Starting phenix.real_space_refine
on Sun Aug 24 08:45:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ynd_33959/08_2025/7ynd_33959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ynd_33959/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ynd_33959/08_2025/7ynd_33959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ynd_33959/08_2025/7ynd_33959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ynd_33959/08_2025/7ynd_33959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ynd_33959/08_2025/7ynd_33959.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.66, per 1000 atoms: 0.20
  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: 1.60
  Conformation dependent library (CDL) restraints added in 773.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 2.11
  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: 3.76

  Time building geometry restraints manager: 2.03 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:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     18.740
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.810
-------------------------------------------------------------------------------
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 : 8.11
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG A 441 
 TYR   0.013   0.002   TYR C  84 
 PHE   0.018   0.002   PHE A 776 
 TRP   0.016   0.002   TRP C 324 
 HIS   0.008   0.001   HIS A 691 

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

*********************** 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  : 0.632 
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: 0.1791
  time to fit residues: 41.4238
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  : 0.740 
-------------------------------------------------------------------------------
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 98 optimal weight:    4.9990
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    0.6980
   chunk 212 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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
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: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.106029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.076291 restraints weight = 34965.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.58
r_work: 0.2843 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.0995

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= 0.155
  Angle     :  0.635  12.471  25246  Z= 0.333
  Chirality :  0.044   0.207   2635
  Planarity :  0.005   0.074   3169
  Dihedral  : 13.285 177.551   2923
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.57 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.17), residues: 2105
  helix: -0.26 (0.21), residues: 611
  sheet: -1.10 (0.29), residues: 292
  loop : -3.49 (0.14), residues: 1202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 978 
 TYR   0.011   0.001   TYR C 325 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.011   0.001   TRP C 474 
 HIS   0.009   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (18603)
  covalent geometry    : angle       0.63375 (25242)
  SS BOND              : bond        0.00927 (    2)
  SS BOND              : angle       3.54295 (    4)
  hydrogen bonds       : bond        0.04364 (  533)
  hydrogen bonds       : angle       4.48071 ( 1566)

*********************** 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
  149 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8570 (mttt)
REVERT: A  311 ASP cc_start: 0.8684 (t0) cc_final: 0.7656 (m-30)
REVERT: A  391 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7474 (mmtt)
REVERT: A  473 MET cc_start: 0.9576 (mmt) cc_final: 0.9344 (mmp)
REVERT: A  503 ARG cc_start: 0.8880 (tmt170) cc_final: 0.8335 (ttt-90)
REVERT: A  559 MET cc_start: 0.9278 (mmm) cc_final: 0.8811 (mmt)
REVERT: A 1063 TRP cc_start: 0.7155 (m100) cc_final: 0.6914 (m100)
REVERT: A 1578 GLU cc_start: 0.8652 (mp0) cc_final: 0.7935 (mp0)
REVERT: C   16 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6469 (mttp)
REVERT: C  377 ARG cc_start: 0.8011 (mmp-170) cc_final: 0.7588 (mmm160)
  outliers start: 42
  outliers final: 20
  residues processed: 143
  average time/residue: 0.1258
  time to fit residues: 27.3450
Evaluate side-chains
  117 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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 52 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 148 optimal weight:    1.9990
   chunk 204 optimal weight:    8.9990
   chunk 211 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 159 optimal weight:    3.9990
   chunk 177 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 200 optimal weight:    0.0010
   chunk 179 optimal weight:    0.3980
   overall best weight:    1.2390

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.106125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.076439 restraints weight = 35035.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.58
r_work: 0.2851 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18605  Z= 0.146
  Angle     :  0.603  10.126  25246  Z= 0.314
  Chirality :  0.044   0.200   2635
  Planarity :  0.005   0.065   3169
  Dihedral  : 13.103 175.767   2912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.97 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.17), residues: 2105
  helix:  0.52 (0.22), residues: 608
  sheet: -0.84 (0.29), residues: 302
  loop : -3.29 (0.15), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 978 
 TYR   0.009   0.001   TYR C 325 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.010   0.001   TRP C 326 
 HIS   0.004   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (18603)
  covalent geometry    : angle       0.60203 (25242)
  SS BOND              : bond        0.00837 (    2)
  SS BOND              : angle       3.18614 (    4)
  hydrogen bonds       : bond        0.03968 (  533)
  hydrogen bonds       : angle       4.21242 ( 1566)

