Starting phenix.real_space_refine
on Wed Jan 22 03:09:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ffb_50353/01_2025/9ffb_50353.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 491 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      42      5.49       5
     S      96      5.16       5
     C   10940      2.51       5
     N    2905      2.21       5
     O    3272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 17255
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "S"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 453
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "T"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 407
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 8884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1118, 8884
          Classifications: {'peptide': 1118}
          Link IDs: {'PTRANS': 46, 'TRANS': 1071}
          Chain breaks: 10
    Chain: "B"
      Number of atoms: 7511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 948, 7511
          Classifications: {'peptide': 948}
          Link IDs: {'PTRANS': 27, 'TRANS': 920}
          Chain breaks: 12
  Residues with excluded nonbonded symmetry interactions: 70
    residue:
      pdb=" N   ARG A  55 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  55 " occ=0.00
    residue:
      pdb=" N   ILE A  60 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD1 ILE A  60 " occ=0.19
    residue:
      pdb=" N   GLY A  64 " occ=0.48
      ... (2 atoms not shown)
      pdb=" O   GLY A  64 " occ=0.00
    residue:
      pdb=" N   GLU A  65 " occ=0.45
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  65 " occ=0.82
    residue:
      pdb=" N   GLU A  69 " occ=0.29
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  69 " occ=0.61
    residue:
      pdb=" N   ASP A  73 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  73 " occ=0.00
    residue:
      pdb=" N   SER A  90 " occ=0.09
      ... (4 atoms not shown)
      pdb=" OG  SER A  90 " occ=0.36
    residue:
      pdb=" N   PRO A  92 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO A  92 " occ=0.00
    residue:
      pdb=" N   GLY A  93 " occ=0.33
      ... (2 atoms not shown)
      pdb=" O   GLY A  93 " occ=0.00
    residue:
      pdb=" N   VAL A  94 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 VAL A  94 " occ=0.71
    residue:
      pdb=" N   GLU A  97 " occ=0.97
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  97 " occ=0.60
    residue:
      pdb=" N   ASN A 114 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN A 114 " occ=0.35
    ... (remaining 58 not shown)
  Time building chain proxies: 10.37, per 1000 atoms: 0.60
  Number of scatterers: 17255
  At special positions: 0
  Unit cell: (109.692, 169.524, 133.791, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     P      42     15.00
     O    3272      8.00
     N    2905      7.00
     C   10940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.74
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  4034 Ramachandran restraints generated.
    2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3968

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 2 sheets defined
      76.7% alpha, 0.5% beta
      8 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 5.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 76 through 88
    Processing helix  chain 'A' and resid 91 through 107
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 3.669A  pdb=" N   LEU A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 144
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 148 through 160
      removed outlier: 3.927A  pdb=" N   VAL A 153 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 3.675A  pdb=" N   LYS A 197 " --> pdb=" O   GLN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 222
      Proline residue:  A 219  - end of helix
      removed outlier: 3.545A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 241
    Processing helix  chain 'A' and resid 244 through 255
      removed outlier: 4.032A  pdb=" N   ILE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 272
      removed outlier: 3.687A  pdb=" N   LYS A 264 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 4.374A  pdb=" N   VAL A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 4.143A  pdb=" N   SER A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 360
      removed outlier: 4.121A  pdb=" N   GLN A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 378
      removed outlier: 3.735A  pdb=" N   ASN A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   SER A 376 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 394
    Processing helix  chain 'A' and resid 400 through 413
    Processing helix  chain 'A' and resid 417 through 427
    Processing helix  chain 'A' and resid 428 through 431
    Processing helix  chain 'A' and resid 433 through 446
      removed outlier: 4.382A  pdb=" N   ILE A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   LEU A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLN A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   THR A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   PHE A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 466
      removed outlier: 4.265A  pdb=" N   VAL A 454 " --> pdb=" O   HIS A 450 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 486
    Processing helix  chain 'A' and resid 488 through 506
      removed outlier: 3.620A  pdb=" N   LEU A 492 " --> pdb=" O   ASN A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 524
      removed outlier: 4.363A  pdb=" N   LEU A 510 " --> pdb=" O   HIS A 506 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   THR A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   PHE A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 540
      removed outlier: 3.985A  pdb=" N   TYR A 537 " --> pdb=" O   ARG A 533 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 564
    Processing helix  chain 'A' and resid 570 through 588
      removed outlier: 4.081A  pdb=" N   GLN A 574 " --> pdb=" O   PRO A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 626 through 644
      removed outlier: 3.664A  pdb=" N   LEU A 630 " --> pdb=" O   THR A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 657
    Processing helix  chain 'A' and resid 659 through 664
      removed outlier: 3.874A  pdb=" N   PHE A 664 " --> pdb=" O   LEU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 747
      removed outlier: 3.727A  pdb=" N   ARG A 737 " --> pdb=" O   SER A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 758
      removed outlier: 3.650A  pdb=" N   LEU A 758 " --> pdb=" O   ASP A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 776
      removed outlier: 3.546A  pdb=" N   VAL A 769 " --> pdb=" O   ASP A 766 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU A 770 " --> pdb=" O   LEU A 767 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP A 774 " --> pdb=" O   GLY A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 803
      removed outlier: 3.609A  pdb=" N   SER A 786 " --> pdb=" O   GLU A 782 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   CYS A 803 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 835
      removed outlier: 3.941A  pdb=" N   LYS A 830 " --> pdb=" O   ASN A 826 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS A 831 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 924
    Processing helix  chain 'A' and resid 931 through 935
    Processing helix  chain 'A' and resid 961 through 979
      removed outlier: 3.886A  pdb=" N   TRP A 973 " --> pdb=" O   ASP A 969 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS A 974 " --> pdb=" O   ASP A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1018
    Processing helix  chain 'A' and resid 1019 through 1036
      removed outlier: 3.889A  pdb=" N   VAL A1036 " --> pdb=" O   TYR A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1072
