Starting phenix.real_space_refine
on Sat Aug 23 08:17:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qm6_4589/08_2025/6qm6_4589.map"
  }
  resolution = 3.7
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    7056      2.51       5
     N    1814      2.21       5
     O    1942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  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: 10852
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 672, 5426
          Classifications: {'peptide': 672}
          Link IDs: {'PTRANS': 29, 'TRANS': 642}
          Chain breaks: 5
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.70, per 1000 atoms: 0.43
  Number of scatterers: 10852
  At special positions: 0
  Unit cell: (88.044, 141.68, 107.272, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1942      8.00
     N    1814      7.00
     C    7056      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 509.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      70.5% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 50
      removed outlier: 3.753A  pdb=" N   THR A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.776A  pdb=" N   LYS A  78 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 111 through 123
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 3.540A  pdb=" N   ASN A 138 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA A 139 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 135 through 139'
    Processing helix  chain 'A' and resid 152 through 166
      removed outlier: 3.573A  pdb=" N   SER A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 199
      removed outlier: 3.779A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   GLU A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   SER A 184 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   VAL A 185 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   TYR A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 244
      removed outlier: 3.513A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
    Processing helix  chain 'A' and resid 290 through 318
      removed outlier: 3.554A  pdb=" N   LEU A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A 318 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 338
      removed outlier: 3.519A  pdb=" N   PHE A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 359
      removed outlier: 3.644A  pdb=" N   SER A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET A 357 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASN A 359 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 4.252A  pdb=" N   VAL A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A 382 " --> pdb=" O   ASN A 378 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 415
      removed outlier: 4.154A  pdb=" N   PHE A 403 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TRP A 407 " --> pdb=" O   PHE A 403 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN A 412 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 442
    Processing helix  chain 'A' and resid 442 through 453
      removed outlier: 3.630A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 467
      removed outlier: 3.504A  pdb=" N   GLN A 464 " --> pdb=" O   GLN A 460 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 494
      removed outlier: 3.919A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 516
      removed outlier: 4.085A  pdb=" N   ASP A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR A 513 " --> pdb=" O   MET A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 546
      removed outlier: 3.623A  pdb=" N   ASN A 531 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TRP A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 534 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.680A  pdb=" N   SER A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 581 " --> pdb=" O   SER A 577 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 627
      removed outlier: 3.584A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 649
      removed outlier: 3.540A  pdb=" N   GLN A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 634 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 638 " --> pdb=" O   LYS A 634 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS A 643 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU A 649 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 678
      removed outlier: 3.637A  pdb=" N   ILE A 670 " --> pdb=" O   HIS A 666 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   THR A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A 673 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU A 676 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLU A 678 " --> pdb=" O   ALA A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 693
    Processing helix  chain 'A' and resid 700 through 718
      removed outlier: 3.914A  pdb=" N   THR A 704 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET A 711 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A 712 " --> pdb=" O   GLY A 708 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLU A 713 " --> pdb=" O   ARG A 709 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN A 714 " --> pdb=" O   ARG A 710 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA A 718 " --> pdb=" O   GLN A 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 50
