Starting phenix.real_space_refine
on Mon Jun 16 09:56:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ynd_33959/06_2025/7ynd_33959.cif"
  }
  resolution = 3.29
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      76      5.16       5
     C   11305      2.51       5
     N    3222      2.21       5
     O    3457      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 18098
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1567, 12683
          Classifications: {'peptide': 1567}
          Link IDs: {'PTRANS': 85, 'TRANS': 1481}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNA': 38}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 5, 'rna3p_pur': 6, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 20, 'rna3p': 17}
    Chain: "C"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4605
          Classifications: {'peptide': 548}
          Link IDs: {'PTRANS': 19, 'TRANS': 528}
          Chain breaks: 1
  Time building chain proxies: 11.50, per 1000 atoms: 0.64
  Number of scatterers: 18098
  At special positions: 0
  Unit cell: (130.54, 199.02, 130.54, 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      76     16.00
     P      38     15.00
     O    3457      8.00
     N    3222      7.00
     C   11305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  86 " - pdb=" SG  CYS A 123 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 708 " - pdb=" SG  CYS A 711 " distance=2.04

  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: 4.47
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3964

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 23 sheets defined
      32.3% alpha, 15.3% beta
      0 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 5.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 3.749A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   THR A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 163 through 166
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 261 through 276
      removed outlier: 3.702A  pdb=" N   THR A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 294 through 299
      removed outlier: 7.111A  pdb=" N   LYS A 297 " --> pdb=" O   ARG A 294 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 298 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 294 through 299'
    Processing helix  chain 'A' and resid 328 through 337
    Processing helix  chain 'A' and resid 344 through 365
      removed outlier: 3.711A  pdb=" N   TRP A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 351 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ASP A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.668A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 481
      removed outlier: 3.667A  pdb=" N   ARG A 478 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 555
      removed outlier: 3.518A  pdb=" N   LYS A 546 " --> pdb=" O   PRO A 542 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 555 " --> pdb=" O   TRP A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 585 through 593
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 642 through 649
    Processing helix  chain 'A' and resid 675 through 689
      removed outlier: 3.736A  pdb=" N   PHE A 679 " --> pdb=" O   LYS A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 714
      removed outlier: 3.642A  pdb=" N   ILE A 713 " --> pdb=" O   LEU A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
    Processing helix  chain 'A' and resid 786 through 801
    Processing helix  chain 'A' and resid 809 through 813
      removed outlier: 3.676A  pdb=" N   ILE A 812 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 4.204A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1030
    Processing helix  chain 'A' and resid 1163 through 1168
    Processing helix  chain 'A' and resid 1231 through 1247
      removed outlier: 3.691A  pdb=" N   ARG A1235 " --> pdb=" O   PRO A1231 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN A1247 " --> pdb=" O   ARG A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1264
    Processing helix  chain 'A' and resid 1300 through 1304
      removed outlier: 3.563A  pdb=" N   LYS A1303 " --> pdb=" O   MET A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1326
      removed outlier: 3.890A  pdb=" N   ALA A1324 " --> pdb=" O   ASP A1321 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN A1326 " --> pdb=" O   SER A1323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1335
      removed outlier: 3.623A  pdb=" N   LEU A1335 " --> pdb=" O   ARG A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1348
      removed outlier: 3.812A  pdb=" N   LEU A1347 " --> pdb=" O   PRO A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1425
      removed outlier: 3.756A  pdb=" N   ILE A1424 " --> pdb=" O   ALA A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1464 through 1476
      removed outlier: 3.773A  pdb=" N   LEU A1468 " --> pdb=" O   LYS A1464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1488 through 1492
      removed outlier: 3.763A  pdb=" N   GLY A1492 " --> pdb=" O   LYS A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1517
      No H-bonds generated for 'chain 'A' and resid 1515 through 1517'
    Processing helix  chain 'A' and resid 1518 through 1534
      removed outlier: 3.952A  pdb=" N   GLY A1524 " --> pdb=" O   PRO A1520 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TRP A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A1534 " --> pdb=" O   LEU A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1540 through 1548
    Processing helix  chain 'A' and resid 1575 through 1580
      removed outlier: 3.640A  pdb=" N   LEU A1579 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A1580 " --> pdb=" O   TYR A1576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1575 through 1580'
    Processing helix  chain 'C' and resid 5 through 14
      removed outlier: 3.624A  pdb=" N   GLN C   9 " --> pdb=" O   ILE C   5 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   THR C  14 " --> pdb=" O   ASP C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 39
      removed outlier: 3.978A  pdb=" N   ASP C  39 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.645A  pdb=" N   THR C  44 " --> pdb=" O   SER C  41 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU C  45 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 41 through 45'