      removed outlier: 3.718A  pdb=" N   LEU A1055 " --> pdb=" O   GLN A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1078
    Processing helix  chain 'A' and resid 1079 through 1080
      No H-bonds generated for 'chain 'A' and resid 1079 through 1080'
    Processing helix  chain 'A' and resid 1081 through 1097
    Processing helix  chain 'A' and resid 1105 through 1118
    Processing helix  chain 'A' and resid 1126 through 1141
    Processing helix  chain 'A' and resid 1146 through 1163
    Processing helix  chain 'A' and resid 1176 through 1193
    Processing helix  chain 'A' and resid 1195 through 1206
    Processing helix  chain 'A' and resid 1208 through 1214
    Processing helix  chain 'A' and resid 1230 through 1248
      removed outlier: 3.873A  pdb=" N   PHE A1234 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1285
      removed outlier: 3.848A  pdb=" N   LEU A1266 " --> pdb=" O   LEU A1262 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A1267 " --> pdb=" O   GLU A1263 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   TRP A1268 " --> pdb=" O   LYS A1264 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A1283 " --> pdb=" O   ILE A1279 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL A1284 " --> pdb=" O   ASN A1280 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A1285 " --> pdb=" O   LEU A1281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1287 through 1320
      removed outlier: 3.680A  pdb=" N   LYS A1296 " --> pdb=" O   SER A1292 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   MET A1310 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
      Proline residue:  A1311  - end of helix
      removed outlier: 3.866A  pdb=" N   HIS A1315 " --> pdb=" O   PRO A1311 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LYS A1318 " --> pdb=" O   ASP A1314 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LYS A1319 " --> pdb=" O   HIS A1315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1348
      removed outlier: 4.527A  pdb=" N   GLN A1337 " --> pdb=" O   LEU A1333 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LEU A1338 " --> pdb=" O   SER A1334 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   HIS A1339 " --> pdb=" O   THR A1335 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   HIS A1340 " --> pdb=" O   ARG A1336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1353 through 1355
      No H-bonds generated for 'chain 'A' and resid 1353 through 1355'
    Processing helix  chain 'A' and resid 1356 through 1378
      removed outlier: 3.551A  pdb=" N   LEU A1360 " --> pdb=" O   HIS A1356 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A1372 " --> pdb=" O   VAL A1368 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN A1378 " --> pdb=" O   MET A1374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 224
      removed outlier: 3.743A  pdb=" N   LYS B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 245
    Processing helix  chain 'B' and resid 264 through 284
      removed outlier: 3.751A  pdb=" N   VAL B 269 " --> pdb=" O   GLN B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 290
      removed outlier: 4.494A  pdb=" N   GLU B 289 " --> pdb=" O   GLN B 285 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLU B 290 " --> pdb=" O   ASP B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 285 through 290'
    Processing helix  chain 'B' and resid 293 through 302
    Processing helix  chain 'B' and resid 308 through 319
    Processing helix  chain 'B' and resid 324 through 349
    Processing helix  chain 'B' and resid 349 through 356
      removed outlier: 3.572A  pdb=" N   GLN B 353 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
      removed outlier: 3.629A  pdb=" N   VAL B 365 " --> pdb=" O   ASP B 361 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   VAL B 370 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LYS B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 396
      removed outlier: 4.375A  pdb=" N   GLU B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 435
    Processing helix  chain 'B' and resid 438 through 451
      removed outlier: 4.088A  pdb=" N   LEU B 451 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 472
      removed outlier: 3.990A  pdb=" N   ILE B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 483 through 491
      removed outlier: 3.577A  pdb=" N   ASP B 488 " --> pdb=" O   GLU B 485 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU B 490 " --> pdb=" O   PHE B 487 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER B 491 " --> pdb=" O   ASP B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 512
      Proline residue:  B 507  - end of helix
    Processing helix  chain 'B' and resid 512 through 528
      removed outlier: 4.295A  pdb=" N   PHE B 528 " --> pdb=" O   GLN B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 549
      removed outlier: 3.555A  pdb=" N   LEU B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 546 " --> pdb=" O   PHE B 542 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   ARG B 547 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE B 549 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 589
      removed outlier: 3.748A  pdb=" N   ILE B 589 " --> pdb=" O   PHE B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 597
      removed outlier: 4.576A  pdb=" N   LEU B 593 " --> pdb=" O   ILE B 589 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 616
      removed outlier: 4.487A  pdb=" N   MET B 606 " --> pdb=" O   ASP B 602 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   LEU B 607 " --> pdb=" O   VAL B 603 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   TYR B 608 " --> pdb=" O   ARG B 604 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU B 609 " --> pdb=" O   LEU B 605 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   TYR B 612 " --> pdb=" O   TYR B 608 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ASP B 613 " --> pdb=" O   GLU B 609 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL B 614 " --> pdb=" O   GLY B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 634
      removed outlier: 3.663A  pdb=" N   SER B 623 " --> pdb=" O   SER B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 637
      No H-bonds generated for 'chain 'B' and resid 635 through 637'
    Processing helix  chain 'B' and resid 648 through 652
    Processing helix  chain 'B' and resid 665 through 684
      removed outlier: 3.579A  pdb=" N   VAL B 684 " --> pdb=" O   TYR B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 3.624A  pdb=" N   LYS B 718 " --> pdb=" O   ARG B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 764
      removed outlier: 3.579A  pdb=" N   LEU B 756 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 767 through 786
      removed outlier: 3.638A  pdb=" N   ASP B 773 " --> pdb=" O   ASN B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 821
    Processing helix  chain 'B' and resid 830 through 836
      removed outlier: 3.816A  pdb=" N   VAL B 834 " --> pdb=" O   GLU B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 838 through 859
      removed outlier: 4.508A  pdb=" N   ALA B 849 " --> pdb=" O   ALA B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 869 through 891
      removed outlier: 3.633A  pdb=" N   MET B 873 " --> pdb=" O   ASN B 869 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ARG B 882 " --> pdb=" O   CYS B 878 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL B 883 " --> pdb=" O   LYS B 879 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE B 891 " --> pdb=" O   ARG B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 906 through 924
      removed outlier: 3.552A  pdb=" N   CYS B 910 " --> pdb=" O   ILE B 906 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 936