      removed outlier: 3.753A  pdb=" N   THR B  48 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B  49 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.776A  pdb=" N   LYS B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS B  90 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 111 through 123
    Processing helix  chain 'B' and resid 135 through 139
      removed outlier: 3.539A  pdb=" N   ASN B 138 " --> pdb=" O   THR B 135 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA B 139 " --> pdb=" O   PRO B 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 135 through 139'
    Processing helix  chain 'B' and resid 152 through 166
      removed outlier: 3.573A  pdb=" N   SER B 165 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS B 166 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 199
      removed outlier: 3.779A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS B 180 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   GLU B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   SER B 184 " --> pdb=" O   LYS B 180 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   VAL B 185 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   TYR B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE B 198 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 244
      removed outlier: 3.513A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL B 229 " --> pdb=" O   GLY B 225 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 289
    Processing helix  chain 'B' and resid 290 through 318
      removed outlier: 3.554A  pdb=" N   LEU B 305 " --> pdb=" O   ALA B 301 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   THR B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 338
      removed outlier: 3.518A  pdb=" N   PHE B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 359
      removed outlier: 3.644A  pdb=" N   SER B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   MET B 357 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASN B 359 " --> pdb=" O   ASN B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 4.252A  pdb=" N   VAL B 376 " --> pdb=" O   GLN B 372 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B 382 " --> pdb=" O   ASN B 378 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 415
      removed outlier: 4.153A  pdb=" N   PHE B 403 " --> pdb=" O   ILE B 399 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TRP B 407 " --> pdb=" O   PHE B 403 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN B 412 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 442
    Processing helix  chain 'B' and resid 442 through 453
      removed outlier: 3.630A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 467
      removed outlier: 3.504A  pdb=" N   GLN B 464 " --> pdb=" O   GLN B 460 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 494
      removed outlier: 3.919A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 516
      removed outlier: 4.086A  pdb=" N   ASP B 503 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU B 506 " --> pdb=" O   GLY B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 546
      removed outlier: 3.623A  pdb=" N   ASN B 531 " --> pdb=" O   CYS B 527 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TRP B 533 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL B 534 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER B 546 " --> pdb=" O   LYS B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.681A  pdb=" N   SER B 576 " --> pdb=" O   GLY B 572 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR B 581 " --> pdb=" O   SER B 577 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 627
      removed outlier: 3.585A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA B 609 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 649
      removed outlier: 3.540A  pdb=" N   GLN B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS B 634 " --> pdb=" O   PRO B 630 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU B 638 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS B 643 " --> pdb=" O   ARG B 639 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 678
      removed outlier: 3.637A  pdb=" N   ILE B 670 " --> pdb=" O   HIS B 666 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR B 671 " --> pdb=" O   SER B 667 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU B 673 " --> pdb=" O   LYS B 669 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU B 676 " --> pdb=" O   ARG B 672 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLU B 678 " --> pdb=" O   ALA B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 693
    Processing helix  chain 'B' and resid 700 through 718
      removed outlier: 3.914A  pdb=" N   THR B 704 " --> pdb=" O   GLY B 700 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET B 711 " --> pdb=" O   ILE B 707 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B 712 " --> pdb=" O   GLY B 708 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLU B 713 " --> pdb=" O   ARG B 709 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN B 714 " --> pdb=" O   ARG B 710 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B 718 " --> pdb=" O   GLN B 714 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 3.576A  pdb=" N   PHE A  22 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268
      removed outlier: 3.725A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 267 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56