    Processing helix  chain 'C' and resid 52 through 66
    Processing helix  chain 'C' and resid 75 through 89
      removed outlier: 4.145A  pdb=" N   ASN C  89 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 108
      removed outlier: 4.091A  pdb=" N   ARG C  96 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 132
    Processing helix  chain 'C' and resid 143 through 161
      removed outlier: 3.837A  pdb=" N   VAL C 147 " --> pdb=" O   PRO C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 183
      removed outlier: 3.867A  pdb=" N   ARG C 183 " --> pdb=" O   MET C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 201
      removed outlier: 3.512A  pdb=" N   LYS C 195 " --> pdb=" O   ASN C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 222
      removed outlier: 3.849A  pdb=" N   ARG C 212 " --> pdb=" O   LEU C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 3.815A  pdb=" N   GLN C 232 " --> pdb=" O   MET C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 254
      removed outlier: 3.795A  pdb=" N   LEU C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   HIS C 253 " --> pdb=" O   ARG C 249 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU C 254 " --> pdb=" O   ALA C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 269
      removed outlier: 3.661A  pdb=" N   TYR C 263 " --> pdb=" O   ASP C 259 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASP C 269 " --> pdb=" O   GLU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 292
    Processing helix  chain 'C' and resid 297 through 310
      removed outlier: 3.846A  pdb=" N   ILE C 301 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 340
    Processing helix  chain 'C' and resid 342 through 351
    Processing helix  chain 'C' and resid 360 through 374
    Processing helix  chain 'C' and resid 382 through 391
      removed outlier: 3.803A  pdb=" N   ILE C 386 " --> pdb=" O   LYS C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.517A  pdb=" N   ARG C 418 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU C 419 " --> pdb=" O   PHE C 416 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 415 through 419'
    Processing helix  chain 'C' and resid 432 through 437
      removed outlier: 3.863A  pdb=" N   GLU C 437 " --> pdb=" O   LEU C 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 479
      removed outlier: 3.692A  pdb=" N   ILE C 479 " --> pdb=" O   GLN C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 486 through 500
      removed outlier: 3.927A  pdb=" N   VAL C 490 " --> pdb=" O   ALA C 486 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   MET C 500 " --> pdb=" O   ILE C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 501 through 505
      removed outlier: 3.816A  pdb=" N   PHE C 504 " --> pdb=" O   PRO C 501 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LYS C 505 " --> pdb=" O   PHE C 502 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 501 through 505'
    Processing helix  chain 'C' and resid 520 through 526
      removed outlier: 3.813A  pdb=" N   LEU C 523 " --> pdb=" O   HIS C 520 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   HIS C 524 " --> pdb=" O   GLY C 521 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG C 525 " --> pdb=" O   PHE C 522 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU C 526 " --> pdb=" O   LEU C 523 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 520 through 526'
    Processing helix  chain 'C' and resid 554 through 558
      removed outlier: 3.702A  pdb=" N   LEU C 557 " --> pdb=" O   ALA C 554 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE C 558 " --> pdb=" O   TRP C 555 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 554 through 558'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107
      removed outlier: 6.049A  pdb=" N   THR A 106 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485
      removed outlier: 4.408A  pdb=" N   GLU A 409 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ASN A 574 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A 411 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   MET A 572 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 557 " --> pdb=" O   PHE A 570 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485
      removed outlier: 4.408A  pdb=" N   GLU A 409 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ASN A 574 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A 411 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   MET A 572 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 611 " --> pdb=" O   TYR A 577 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504
      removed outlier: 3.725A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 724
    Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 663
    Processing sheet with id=AB1, first strand: chain 'A' and resid 739 through 742
    Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945
      removed outlier: 5.608A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A1462 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945
      removed outlier: 6.999A  pdb=" N   LYS A 894 " --> pdb=" O   VAL A1503 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   VAL A1503 " --> pdb=" O   LYS A 894 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ARG A 896 " --> pdb=" O   GLU A1501 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER A1495 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978
    Processing sheet with id=AB5, first strand: chain 'A' and resid 993 through 995
      removed outlier: 6.751A  pdb=" N   GLU A1226 " --> pdb=" O   LYS A1004 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012
      removed outlier: 9.032A  pdb=" N   THR A1008 " --> pdb=" O   GLN A1127 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   ALA A1129 " --> pdb=" O   THR A1008 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ARG A1010 " --> pdb=" O   ALA A1129 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ARG A1041 " --> pdb=" O   TYR A1126 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LYS A1128 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   VAL A1039 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   PHE A1130 " --> pdb=" O   MET A1037 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   MET A1037 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1070 through 1071
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1156 through 1159