*********************** 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
  139 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8553 (mttt)
REVERT: A  311 ASP cc_start: 0.8715 (t0) cc_final: 0.7716 (m-30)
REVERT: A  473 MET cc_start: 0.9597 (mmt) cc_final: 0.9371 (mmp)
REVERT: A  503 ARG cc_start: 0.8852 (tmt170) cc_final: 0.8343 (ttt-90)
REVERT: A 1578 GLU cc_start: 0.8611 (mp0) cc_final: 0.8159 (mp0)
REVERT: C   16 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6563 (mttp)
REVERT: C  363 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7425 (pm20)
REVERT: C  377 ARG cc_start: 0.7995 (mmp-170) cc_final: 0.7562 (mmm160)
  outliers start: 37
  outliers final: 23
  residues processed: 134
  average time/residue: 0.1342
  time to fit residues: 26.9311
Evaluate side-chains
  119 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  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 38 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 165 optimal weight:    6.9990
   chunk 142 optimal weight:    0.8980
   chunk 195 optimal weight:   10.0000
   chunk 211 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 178 optimal weight:    2.9990
   chunk 201 optimal weight:    0.9980
   chunk 148 optimal weight:    3.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 691 HIS
A1280 ASN
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.104628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.074781 restraints weight = 35262.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.58
r_work: 0.2826 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  18605  Z= 0.203
  Angle     :  0.637  10.631  25246  Z= 0.332
  Chirality :  0.045   0.200   2635
  Planarity :  0.005   0.071   3169
  Dihedral  : 13.163 176.566   2912
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.05 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.18), residues: 2105
  helix:  0.77 (0.22), residues: 607
  sheet: -0.60 (0.29), residues: 302
  loop : -3.21 (0.15), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 373 
 TYR   0.011   0.001   TYR C 325 
 PHE   0.013   0.001   PHE A 187 
 TRP   0.012   0.001   TRP C 326 
 HIS   0.007   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (18603)
  covalent geometry    : angle       0.63543 (25242)
  SS BOND              : bond        0.00981 (    2)
  SS BOND              : angle       3.48226 (    4)
  hydrogen bonds       : bond        0.04586 (  533)
  hydrogen bonds       : angle       4.26027 ( 1566)

*********************** 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
  144 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 98
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8540 (mttt)
REVERT: A  311 ASP cc_start: 0.8770 (t0) cc_final: 0.7782 (m-30)
REVERT: A  984 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7626 (tp-100)
REVERT: A 1578 GLU cc_start: 0.8646 (mp0) cc_final: 0.8068 (mp0)
REVERT: C   16 LYS cc_start: 0.7333 (mmmt) cc_final: 0.6687 (mttp)
REVERT: C   98 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7779 (mp0)
REVERT: C  265 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8458 (mt-10)
REVERT: C  377 ARG cc_start: 0.8019 (mmp-170) cc_final: 0.7598 (mmm160)
  outliers start: 46
  outliers final: 31
  residues processed: 137
  average time/residue: 0.1352
  time to fit residues: 28.0500
Evaluate side-chains
  126 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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  389 LEU
Chi-restraints excluded: chain A residue  400 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  742 VAL
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 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  285 GLU
Chi-restraints excluded: chain C residue  353 LEU
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 47 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 172 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 468 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.104454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.074618 restraints weight = 35185.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.58
r_work: 0.2819 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  18605  Z= 0.204
  Angle     :  0.637  10.695  25246  Z= 0.332
  Chirality :  0.046   0.205   2635
  Planarity :  0.005   0.072   3169
  Dihedral  : 13.169 176.830   2912
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.19 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.13 (0.18), residues: 2105
  helix:  0.93 (0.22), residues: 607
  sheet: -0.59 (0.29), residues: 309
  loop : -3.13 (0.16), residues: 1189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 373 
 TYR   0.010   0.001   TYR C 325 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.013   0.001   TRP C 326 
 HIS   0.004   0.001   HIS A1313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (18603)
  covalent geometry    : angle       0.63543 (25242)
  SS BOND              : bond        0.00972 (    2)
  SS BOND              : angle       3.45887 (    4)
  hydrogen bonds       : bond        0.04540 (  533)
  hydrogen bonds       : angle       4.24449 ( 1566)