      removed outlier: 3.576A  pdb=" N   PHE B  22 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268
      removed outlier: 3.724A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA B 267 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    601 hydrogen bonds defined for protein.
    1797 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3436
        1.34 -     1.46: 2295
        1.46 -     1.58: 5335
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 11132
  Sorted by residual:
  bond pdb=" C   SER B 595 "
       pdb=" N   PRO B 596 "
    ideal  model  delta    sigma   weight residual
    1.330  1.372 -0.041 1.23e-02 6.61e+03 1.13e+01
  bond pdb=" C   SER A 595 "
       pdb=" N   PRO A 596 "
    ideal  model  delta    sigma   weight residual
    1.330  1.371 -0.041 1.23e-02 6.61e+03 1.12e+01
  bond pdb=" C   ILE B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 2.34e-02 1.83e+03 6.09e+00
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.334  1.391 -0.057 2.34e-02 1.83e+03 6.01e+00
  bond pdb=" N   GLU B  32 "
       pdb=" CA  GLU B  32 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.88e+00
  ... (remaining 11127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 14619
        1.98 -     3.97: 400
        3.97 -     5.95: 55
        5.95 -     7.93: 14
        7.93 -     9.91: 8
  Bond angle restraints: 15096
  Sorted by residual:
  angle pdb=" CA  ILE A 394 "
        pdb=" C   ILE A 394 "
        pdb=" N   PRO A 395 "
      ideal   model   delta    sigma   weight residual
     118.88  124.52   -5.64 1.54e+00 4.22e-01 1.34e+01
  angle pdb=" CA  ILE B 394 "
        pdb=" C   ILE B 394 "
        pdb=" N   PRO B 395 "
      ideal   model   delta    sigma   weight residual
     118.88  124.49   -5.61 1.54e+00 4.22e-01 1.33e+01
  angle pdb=" CA  GLU A  32 "
        pdb=" CB  GLU A  32 "
        pdb=" CG  GLU A  32 "
      ideal   model   delta    sigma   weight residual
     114.10  120.84   -6.74 2.00e+00 2.50e-01 1.13e+01
  angle pdb=" CA  GLU B  32 "
        pdb=" CB  GLU B  32 "
        pdb=" CG  GLU B  32 "
      ideal   model   delta    sigma   weight residual
     114.10  120.83   -6.73 2.00e+00 2.50e-01 1.13e+01
  angle pdb=" CA  THR A 340 "
        pdb=" C   THR A 340 "
        pdb=" N   PRO A 341 "
      ideal   model   delta    sigma   weight residual
     118.44  123.43   -4.99 1.59e+00 3.96e-01 9.83e+00
  ... (remaining 15091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.20: 5737
       16.20 -    32.40: 661
       32.40 -    48.59: 124
       48.59 -    64.79: 20
       64.79 -    80.99: 14
  Dihedral angle restraints: 6556
    sinusoidal: 2636
      harmonic: 3920
  Sorted by residual:
  dihedral pdb=" CA  HIS B 401 "
           pdb=" C   HIS B 401 "
           pdb=" N   PRO B 402 "
           pdb=" CA  PRO B 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.21   17.79     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  HIS A 401 "
           pdb=" C   HIS A 401 "
           pdb=" N   PRO A 402 "
           pdb=" CA  PRO A 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.24   17.76     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  THR A 340 "
           pdb=" C   THR A 340 "
           pdb=" N   PRO A 341 "
           pdb=" CA  PRO A 341 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.50   16.50     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 6553 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1283
       0.047 -    0.094: 271
       0.094 -    0.141: 82
       0.141 -    0.188: 18
       0.188 -    0.235: 2
  Chirality restraints: 1656
  Sorted by residual:
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  THR B 340 "
            pdb=" N   THR B 340 "
            pdb=" C   THR B 340 "
            pdb=" CB  THR B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  VAL A 229 "
            pdb=" CA  VAL A 229 "
            pdb=" CG1 VAL A 229 "
            pdb=" CG2 VAL A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 1653 not shown)

  Planarity restraints: 1916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 401 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.34e+00
        pdb=" N   PRO A 402 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 402 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 402 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 401 "    0.045 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO B 402 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 402 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 402 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 595 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.08e+00
        pdb=" N   PRO A 596 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 596 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 596 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1913 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3674
        2.85 -     3.36: 10232
        3.36 -     3.88: 17348
        3.88 -     4.39: 20232
        4.39 -     4.90: 34081
  Nonbonded interactions: 85567
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   PHE A 528 "
            pdb=" ND2 ASN A 532 "
     model   vdw
     2.376 3.120
  nonbonded pdb=" O   PHE B 528 "
            pdb=" ND2 ASN B 532 "
     model   vdw
     2.376 3.120
  nonbonded pdb=" O   GLN A 374 "
            pdb=" ND2 ASN A 378 "
     model   vdw
     2.382 3.120