      removed outlier: 3.598A  pdb=" N   PHE B 932 " --> pdb=" O   ARG B 928 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B 936 " --> pdb=" O   PHE B 932 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 949 through 971
      removed outlier: 3.827A  pdb=" N   LYS B 953 " --> pdb=" O   ASN B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 976
      removed outlier: 3.583A  pdb=" N   PHE B 976 " --> pdb=" O   GLU B 973 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 977 through 992
      removed outlier: 3.654A  pdb=" N   THR B 981 " --> pdb=" O   ASN B 977 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 993 through 995
      No H-bonds generated for 'chain 'B' and resid 993 through 995'
    Processing helix  chain 'B' and resid 1000 through 1016
      removed outlier: 3.506A  pdb=" N   GLN B1004 " --> pdb=" O   GLN B1000 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1020 through 1035
      removed outlier: 3.601A  pdb=" N   CYS B1024 " --> pdb=" O   ASP B1020 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1041 through 1056
    Processing helix  chain 'B' and resid 1080 through 1106
      removed outlier: 4.211A  pdb=" N   LEU B1086 " --> pdb=" O   THR B1082 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1122 through 1146
      removed outlier: 3.518A  pdb=" N   GLY B1129 " --> pdb=" O   ALA B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1167
      removed outlier: 3.728A  pdb=" N   ASP B1156 " --> pdb=" O   GLY B1152 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B1167 " --> pdb=" O   SER B1163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1170 through 1176
    Processing helix  chain 'B' and resid 1177 through 1179
      No H-bonds generated for 'chain 'B' and resid 1177 through 1179'
    Processing helix  chain 'B' and resid 1188 through 1202
    Processing helix  chain 'B' and resid 1202 through 1222
      removed outlier: 3.643A  pdb=" N   SER B1208 " --> pdb=" O   PRO B1204 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE B1210 " --> pdb=" O   CYS B1206 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ASN B1215 " --> pdb=" O   THR B1211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1242 through 1247
    Processing helix  chain 'B' and resid 1251 through 1274
      removed outlier: 3.844A  pdb=" N   ASN B1255 " --> pdb=" O   LYS B1251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1293 through 1297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 685 through 687
      removed outlier: 3.507A  pdb=" N   LEU A 687 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1386 through 1389
      removed outlier: 4.612A  pdb=" N   SER B1287 " --> pdb=" O   LEU A1389 " (cutoff:3.500A)

    1042 hydrogen bonds defined for protein.
    3054 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      42 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 6.24

  Time building geometry restraints manager: 5.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.40: 6836
        1.40 -     1.58: 10564
        1.58 -     1.77: 88
        1.77 -     1.95: 141
        1.95 -     2.13: 5
  Bond restraints: 17634
  Sorted by residual:
  bond pdb=" C   ASN A 174 "
       pdb=" N   PHE A 175 "
    ideal  model  delta    sigma   weight residual
    1.331  2.003 -0.672 2.07e-02 2.33e+03 1.06e+03
  bond pdb=" CE2 PHE A 163 "
       pdb=" CZ  PHE A 163 "
    ideal  model  delta    sigma   weight residual
    1.382  2.134 -0.752 3.00e-02 1.11e+03 6.28e+02
  bond pdb=" CD1 PHE A 163 "
       pdb=" CE1 PHE A 163 "
    ideal  model  delta    sigma   weight residual
    1.382  2.125 -0.743 3.00e-02 1.11e+03 6.13e+02
  bond pdb=" CD2 PHE A 163 "
       pdb=" CE2 PHE A 163 "
    ideal  model  delta    sigma   weight residual
    1.382  2.120 -0.738 3.00e-02 1.11e+03 6.05e+02
  bond pdb=" CE1 PHE A 163 "
       pdb=" CZ  PHE A 163 "
    ideal  model  delta    sigma   weight residual
    1.382  2.059 -0.677 3.00e-02 1.11e+03 5.09e+02
  ... (remaining 17629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.78: 23926
        7.78 -    15.56: 69
       15.56 -    23.34: 1
       23.34 -    31.12: 0
       31.12 -    38.90: 1
  Bond angle restraints: 23997
  Sorted by residual:
  angle pdb=" C   ASN A 174 "
        pdb=" N   PHE A 175 "
        pdb=" CA  PHE A 175 "
      ideal   model   delta    sigma   weight residual
     121.80  160.70  -38.90 2.44e+00 1.68e-01 2.54e+02
  angle pdb=" CA  ASN A 174 "
        pdb=" C   ASN A 174 "
        pdb=" O   ASN A 174 "
      ideal   model   delta    sigma   weight residual
     120.80  105.50   15.30 1.70e+00 3.46e-01 8.10e+01
  angle pdb=" CA  PRO A 207 "
        pdb=" N   PRO A 207 "
        pdb=" CD  PRO A 207 "
      ideal   model   delta    sigma   weight residual
     112.00  101.99   10.01 1.40e+00 5.10e-01 5.11e+01
  angle pdb=" CA  PRO A1105 "
        pdb=" N   PRO A1105 "
        pdb=" CD  PRO A1105 "
      ideal   model   delta    sigma   weight residual
     112.00  103.51    8.49 1.40e+00 5.10e-01 3.68e+01
  angle pdb=" CA  ASN A 174 "
        pdb=" C   ASN A 174 "
        pdb=" N   PHE A 175 "
      ideal   model   delta    sigma   weight residual
     116.20  128.31  -12.11 2.00e+00 2.50e-01 3.67e+01
  ... (remaining 23992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.78: 10079
       35.78 -    71.55: 537
       71.55 -   107.33: 35
      107.33 -   143.10: 1
      143.10 -   178.88: 3
  Dihedral angle restraints: 10655
    sinusoidal: 4601
      harmonic: 6054
  Sorted by residual:
  dihedral pdb=" C4'  DT S  18 "
           pdb=" C3'  DT S  18 "
           pdb=" O3'  DT S  18 "
           pdb=" P    DC S  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.12  178.88     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC S   5 "
           pdb=" C3'  DC S   5 "
           pdb=" O3'  DC S   5 "
           pdb=" P    DT S   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   31.84 -171.84     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DA S  11 "
           pdb=" C3'  DA S  11 "
           pdb=" O3'  DA S  11 "
           pdb=" P    DG S  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   59.54  160.46     1      3.50e+01 8.16e-04 1.52e+01
  ... (remaining 10652 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 2779
       0.121 -    0.242: 26
       0.242 -    0.363: 3
       0.363 -    0.484: 18
       0.484 -    0.605: 5
  Chirality restraints: 2831
  Sorted by residual:
  chirality pdb=" P    DA T  49 "
            pdb=" OP1  DA T  49 "
            pdb=" OP2  DA T  49 "
            pdb=" O5'  DA T  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.61 2.00e-01 2.50e+01 9.16e+00
  chirality pdb=" P    DG S  12 "
            pdb=" OP1  DG S  12 "
            pdb=" OP2  DG S  12 "
            pdb=" O5'  DG S  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.94   -0.60 2.00e-01 2.50e+01 8.89e+00
  chirality pdb=" P    DG T  50 "
            pdb=" OP1  DG T  50 "
            pdb=" OP2  DG T  50 "
            pdb=" O5'  DG T  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.55 2.00e-01 2.50e+01 7.46e+00
  ... (remaining 2828 not shown)

  Planarity restraints: 2874
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 206 "    0.107 5.00e-02 4.00e+02   1.55e-01 3.85e+01
        pdb=" N   PRO A 207 "   -0.268 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "    0.083 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "    0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1104 "   -0.067 5.00e-02 4.00e+02   9.59e-02 1.47e+01
        pdb=" N   PRO A1105 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A1105 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A1105 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 175 "    0.058 5.00e-02 4.00e+02   8.69e-02 1.21e+01
        pdb=" N   PRO A 176 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 176 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 176 "    0.048 5.00e-02 4.00e+02
  ... (remaining 2871 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 217
