb=" O   GLU A1346 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   GLU A1346 " --> pdb=" O   ASN A1293 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG A1297 " --> pdb=" O   ALA A1342 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ALA A1342 " --> pdb=" O   ARG A1297 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1368 through 1369
      removed outlier: 3.823A  pdb=" N   ILE A1369 " --> pdb=" O   VAL A1448 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A1480 " --> pdb=" O   LEU A1449 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLY A1320 " --> pdb=" O   LEU A1494 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU A1496 " --> pdb=" O   GLY A1320 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL A1322 " --> pdb=" O   LEU A1496 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   VAL A1493 " --> pdb=" O   PHE A1504 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   PHE A1504 " --> pdb=" O   VAL A1493 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL A1495 " --> pdb=" O   ALA A1502 " (cutoff:3.500A)

    514 hydrogen bonds defined for protein.
    1476 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: 4.30

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1711
        1.32 -     1.44: 2999
        1.44 -     1.57: 6300
        1.57 -     1.69: 12
        1.69 -     1.82: 91
  Bond restraints: 11113
  Sorted by residual:
  bond pdb=" C10 U38 A1602 "
       pdb=" C11 U38 A1602 "
    ideal  model  delta    sigma   weight residual
    1.389  1.604 -0.215 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C10 U38 A1601 "
       pdb=" C11 U38 A1601 "
    ideal  model  delta    sigma   weight residual
    1.389  1.603 -0.214 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C23 U38 A1602 "
       pdb=" C7  U38 A1602 "
    ideal  model  delta    sigma   weight residual
    1.391  1.603 -0.212 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C23 U38 A1601 "
       pdb=" C7  U38 A1601 "
    ideal  model  delta    sigma   weight residual
    1.391  1.602 -0.211 2.00e-02 2.50e+03 1.12e+02
  bond pdb=" C8  U38 A1601 "
       pdb=" C9  U38 A1601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.196  0.194 2.00e-02 2.50e+03 9.45e+01
  ... (remaining 11108 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 14795
        2.43 -     4.86: 270
        4.86 -     7.29: 50
        7.29 -     9.72: 10
        9.72 -    12.14: 3
  Bond angle restraints: 15128
  Sorted by residual:
  angle pdb=" N   VAL A1026 "
        pdb=" CA  VAL A1026 "
        pdb=" C   VAL A1026 "
      ideal   model   delta    sigma   weight residual
     113.71  107.72    5.99 9.50e-01 1.11e+00 3.98e+01
  angle pdb=" N   VAL A 114 "
        pdb=" CA  VAL A 114 "
        pdb=" C   VAL A 114 "
      ideal   model   delta    sigma   weight residual
     112.96  107.58    5.38 1.00e+00 1.00e+00 2.89e+01
  angle pdb=" C   PHE A 420 "
        pdb=" N   MET A 421 "
        pdb=" CA  MET A 421 "
      ideal   model   delta    sigma   weight residual
     121.54  131.38   -9.84 1.91e+00 2.74e-01 2.65e+01
  angle pdb=" N   VAL A1199 "
        pdb=" CA  VAL A1199 "
        pdb=" C   VAL A1199 "
      ideal   model   delta    sigma   weight residual
     111.62  108.22    3.40 7.90e-01 1.60e+00 1.85e+01
  angle pdb=" C20 U38 A1601 "
        pdb=" C21 U38 A1601 "
        pdb=" C22 U38 A1601 "
      ideal   model   delta    sigma   weight residual
     112.77  124.91  -12.14 3.00e+00 1.11e-01 1.64e+01
  ... (remaining 15123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 6258
       24.42 -    48.85: 378
       48.85 -    73.27: 36
       73.27 -    97.69: 11
       97.69 -   122.12: 5
  Dihedral angle restraints: 6688
    sinusoidal: 2694
      harmonic: 3994
  Sorted by residual:
  dihedral pdb=" CD  ARG A1245 "
           pdb=" NE  ARG A1245 "
           pdb=" CZ  ARG A1245 "
           pdb=" NH1 ARG A1245 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -66.78   66.78     1      1.00e+01 1.00e-02 5.81e+01
  dihedral pdb=" CA  TRP A1283 "
           pdb=" C   TRP A1283 "
           pdb=" N   PRO A1284 "
           pdb=" CA  PRO A1284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.73   32.27     0      5.00e+00 4.00e-02 4.16e+01
  dihedral pdb=" CA  PHE A 196 "
           pdb=" C   PHE A 196 "
           pdb=" N   PHE A 197 "