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1187 through 1188
      removed outlier: 3.706A  pdb=" N   ASP A1187 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1276 through 1280
      removed outlier: 6.719A  pdb=" N   TYR A1276 " --> pdb=" O   ILE A1287 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ILE A1287 " --> pdb=" O   TYR A1276 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LYS A1278 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1385 through 1387
    Processing sheet with id=AC4, first strand: chain 'C' and resid 314 through 315
    Processing sheet with id=AC5, first strand: chain 'C' and resid 457 through 462
      removed outlier: 6.416A  pdb=" N   ILE C 424 " --> pdb=" O   LEU C 516 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   ILE C 518 " --> pdb=" O   ILE C 424 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL C 426 " --> pdb=" O   ILE C 518 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG C 550 " --> pdb=" O   VAL C 515 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1566 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 7.37

  Time building geometry restraints manager: 5.39 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 5666
        1.33 -     1.46: 3873
        1.46 -     1.58: 8878
        1.58 -     1.70: 75
        1.70 -     1.83: 111
  Bond restraints: 18603
  Sorted by residual:
  bond pdb=" N   VAL A 842 "
       pdb=" CA  VAL A 842 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.53e+00
  bond pdb=" N   VAL A 986 "
       pdb=" CA  VAL A 986 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.22e-02 6.72e+03 8.36e+00
  bond pdb=" N   GLN A1056 "
       pdb=" CA  GLN A1056 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.09e+00
  bond pdb=" N   ASP A 838 "
       pdb=" CA  ASP A 838 "
    ideal  model  delta    sigma   weight residual
    1.452  1.488 -0.037 1.30e-02 5.92e+03 8.01e+00
  bond pdb=" N   LEU A 987 "
       pdb=" CA  LEU A 987 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 1.18e-02 7.18e+03 7.62e+00
  ... (remaining 18598 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 24529
        2.01 -     4.03: 631
        4.03 -     6.04: 57
        6.04 -     8.05: 18
        8.05 -    10.06: 7
  Bond angle restraints: 25242
  Sorted by residual:
  angle pdb=" N   TYR A 866 "
        pdb=" CA  TYR A 866 "
        pdb=" C   TYR A 866 "
      ideal   model   delta    sigma   weight residual
     111.02  117.62   -6.60 1.25e+00 6.40e-01 2.79e+01
  angle pdb=" C   GLU A 633 "
        pdb=" N   MET A 634 "
        pdb=" CA  MET A 634 "
      ideal   model   delta    sigma   weight residual
     121.54  112.85    8.69 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" C   ASP A 841 "
        pdb=" CA  ASP A 841 "
        pdb=" CB  ASP A 841 "
      ideal   model   delta    sigma   weight residual
     111.26  118.60   -7.34 1.67e+00 3.59e-01 1.93e+01
  angle pdb=" N   ASP A 649 "
        pdb=" CA  ASP A 649 "
        pdb=" C   ASP A 649 "
      ideal   model   delta    sigma   weight residual
     110.24  115.73   -5.49 1.30e+00 5.92e-01 1.78e+01
  angle pdb=" C   GLU A1392 "
        pdb=" N   ARG A1393 "
        pdb=" CA  ARG A1393 "
      ideal   model   delta    sigma   weight residual
     121.80  131.79   -9.99 2.44e+00 1.68e-01 1.68e+01
  ... (remaining 25237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.62: 10902
       35.62 -    71.24: 404
       71.24 -   106.86: 28
      106.86 -   142.48: 0
      142.48 -   178.10: 3
  Dihedral angle restraints: 11337
    sinusoidal: 5198
      harmonic: 6139
  Sorted by residual:
  dihedral pdb=" O4'   U B  21 "
           pdb=" C1'   U B  21 "
           pdb=" N1    U B  21 "
           pdb=" C2    U B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   18.10 -178.10     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" CA  GLU A 633 "
           pdb=" C   GLU A 633 "
           pdb=" N   MET A 634 "
           pdb=" CA  MET A 634 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.70   25.30     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  HIS A 383 "
           pdb=" C   HIS A 383 "
           pdb=" N   GLY A 384 "
           pdb=" CA  GLY A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.88  -24.12     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 11334 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 2209
       0.065 -    0.130: 388
       0.130 -    0.195: 34
       0.195 -    0.260: 2
       0.260 -    0.325: 2
  Chirality restraints: 2635
  Sorted by residual:
  chirality pdb=" CA  ASP A 841 "
            pdb=" N   ASP A 841 "
            pdb=" C   ASP A 841 "
            pdb=" CB  ASP A 841 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE A 376 "
            pdb=" CA  ILE A 376 "
            pdb=" CG1 ILE A 376 "
            pdb=" CG2 ILE A 376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  PRO A 864 "
            pdb=" N   PRO A 864 "
            pdb=" C   PRO A 864 "
            pdb=" CB  PRO A 864 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2632 not shown)

  Planarity restraints: 3169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "    0.055 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO A 864 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 768 "    0.045 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO A 769 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 769 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 769 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 903 "    0.042 5.00e-02 4.00e+02   6.28e-02 6.30e+00
        pdb=" N   PRO A 904 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 904 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 904 "    0.035 5.00e-02 4.00e+02
  ... (remaining 3166 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2892
        2.75 -     3.29: 15852
        3.29 -     3.83: 27936
        3.83 -     4.36: 32550
        4.36 -     4.90: 57742
  Nonbonded interactions: 136972
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  13 "
            pdb=" OP1   A B  14 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" NZ  LYS A 304 "
            pdb=" OD1 ASP A 310 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   ARG A 489 "
            pdb=" OG  SER A 490 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE2 GLU A1226 "