        2.59 -     3.17: 15650
        3.17 -     3.75: 30274
        3.75 -     4.32: 37750
        4.32 -     4.90: 59082
  Nonbonded interactions: 142973
  Sorted by model distance:
  nonbonded pdb=" CD1 PHE A 163 "
            pdb=" N   PHE A 175 "
     model   vdw
     2.015 3.420
  nonbonded pdb=" CD2 PHE A 163 "
            pdb=" N   PHE A 175 "
     model   vdw
     2.036 3.420
  nonbonded pdb=" CG  PHE A 163 "
            pdb=" N   PHE A 175 "
     model   vdw
     2.050 3.340
  nonbonded pdb=" OD1 ASP B 361 "
            pdb=" OG1 THR B 363 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" CE1 PHE A 163 "
            pdb=" N   PHE A 175 "
     model   vdw
     2.073 3.420
  ... (remaining 142968 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.73
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.080
  Set scattering table:                    0.160
  Process input model:                     43.470
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
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      :  0.013   0.752  17634  Z= 0.786
  Angle     :  0.950  38.896  23997  Z= 0.442
  Chirality :  0.056   0.605   2831
  Planarity :  0.006   0.155   2874
  Dihedral  : 20.149 178.879   6687
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.45 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 31.82 %
    Favored  : 68.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.19), residues: 2017
  helix:  0.51 (0.14), residues: 1431
  sheet:  None (None), residues: 0
  loop : -2.34 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 794 
 HIS   0.008   0.001   HIS A 290 
 PHE   0.041   0.002   PHE A1067 
 TYR   0.018   0.001   TYR A 461 
 ARG   0.007   0.000   ARG A1370 

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

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

  4034 Ramachandran restraints generated.
    2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4034 Ramachandran restraints generated.
    2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 1.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.7502 (mpp) cc_final: 0.7279 (mpp)
REVERT: A 1127 PHE cc_start: 0.8488 (t80) cc_final: 0.8186 (t80)
REVERT: B  996 ASP cc_start: 0.8658 (p0) cc_final: 0.7869 (p0)
  outliers start: 3
  outliers final: 3
  residues processed: 118
  average time/residue: 0.2788
  time to fit residues: 53.3129
Evaluate side-chains
  115 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 1.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue 1005 GLN
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 176 optimal weight:    9.9990
   chunk 158 optimal weight:    0.1980
   chunk 87 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 163 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9990
   chunk 121 optimal weight:   20.0000
   chunk 189 optimal weight:    3.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 531 GLN
A1024 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1119 ASN
A1344 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.057574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.043756 restraints weight = 109696.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.044684 restraints weight = 54504.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.045296 restraints weight = 35397.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3194 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.739  17634  Z= 0.778
  Angle     :  0.759  38.475  23997  Z= 0.378
  Chirality :  0.040   0.165   2831
  Planarity :  0.005   0.085   2874
  Dihedral  : 16.664 179.256   2624
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.95 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.04 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.19), residues: 2018
  helix:  0.72 (0.14), residues: 1457
  sheet:  None (None), residues: 0
  loop : -2.41 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1073 
 HIS   0.006   0.001   HIS A 290 
 PHE   0.029   0.002   PHE A 163 
 TYR   0.013   0.001   TYR A1297 
 ARG   0.008   0.001   ARG B1160 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 123
  time to evaluate  : 1.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 MET cc_start: 0.8394 (ppp) cc_final: 0.8173 (ptm)
REVERT: A  461 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.7118 (m-80)
REVERT: A  538 ILE cc_start: 0.7937 (mm) cc_final: 0.7663 (tt)
REVERT: A  618 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5956 (tp)
REVERT: A 1127 PHE cc_start: 0.8608 (t80) cc_final: 0.8183 (t80)
REVERT: B  237 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8100 (t80)
REVERT: B  330 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.9001 (p0)
REVERT: B  363 THR cc_start: 0.9207 (p) cc_final: 0.9006 (p)
REVERT: B  440 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8012 (p)
REVERT: B  488 ASP cc_start: 0.9387 (p0) cc_final: 0.8761 (p0)
REVERT: B  528 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7448 (m-10)
REVERT: B  716 MET cc_start: 0.9547 (mmp) cc_final: 0.9126 (mmp)
REVERT: B  817 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8662 (mm)
REVERT: B  996 ASP cc_start: 0.8614 (p0) cc_final: 0.7896 (p0)
  outliers start: 62
  outliers final: 15
  residues processed: 181
  average time/residue: 0.2603
  time to fit residues: 75.7109
Evaluate side-chains
  140 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  381 LYS
Chi-restraints excluded: chain A residue  461 TYR
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  330 ASP
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 181 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 119 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 136 optimal weight:    1.9990
   chunk 200 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 182 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 GLN
A 644 GLN
A1005 GLN
** A1025 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.055892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.042105 restraints weight = 110097.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.043136 restraints weight = 63507.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.043112 restraints weight = 36187.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3194 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3247 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.750  17634  Z= 0.799
  Angle     :  0.782  38.685  23997  Z= 0.389
  Chirality :  0.042   0.337   2831
  Planarity :  0.005   0.089   2874
  Dihedral  : 16.610 177.539   2617
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.59 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.34 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.19), residues: 2018
  helix:  0.69 (0.13), residues: 1445
  sheet:  None (None), residues: 0
  loop : -2.43 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1073 
 HIS   0.005   0.001   HIS A 572 
 PHE   0.023   0.002   PHE A 163 
 TYR   0.020   0.002   TYR A1297 
 ARG   0.006   0.001   ARG B 916 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 119
  time to evaluate  : 2.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.7578 (mpp) cc_final: 0.7015 (mpp)
REVERT: A  279 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7261 (pp20)
REVERT: A  538 ILE cc_start: 0.8103 (mm) cc_final: 0.7826 (tt)
REVERT: A  618 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6127 (tp)
REVERT: A  745 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8698 (tm-30)
REVERT: A  764 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6779 (tp)
REVERT: A  920 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8530 (t80)
REVERT: A 1029 MET cc_start: 0.9077 (ppp) cc_final: 0.8792 (ppp)
REVERT: B  237 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8126 (t80)
REVERT: B  363 THR cc_start: 0.9230 (p) cc_final: 0.9024 (p)
REVERT: B  440 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.7953 (p)