           pdb=" CA  PHE A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.37  -25.63     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 6685 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 1697
       0.102 -    0.204: 63
       0.204 -    0.306: 3
       0.306 -    0.409: 2
       0.409 -    0.511: 3
  Chirality restraints: 1768
  Sorted by residual:
  chirality pdb=" C15 U38 A1601 "
            pdb=" C14 U38 A1601 "
            pdb=" C16 U38 A1601 "
            pdb=" C19 U38 A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.38    2.89   -0.51 2.00e-01 2.50e+01 6.52e+00
  chirality pdb=" C22 U38 A1602 "
            pdb=" C14 U38 A1602 "
            pdb=" C21 U38 A1602 "
            pdb=" C23 U38 A1602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.92   -0.45 2.00e-01 2.50e+01 5.06e+00
  chirality pdb=" C22 U38 A1601 "
            pdb=" C14 U38 A1601 "
            pdb=" C21 U38 A1601 "
            pdb=" C23 U38 A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.92   -0.45 2.00e-01 2.50e+01 5.02e+00
  ... (remaining 1765 not shown)

  Planarity restraints: 1883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1245 "   -1.007 9.50e-02 1.11e+02   4.51e-01 1.23e+02
        pdb=" NE  ARG A1245 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1245 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1245 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1245 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A1283 "   -0.065 5.00e-02 4.00e+02   9.87e-02 1.56e+01
        pdb=" N   PRO A1284 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO A1284 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A1284 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 205 "   -0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO A 206 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1880 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 381
        2.70 -     3.25: 12029
        3.25 -     3.80: 17578
        3.80 -     4.35: 22027
        4.35 -     4.90: 34946
  Nonbonded interactions: 86961
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 364 "
            pdb=" OE1 GLU A1200 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OD1 ASP A 416 "
            pdb=" OG  SER A 598 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG1 THR A 383 "
            pdb=" OE1 GLN A1182 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   SER A 844 "
            pdb=" ND2 ASN A 847 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   HIS A1050 "
            pdb=" NH1 ARG A1054 "
     model   vdw
     2.196 3.120
  ... (remaining 86956 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     27.980
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
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      :  0.011   0.679  11115  Z= 0.871
  Angle     :  0.850  12.144  15128  Z= 0.440
  Chirality :  0.052   0.511   1768
  Planarity :  0.012   0.451   1883
  Dihedral  : 15.684 122.116   4108
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.17 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.22), residues: 1369
  helix: -1.37 (0.18), residues: 812
  sheet: -0.87 (0.62), residues: 76
  loop : -1.68 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 431 
 HIS   0.004   0.001   HIS A 177 
 PHE   0.028   0.002   PHE A  89 
 TYR   0.017   0.002   TYR A  90 
 ARG   0.007   0.001   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17817 (  512)
  hydrogen bonds       : angle       7.32454 ( 1476)
  covalent geometry    : bond        0.00761 (11113)
  covalent geometry    : angle       0.84990 (15128)
  Misc. bond           : bond        0.58600 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  459 MET cc_start: 0.7916 (mmt) cc_final: 0.7295 (mmt)
REVERT: A  493 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A  496 ASN cc_start: 0.8682 (m-40) cc_final: 0.8352 (m-40)
REVERT: A  504 TYR cc_start: 0.8447 (p90) cc_final: 0.7900 (p90)
REVERT: A  540 MET cc_start: 0.8023 (mmm) cc_final: 0.7004 (mmm)
REVERT: A  820 PHE cc_start: 0.7268 (t80) cc_final: 0.6325 (t80)
REVERT: A  835 TYR cc_start: 0.7405 (t80) cc_final: 0.7157 (t80)
REVERT: A 1294 TYR cc_start: 0.7911 (t80) cc_final: 0.7053 (t80)
REVERT: A 1472 PHE cc_start: 0.7862 (m-80) cc_final: 0.7625 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 194
  average time/residue: 0.2021
  time to fit residues: 58.6569
Evaluate side-chains
  146 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1245 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 55 optimal weight:    0.3980