*********************** 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
  151 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8476 (mttt)
REVERT: A  104 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7480 (mtp180)
REVERT: A 1145 GLU cc_start: 0.6266 (mm-30) cc_final: 0.6026 (mm-30)
REVERT: A 1578 GLU cc_start: 0.8611 (mp0) cc_final: 0.8114 (mp0)
REVERT: C   16 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6708 (mttp)
REVERT: C   98 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7780 (mp0)
REVERT: C  265 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8450 (mt-10)
REVERT: C  377 ARG cc_start: 0.7961 (mmp-170) cc_final: 0.7549 (mmm160)
REVERT: C  399 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8045 (pp)
  outliers start: 50
  outliers final: 35
  residues processed: 145
  average time/residue: 0.1601
  time to fit residues: 35.4669
Evaluate side-chains
  131 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
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  104 ARG
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  400 VAL
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  742 VAL
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 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  399 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 13 optimal weight:    5.9990
   chunk 182 optimal weight:    8.9990
   chunk 152 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 208 optimal weight:    0.8980
   chunk 180 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 204 optimal weight:    6.9990
   chunk 169 optimal weight:    2.9990
   chunk 191 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 984 GLN
A1247 ASN
A1516 ASN
C 436 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.103612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.073750 restraints weight = 34926.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.60
r_work: 0.2809 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  18605  Z= 0.218
  Angle     :  0.654  11.076  25246  Z= 0.340
  Chirality :  0.046   0.207   2635
  Planarity :  0.005   0.073   3169
  Dihedral  : 13.189 177.156   2912
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.40 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.18), residues: 2105
  helix:  1.02 (0.22), residues: 607
  sheet: -0.42 (0.29), residues: 303
  loop : -3.11 (0.16), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1193 
 TYR   0.012   0.001   TYR C 325 
 PHE   0.014   0.002   PHE A 776 
 TRP   0.014   0.001   TRP C 326 
 HIS   0.009   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (18603)
  covalent geometry    : angle       0.65209 (25242)
  SS BOND              : bond        0.01006 (    2)
  SS BOND              : angle       3.52621 (    4)
  hydrogen bonds       : bond        0.04698 (  533)
  hydrogen bonds       : angle       4.25699 ( 1566)

*********************** 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
  158 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 100
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8470 (mttt)
REVERT: A  104 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7548 (mtp180)
REVERT: A  311 ASP cc_start: 0.8777 (t0) cc_final: 0.7763 (m-30)
REVERT: A  340 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8805 (tptt)
REVERT: A  473 MET cc_start: 0.9587 (mmt) cc_final: 0.9369 (mmp)
REVERT: A  692 MET cc_start: 0.8128 (tpp) cc_final: 0.7625 (tpt)
REVERT: A  984 GLN cc_start: 0.7551 (tp40) cc_final: 0.7204 (tp-100)
REVERT: A 1145 GLU cc_start: 0.5992 (mm-30) cc_final: 0.5600 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8837 (t0)
REVERT: A 1578 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8165 (mp0)
REVERT: C   16 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6703 (mttp)
REVERT: C   98 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7800 (mp0)
REVERT: C  265 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8399 (mt-10)
REVERT: C  377 ARG cc_start: 0.7896 (mmp-170) cc_final: 0.7505 (mmm160)
REVERT: C  399 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (pp)
  outliers start: 58
  outliers final: 42
  residues processed: 149
  average time/residue: 0.1604
  time to fit residues: 36.3775
Evaluate side-chains
  139 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 92
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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  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  717 GLU
Chi-restraints excluded: chain A residue  742 VAL
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 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  399 LEU
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 36 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 189 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 155 optimal weight:    2.9990
   chunk 210 optimal weight:    3.9990
   chunk 174 optimal weight:    1.9990
   chunk 153 optimal weight:    6.9990
   chunk 188 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.104586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.074846 restraints weight = 35188.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.58
r_work: 0.2827 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1612