            pdb=" OH  TYR A1228 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   GLN C 421 "
            pdb=" NH2 ARG C 513 "
     model   vdw
     2.235 3.120
  ... (remaining 136967 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.780
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     48.130
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
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      :  0.007   0.043  18605  Z= 0.306
  Angle     :  0.786  10.063  25246  Z= 0.458
  Chirality :  0.049   0.325   2635
  Planarity :  0.006   0.084   3169
  Dihedral  : 17.739 178.105   7367
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.55 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.11 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.05 %
  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: -4.25 (0.14), residues: 2105
  helix: -1.85 (0.18), residues: 591
  sheet: -1.64 (0.28), residues: 297
  loop : -3.85 (0.13), residues: 1217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 324 
 HIS   0.008   0.001   HIS A 691 
 PHE   0.018   0.002   PHE A 776 
 TYR   0.013   0.002   TYR C  84 
 ARG   0.008   0.001   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16598 (  533)
  hydrogen bonds       : angle       6.09579 ( 1566)
  SS BOND              : bond        0.00789 (    2)
  SS BOND              : angle       2.85490 (    4)
  covalent geometry    : bond        0.00673 (18603)
  covalent geometry    : angle       0.78495 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 2.110 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8425 (mttt)
REVERT: A  473 MET cc_start: 0.9233 (mmt) cc_final: 0.8998 (mmp)
REVERT: A  503 ARG cc_start: 0.8536 (tmt170) cc_final: 0.8021 (ttt-90)
REVERT: A  559 MET cc_start: 0.8952 (mmm) cc_final: 0.8287 (mmt)
REVERT: A 1063 TRP cc_start: 0.7061 (m100) cc_final: 0.6752 (m100)
REVERT: A 1268 LYS cc_start: 0.8275 (tptt) cc_final: 0.8059 (mmmt)
REVERT: A 1326 ASN cc_start: 0.8863 (t0) cc_final: 0.8660 (m-40)
REVERT: A 1578 GLU cc_start: 0.8181 (mp0) cc_final: 0.7576 (mp0)
REVERT: C   16 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6583 (mttp)
REVERT: C   65 ASP cc_start: 0.8275 (t70) cc_final: 0.7912 (t70)
  outliers start: 27
  outliers final: 14
  residues processed: 161
  average time/residue: 0.3735
  time to fit residues: 87.7188
Evaluate side-chains
  114 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  518 ASN
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  702 THR
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  839 GLU
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  254 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 179 optimal weight:    3.9990
   chunk 161 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 166 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 193 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 149 HIS
A 260 ASN
A 276 ASN
A 456 GLN
A 493 ASN
** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1280 ASN
A1337 HIS
A1419 HIS
A1428 ASN
A1483 HIS
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 ASN
C 391 ASN
C 436 HIS
C 477 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.076648 restraints weight = 35118.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.60
r_work: 0.2856 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18605  Z= 0.142
  Angle     :  0.626  12.040  25246  Z= 0.329
  Chirality :  0.044   0.207   2635
  Planarity :  0.005   0.073   3169
  Dihedral  : 13.270 177.399   2923
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.09 %
    Favored  : 83.65 %
  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: -3.12 (0.16), residues: 2105
  helix: -0.30 (0.21), residues: 611
  sheet: -1.11 (0.29), residues: 292
  loop : -3.50 (0.14), residues: 1202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 474 
 HIS   0.008   0.001   HIS C 436 
 PHE   0.013   0.001   PHE A1407 
 TYR   0.011   0.001   TYR C 325 
 ARG   0.003   0.000   ARG A 917 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  533)
  hydrogen bonds       : angle       4.48839 ( 1566)
  SS BOND              : bond        0.00822 (    2)
  SS BOND              : angle       3.26809 (    4)
  covalent geometry    : bond        0.00324 (18603)
  covalent geometry    : angle       0.62506 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 108
  time to evaluate  : 2.172 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8567 (mttt)
REVERT: A  311 ASP cc_start: 0.8698 (t0) cc_final: 0.7668 (m-30)
REVERT: A  473 MET cc_start: 0.9567 (mmt) cc_final: 0.9330 (mmp)
REVERT: A  503 ARG cc_start: 0.8880 (tmt170) cc_final: 0.8335 (ttt-90)
REVERT: A  559 MET cc_start: 0.9267 (mmm) cc_final: 0.8797 (mmt)
REVERT: A 1063 TRP cc_start: 0.7164 (m100) cc_final: 0.6923 (m100)
REVERT: A 1578 GLU cc_start: 0.8648 (mp0) cc_final: 0.7912 (mp0)
REVERT: C   16 LYS cc_start: 0.7168 (mmmt) cc_final: 0.6465 (mttp)
REVERT: C  377 ARG cc_start: 0.8004 (mmp-170) cc_final: 0.7591 (mmm160)
  outliers start: 42
  outliers final: 20
  residues processed: 144
  average time/residue: 0.3832
  time to fit residues: 84.7128
Evaluate side-chains
  116 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 2.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  401 ARG
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  559 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 209 optimal weight:    0.0770
   chunk 108 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0570
   chunk 207 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 191 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.6060

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

Flipped N/Q/H residues before XYZ refinement:
A 691 HIS
** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 468 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.105361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.075517 restraints weight = 34972.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.59
r_work: 0.2827 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18605  Z= 0.175
  Angle     :  0.629  10.396  25246  Z= 0.328
  Chirality :  0.044   0.199   2635
  Planarity :  0.005   0.068   3169
  Dihedral  : 13.148 176.052   2912
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.03 %
    Favored  : 81.92 %
  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: -2.55 (0.17), residues: 2105