   chunk 107 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 428 ASN
A1165 ASN
A1430 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.152232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.106298 restraints weight = 18225.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106536 restraints weight = 11085.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106726 restraints weight = 7834.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11115  Z= 0.153
  Angle     :  0.741   9.878  15128  Z= 0.372
  Chirality :  0.045   0.188   1768
  Planarity :  0.005   0.096   1883
  Dihedral  :  8.663 101.197   1623
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.90 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.22), residues: 1369
  helix: -1.02 (0.18), residues: 840
  sheet: -0.66 (0.65), residues: 71
  loop : -1.87 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1242 
 HIS   0.006   0.001   HIS A1050 
 PHE   0.027   0.002   PHE A1111 
 TYR   0.012   0.001   TYR A  90 
 ARG   0.005   0.000   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04839 (  512)
  hydrogen bonds       : angle       5.28728 ( 1476)
  covalent geometry    : bond        0.00327 (11113)
  covalent geometry    : angle       0.74057 (15128)
  Misc. bond           : bond        0.00291 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LYS cc_start: 0.8274 (pttm) cc_final: 0.7859 (tptt)
REVERT: A  171 PHE cc_start: 0.8023 (t80) cc_final: 0.7696 (t80)
REVERT: A  493 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: A  496 ASN cc_start: 0.8866 (m-40) cc_final: 0.8581 (m-40)
REVERT: A  504 TYR cc_start: 0.8430 (p90) cc_final: 0.7854 (p90)
REVERT: A  513 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: A  687 MET cc_start: 0.7297 (mmp) cc_final: 0.6946 (mmp)
REVERT: A 1094 PHE cc_start: 0.8642 (t80) cc_final: 0.8193 (t80)
REVERT: A 1105 MET cc_start: 0.8256 (mmm) cc_final: 0.8005 (mmm)
REVERT: A 1294 TYR cc_start: 0.7628 (t80) cc_final: 0.7376 (t80)
REVERT: A 1449 LEU cc_start: 0.9041 (tt) cc_final: 0.8336 (mp)
REVERT: A 1472 PHE cc_start: 0.7912 (m-80) cc_final: 0.7619 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 173
  average time/residue: 0.1881
  time to fit residues: 49.0342
Evaluate side-chains
  154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue 1098 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0670
   chunk 94 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0770
   chunk 86 optimal weight:    0.9980
   chunk 131 optimal weight:    0.0670
   chunk 55 optimal weight:    0.8980
   chunk 128 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.4214

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A1165 ASN
A1312 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.154757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.109342 restraints weight = 18296.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.109651 restraints weight = 10865.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.110007 restraints weight = 8040.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11115  Z= 0.125
  Angle     :  0.691  10.623  15128  Z= 0.341
  Chirality :  0.044   0.189   1768
  Planarity :  0.005   0.096   1883
  Dihedral  :  6.755 109.617   1619
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.14 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.23), residues: 1369
  helix: -0.81 (0.18), residues: 845
  sheet: -0.50 (0.66), residues: 71
  loop : -1.79 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 241 
 HIS   0.007   0.001   HIS A1050 
 PHE   0.026   0.002   PHE A 820 
 TYR   0.021   0.001   TYR A 835 
 ARG   0.004   0.000   ARG A1278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  512)
  hydrogen bonds       : angle       4.70086 ( 1476)
  covalent geometry    : bond        0.00267 (11113)
  covalent geometry    : angle       0.69117 (15128)
  Misc. bond           : bond        0.00080 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.6305 (ttt) cc_final: 0.6022 (ttp)
REVERT: A  155 LYS cc_start: 0.8275 (pttm) cc_final: 0.7835 (tptt)
REVERT: A  171 PHE cc_start: 0.8106 (t80) cc_final: 0.7835 (t80)
REVERT: A  421 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7964 (ptm)
REVERT: A  459 MET cc_start: 0.7776 (mtt) cc_final: 0.7466 (mtt)
REVERT: A  496 ASN cc_start: 0.8860 (m-40) cc_final: 0.8593 (m-40)
REVERT: A  504 TYR cc_start: 0.8402 (p90) cc_final: 0.7772 (p90)