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= 0.184
  Angle     :  0.634  10.962  25246  Z= 0.329
  Chirality :  0.045   0.215   2635
  Planarity :  0.005   0.072   3169
  Dihedral  : 13.143 176.825   2912
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.73 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.18), residues: 2105
  helix:  1.13 (0.22), residues: 609
  sheet: -0.39 (0.29), residues: 303
  loop : -3.07 (0.16), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1193 
 TYR   0.011   0.001   TYR C 325 
 PHE   0.015   0.001   PHE A 776 
 TRP   0.014   0.001   TRP C 326 
 HIS   0.008   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (18603)
  covalent geometry    : angle       0.63279 (25242)
  SS BOND              : bond        0.00934 (    2)
  SS BOND              : angle       3.34904 (    4)
  hydrogen bonds       : bond        0.04295 (  533)
  hydrogen bonds       : angle       4.19015 ( 1566)

*********************** 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: 54
    poor density    : 100
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8487 (mttt)
REVERT: A  104 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7488 (mtp180)
REVERT: A  311 ASP cc_start: 0.8770 (t0) cc_final: 0.7738 (m-30)
REVERT: A  473 MET cc_start: 0.9597 (mmt) cc_final: 0.9351 (mmp)
REVERT: A  692 MET cc_start: 0.8152 (tpp) cc_final: 0.7749 (tpt)
REVERT: A  984 GLN cc_start: 0.7618 (tp40) cc_final: 0.7209 (tp-100)
REVERT: A 1145 GLU cc_start: 0.5912 (mm-30) cc_final: 0.5492 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8784 (t0)
REVERT: A 1578 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8181 (mp0)
REVERT: C   16 LYS cc_start: 0.7308 (mmmt) cc_final: 0.7019 (mmtm)
REVERT: C   98 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7736 (mp0)
REVERT: C  265 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8380 (mt-10)
REVERT: C  377 ARG cc_start: 0.7920 (mmp-170) cc_final: 0.7511 (mmm160)
  outliers start: 54
  outliers final: 42
  residues processed: 144
  average time/residue: 0.1633
  time to fit residues: 35.3780
Evaluate side-chains
  142 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 97
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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   99 LEU
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  176 VAL
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  717 GLU
Chi-restraints excluded: chain A residue  742 VAL
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  955 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 1247 ASN
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1312 CYS
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 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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 203 optimal weight:    0.9990
   chunk 143 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 180 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.076232 restraints weight = 34911.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.60
r_work: 0.2852 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18605  Z= 0.137
  Angle     :  0.597  10.774  25246  Z= 0.309
  Chirality :  0.044   0.205   2635
  Planarity :  0.005   0.068   3169
  Dihedral  : 13.028 175.763   2912
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.00 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.18), residues: 2105
  helix:  1.29 (0.22), residues: 609
  sheet: -0.32 (0.29), residues: 303
  loop : -2.99 (0.16), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1193 
 TYR   0.009   0.001   TYR C 325 
 PHE   0.014   0.001   PHE A 776 
 TRP   0.015   0.001   TRP C 326 
 HIS   0.008   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (18603)
  covalent geometry    : angle       0.59621 (25242)
  SS BOND              : bond        0.00750 (    2)
  SS BOND              : angle       2.98785 (    4)
  hydrogen bonds       : bond        0.03676 (  533)
  hydrogen bonds       : angle       4.06119 ( 1566)