  ... (remaining 85562 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.130
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
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      :  0.004   0.058  11132  Z= 0.207
  Angle     :  0.844   9.915  15096  Z= 0.500
  Chirality :  0.045   0.235   1656
  Planarity :  0.006   0.068   1916
  Dihedral  : 14.338  80.989   4012
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  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: -6.02 (0.14), residues: 1320
  helix: -4.55 (0.06), residues: 874
  sheet: -2.94 (0.54), residues: 50
  loop : -1.98 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  33 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.021   0.001   PHE A 205 
 TRP   0.015   0.001   TRP A 235 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (11132)
  covalent geometry    : angle       0.84357 (15096)
  hydrogen bonds       : bond        0.30865 (  601)
  hydrogen bonds       : angle      10.15334 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 TYR cc_start: 0.9496 (t80) cc_final: 0.9094 (t80)
REVERT: A  211 LEU cc_start: 0.9046 (tp) cc_final: 0.8834 (tt)
REVERT: A  286 LYS cc_start: 0.7578 (mttt) cc_final: 0.6672 (mmtt)
REVERT: A  507 MET cc_start: 0.8684 (mmp) cc_final: 0.8173 (mmt)
REVERT: B  211 LEU cc_start: 0.9074 (tp) cc_final: 0.8835 (tt)
REVERT: B  286 LYS cc_start: 0.7415 (mttt) cc_final: 0.6536 (mmtt)
REVERT: B  357 MET cc_start: 0.8451 (mtp) cc_final: 0.8234 (ttm)
REVERT: B  507 MET cc_start: 0.8816 (mmp) cc_final: 0.8361 (mmt)
REVERT: B  693 MET cc_start: 0.7774 (ppp) cc_final: 0.7475 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.1104
  time to fit residues: 34.4372
Evaluate side-chains
  151 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  42 GLN
A  98 HIS
A  99 ASN
A 143 HIS
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
A 461 GLN
A 510 GLN
A 532 ASN
B  17 ASN
B  42 GLN
B  98 HIS
B  99 ASN
B 143 HIS
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 HIS
B 461 GLN
B 510 GLN
B 532 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.110757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.082409 restraints weight = 19996.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.085020 restraints weight = 10546.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.086677 restraints weight = 7268.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.087555 restraints weight = 5889.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.088231 restraints weight = 5255.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11132  Z= 0.147
  Angle     :  0.593   7.208  15096  Z= 0.310
  Chirality :  0.040   0.182   1656
  Planarity :  0.005   0.042   1916
  Dihedral  :  4.388  15.710   1444
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.82 %
    Favored  : 86.22 %
  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: -2.79 (0.19), residues: 1320
  helix: -1.79 (0.14), residues: 892
  sheet: -0.80 (0.59), residues: 58
  loop : -1.63 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  82 
 TYR   0.016   0.001   TYR B 360 
 PHE   0.025   0.001   PHE A 205 
 TRP   0.020   0.002   TRP B 141 
 HIS   0.005   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11132)
  covalent geometry    : angle       0.59332 (15096)
  hydrogen bonds       : bond        0.04392 (  601)
  hydrogen bonds       : angle       4.36089 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 193
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 TYR cc_start: 0.9515 (t80) cc_final: 0.9159 (t80)
REVERT: A  197 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8347 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9082 (tp) cc_final: 0.8809 (tt)
REVERT: A  268 GLU cc_start: 0.7634 (tp30) cc_final: 0.7154 (tp30)
REVERT: A  277 LYS cc_start: 0.9016 (mttt) cc_final: 0.8539 (mmtp)
REVERT: A  286 LYS cc_start: 0.7478 (mttt) cc_final: 0.6670 (tttt)
REVERT: A  298 CYS cc_start: 0.8394 (m) cc_final: 0.8178 (m)
REVERT: A  697 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7492 (ptm160)
REVERT: B  211 LEU cc_start: 0.9144 (tp) cc_final: 0.8870 (tt)
REVERT: B  268 GLU cc_start: 0.7678 (tp30) cc_final: 0.7342 (tp30)
REVERT: B  274 GLU cc_start: 0.8200 (tt0) cc_final: 0.7625 (tm-30)
REVERT: B  286 LYS cc_start: 0.7180 (mttt) cc_final: 0.6363 (tttt)
REVERT: B  298 CYS cc_start: 0.8350 (m) cc_final: 0.8127 (m)
  outliers start: 11
  outliers final: 6
  residues processed: 199
  average time/residue: 0.0912
  time to fit residues: 27.1737
Evaluate side-chains
  166 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  697 ARG
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  626 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 291 GLN
A 378 ASN
A 532 ASN
B  79 GLN
B 378 ASN
B 532 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.106113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.077705 restraints weight = 20540.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.080147 restraints weight = 11028.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.081670 restraints weight = 7703.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.082567 restraints weight = 6298.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.082925 restraints weight = 5634.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  11132  Z= 0.313
  Angle     :  0.701   7.110  15096  Z= 0.363
  Chirality :  0.045   0.204   1656
  Planarity :  0.005   0.038   1916