REVERT: A  678 MET cc_start: 0.8291 (ttt) cc_final: 0.7878 (mtp)
REVERT: A  679 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7585 (pm20)
REVERT: A 1094 PHE cc_start: 0.8694 (t80) cc_final: 0.8320 (t80)
REVERT: A 1105 MET cc_start: 0.8258 (mmm) cc_final: 0.8029 (mmm)
REVERT: A 1110 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: A 1195 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8050 (tp)
REVERT: A 1232 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7409 (m-10)
REVERT: A 1449 LEU cc_start: 0.9052 (tt) cc_final: 0.8431 (mt)
REVERT: A 1472 PHE cc_start: 0.7780 (m-80) cc_final: 0.7565 (m-80)
  outliers start: 25
  outliers final: 13
  residues processed: 192
  average time/residue: 0.1959
  time to fit residues: 57.2279
Evaluate side-chains
  175 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  847 ASN
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1165 ASN
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1336 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 104 optimal weight:    0.0370
   chunk 57 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0010
   chunk 108 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.4466

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

Flipped N/Q/H residues before XYZ refinement:
A 560 ASN
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.154815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.109282 restraints weight = 18284.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.108117 restraints weight = 10750.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.109276 restraints weight = 7951.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11115  Z= 0.123
  Angle     :  0.674  11.189  15128  Z= 0.330
  Chirality :  0.043   0.171   1768
  Planarity :  0.005   0.094   1883
  Dihedral  :  6.463 116.650   1619
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.71 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.23), residues: 1369
  helix: -0.70 (0.18), residues: 849
  sheet: -0.18 (0.68), residues: 70
  loop : -1.74 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 991 
 HIS   0.005   0.001   HIS A1050 
 PHE   0.022   0.001   PHE A 820 
 TYR   0.015   0.001   TYR A1294 
 ARG   0.003   0.000   ARG A1278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  512)
  hydrogen bonds       : angle       4.47798 ( 1476)
  covalent geometry    : bond        0.00263 (11113)
  covalent geometry    : angle       0.67434 (15128)
  Misc. bond           : bond        0.00058 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8624 (tt) cc_final: 0.8190 (mm)
REVERT: A   74 MET cc_start: 0.6326 (ttt) cc_final: 0.6107 (ttp)
REVERT: A  155 LYS cc_start: 0.8198 (pttm) cc_final: 0.7789 (tptt)
REVERT: A  171 PHE cc_start: 0.8083 (t80) cc_final: 0.7821 (t80)
REVERT: A  247 ASP cc_start: 0.7667 (t0) cc_final: 0.7460 (t0)
REVERT: A  459 MET cc_start: 0.7719 (mtt) cc_final: 0.7473 (mtt)
REVERT: A  496 ASN cc_start: 0.8882 (m-40) cc_final: 0.8419 (m-40)
REVERT: A  504 TYR cc_start: 0.8375 (p90) cc_final: 0.7783 (p90)
REVERT: A  551 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9221 (mm)
REVERT: A 1094 PHE cc_start: 0.8693 (t80) cc_final: 0.8255 (t80)
REVERT: A 1110 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7722 (tt)
REVERT: A 1145 SER cc_start: 0.8973 (m) cc_final: 0.8656 (p)
REVERT: A 1195 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8064 (tp)
REVERT: A 1232 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7418 (m-10)
REVERT: A 1449 LEU cc_start: 0.9060 (tt) cc_final: 0.8451 (mt)
REVERT: A 1472 PHE cc_start: 0.7833 (m-80) cc_final: 0.7581 (m-80)
  outliers start: 31
  outliers final: 15
  residues processed: 193
  average time/residue: 0.1894
  time to fit residues: 55.7943
Evaluate side-chains
  183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1336 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:   30.0000
   chunk 85 optimal weight:    5.9990
   chunk 117 optimal weight:    0.0470
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.151871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.105546 restraints weight = 18227.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.104475 restraints weight = 10899.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105678 restraints weight = 8007.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11115  Z= 0.183
  Angle     :  0.705  10.450  15128  Z= 0.351