*********************** 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
  158 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 105
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8489 (mttt)
REVERT: A  104 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7390 (mtp180)
REVERT: A  311 ASP cc_start: 0.8758 (t0) cc_final: 0.7776 (m-30)
REVERT: A  340 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8761 (tptt)
REVERT: A  431 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8293 (mt0)
REVERT: A  473 MET cc_start: 0.9601 (mmt) cc_final: 0.9341 (mmp)
REVERT: A  633 GLU cc_start: 0.7407 (pp20) cc_final: 0.6998 (pp20)
REVERT: A  692 MET cc_start: 0.8154 (tpp) cc_final: 0.7791 (tpt)
REVERT: A  896 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8326 (mtp-110)
REVERT: A  984 GLN cc_start: 0.7730 (tp40) cc_final: 0.7254 (tp-100)
REVERT: A 1145 GLU cc_start: 0.5901 (mm-30) cc_final: 0.5511 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8750 (t0)
REVERT: A 1578 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8250 (mp0)
REVERT: C   16 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7087 (mmtm)
REVERT: C   98 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7686 (mp0)
REVERT: C  229 MET cc_start: 0.8111 (tmm) cc_final: 0.7801 (tmm)
REVERT: C  265 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8387 (mt-10)
REVERT: C  377 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7485 (mmm160)
  outliers start: 53
  outliers final: 37
  residues processed: 151
  average time/residue: 0.1666
  time to fit residues: 37.4313
Evaluate side-chains
  145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   19 LYS
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  414 THR
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  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  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  955 SER
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1247 ASN
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 1386 VAL
Chi-restraints excluded: chain A residue 1399 SER
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  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 187 optimal weight:    4.9990
   chunk 112 optimal weight:    9.9990
   chunk 58 optimal weight:    0.3980
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 164 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.106366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.076769 restraints weight = 34689.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.57
r_work: 0.2864 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18605  Z= 0.132
  Angle     :  0.589  10.361  25246  Z= 0.305
  Chirality :  0.043   0.199   2635
  Planarity :  0.004   0.066   3169
  Dihedral  : 12.945 175.340   2912
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.37 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.18), residues: 2105
  helix:  1.39 (0.22), residues: 607
  sheet: -0.24 (0.30), residues: 303
  loop : -2.90 (0.16), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1193 
 TYR   0.008   0.001   TYR A 866 
 PHE   0.014   0.001   PHE A 776 
 TRP   0.016   0.001   TRP A1063 
 HIS   0.008   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (18603)
  covalent geometry    : angle       0.58802 (25242)
  SS BOND              : bond        0.00722 (    2)
  SS BOND              : angle       2.85782 (    4)
  hydrogen bonds       : bond        0.03561 (  533)
  hydrogen bonds       : angle       4.01023 ( 1566)

*********************** 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
  148 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 103
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8561 (mttt)
REVERT: A  311 ASP cc_start: 0.8756 (t0) cc_final: 0.7778 (m-30)
REVERT: A  340 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (tptt)
REVERT: A  391 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7314 (mmtt)
REVERT: A  431 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8265 (mt0)
REVERT: A  473 MET cc_start: 0.9634 (mmt) cc_final: 0.9377 (mmp)
REVERT: A  633 GLU cc_start: 0.7061 (pp20) cc_final: 0.6852 (pp20)
REVERT: A  896 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.8262 (mtp-110)
REVERT: A 1145 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5581 (mm-30)
REVERT: A 1539 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8729 (t0)
REVERT: A 1578 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8115 (mp0)
REVERT: C   16 LYS cc_start: 0.7393 (mmmt) cc_final: 0.7125 (mmtm)
REVERT: C   98 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7632 (mp0)
REVERT: C  229 MET cc_start: 0.8118 (tmm) cc_final: 0.7816 (tmm)
REVERT: C  265 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8373 (mt-10)
REVERT: C  377 ARG cc_start: 0.7959 (mmp-170) cc_final: 0.7468 (mmm160)
  outliers start: 45
  outliers final: 39
  residues processed: 143
  average time/residue: 0.1686
  time to fit residues: 36.0630
Evaluate side-chains
  145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 100
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   19 LYS
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  431 GLN
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  955 SER
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 1287 ILE
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1399 SER
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   90 PHE
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 GLU
Chi-restraints excluded: chain C residue  490 VAL
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 36 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 210 optimal weight:    0.7980
   chunk 152 optimal weight:    6.9990
   chunk 193 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 115 optimal weight:    4.9990
   chunk 201 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.105007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.075325 restraints weight = 34918.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.58
r_work: 0.2837 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  18605  Z= 0.181
  Angle     :  0.625  10.591  25246  Z= 0.323
  Chirality :  0.045   0.193   2635
  Planarity :  0.005   0.068   3169
  Dihedral  : 12.989 176.137   2912
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.32 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.70 (0.18), residues: 2105
  helix:  1.37 (0.22), residues: 607
  sheet: -0.23 (0.30), residues: 303
  loop : -2.92 (0.16), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1193 
 TYR   0.010   0.001   TYR C 198 
 PHE   0.014   0.001   PHE A 776 
 TRP   0.016   0.001   TRP A1063 
 HIS   0.008   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (18603)
  covalent geometry    : angle       0.62361 (25242)
  SS BOND              : bond        0.00854 (    2)
  SS BOND              : angle       3.13798 (    4)
  hydrogen bonds       : bond        0.04177 (  533)
  hydrogen bonds       : angle       4.10561 ( 1566)