  Dihedral  :  4.394  16.931   1444
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.34 %
    Favored  : 82.41 %
  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: -1.19 (0.22), residues: 1320
  helix: -0.43 (0.17), residues: 900
  sheet: -0.93 (0.60), residues: 68
  loop : -1.32 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 548 
 TYR   0.020   0.002   TYR A  26 
 PHE   0.028   0.002   PHE A 315 
 TRP   0.013   0.002   TRP A 561 
 HIS   0.005   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 (11132)
  covalent geometry    : angle       0.70100 (15096)
  hydrogen bonds       : bond        0.04806 (  601)
  hydrogen bonds       : angle       4.24136 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8406 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9169 (tp) cc_final: 0.8919 (tt)
REVERT: A  268 GLU cc_start: 0.7717 (tp30) cc_final: 0.7277 (tp30)
REVERT: A  274 GLU cc_start: 0.8303 (tt0) cc_final: 0.7669 (tm-30)
REVERT: A  697 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7538 (ptm160)
REVERT: B  211 LEU cc_start: 0.9172 (tp) cc_final: 0.8908 (tt)
REVERT: B  268 GLU cc_start: 0.7697 (tp30) cc_final: 0.7290 (tp30)
REVERT: B  274 GLU cc_start: 0.8376 (tt0) cc_final: 0.7767 (tm-30)
  outliers start: 26
  outliers final: 17
  residues processed: 166
  average time/residue: 0.0879
  time to fit residues: 22.3266
Evaluate side-chains
  153 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  625 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  697 ARG
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  626 LYS
Chi-restraints excluded: chain B residue  666 HIS
Chi-restraints excluded: chain B residue  701 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 95 optimal weight:    4.9990
   chunk 118 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   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 666 HIS
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.109583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.081161 restraints weight = 20333.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.083773 restraints weight = 10705.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.085406 restraints weight = 7398.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.086373 restraints weight = 6012.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.086836 restraints weight = 5352.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11132  Z= 0.144
  Angle     :  0.575  11.009  15096  Z= 0.289
  Chirality :  0.040   0.197   1656
  Planarity :  0.004   0.037   1916
  Dihedral  :  4.098  14.487   1444
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.86 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.23), residues: 1320
  helix:  0.34 (0.18), residues: 902
  sheet: -0.15 (0.65), residues: 58
  loop : -1.13 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  45 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.027   0.001   PHE B 315 
 TRP   0.013   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11132)
  covalent geometry    : angle       0.57494 (15096)
  hydrogen bonds       : bond        0.03714 (  601)
  hydrogen bonds       : angle       3.83801 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8339 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9148 (tp) cc_final: 0.8863 (tt)
REVERT: A  268 GLU cc_start: 0.7603 (tp30) cc_final: 0.7190 (tp30)
REVERT: A  298 CYS cc_start: 0.8211 (m) cc_final: 0.7902 (m)
REVERT: A  457 TYR cc_start: 0.6352 (t80) cc_final: 0.5776 (t80)
REVERT: A  697 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7578 (ptm160)
REVERT: B  211 LEU cc_start: 0.9173 (tp) cc_final: 0.8896 (tt)
REVERT: B  268 GLU cc_start: 0.7667 (tp30) cc_final: 0.7200 (tp30)
REVERT: B  298 CYS cc_start: 0.8220 (m) cc_final: 0.7900 (m)
REVERT: B  457 TYR cc_start: 0.6497 (t80) cc_final: 0.5951 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 181
  average time/residue: 0.0851
  time to fit residues: 23.6665
Evaluate side-chains
  166 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  697 ARG
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  574 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  626 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 126 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
B 291 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.080696 restraints weight = 20148.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.083279 restraints weight = 10637.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.084888 restraints weight = 7373.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.085777 restraints weight = 6003.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.086381 restraints weight = 5386.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  11132  Z= 0.163
  Angle     :  0.594  12.145  15096  Z= 0.296
  Chirality :  0.041   0.187   1656
  Planarity :  0.004   0.036   1916
  Dihedral  :  3.990  15.185   1444
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.07 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.24), residues: 1320
  helix:  0.74 (0.18), residues: 902
  sheet: -0.18 (0.67), residues: 58
  loop : -0.97 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  45 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.028   0.001   PHE A 315 
 TRP   0.013   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11132)
  covalent geometry    : angle       0.59363 (15096)