  Chirality :  0.045   0.167   1768
  Planarity :  0.005   0.093   1883
  Dihedral  :  6.590 120.377   1619
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.15 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.23), residues: 1369
  helix: -0.65 (0.18), residues: 850
  sheet: -0.34 (0.66), residues: 70
  loop : -1.77 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1242 
 HIS   0.006   0.001   HIS A1050 
 PHE   0.017   0.002   PHE A 544 
 TYR   0.013   0.001   TYR A 231 
 ARG   0.005   0.000   ARG A1431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  512)
  hydrogen bonds       : angle       4.53139 ( 1476)
  covalent geometry    : bond        0.00418 (11113)
  covalent geometry    : angle       0.70467 (15128)
  Misc. bond           : bond        0.00053 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.6361 (ttt) cc_final: 0.6136 (ttp)
REVERT: A  155 LYS cc_start: 0.8218 (pttm) cc_final: 0.7818 (tptt)
REVERT: A  171 PHE cc_start: 0.8105 (t80) cc_final: 0.7864 (t80)
REVERT: A  496 ASN cc_start: 0.8914 (m-40) cc_final: 0.8609 (m-40)
REVERT: A  504 TYR cc_start: 0.8490 (p90) cc_final: 0.7587 (p90)
REVERT: A  551 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9311 (mm)
REVERT: A  572 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.9008 (p)
REVERT: A  635 THR cc_start: 0.8373 (m) cc_final: 0.7486 (m)
REVERT: A 1110 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: A 1145 SER cc_start: 0.9036 (m) cc_final: 0.8706 (p)
REVERT: A 1195 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8100 (tp)
REVERT: A 1232 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7568 (m-10)
REVERT: A 1449 LEU cc_start: 0.9038 (tt) cc_final: 0.8411 (mt)
REVERT: A 1472 PHE cc_start: 0.8046 (m-80) cc_final: 0.7714 (m-80)
  outliers start: 37
  outliers final: 22
  residues processed: 192
  average time/residue: 0.1889
  time to fit residues: 55.5008
Evaluate side-chains
  183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1075 ASP
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1336 LEU
Chi-restraints excluded: chain A residue 1371 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 129 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 116 optimal weight:   20.0000
   chunk 50 optimal weight:    0.4980
   chunk 107 optimal weight:    4.9990
   chunk 133 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 ASN
A1314 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.150195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104498 restraints weight = 18506.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.104137 restraints weight = 11225.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.105041 restraints weight = 8400.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11115  Z= 0.214
  Angle     :  0.734  11.122  15128  Z= 0.361
  Chirality :  0.046   0.159   1768
  Planarity :  0.005   0.092   1883
  Dihedral  :  6.749 122.311   1619
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.26 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.23), residues: 1369
  helix: -0.64 (0.18), residues: 847
  sheet: -0.67 (0.63), residues: 77
  loop : -1.78 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1242 
 HIS   0.007   0.001   HIS A1050 
 PHE   0.022   0.002   PHE A 820 
 TYR   0.013   0.001   TYR A 207 
 ARG   0.006   0.000   ARG A1278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  512)
  hydrogen bonds       : angle       4.57323 ( 1476)
  covalent geometry    : bond        0.00490 (11113)
  covalent geometry    : angle       0.73433 (15128)
  Misc. bond           : bond        0.00056 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 167
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.6535 (ttt) cc_final: 0.5017 (mmt)
REVERT: A  155 LYS cc_start: 0.8178 (pttm) cc_final: 0.7770 (tptt)
REVERT: A  171 PHE cc_start: 0.8126 (t80) cc_final: 0.7907 (t80)
REVERT: A  496 ASN cc_start: 0.8832 (m-40) cc_final: 0.8478 (m110)
REVERT: A  504 TYR cc_start: 0.8377 (p90) cc_final: 0.7629 (p90)
REVERT: A  551 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9349 (mm)
REVERT: A  635 THR cc_start: 0.7746 (m) cc_final: 0.7473 (m)
REVERT: A 1110 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (tt)
REVERT: A 1145 SER cc_start: 0.9168 (m) cc_final: 0.8873 (p)
REVERT: A 1195 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8180 (tp)
REVERT: A 1232 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7708 (m-10)