REVERT: B  486 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8062 (m)
REVERT: B  488 ASP cc_start: 0.9291 (p0) cc_final: 0.8738 (p0)
REVERT: B  528 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7270 (m-10)
REVERT: B  590 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8736 (mt)
REVERT: B  716 MET cc_start: 0.9641 (mmp) cc_final: 0.9273 (mmp)
REVERT: B  817 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8687 (mm)
REVERT: B  996 ASP cc_start: 0.8543 (p0) cc_final: 0.8005 (p0)
REVERT: B 1009 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9005 (p)
REVERT: B 1078 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8942 (t)
REVERT: B 1127 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8087 (pp20)
  outliers start: 89
  outliers final: 45
  residues processed: 202
  average time/residue: 0.2663
  time to fit residues: 86.5155
Evaluate side-chains
  173 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 114
  time to evaluate  : 1.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  785 CYS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  970 ASP
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1005 GLN
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1063 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1187 CYS
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1295 LEU
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  780 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1009 THR
Chi-restraints excluded: chain B residue 1073 ILE
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1195 VAL
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0670
   chunk 80 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 174 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 109 optimal weight:    0.0470
   chunk 16 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9980
   chunk 188 optimal weight:    3.9990
   overall best weight:    1.2220

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN
A 800 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1034 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.056979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.042846 restraints weight = 108302.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.043709 restraints weight = 61863.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.043835 restraints weight = 36923.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3247 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3292 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.748  17634  Z= 0.772
  Angle     :  0.749  38.787  23997  Z= 0.368
  Chirality :  0.040   0.174   2831
  Planarity :  0.005   0.089   2874
  Dihedral  : 16.580 179.317   2617
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.95 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 29.57 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.19), residues: 2018
  helix:  0.82 (0.14), residues: 1449
  sheet:  None (None), residues: 0
  loop : -2.42 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 794 
 HIS   0.007   0.001   HIS A1002 
 PHE   0.023   0.002   PHE A 163 
 TYR   0.016   0.001   TYR A1297 
 ARG   0.006   0.000   ARG A1006 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 127
  time to evaluate  : 1.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6924 (mpp)
REVERT: A  538 ILE cc_start: 0.8079 (mm) cc_final: 0.7838 (tt)
REVERT: A  764 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6711 (tp)
REVERT: A 1127 PHE cc_start: 0.8605 (t80) cc_final: 0.8221 (t80)
REVERT: B  237 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8052 (t80)
REVERT: B  330 ASP cc_start: 0.9202 (OUTLIER) cc_final: 0.8991 (p0)
REVERT: B  363 THR cc_start: 0.9210 (p) cc_final: 0.9004 (p)
REVERT: B  486 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.8014 (m)
REVERT: B  488 ASP cc_start: 0.9228 (p0) cc_final: 0.8743 (p0)
REVERT: B  528 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7172 (m-10)
REVERT: B  716 MET cc_start: 0.9608 (mmp) cc_final: 0.9244 (mmp)
REVERT: B  817 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: B  996 ASP cc_start: 0.8480 (p0) cc_final: 0.7836 (p0)
REVERT: B 1009 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8998 (p)
REVERT: B 1078 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8784 (t)
REVERT: B 1127 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8119 (pp20)
  outliers start: 82
  outliers final: 40
  residues processed: 199
  average time/residue: 0.2600
  time to fit residues: 82.5051
Evaluate side-chains
  171 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 1.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  330 ASP
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1009 THR
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 186 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   chunk 190 optimal weight:    3.9990
   chunk 125 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 188 optimal weight:    6.9990
   chunk 129 optimal weight:   20.0000
   chunk 96 optimal weight:    0.8980
   chunk 164 optimal weight:    0.6980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN
A 800 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 703 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.056443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.042018 restraints weight = 109236.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.042836 restraints weight = 62090.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.042956 restraints weight = 37685.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3292 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3351 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.750  17634  Z= 0.780
  Angle     :  0.768  39.102  23997  Z= 0.376
  Chirality :  0.040   0.174   2831
  Planarity :  0.005   0.085   2874
  Dihedral  : 16.466 179.417   2617
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.49 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 28.98 %
    Favored  : 66.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.19), residues: 2018
  helix:  0.81 (0.14), residues: 1458
  sheet:  None (None), residues: 0
  loop : -2.43 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1073 
 HIS   0.007   0.001   HIS A1192 
 PHE   0.037   0.002   PHE B 812 
 TYR   0.017   0.001   TYR A1297 
 ARG   0.004   0.000   ARG A1006 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 121
  time to evaluate  : 2.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.8951 (tt) cc_final: 0.8708 (tp)
REVERT: A  200 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6965 (mpp)
REVERT: A  270 MET cc_start: 0.7033 (mmm) cc_final: 0.5411 (mmm)
REVERT: A  279 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7342 (pp20)
REVERT: A  538 ILE cc_start: 0.8122 (mm) cc_final: 0.7871 (tt)
REVERT: A  745 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8551 (tm-30)
REVERT: A  764 LEU cc_start: 0.7337 (mt) cc_final: 0.6933 (tp)
REVERT: A 1056 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6018 (ttm)
REVERT: A 1092 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6861 (pp)
REVERT: A 1127 PHE cc_start: 0.8565 (t80) cc_final: 0.8176 (t80)
REVERT: A 1153 MET cc_start: 0.6891 (mmp) cc_final: 0.6507 (mmp)
REVERT: B  237 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8024 (t80)
REVERT: B  330 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8979 (p0)
REVERT: B  363 THR cc_start: 0.9222 (p) cc_final: 0.9019 (p)
REVERT: B  440 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7964 (p)
REVERT: B  486 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8088 (m)
REVERT: B  488 ASP cc_start: 0.9199 (p0) cc_final: 0.8808 (p0)
REVERT: B  528 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7098 (m-10)
REVERT: B  590 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8755 (mt)
REVERT: B  716 MET cc_start: 0.9629 (mmp) cc_final: 0.9284 (mmp)