  hydrogen bonds       : bond        0.03774 (  601)
  hydrogen bonds       : angle       3.75105 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8349 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9151 (tp) cc_final: 0.8855 (tt)
REVERT: A  268 GLU cc_start: 0.7622 (tp30) cc_final: 0.7182 (tp30)
REVERT: A  298 CYS cc_start: 0.8211 (m) cc_final: 0.7900 (m)
REVERT: A  457 TYR cc_start: 0.6042 (t80) cc_final: 0.5547 (t80)
REVERT: A  677 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6821 (mm-30)
REVERT: A  697 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7633 (ptm160)
REVERT: B  211 LEU cc_start: 0.9114 (tp) cc_final: 0.8853 (tt)
REVERT: B  268 GLU cc_start: 0.7666 (tp30) cc_final: 0.7189 (tp30)
REVERT: B  298 CYS cc_start: 0.8256 (m) cc_final: 0.7938 (m)
REVERT: B  457 TYR cc_start: 0.6169 (t80) cc_final: 0.5725 (t80)
REVERT: B  677 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6670 (mm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 171
  average time/residue: 0.0838
  time to fit residues: 22.1484
Evaluate side-chains
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  697 ARG
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  574 ILE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  626 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 123 optimal weight:    0.0020
   chunk 78 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 101 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.083629 restraints weight = 20052.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.086301 restraints weight = 10443.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.087974 restraints weight = 7145.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.088962 restraints weight = 5762.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.089382 restraints weight = 5115.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11132  Z= 0.113
  Angle     :  0.576  10.618  15096  Z= 0.278
  Chirality :  0.039   0.172   1656
  Planarity :  0.004   0.034   1916
  Dihedral  :  3.837  13.411   1444
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.20 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.24), residues: 1320
  helix:  1.11 (0.18), residues: 904
  sheet: -0.18 (0.69), residues: 58
  loop : -0.91 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.050   0.001   PHE B 205 
 TRP   0.013   0.001   TRP A 227 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (11132)
  covalent geometry    : angle       0.57578 (15096)
  hydrogen bonds       : bond        0.03343 (  601)
  hydrogen bonds       : angle       3.51756 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8314 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9080 (tp) cc_final: 0.8793 (tt)
REVERT: A  241 ASP cc_start: 0.8288 (t0) cc_final: 0.8081 (t0)
REVERT: A  268 GLU cc_start: 0.7590 (tp30) cc_final: 0.7298 (tp30)
REVERT: A  298 CYS cc_start: 0.8235 (m) cc_final: 0.7915 (m)
REVERT: A  457 TYR cc_start: 0.5901 (t80) cc_final: 0.5428 (t80)
REVERT: B  211 LEU cc_start: 0.9091 (tp) cc_final: 0.8823 (tt)
REVERT: B  268 GLU cc_start: 0.7675 (tp30) cc_final: 0.7390 (tp30)
REVERT: B  286 LYS cc_start: 0.7896 (mttt) cc_final: 0.7070 (tttt)
REVERT: B  298 CYS cc_start: 0.8223 (m) cc_final: 0.7906 (m)
REVERT: B  445 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8169 (mm110)
REVERT: B  457 TYR cc_start: 0.5973 (t80) cc_final: 0.5559 (t80)
REVERT: B  693 MET cc_start: 0.7446 (ppp) cc_final: 0.7023 (tmm)
  outliers start: 23
  outliers final: 19
  residues processed: 183
  average time/residue: 0.0908
  time to fit residues: 25.6507
Evaluate side-chains
  170 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  626 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 97 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 127 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0470
   chunk 102 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.5482

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

Flipped N/Q/H residues before XYZ refinement:
B 460 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.109428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.081612 restraints weight = 20134.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.084206 restraints weight = 10484.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.085809 restraints weight = 7212.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.086773 restraints weight = 5848.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.087135 restraints weight = 5194.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11132  Z= 0.157
  Angle     :  0.600   9.896  15096  Z= 0.295
  Chirality :  0.041   0.181   1656
  Planarity :  0.004   0.035   1916
  Dihedral  :  3.842  13.672   1444
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.28 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.24), residues: 1320
  helix:  1.19 (0.18), residues: 902
  sheet: -0.21 (0.70), residues: 58
  loop : -0.78 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.016   0.001   TYR A  26 
 PHE   0.054   0.002   PHE B 205 
 TRP   0.017   0.001   TRP A 600 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (11132)
  covalent geometry    : angle       0.59969 (15096)
  hydrogen bonds       : bond        0.03619 (  601)
  hydrogen bonds       : angle       3.61859 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8345 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9097 (tp) cc_final: 0.8803 (tt)