REVERT: A 1449 LEU cc_start: 0.9024 (tt) cc_final: 0.8430 (mt)
REVERT: A 1472 PHE cc_start: 0.7909 (m-80) cc_final: 0.7673 (m-80)
  outliers start: 39
  outliers final: 23
  residues processed: 190
  average time/residue: 0.1926
  time to fit residues: 56.0248
Evaluate side-chains
  185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1249 ASP
Chi-restraints excluded: chain A residue 1336 LEU
Chi-restraints excluded: chain A residue 1371 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 103 optimal weight:    0.4980
   chunk 87 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 120 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.151859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106148 restraints weight = 18568.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.106393 restraints weight = 11266.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.107162 restraints weight = 8208.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11115  Z= 0.160
  Angle     :  0.713  11.975  15128  Z= 0.346
  Chirality :  0.045   0.174   1768
  Planarity :  0.005   0.093   1883
  Dihedral  :  6.622 124.221   1619
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.19 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.23), residues: 1369
  helix: -0.56 (0.18), residues: 850
  sheet: -0.77 (0.62), residues: 78
  loop : -1.72 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1242 
 HIS   0.009   0.001   HIS A1050 
 PHE   0.022   0.002   PHE A 820 
 TYR   0.011   0.001   TYR A 207 
 ARG   0.003   0.000   ARG A1278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  512)
  hydrogen bonds       : angle       4.43402 ( 1476)
  covalent geometry    : bond        0.00363 (11113)
  covalent geometry    : angle       0.71336 (15128)
  Misc. bond           : bond        0.00051 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.6577 (ttt) cc_final: 0.5191 (mmt)
REVERT: A  155 LYS cc_start: 0.8306 (pttm) cc_final: 0.7835 (tptt)
REVERT: A  165 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7664 (tt)
REVERT: A  171 PHE cc_start: 0.8106 (t80) cc_final: 0.7901 (t80)
REVERT: A  496 ASN cc_start: 0.8820 (m-40) cc_final: 0.8464 (m110)
REVERT: A  504 TYR cc_start: 0.8352 (p90) cc_final: 0.7653 (p90)
REVERT: A  551 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9292 (mm)
REVERT: A  678 MET cc_start: 0.8231 (tpp) cc_final: 0.7889 (tpt)
REVERT: A 1110 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (tt)
REVERT: A 1145 SER cc_start: 0.9170 (m) cc_final: 0.8845 (p)
REVERT: A 1195 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8149 (tp)
REVERT: A 1232 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7655 (m-10)
REVERT: A 1449 LEU cc_start: 0.8959 (tt) cc_final: 0.8383 (mt)
  outliers start: 38
  outliers final: 22
  residues processed: 189
  average time/residue: 0.1994
  time to fit residues: 56.9610
Evaluate side-chains
  185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1336 LEU
Chi-restraints excluded: chain A residue 1371 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 126 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 131 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0030
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 250 GLN
A 560 ASN
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106661 restraints weight = 18721.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.105846 restraints weight = 11377.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105995 restraints weight = 9066.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11115  Z= 0.128
  Angle     :  0.699  12.334  15128  Z= 0.334
  Chirality :  0.043   0.165   1768
  Planarity :  0.005   0.093   1883
  Dihedral  :  6.480 125.894   1619
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.62 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.23), residues: 1369
  helix: -0.45 (0.18), residues: 850
  sheet: -0.53 (0.64), residues: 71
  loop : -1.65 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 241 
 HIS   0.008   0.001   HIS A1050 
 PHE   0.021   0.001   PHE A1472 
 TYR   0.015   0.001   TYR A1294 
 ARG   0.007   0.000   ARG A1054 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  512)
  hydrogen bonds       : angle       4.32040 ( 1476)
  covalent geometry    : bond        0.00284 (11113)
  covalent geometry    : angle       0.69930 (15128)
  Misc. bond           : bond        0.00049 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8556 (tt) cc_final: 0.8090 (mm)