REVERT: B  817 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8684 (mm)
REVERT: B  824 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8331 (m-40)
REVERT: B  996 ASP cc_start: 0.8404 (p0) cc_final: 0.7878 (p0)
REVERT: B 1009 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9051 (p)
REVERT: B 1078 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8898 (t)
REVERT: B 1289 ASP cc_start: 0.3571 (p0) cc_final: 0.3286 (p0)
  outliers start: 92
  outliers final: 48
  residues processed: 204
  average time/residue: 0.2493
  time to fit residues: 83.5190
Evaluate side-chains
  183 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 120
  time to evaluate  : 2.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  970 ASP
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  330 ASP
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  780 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  824 ASN
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1009 THR
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1195 VAL
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 174 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 134 optimal weight:    0.7980
   chunk 187 optimal weight:    4.9990
   chunk 147 optimal weight:    0.2980
   chunk 204 optimal weight:    9.9990
   chunk 206 optimal weight:    2.9990
   chunk 193 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 197 optimal weight:    4.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 ASN
** A1025 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.056506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.041303 restraints weight = 107984.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.042176 restraints weight = 54722.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.042743 restraints weight = 36134.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3351 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3410 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.750  17634  Z= 0.777
  Angle     :  0.764  38.935  23997  Z= 0.373
  Chirality :  0.040   0.184   2831
  Planarity :  0.005   0.084   2874
  Dihedral  : 16.420 179.800   2617
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.49 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 29.36 %
    Favored  : 65.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.19), residues: 2018
  helix:  0.85 (0.14), residues: 1453
  sheet:  None (None), residues: 0
  loop : -2.40 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1165 
 HIS   0.011   0.001   HIS A 290 
 PHE   0.023   0.002   PHE B 812 
 TYR   0.017   0.001   TYR A1297 
 ARG   0.004   0.000   ARG B 243 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 123
  time to evaluate  : 1.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.9028 (tt) cc_final: 0.8783 (tp)
REVERT: A  200 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7042 (mpp)
REVERT: A  270 MET cc_start: 0.7177 (mmm) cc_final: 0.5792 (mmm)
REVERT: A  279 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7370 (pp20)
REVERT: A  538 ILE cc_start: 0.8090 (mm) cc_final: 0.7841 (tt)
REVERT: A  745 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8383 (tm-30)
REVERT: A  764 LEU cc_start: 0.7061 (mt) cc_final: 0.6655 (mt)
REVERT: A 1092 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6912 (pp)
REVERT: A 1127 PHE cc_start: 0.8588 (t80) cc_final: 0.8206 (t80)
REVERT: B  237 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8153 (t80)
REVERT: B  440 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8237 (p)
REVERT: B  486 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8194 (m)
REVERT: B  488 ASP cc_start: 0.9197 (p0) cc_final: 0.8894 (p0)
REVERT: B  528 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7013 (m-10)
REVERT: B  590 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8765 (mt)
REVERT: B  716 MET cc_start: 0.9593 (mmp) cc_final: 0.9266 (mmp)
REVERT: B  817 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8666 (mm)
REVERT: B  996 ASP cc_start: 0.8363 (p0) cc_final: 0.7738 (p0)
REVERT: B 1078 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8884 (t)
REVERT: B 1127 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8153 (pp20)
  outliers start: 95
  outliers final: 59
  residues processed: 206
  average time/residue: 0.2446
  time to fit residues: 82.1769
Evaluate side-chains
  192 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 121
  time to evaluate  : 1.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  966 PHE
Chi-restraints excluded: chain A residue  970 ASP
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1187 CYS
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Chi-restraints excluded: chain B residue 1276 VAL
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:   20.0000
   chunk 166 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 205 optimal weight:    0.0980
   chunk 87 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1325 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 = 0.3676 r_free = 0.3676 target = 0.056340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.041192 restraints weight = 107031.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.042037 restraints weight = 54240.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.042594 restraints weight = 35885.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3410 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3435 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.751  17634  Z= 0.781
  Angle     :  0.776  38.954  23997  Z= 0.380
  Chirality :  0.041   0.366   2831
  Planarity :  0.005   0.085   2874
  Dihedral  : 16.397 179.258   2617
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.54 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 29.14 %
    Favored  : 65.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.19), residues: 2018
  helix:  0.82 (0.14), residues: 1454
  sheet:  None (None), residues: 0
  loop : -2.42 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1073 
 HIS   0.005   0.001   HIS A1192 
 PHE   0.023   0.002   PHE B 329 
 TYR   0.017   0.001   TYR A1297 
 ARG   0.004   0.000   ARG B 243 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 123
  time to evaluate  : 2.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.9061 (tt) cc_final: 0.8813 (tp)
REVERT: A  200 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6912 (mpp)
REVERT: A  270 MET cc_start: 0.7214 (mmm) cc_final: 0.5867 (mmm)
REVERT: A  279 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7409 (pp20)
REVERT: A  538 ILE cc_start: 0.8078 (mm) cc_final: 0.7835 (tt)
REVERT: A  745 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8256 (tm-30)
REVERT: A  764 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6411 (tp)
REVERT: A  920 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8313 (t80)
REVERT: A 1056 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.5955 (ttm)
REVERT: A 1060 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: A 1092 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6902 (pp)
REVERT: A 1127 PHE cc_start: 0.8566 (t80) cc_final: 0.8180 (t80)
REVERT: B  237 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8157 (t80)
REVERT: B  440 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8237 (p)
REVERT: B  486 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8287 (m)
REVERT: B  488 ASP cc_start: 0.9194 (p0) cc_final: 0.8899 (p0)
REVERT: B  528 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6900 (m-10)
REVERT: B  590 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8778 (mt)
REVERT: B  716 MET cc_start: 0.9580 (mmp) cc_final: 0.9272 (mmp)
REVERT: B  817 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8660 (mm)
REVERT: B  824 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8248 (m-40)
REVERT: B  996 ASP cc_start: 0.8375 (p0) cc_final: 0.7801 (p0)