********************** 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
  148 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 99
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8515 (mttt)
REVERT: A  104 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7492 (mtp180)
REVERT: A  311 ASP cc_start: 0.8798 (t0) cc_final: 0.7790 (m-30)
REVERT: A  340 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8763 (tptt)
REVERT: A  431 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8310 (mt0)
REVERT: A  473 MET cc_start: 0.9615 (mmt) cc_final: 0.9365 (mmp)
REVERT: A  633 GLU cc_start: 0.7014 (pp20) cc_final: 0.6719 (pp20)
REVERT: A  692 MET cc_start: 0.8107 (tpp) cc_final: 0.7883 (tpp)
REVERT: A 1145 GLU cc_start: 0.5614 (mm-30) cc_final: 0.5211 (mm-30)
REVERT: A 1539 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8778 (t0)
REVERT: A 1578 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8131 (mp0)
REVERT: C   16 LYS cc_start: 0.7363 (mmmt) cc_final: 0.7081 (mmtm)
REVERT: C   98 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7700 (mp0)
REVERT: C  204 PHE cc_start: 0.8162 (t80) cc_final: 0.7908 (t80)
REVERT: C  229 MET cc_start: 0.8134 (tmm) cc_final: 0.7814 (tmm)
REVERT: C  265 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8373 (mt-10)
REVERT: C  377 ARG cc_start: 0.7931 (mmp-170) cc_final: 0.7458 (mmm160)
  outliers start: 49
  outliers final: 40
  residues processed: 141
  average time/residue: 0.1588
  time to fit residues: 34.0635
Evaluate side-chains
  141 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 95
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   19 LYS
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  414 THR
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  445 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  483 ILE
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  955 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 1287 ILE
Chi-restraints excluded: chain A residue 1312 CYS
Chi-restraints excluded: chain A residue 1399 SER
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   90 PHE
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 GLU
Chi-restraints excluded: chain C residue  490 VAL
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 100 optimal weight:    5.9990
   chunk 172 optimal weight:    2.9990
   chunk 174 optimal weight:    1.9990
   chunk 161 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 193 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

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 = 0.105950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.076287 restraints weight = 35043.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.59
r_work: 0.2854 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18605  Z= 0.146
  Angle     :  0.603  10.360  25246  Z= 0.310
  Chirality :  0.044   0.195   2635
  Planarity :  0.005   0.067   3169
  Dihedral  : 12.929 175.667   2912
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.43 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.18), residues: 2105
  helix:  1.36 (0.22), residues: 613
  sheet: -0.20 (0.30), residues: 303
  loop : -2.85 (0.16), residues: 1189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1193 
 TYR   0.008   0.001   TYR C 198 
 PHE   0.015   0.001   PHE A 776 
 TRP   0.015   0.001   TRP A1063 
 HIS   0.008   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (18603)
  covalent geometry    : angle       0.60193 (25242)
  SS BOND              : bond        0.00765 (    2)
  SS BOND              : angle       2.93656 (    4)
  hydrogen bonds       : bond        0.03735 (  533)
  hydrogen bonds       : angle       4.03331 ( 1566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5111.57 seconds
wall clock time: 88 minutes 15.84 seconds (5295.84 seconds total)