  helix:  0.48 (0.22), residues: 608
  sheet: -0.86 (0.29), residues: 302
  loop : -3.31 (0.15), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 326 
 HIS   0.005   0.001   HIS A 691 
 PHE   0.013   0.001   PHE A 776 
 TYR   0.011   0.001   TYR C 325 
 ARG   0.004   0.000   ARG A 978 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04391 (  533)
  hydrogen bonds       : angle       4.27050 ( 1566)
  SS BOND              : bond        0.00902 (    2)
  SS BOND              : angle       3.40405 (    4)
  covalent geometry    : bond        0.00413 (18603)
  covalent geometry    : angle       0.62799 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 104
  time to evaluate  : 2.102 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8569 (mttt)
REVERT: A  311 ASP cc_start: 0.8696 (t0) cc_final: 0.7677 (m-30)
REVERT: A  473 MET cc_start: 0.9601 (mmt) cc_final: 0.9391 (mmp)
REVERT: A  503 ARG cc_start: 0.8886 (tmt170) cc_final: 0.8382 (ttt-90)
REVERT: A  692 MET cc_start: 0.8185 (tpp) cc_final: 0.7816 (tpt)
REVERT: A 1578 GLU cc_start: 0.8645 (mp0) cc_final: 0.8215 (mp0)
REVERT: C   16 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6578 (mttp)
REVERT: C   98 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7705 (mp0)
REVERT: C  265 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8500 (mt-10)
REVERT: C  363 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7371 (pm20)
REVERT: C  377 ARG cc_start: 0.7991 (mmp-170) cc_final: 0.7566 (mmm160)
  outliers start: 38
  outliers final: 24
  residues processed: 138
  average time/residue: 0.4434
  time to fit residues: 95.7419
Evaluate side-chains
  121 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 4.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  363 GLU
Chi-restraints excluded: chain C residue  490 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 185 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 174 optimal weight:    1.9990
   chunk 204 optimal weight:    9.9990
   chunk 162 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 202 optimal weight:    8.9990
   chunk 179 optimal weight:    6.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A1020 HIS
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.076082 restraints weight = 35062.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.60
r_work: 0.2847 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  18605  Z= 0.157
  Angle     :  0.601  10.469  25246  Z= 0.313
  Chirality :  0.044   0.199   2635
  Planarity :  0.005   0.068   3169
  Dihedral  : 13.084 176.123   2912
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.32 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.18), residues: 2105
  helix:  0.82 (0.22), residues: 607
  sheet: -0.60 (0.29), residues: 302
  loop : -3.17 (0.15), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 326 
 HIS   0.003   0.001   HIS A1313 
 PHE   0.013   0.001   PHE A 776 
 TYR   0.009   0.001   TYR C 325 
 ARG   0.004   0.000   ARG A 978 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  533)
  hydrogen bonds       : angle       4.15299 ( 1566)
  SS BOND              : bond        0.00851 (    2)
  SS BOND              : angle       3.15317 (    4)
  covalent geometry    : bond        0.00369 (18603)
  covalent geometry    : angle       0.59999 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 103
  time to evaluate  : 1.898 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8536 (mttt)
REVERT: A  311 ASP cc_start: 0.8757 (t0) cc_final: 0.7790 (m-30)
REVERT: A  503 ARG cc_start: 0.8895 (tmt170) cc_final: 0.8413 (ttt-90)
REVERT: A  984 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7613 (tp-100)
REVERT: A 1356 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.9201 (ptt90)
REVERT: A 1578 GLU cc_start: 0.8601 (mp0) cc_final: 0.8027 (mp0)
REVERT: C   16 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6710 (mttp)
REVERT: C   98 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7678 (mp0)
REVERT: C  265 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8456 (mt-10)
REVERT: C  363 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7484 (pm20)
REVERT: C  377 ARG cc_start: 0.8031 (mmp-170) cc_final: 0.7580 (mmm160)
  outliers start: 39
  outliers final: 24
  residues processed: 137
  average time/residue: 0.3323
  time to fit residues: 68.2960
Evaluate side-chains
  125 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 1.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1356 ARG
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1514 ASN
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  363 GLU
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  559 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 176 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 161 optimal weight:    4.9990
   chunk 135 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 187 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0020
   chunk 33 optimal weight:    0.2980
   chunk 183 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.8594

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

Flipped N/Q/H residues before XYZ refinement:
A1405 ASN
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 436 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.074953 restraints weight = 35278.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.59
r_work: 0.2828 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  18605  Z= 0.193
  Angle     :  0.624  10.557  25246  Z= 0.325
  Chirality :  0.045   0.198   2635
  Planarity :  0.005   0.069   3169
  Dihedral  : 13.130 176.818   2912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.38 %
    Favored  : 79.87 %
  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: -2.09 (0.18), residues: 2105
  helix:  0.98 (0.22), residues: 607
  sheet: -0.57 (0.29), residues: 309
  loop : -3.11 (0.15), residues: 1189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 326 
 HIS   0.009   0.001   HIS C 436 
 PHE   0.013   0.001   PHE A 187 
 TYR   0.010   0.001   TYR C 325 
 ARG   0.006   0.000   ARG C 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04424 (  533)
  hydrogen bonds       : angle       4.18919 ( 1566)
  SS BOND              : bond        0.00947 (    2)
  SS BOND              : angle       3.32724 (    4)
  covalent geometry    : bond        0.00460 (18603)