REVERT: A  268 GLU cc_start: 0.7636 (tp30) cc_final: 0.7323 (tp30)
REVERT: A  298 CYS cc_start: 0.8199 (m) cc_final: 0.7891 (m)
REVERT: A  457 TYR cc_start: 0.5855 (t80) cc_final: 0.5329 (t80)
REVERT: B  211 LEU cc_start: 0.9107 (tp) cc_final: 0.8840 (tt)
REVERT: B  268 GLU cc_start: 0.7680 (tp30) cc_final: 0.7367 (tp30)
REVERT: B  298 CYS cc_start: 0.8244 (m) cc_final: 0.7931 (m)
REVERT: B  457 TYR cc_start: 0.5928 (t80) cc_final: 0.5521 (t80)
REVERT: B  693 MET cc_start: 0.7565 (ppp) cc_final: 0.7100 (tmm)
  outliers start: 36
  outliers final: 29
  residues processed: 180
  average time/residue: 0.0885
  time to fit residues: 24.9483
Evaluate side-chains
  178 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  460 GLN
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  626 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 90 optimal weight:    0.3980
   chunk 31 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 460 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.083966 restraints weight = 20127.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.086651 restraints weight = 10574.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.088326 restraints weight = 7285.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.089208 restraints weight = 5910.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.089876 restraints weight = 5287.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11132  Z= 0.111
  Angle     :  0.581   9.373  15096  Z= 0.285
  Chirality :  0.040   0.183   1656
  Planarity :  0.003   0.033   1916
  Dihedral  :  3.782  12.573   1444
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.54 %
    Favored  : 79.03 %
  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:  0.99 (0.24), residues: 1320
  helix:  1.33 (0.18), residues: 902
  sheet: -0.16 (0.71), residues: 58
  loop : -0.83 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  33 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.029   0.001   PHE B 315 
 TRP   0.016   0.001   TRP A 600 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (11132)
  covalent geometry    : angle       0.58127 (15096)
  hydrogen bonds       : bond        0.03321 (  601)
  hydrogen bonds       : angle       3.52954 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8309 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9093 (tp) cc_final: 0.8799 (tt)
REVERT: A  241 ASP cc_start: 0.8316 (t0) cc_final: 0.8079 (t0)
REVERT: A  268 GLU cc_start: 0.7643 (tp30) cc_final: 0.7329 (tp30)
REVERT: A  298 CYS cc_start: 0.8228 (m) cc_final: 0.7910 (m)
REVERT: A  457 TYR cc_start: 0.5809 (t80) cc_final: 0.5322 (t80)
REVERT: A  693 MET cc_start: 0.7521 (ppp) cc_final: 0.7249 (tmm)
REVERT: B  211 LEU cc_start: 0.9097 (tp) cc_final: 0.8819 (tt)
REVERT: B  268 GLU cc_start: 0.7682 (tp30) cc_final: 0.7383 (tp30)
REVERT: B  286 LYS cc_start: 0.7967 (mttt) cc_final: 0.7150 (tttt)
REVERT: B  298 CYS cc_start: 0.8253 (m) cc_final: 0.7929 (m)
REVERT: B  353 LYS cc_start: 0.7633 (mttp) cc_final: 0.7092 (ttpt)
REVERT: B  693 MET cc_start: 0.7518 (ppp) cc_final: 0.7075 (tmm)
  outliers start: 28
  outliers final: 25
  residues processed: 186
  average time/residue: 0.0842
  time to fit residues: 24.3923
Evaluate side-chains
  182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  460 GLN
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  574 ILE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  626 LYS
Chi-restraints excluded: chain B residue  701 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0470
   chunk 79 optimal weight:    6.9990
   chunk 130 optimal weight:    9.9990
   chunk 98 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0060
   chunk 122 optimal weight:    3.9990
   chunk 126 optimal weight:    6.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.7096

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

Flipped N/Q/H residues before XYZ refinement:
A 531 ASN
B 460 GLN
B 531 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.084548 restraints weight = 19948.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.087247 restraints weight = 10521.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.088921 restraints weight = 7283.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.089937 restraints weight = 5923.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.090376 restraints weight = 5268.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11132  Z= 0.113
  Angle     :  0.579   9.411  15096  Z= 0.284
  Chirality :  0.040   0.174   1656
  Planarity :  0.003   0.034   1916
  Dihedral  :  3.708  12.020   1444
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.72 %
    Favored  : 78.51 %
  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:  1.09 (0.24), residues: 1320
  helix:  1.43 (0.18), residues: 906
  sheet: -0.10 (0.73), residues: 58
  loop : -0.88 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  33 
 TYR   0.029   0.001   TYR B 457 
 PHE   0.052   0.001   PHE A 205 
 TRP   0.020   0.001   TRP B 533 
 HIS   0.002   0.000   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11132)
  covalent geometry    : angle       0.57859 (15096)
  hydrogen bonds       : bond        0.03268 (  601)
  hydrogen bonds       : angle       3.46109 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8317 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9084 (tp) cc_final: 0.8787 (tt)