REVERT: A   74 MET cc_start: 0.6323 (ttt) cc_final: 0.5067 (mmt)
REVERT: A  155 LYS cc_start: 0.8368 (pttm) cc_final: 0.7933 (tptt)
REVERT: A  165 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7562 (tt)
REVERT: A  171 PHE cc_start: 0.8147 (t80) cc_final: 0.7902 (t80)
REVERT: A  496 ASN cc_start: 0.8921 (m-40) cc_final: 0.8505 (m110)
REVERT: A  504 TYR cc_start: 0.8365 (p90) cc_final: 0.7597 (p90)
REVERT: A  551 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9243 (mm)
REVERT: A  678 MET cc_start: 0.8293 (tpp) cc_final: 0.8019 (tpt)
REVERT: A 1145 SER cc_start: 0.9064 (m) cc_final: 0.8741 (p)
REVERT: A 1195 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8063 (tp)
REVERT: A 1232 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7555 (m-10)
REVERT: A 1449 LEU cc_start: 0.8947 (tt) cc_final: 0.8404 (pp)
  outliers start: 34
  outliers final: 22
  residues processed: 194
  average time/residue: 0.2319
  time to fit residues: 68.2236
Evaluate side-chains
  186 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1249 ASP
Chi-restraints excluded: chain A residue 1336 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0040
   chunk 67 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.9994

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

Flipped N/Q/H residues before XYZ refinement:
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.153603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.109575 restraints weight = 18284.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.108627 restraints weight = 10866.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.108446 restraints weight = 9001.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11115  Z= 0.143
  Angle     :  0.714  12.385  15128  Z= 0.343
  Chirality :  0.044   0.174   1768
  Planarity :  0.004   0.091   1883
  Dihedral  :  6.488 127.784   1619
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.72 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1369
  helix: -0.39 (0.18), residues: 852
  sheet: -0.81 (0.60), residues: 78
  loop : -1.62 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 241 
 HIS   0.007   0.001   HIS A1050 
 PHE   0.019   0.001   PHE A 105 
 TYR   0.011   0.001   TYR A  90 
 ARG   0.005   0.000   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  512)
  hydrogen bonds       : angle       4.28493 ( 1476)
  covalent geometry    : bond        0.00326 (11113)
  covalent geometry    : angle       0.71442 (15128)
  Misc. bond           : bond        0.00040 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8571 (tt) cc_final: 0.8081 (mm)
REVERT: A   74 MET cc_start: 0.6454 (ttt) cc_final: 0.5145 (mmt)
REVERT: A  155 LYS cc_start: 0.8341 (pttm) cc_final: 0.7882 (tptt)
REVERT: A  165 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7576 (tt)
REVERT: A  171 PHE cc_start: 0.8155 (t80) cc_final: 0.7950 (t80)
REVERT: A  493 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: A  496 ASN cc_start: 0.8852 (m-40) cc_final: 0.8461 (m110)
REVERT: A  504 TYR cc_start: 0.8336 (p90) cc_final: 0.7580 (p90)
REVERT: A  551 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9278 (mm)
REVERT: A  678 MET cc_start: 0.8295 (tpp) cc_final: 0.7940 (tpt)
REVERT: A 1110 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7813 (tt)
REVERT: A 1145 SER cc_start: 0.9032 (m) cc_final: 0.8722 (p)
REVERT: A 1195 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8119 (tp)
REVERT: A 1232 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7554 (m-10)
REVERT: A 1336 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9179 (mm)
REVERT: A 1449 LEU cc_start: 0.8917 (tt) cc_final: 0.8431 (pp)
  outliers start: 30
  outliers final: 22
  residues processed: 182
  average time/residue: 0.1946
  time to fit residues: 53.0910
Evaluate side-chains
  184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1110 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1249 ASP
Chi-restraints excluded: chain A residue 1336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 119 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 128 optimal weight:    3.9990
   chunk 104 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0570
   chunk 77 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 560 ASN