REVERT: B 1009 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9045 (p)
REVERT: B 1078 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8912 (t)
REVERT: B 1127 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8146 (pp20)
REVERT: B 1216 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7968 (tp)
  outliers start: 102
  outliers final: 66
  residues processed: 210
  average time/residue: 0.2478
  time to fit residues: 85.2520
Evaluate side-chains
  207 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 122
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  966 PHE
Chi-restraints excluded: chain A residue  970 ASP
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1187 CYS
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  422 LYS
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  548 ASN
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  780 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  824 ASN
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  988 LEU
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1009 THR
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1195 VAL
Chi-restraints excluded: chain B residue 1216 ILE
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Chi-restraints excluded: chain B residue 1276 VAL
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 140 optimal weight:   40.0000
   chunk 5 optimal weight:   20.0000
   chunk 173 optimal weight:    2.9990
   chunk 137 optimal weight:    0.0070
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0070
   chunk 208 optimal weight:   10.0000
   chunk 146 optimal weight:    7.9990
   chunk 201 optimal weight:    0.9990
   overall best weight:    1.4022

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 HIS ** 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 = 0.3696 r_free = 0.3696 target = 0.056965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.042223 restraints weight = 106080.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.042977 restraints weight = 60993.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.043171 restraints weight = 35766.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3435 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3456 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.750  17634  Z= 0.772
  Angle     :  0.777  38.946  23997  Z= 0.376
  Chirality :  0.041   0.277   2831
  Planarity :  0.005   0.084   2874
  Dihedral  : 16.323 178.055   2617
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.05 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 30.11 %
    Favored  : 65.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.19), residues: 2018
  helix:  0.89 (0.14), residues: 1453
  sheet:  None (None), residues: 0
  loop : -2.39 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1073 
 HIS   0.005   0.001   HIS A1192 
 PHE   0.022   0.002   PHE A 163 
 TYR   0.015   0.001   TYR A1297 
 ARG   0.005   0.000   ARG A 232 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 132
  time to evaluate  : 1.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.9031 (tt) cc_final: 0.8702 (tp)
REVERT: A  200 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6759 (mpp)
REVERT: A  538 ILE cc_start: 0.8001 (mm) cc_final: 0.7753 (tt)
REVERT: A  745 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8238 (tm-30)
REVERT: A  764 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6786 (tp)
REVERT: A  920 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (t80)
REVERT: A 1056 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5807 (ttm)
REVERT: A 1060 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6975 (t80)
REVERT: A 1092 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6855 (pp)
REVERT: A 1127 PHE cc_start: 0.8603 (t80) cc_final: 0.8237 (t80)
REVERT: B  363 THR cc_start: 0.9312 (p) cc_final: 0.8945 (t)
REVERT: B  368 GLU cc_start: 0.9077 (pp20) cc_final: 0.8869 (tm-30)
REVERT: B  440 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7885 (p)
REVERT: B  486 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (m)
REVERT: B  488 ASP cc_start: 0.9178 (p0) cc_final: 0.8861 (p0)
REVERT: B  528 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6771 (m-10)
REVERT: B  590 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8759 (mt)
REVERT: B  716 MET cc_start: 0.9592 (mmp) cc_final: 0.9267 (mmp)
REVERT: B  817 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8653 (mm)
REVERT: B  824 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8296 (m-40)
REVERT: B  996 ASP cc_start: 0.8395 (p0) cc_final: 0.7696 (p0)
REVERT: B 1078 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8821 (t)
REVERT: B 1127 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8183 (pp20)
  outliers start: 87
  outliers final: 59
  residues processed: 208
  average time/residue: 0.2556
  time to fit residues: 86.0705
Evaluate side-chains
  199 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 125
  time to evaluate  : 2.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  966 PHE
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1187 CYS
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  548 ASN
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  824 ASN
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1086 LEU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1138 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Chi-restraints excluded: chain B residue 1276 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 141 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 132 optimal weight:    0.4980
   chunk 17 optimal weight:   40.0000
   chunk 147 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 696 GLN
A 747 ASN
A 800 ASN
A 825 GLN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.056446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.041472 restraints weight = 107081.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.042363 restraints weight = 61563.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.042386 restraints weight = 36143.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3456 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3477 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.751  17634  Z= 0.782
  Angle     :  0.798  38.933  23997  Z= 0.387
  Chirality :  0.041   0.221   2831
  Planarity :  0.005   0.084   2874
  Dihedral  : 16.290 178.241   2617
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.44 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 30.27 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.19), residues: 2018
  helix:  0.80 (0.14), residues: 1460
  sheet:  None (None), residues: 0
  loop : -2.40 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 794 
 HIS   0.005   0.001   HIS A1192 
 PHE   0.022   0.002   PHE A 163 
 TYR   0.024   0.001   TYR A 461 
 ARG   0.013   0.000   ARG A 232 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 121
  time to evaluate  : 1.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.4717 (mt0)
REVERT: A  186 LEU cc_start: 0.9080 (tt) cc_final: 0.8792 (tp)
REVERT: A  279 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7432 (pp20)
REVERT: A  538 ILE cc_start: 0.8041 (mm) cc_final: 0.7788 (tt)
REVERT: A  745 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8332 (tm-30)
REVERT: A  764 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6998 (tp)
REVERT: A  920 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8393 (t80)
REVERT: A 1056 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.5923 (ttm)
REVERT: A 1060 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7039 (t80)
REVERT: A 1069 LEU cc_start: 0.8095 (mt) cc_final: 0.7808 (mt)
REVERT: A 1092 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6764 (pp)
REVERT: A 1127 PHE cc_start: 0.8556 (t80) cc_final: 0.8169 (t80)
REVERT: B  363 THR cc_start: 0.9306 (p) cc_final: 0.8930 (t)
REVERT: B  440 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8044 (p)