REVERT: A  241 ASP cc_start: 0.8287 (t0) cc_final: 0.8079 (t0)
REVERT: A  268 GLU cc_start: 0.7646 (tp30) cc_final: 0.7325 (tp30)
REVERT: A  298 CYS cc_start: 0.8224 (m) cc_final: 0.7901 (m)
REVERT: A  353 LYS cc_start: 0.7601 (mttp) cc_final: 0.7070 (ttpt)
REVERT: A  445 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7957 (mm-40)
REVERT: A  457 TYR cc_start: 0.5765 (t80) cc_final: 0.5272 (t80)
REVERT: A  693 MET cc_start: 0.7494 (ppp) cc_final: 0.7225 (tmm)
REVERT: B  211 LEU cc_start: 0.9079 (tp) cc_final: 0.8802 (tt)
REVERT: B  268 GLU cc_start: 0.7687 (tp30) cc_final: 0.7381 (tp30)
REVERT: B  286 LYS cc_start: 0.7967 (mttt) cc_final: 0.7111 (ttpt)
REVERT: B  298 CYS cc_start: 0.8235 (m) cc_final: 0.7928 (m)
REVERT: B  353 LYS cc_start: 0.7601 (mttp) cc_final: 0.7030 (ttpt)
REVERT: B  445 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7965 (mm-40)
REVERT: B  693 MET cc_start: 0.7595 (ppp) cc_final: 0.7132 (tmm)
  outliers start: 32
  outliers final: 29
  residues processed: 183
  average time/residue: 0.0906
  time to fit residues: 25.5980
Evaluate side-chains
  183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  460 GLN
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  626 LYS
Chi-restraints excluded: chain B residue  701 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 460 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.084680 restraints weight = 19991.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.087350 restraints weight = 10558.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.089045 restraints weight = 7297.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.090046 restraints weight = 5919.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.090444 restraints weight = 5277.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11132  Z= 0.116
  Angle     :  0.593   9.922  15096  Z= 0.291
  Chirality :  0.040   0.172   1656
  Planarity :  0.003   0.033   1916
  Dihedral  :  3.692  11.903   1444
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.89 %
    Favored  : 78.42 %
  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:  1.21 (0.24), residues: 1320
  helix:  1.50 (0.18), residues: 904
  sheet: -0.05 (0.74), residues: 58
  loop : -0.80 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  33 
 TYR   0.014   0.001   TYR B  26 
 PHE   0.031   0.001   PHE B 315 
 TRP   0.020   0.001   TRP A 533 
 HIS   0.002   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11132)
  covalent geometry    : angle       0.59315 (15096)
  hydrogen bonds       : bond        0.03296 (  601)
  hydrogen bonds       : angle       3.47319 ( 1797)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8313 (mtt-85)
REVERT: A  211 LEU cc_start: 0.9075 (tp) cc_final: 0.8783 (tt)
REVERT: A  268 GLU cc_start: 0.7650 (tp30) cc_final: 0.7326 (tp30)
REVERT: A  298 CYS cc_start: 0.8213 (m) cc_final: 0.7919 (m)
REVERT: A  353 LYS cc_start: 0.7587 (mttp) cc_final: 0.7008 (ttpt)
REVERT: A  693 MET cc_start: 0.7530 (ppp) cc_final: 0.7263 (tmm)
REVERT: B  211 LEU cc_start: 0.9069 (tp) cc_final: 0.8796 (tt)
REVERT: B  268 GLU cc_start: 0.7684 (tp30) cc_final: 0.7378 (tp30)
REVERT: B  286 LYS cc_start: 0.7971 (mttt) cc_final: 0.7115 (ttpt)
REVERT: B  298 CYS cc_start: 0.8225 (m) cc_final: 0.7919 (m)
REVERT: B  353 LYS cc_start: 0.7569 (mttp) cc_final: 0.7000 (ttpt)
REVERT: B  693 MET cc_start: 0.7611 (ppp) cc_final: 0.7135 (tmm)
  outliers start: 31
  outliers final: 30
  residues processed: 177
  average time/residue: 0.0871
  time to fit residues: 23.7981
Evaluate side-chains
  178 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  626 LYS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  460 GLN
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  605 SER
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  626 LYS
Chi-restraints excluded: chain B residue  701 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 117 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
B 460 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.083356 restraints weight = 20114.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.085977 restraints weight = 10532.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.087641 restraints weight = 7246.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.088597 restraints weight = 5850.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.088946 restraints weight = 5218.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11132  Z= 0.147
  Angle     :  0.609  10.577  15096  Z= 0.301
  Chirality :  0.041   0.174   1656
  Planarity :  0.004   0.034   1916
  Dihedral  :  3.749  14.316   1444
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.89 %
    Favored  : 78.25 %
  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:  1.14 (0.24), residues: 1320
  helix:  1.44 (0.18), residues: 906
  sheet: -0.12 (0.73), residues: 58
  loop : -0.78 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  33 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.033   0.001   PHE B 315 
 TRP   0.022   0.001   TRP B 533 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11132)
  covalent geometry    : angle       0.60873 (15096)
  hydrogen bonds       : bond        0.03524 (  601)
  hydrogen bonds       : angle       3.54252 ( 1797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1833.11 seconds
wall clock time: 32 minutes 33.85 seconds (1953.85 seconds total)