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.155639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.110196 restraints weight = 18248.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.109181 restraints weight = 10290.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.110414 restraints weight = 7805.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11115  Z= 0.122
  Angle     :  0.708  12.585  15128  Z= 0.335
  Chirality :  0.043   0.166   1768
  Planarity :  0.004   0.089   1883
  Dihedral  :  6.345 129.680   1619
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.72 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.23), residues: 1369
  helix: -0.30 (0.18), residues: 842
  sheet: -0.79 (0.60), residues: 76
  loop : -1.56 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 241 
 HIS   0.007   0.001   HIS A1050 
 PHE   0.016   0.001   PHE A 105 
 TYR   0.016   0.001   TYR A1294 
 ARG   0.005   0.000   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  512)
  hydrogen bonds       : angle       4.19110 ( 1476)
  covalent geometry    : bond        0.00270 (11113)
  covalent geometry    : angle       0.70794 (15128)
  Misc. bond           : bond        0.00063 (    2)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8545 (tt) cc_final: 0.8068 (mm)
REVERT: A   74 MET cc_start: 0.6480 (ttt) cc_final: 0.5181 (mmt)
REVERT: A  155 LYS cc_start: 0.8332 (pttm) cc_final: 0.7874 (tptt)
REVERT: A  165 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7542 (tt)
REVERT: A  411 ASN cc_start: 0.8984 (t0) cc_final: 0.8232 (t0)
REVERT: A  421 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7809 (ptm)
REVERT: A  493 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: A  496 ASN cc_start: 0.8855 (m-40) cc_final: 0.8144 (m110)
REVERT: A  504 TYR cc_start: 0.8167 (p90) cc_final: 0.7477 (p90)
REVERT: A  551 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9237 (mm)
REVERT: A  678 MET cc_start: 0.8295 (tpp) cc_final: 0.7919 (tpt)
REVERT: A 1094 PHE cc_start: 0.8815 (t80) cc_final: 0.8378 (t80)
REVERT: A 1145 SER cc_start: 0.8960 (m) cc_final: 0.8661 (p)
REVERT: A 1195 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8170 (tp)
REVERT: A 1232 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7447 (m-10)
REVERT: A 1278 ARG cc_start: 0.8013 (mmp-170) cc_final: 0.6979 (mmp80)
REVERT: A 1336 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9176 (mm)
REVERT: A 1449 LEU cc_start: 0.8905 (tt) cc_final: 0.8452 (pp)
  outliers start: 31
  outliers final: 20
  residues processed: 198
  average time/residue: 0.1933
  time to fit residues: 57.9440
Evaluate side-chains
  189 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   89 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue 1112 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1249 ASP
Chi-restraints excluded: chain A residue 1336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 94 optimal weight:    0.1980
   chunk 39 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 124 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 128 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A 614 GLN
** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1182 GLN
** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.155367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.112527 restraints weight = 18229.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.110726 restraints weight = 10932.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.110765 restraints weight = 9189.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11115  Z= 0.131
  Angle     :  0.716  12.514  15128  Z= 0.339
  Chirality :  0.044   0.163   1768
  Planarity :  0.005   0.088   1883
  Dihedral  :  6.354 131.676   1619
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.74 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.23), residues: 1369
  helix: -0.25 (0.18), residues: 843
  sheet: -0.78 (0.60), residues: 76
  loop : -1.50 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 431 
 HIS   0.006   0.001   HIS A1050 
 PHE   0.030   0.001   PHE A1059 
 TYR   0.011   0.001   TYR A  90 
 ARG   0.005   0.000   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  512)
  hydrogen bonds       : angle       4.15879 ( 1476)
  covalent geometry    : bond        0.00296 (11113)
  covalent geometry    : angle       0.71587 (15128)
  Misc. bond           : bond        0.00043 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3373.48 seconds
wall clock time: 59 minutes 22.33 seconds (3562.33 seconds total)