  covalent geometry    : angle       0.62291 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 101
  time to evaluate  : 2.110 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8522 (mttt)
REVERT: A  104 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7429 (mtp180)
REVERT: A  311 ASP cc_start: 0.8749 (t0) cc_final: 0.7758 (m-30)
REVERT: A  984 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7678 (tp-100)
REVERT: A 1145 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5999 (mm-30)
REVERT: A 1578 GLU cc_start: 0.8604 (mp0) cc_final: 0.8081 (mp0)
REVERT: C   16 LYS cc_start: 0.7356 (mmmt) cc_final: 0.6685 (mttp)
REVERT: C   98 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7681 (mp0)
REVERT: C  265 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8439 (mt-10)
REVERT: C  377 ARG cc_start: 0.7946 (mmp-170) cc_final: 0.7544 (mmm160)
  outliers start: 51
  outliers final: 35
  residues processed: 146
  average time/residue: 0.3379
  time to fit residues: 75.2012
Evaluate side-chains
  132 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 2.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  445 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1483 HIS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1514 ASN
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 183 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 174 optimal weight:    2.9990
   chunk 208 optimal weight:    0.8980
   chunk 99 optimal weight:    7.9990
   chunk 131 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 202 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 172 optimal weight:    4.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
A1516 ASN
C 556 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.074158 restraints weight = 35261.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.60
r_work: 0.2813 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  18605  Z= 0.219
  Angle     :  0.649  10.745  25246  Z= 0.337
  Chirality :  0.046   0.203   2635
  Planarity :  0.005   0.072   3169
  Dihedral  : 13.184 177.040   2912
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.13 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.18), residues: 2105
  helix:  1.05 (0.22), residues: 607
  sheet: -0.51 (0.29), residues: 309
  loop : -3.10 (0.15), residues: 1189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 326 
 HIS   0.004   0.001   HIS A1313 
 PHE   0.013   0.002   PHE A 187 
 TYR   0.013   0.001   TYR C 325 
 ARG   0.004   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  533)
  hydrogen bonds       : angle       4.24591 ( 1566)
  SS BOND              : bond        0.01012 (    2)
  SS BOND              : angle       3.48556 (    4)
  covalent geometry    : bond        0.00525 (18603)
  covalent geometry    : angle       0.64775 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 97
  time to evaluate  : 2.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8459 (mttt)
REVERT: A  104 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7450 (mtp180)
REVERT: A  340 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8856 (tptt)
REVERT: A  896 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8371 (mtp-110)
REVERT: A 1145 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5736 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8820 (t0)
REVERT: A 1578 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8125 (mp0)
REVERT: C   16 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6704 (mttp)
REVERT: C   98 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7792 (mp0)
REVERT: C  265 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8380 (mt-10)
REVERT: C  377 ARG cc_start: 0.7900 (mmp-170) cc_final: 0.7486 (mmm160)
  outliers start: 56
  outliers final: 44
  residues processed: 144
  average time/residue: 0.3397
  time to fit residues: 74.4090
Evaluate side-chains
  145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 97
  time to evaluate  : 2.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  445 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  702 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1390 LEU
Chi-restraints excluded: chain A residue 1483 HIS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1514 ASN
Chi-restraints excluded: chain A residue 1516 ASN
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1578 GLU
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 196 optimal weight:    7.9990
   chunk 148 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9990
   chunk 166 optimal weight:    6.9990
   chunk 163 optimal weight:    2.9990
   chunk 191 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 170 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 984 GLN
A1516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.106159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.076439 restraints weight = 34890.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.61
r_work: 0.2853 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18605  Z= 0.132
  Angle     :  0.591  10.600  25246  Z= 0.306
  Chirality :  0.043   0.199   2635
  Planarity :  0.004   0.067   3169
  Dihedral  : 13.040 175.985   2912
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.00 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.18), residues: 2105
  helix:  1.27 (0.22), residues: 609
  sheet: -0.30 (0.30), residues: 303
  loop : -3.00 (0.16), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 326 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.014   0.001   PHE A 776 
 TYR   0.009   0.001   TYR C 325 
 ARG   0.005   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  533)
  hydrogen bonds       : angle       4.06479 ( 1566)
  SS BOND              : bond        0.00774 (    2)
  SS BOND              : angle       2.93255 (    4)
  covalent geometry    : bond        0.00308 (18603)
  covalent geometry    : angle       0.59005 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 106
  time to evaluate  : 1.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8529 (mttt)
REVERT: A  311 ASP cc_start: 0.8755 (t0) cc_final: 0.7772 (m-30)
REVERT: A  391 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7112 (mmtt)
REVERT: A  633 GLU cc_start: 0.7297 (pp20) cc_final: 0.7017 (pp20)
REVERT: A  896 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8321 (mtp-110)
REVERT: A  984 GLN cc_start: 0.7412 (tp40) cc_final: 0.7159 (tp-100)