REVERT: B  486 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8386 (m)
REVERT: B  488 ASP cc_start: 0.9153 (p0) cc_final: 0.8878 (p0)
REVERT: B  528 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6826 (m-10)
REVERT: B  590 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8781 (mt)
REVERT: B  716 MET cc_start: 0.9618 (mmp) cc_final: 0.9302 (mmp)
REVERT: B  817 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8673 (mm)
REVERT: B  988 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9106 (mt)
REVERT: B  996 ASP cc_start: 0.8352 (p0) cc_final: 0.7776 (p0)
REVERT: B 1078 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8903 (t)
REVERT: B 1127 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8135 (pp20)
  outliers start: 87
  outliers final: 58
  residues processed: 197
  average time/residue: 0.2585
  time to fit residues: 82.5995
Evaluate side-chains
  193 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 119
  time to evaluate  : 1.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  966 PHE
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1187 CYS
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  548 ASN
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  988 LEU
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Chi-restraints excluded: chain B residue 1276 VAL
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 144 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 102 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 86 optimal weight:    0.3980
   chunk 126 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 202 optimal weight:    0.9990
   chunk 151 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 825 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.057440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.042427 restraints weight = 106237.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.043299 restraints weight = 61420.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.043423 restraints weight = 36526.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3477 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3537 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.750  17634  Z= 0.773
  Angle     :  0.803  38.929  23997  Z= 0.386
  Chirality :  0.042   0.424   2831
  Planarity :  0.004   0.084   2874
  Dihedral  : 16.242 177.465   2617
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.05 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 30.80 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.19), residues: 2018
  helix:  0.83 (0.14), residues: 1459
  sheet:  None (None), residues: 0
  loop : -2.40 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1268 
 HIS   0.005   0.001   HIS A1192 
 PHE   0.026   0.002   PHE A1231 
 TYR   0.020   0.001   TYR A 461 
 ARG   0.007   0.000   ARG A 232 

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

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

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4036 Ramachandran restraints generated.
    2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 129
  time to evaluate  : 1.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.4799 (mt0)
REVERT: A  186 LEU cc_start: 0.9083 (tt) cc_final: 0.8791 (tp)
REVERT: A  200 MET cc_start: 0.7645 (mpp) cc_final: 0.6894 (mpp)
REVERT: A  279 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7492 (pp20)
REVERT: A  538 ILE cc_start: 0.8015 (mm) cc_final: 0.7769 (tt)
REVERT: A  691 ASP cc_start: 0.8502 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  745 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8282 (tm-30)
REVERT: A  764 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.6938 (tp)
REVERT: A  920 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8397 (t80)
REVERT: A 1056 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5926 (ttm)
REVERT: A 1060 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6706 (t80)
REVERT: A 1092 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6764 (pp)
REVERT: A 1127 PHE cc_start: 0.8589 (t80) cc_final: 0.8231 (t80)
REVERT: B  363 THR cc_start: 0.9300 (p) cc_final: 0.8943 (t)
REVERT: B  440 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8050 (p)
REVERT: B  486 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (m)
REVERT: B  488 ASP cc_start: 0.9148 (p0) cc_final: 0.8903 (p0)
REVERT: B  528 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6807 (m-10)
REVERT: B  590 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8762 (mt)
REVERT: B  716 MET cc_start: 0.9620 (mmp) cc_final: 0.9290 (mmp)
REVERT: B  817 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8642 (mm)
REVERT: B  988 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9063 (mt)
REVERT: B  996 ASP cc_start: 0.8345 (p0) cc_final: 0.7538 (p0)
REVERT: B 1078 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8809 (t)
REVERT: B 1127 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8190 (pp20)
  outliers start: 77
  outliers final: 59
  residues processed: 196
  average time/residue: 0.2611
  time to fit residues: 82.8882
Evaluate side-chains
  200 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 125
  time to evaluate  : 1.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  740 ARG
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  966 PHE
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1094 ASP
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1219 CYS
Chi-restraints excluded: chain A residue 1281 LEU
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1320 HIS
Chi-restraints excluded: chain A residue 1334 SER
Chi-restraints excluded: chain A residue 1390 LYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  528 PHE
Chi-restraints excluded: chain B residue  548 ASN
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  671 CYS
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  924 LEU
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue  988 LEU
Chi-restraints excluded: chain B residue  991 LEU
Chi-restraints excluded: chain B residue 1002 PHE
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1127 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1138 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1155 VAL
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1221 LEU
Chi-restraints excluded: chain B residue 1267 LEU
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 165 optimal weight:    8.9990
   chunk 173 optimal weight:    0.6980
   chunk 183 optimal weight:    5.9990
   chunk 201 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 825 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.056985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.041980 restraints weight = 105595.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.042872 restraints weight = 61054.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.042901 restraints weight = 35299.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3537 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     3574 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.751  17634  Z= 0.774
  Angle     :  0.801  38.922  23997  Z= 0.387
  Chirality :  0.041   0.203   2831
  Planarity :  0.005   0.084   2874
  Dihedral  : 16.248 176.648   2617
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.29 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 30.96 %
    Favored  : 64.87 %
  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: -0.08 (0.19), residues: 2018
  helix:  0.82 (0.14), residues: 1459
  sheet:  None (None), residues: 0
  loop : -2.38 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 794 
 HIS   0.005   0.001   HIS A1192 
 PHE   0.026   0.002   PHE A1231 
 TYR   0.019   0.001   TYR A 461 
 ARG   0.012   0.000   ARG B1160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5314.08 seconds
wall clock time: 95 minutes 46.77 seconds (5746.77 seconds total)