REVERT: A 1145 GLU cc_start: 0.6094 (mm-30) cc_final: 0.5833 (mm-30)
REVERT: A 1578 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8056 (mp0)
REVERT: C   16 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7064 (mmtm)
REVERT: C   98 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7669 (mp0)
REVERT: C  229 MET cc_start: 0.8106 (tmm) cc_final: 0.7830 (tmm)
REVERT: C  265 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8401 (mt-10)
REVERT: C  377 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7502 (mmm160)
  outliers start: 48
  outliers final: 39
  residues processed: 148
  average time/residue: 0.3400
  time to fit residues: 76.6610
Evaluate side-chains
  140 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 2.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  445 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  702 THR
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  859 GLU
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1221 ASP
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1483 HIS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1516 ASN
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1578 GLU
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  360 ARG
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 201 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 209 optimal weight:    1.9990
   chunk 205 optimal weight:    3.9990
   chunk 173 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.106367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.076736 restraints weight = 35018.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.59
r_work: 0.2861 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18605  Z= 0.134
  Angle     :  0.586  10.297  25246  Z= 0.302
  Chirality :  0.043   0.199   2635
  Planarity :  0.004   0.064   3169
  Dihedral  : 12.950 175.687   2912
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.05 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.18), residues: 2105
  helix:  1.38 (0.22), residues: 608
  sheet: -0.22 (0.30), residues: 303
  loop : -2.93 (0.16), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1063 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.013   0.001   PHE A 776 
 TYR   0.008   0.001   TYR C 325 
 ARG   0.005   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  533)
  hydrogen bonds       : angle       4.00047 ( 1566)
  SS BOND              : bond        0.00761 (    2)
  SS BOND              : angle       2.86517 (    4)
  covalent geometry    : bond        0.00313 (18603)
  covalent geometry    : angle       0.58455 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 1.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8528 (mttt)
REVERT: A  311 ASP cc_start: 0.8724 (t0) cc_final: 0.7745 (m-30)
REVERT: A  340 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8788 (tptt)
REVERT: A  391 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7279 (mmtt)
REVERT: A  633 GLU cc_start: 0.7197 (pp20) cc_final: 0.6972 (pp20)
REVERT: A  692 MET cc_start: 0.8023 (tpp) cc_final: 0.7722 (tpp)
REVERT: A  896 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8299 (mtp-110)
REVERT: A  984 GLN cc_start: 0.7569 (tp40) cc_final: 0.7306 (tp-100)
REVERT: A 1145 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5768 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8741 (t0)
REVERT: A 1578 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8077 (mp0)
REVERT: C   16 LYS cc_start: 0.7322 (mmmt) cc_final: 0.7069 (mmtm)
REVERT: C   98 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7667 (mp0)
REVERT: C  204 PHE cc_start: 0.8176 (t80) cc_final: 0.7899 (t80)
REVERT: C  229 MET cc_start: 0.8134 (tmm) cc_final: 0.7867 (tmm)
REVERT: C  265 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8379 (mt-10)
REVERT: C  377 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7485 (mmm160)
  outliers start: 49
  outliers final: 38
  residues processed: 142
  average time/residue: 0.3287
  time to fit residues: 71.1426
Evaluate side-chains
  141 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 99
  time to evaluate  : 2.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  445 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  702 THR
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  859 GLU
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1483 HIS
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1516 ASN
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1578 GLU
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue   90 PHE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  490 VAL
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 209 optimal weight:    0.5980
   chunk 152 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 191 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 14 optimal weight:    0.2980
   chunk 170 optimal weight:    6.9990
   chunk 192 optimal weight:    1.9990
   chunk 184 optimal weight:    0.0270
   chunk 198 optimal weight:    4.9990
   chunk 159 optimal weight:    0.1980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
A 988 GLN
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.109568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.080102 restraints weight = 34851.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.62
r_work: 0.2924 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  18605  Z= 0.097
  Angle     :  0.549   9.926  25246  Z= 0.283
  Chirality :  0.041   0.199   2635
  Planarity :  0.004   0.061   3169
  Dihedral  : 12.702 173.774   2912
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 20.18 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.18), residues: 2105
  helix:  1.54 (0.22), residues: 607
  sheet: -0.16 (0.30), residues: 307
  loop : -2.78 (0.16), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1063 
 HIS   0.003   0.000   HIS A1279 
 PHE   0.017   0.001   PHE A1407 
 TYR   0.008   0.001   TYR C 209 
 ARG   0.006   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02680 (  533)
  hydrogen bonds       : angle       3.82300 ( 1566)
  SS BOND              : bond        0.00548 (    2)
  SS BOND              : angle       2.36939 (    4)
  covalent geometry    : bond        0.00212 (18603)
  covalent geometry    : angle       0.54854 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 1.962 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8568 (mttt)
REVERT: A  174 ASN cc_start: 0.8833 (t0) cc_final: 0.8300 (m-40)
REVERT: A  311 ASP cc_start: 0.8742 (t0) cc_final: 0.7859 (m-30)
REVERT: A  391 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7317 (mmtt)
REVERT: A  692 MET cc_start: 0.7904 (tpp) cc_final: 0.7614 (tpp)
REVERT: A  896 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.8196 (mtp-110)
REVERT: A  984 GLN cc_start: 0.7711 (tp40) cc_final: 0.7343 (tp-100)
REVERT: A  988 GLN cc_start: 0.8596 (pt0) cc_final: 0.8239 (pm20)
REVERT: A 1145 GLU cc_start: 0.6094 (mm-30) cc_final: 0.5810 (mm-30)
REVERT: A 1539 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.7940 (t0)
REVERT: A 1578 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8151 (mp0)
REVERT: C   16 LYS cc_start: 0.7431 (mmmt) cc_final: 0.7033 (mmtm)
REVERT: C  229 MET cc_start: 0.8149 (tmm) cc_final: 0.7891 (tmm)
REVERT: C  265 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8397 (mt-10)
REVERT: C  377 ARG cc_start: 0.8002 (mmp-170) cc_final: 0.7478 (mmm160)
  outliers start: 31
  outliers final: 20
  residues processed: 143
  average time/residue: 0.3600
  time to fit residues: 77.1494
Evaluate side-chains
  131 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 2.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  859 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1221 ASP
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1578 GLU
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue   90 PHE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 187 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 152 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 119 optimal weight:    0.0670
   chunk 111 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 210 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1452 ASN
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 292 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.074083 restraints weight = 35146.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.58
r_work: 0.2812 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  18605  Z= 0.253
  Angle     :  0.683  11.150  25246  Z= 0.353
  Chirality :  0.047   0.194   2635
  Planarity :  0.005   0.062   3169
  Dihedral  : 12.971 177.240   2908
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.24 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.18), residues: 2105
  helix:  1.29 (0.22), residues: 613
  sheet: -0.17 (0.29), residues: 311
  loop : -2.92 (0.16), residues: 1181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1063 
 HIS   0.005   0.001   HIS A 741 
 PHE   0.015   0.002   PHE A1013 
 TYR   0.013   0.001   TYR C 325 
 ARG   0.006   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  533)
  hydrogen bonds       : angle       4.19001 ( 1566)
  SS BOND              : bond        0.01091 (    2)
  SS BOND              : angle       3.37015 (    4)
  covalent geometry    : bond        0.00606 (18603)
  covalent geometry    : angle       0.68182 (25242)

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

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

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4210 Ramachandran restraints generated.
    2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 2.098 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8500 (tttt)
REVERT: A  311 ASP cc_start: 0.8755 (t0) cc_final: 0.7772 (m-30)
REVERT: A  391 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7563 (mmtt)
REVERT: A  431 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8353 (mt0)
REVERT: A 1145 GLU cc_start: 0.5868 (mm-30) cc_final: 0.5429 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.7972 (t0)
REVERT: A 1578 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8149 (mp0)
REVERT: C   16 LYS cc_start: 0.7353 (mmmt) cc_final: 0.7079 (mmtm)
REVERT: C   98 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7722 (mp0)
REVERT: C  229 MET cc_start: 0.8162 (tmm) cc_final: 0.7842 (tmm)
REVERT: C  265 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8458 (mp0)
REVERT: C  377 ARG cc_start: 0.7921 (mmp-170) cc_final: 0.7422 (mmm160)
  outliers start: 33
  outliers final: 25
  residues processed: 127
  average time/residue: 0.3344
  time to fit residues: 65.8481
Evaluate side-chains
  123 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 2.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 GLN
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  702 THR
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  840 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1578 GLU
Chi-restraints excluded: chain A residue 1600 TRP
Chi-restraints excluded: chain C residue   90 PHE
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 GLU
Chi-restraints excluded: chain C residue  503 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 206 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0970
   chunk 109 optimal weight:    1.9990
   chunk 167 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0070
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1452 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.105981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.076894 restraints weight = 35381.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.49
r_work: 0.2874 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18605  Z= 0.111
  Angle     :  0.583  10.802  25246  Z= 0.300
  Chirality :  0.042   0.193   2635
  Planarity :  0.004   0.065   3169
  Dihedral  : 12.763 174.844   2908
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 20.51 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.18), residues: 2105
  helix:  1.48 (0.22), residues: 613
  sheet: -0.11 (0.30), residues: 302
  loop : -2.77 (0.16), residues: 1190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1063 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.015   0.001   PHE A1407 
 TYR   0.008   0.001   TYR A1126 
 ARG   0.007   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  533)
  hydrogen bonds       : angle       3.93285 ( 1566)
  SS BOND              : bond        0.00682 (    2)
  SS BOND              : angle       2.59522 (    4)
  covalent geometry    : bond        0.00253 (18603)
  covalent geometry    : angle       0.58197 (25242)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10728.97 seconds
wall clock time: 187 minutes 38.67 seconds (11258.67 seconds total)