Starting phenix.real_space_refine
on Wed Nov 19 00:18:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6boa_7122/11_2025/6boa_7122.map"
  }
  resolution = 4.2
  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=   0.002 sd=   0.011
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     156      5.16       5
     C   12300      2.51       5
     N    3208      2.21       5
     O    3376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19040
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4760
          Classifications: {'peptide': 593}
          Link IDs: {'PTRANS': 26, 'TRANS': 566}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 4.28, per 1000 atoms: 0.22
  Number of scatterers: 19040
  At special positions: 0
  Unit cell: (139.7, 139.7, 125.4, 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     156     16.00
     O    3376      8.00
     N    3208      7.00
     C   12300      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: 1.68
  Conformation dependent library (CDL) restraints added in 681.0 milliseconds
  

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4504

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 4 sheets defined
      61.9% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 47
      removed outlier: 4.034A  pdb=" N   ARG A  33 " --> pdb=" O   TRP A  29 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP A  34 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 57 through 67
      removed outlier: 3.710A  pdb=" N   LYS A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR A  67 " --> pdb=" O   LYS A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 91 through 102
      removed outlier: 3.580A  pdb=" N   ALA A  95 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU A 100 " --> pdb=" O   MET A  96 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 3.861A  pdb=" N   ILE A 123 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 139
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 3.556A  pdb=" N   VAL A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.790A  pdb=" N   ILE A 202 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 211
      No H-bonds generated for 'chain 'A' and resid 209 through 211'
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.158A  pdb=" N   TYR A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN A 217 " --> pdb=" O   CYS A 213 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
    Processing helix  chain 'A' and resid 252 through 261
      removed outlier: 3.625A  pdb=" N   GLN A 261 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
      removed outlier: 3.755A  pdb=" N   ILE A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 309
      removed outlier: 3.720A  pdb=" N   LEU A 308 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 323
      removed outlier: 3.807A  pdb=" N   LEU A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 349
      removed outlier: 3.649A  pdb=" N   ILE A 335 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   CYS A 346 " --> pdb=" O   CYS A 342 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR A 349 " --> pdb=" O   MET A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 403
      removed outlier: 4.011A  pdb=" N   ILE A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 446
      removed outlier: 3.529A  pdb=" N   ALA A 433 " --> pdb=" O   ILE A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 464
      removed outlier: 3.558A  pdb=" N   MET A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 456 " --> pdb=" O   VAL A 452 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY A 461 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 467
      No H-bonds generated for 'chain 'A' and resid 465 through 467'
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 3.773A  pdb=" N   MET A 485 " --> pdb=" O   MET A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 512
      removed outlier: 4.489A  pdb=" N   TRP A 495 " --> pdb=" O   MET A 491 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   VAL A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 524
      removed outlier: 3.662A  pdb=" N   PHE A 523 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 520 through 524'
    Processing helix  chain 'A' and resid 525 through 538
      removed outlier: 3.663A  pdb=" N   LEU A 530 " --> pdb=" O   TYR A 526 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE A 531 " --> pdb=" O   PRO A 527 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 536 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 538 " --> pdb=" O   PHE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 580
      removed outlier: 3.587A  pdb=" N   ALA A 560 " --> pdb=" O   SER A 556 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE A 565 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   MET A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A 574 " --> pdb=" O   MET A 570 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ILE A 575 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A 576 " --> pdb=" O   ASN A 572 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   MET A 577 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP A 580 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 607
      removed outlier: 3.882A  pdb=" N   GLU A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   ASP A 590 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLU A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE A 597 " --> pdb=" O   TRP A 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 47
      removed outlier: 4.034A  pdb=" N   ARG B  33 " --> pdb=" O   TRP B  29 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP B  34 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN B  36 " --> pdb=" O   SER B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 55
    Processing helix  chain 'B' and resid 57 through 67
      removed outlier: 3.710A  pdb=" N   LYS B  63 " --> pdb=" O   GLN B  59 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TYR B  67 " --> pdb=" O   LYS B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 91 through 102
      removed outlier: 3.580A  pdb=" N   ALA B  95 " --> pdb=" O   ASN B  91 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL B  97 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLU B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA B 101 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 127
      removed outlier: 3.861A  pdb=" N   ILE B 123 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN B 127 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 139
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'B' and resid 165 through 173
      removed outlier: 3.557A  pdb=" N   VAL B 173 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 184
    Processing helix  chain 'B' and resid 198 through 205
      removed outlier: 3.789A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU B 203 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 4.158A  pdb=" N   TYR B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 217 " --> pdb=" O   CYS B 213 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU B 220 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 250
    Processing helix  chain 'B' and resid 252 through 261
      removed outlier: 3.625A  pdb=" N   GLN B 261 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 298
      removed outlier: 3.755A  pdb=" N   ILE B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 309
      removed outlier: 3.500A  pdb=" N   ILE B 307 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 308 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 323
      removed outlier: 3.806A  pdb=" N   LEU B 316 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 349
      removed outlier: 3.648A  pdb=" N   ILE B 335 " --> pdb=" O   MET B 331 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   CYS B 346 " --> pdb=" O   CYS B 342 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR B 349 " --> pdb=" O   MET B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 403
      removed outlier: 4.012A  pdb=" N   ILE B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 386 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR B 392 " --> pdb=" O   GLY B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 446
      removed outlier: 3.529A  pdb=" N   ALA B 433 " --> pdb=" O   ILE B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 464
      removed outlier: 3.559A  pdb=" N   MET B 454 " --> pdb=" O   GLU B 450 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B 456 " --> pdb=" O   VAL B 452 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLY B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 467
      No H-bonds generated for 'chain 'B' and resid 465 through 467'
    Processing helix  chain 'B' and resid 468 through 473
    Processing helix  chain 'B' and resid 480 through 486
      removed outlier: 3.773A  pdb=" N   MET B 485 " --> pdb=" O   MET B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 512
      removed outlier: 4.489A  pdb=" N   TRP B 495 " --> pdb=" O   MET B 491 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   VAL B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 524
      removed outlier: 3.662A  pdb=" N   PHE B 523 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 520 through 524'
    Processing helix  chain 'B' and resid 525 through 538
      removed outlier: 3.661A  pdb=" N   LEU B 530 " --> pdb=" O   TYR B 526 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE B 531 " --> pdb=" O   PRO B 527 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU B 536 " --> pdb=" O   SER B 532 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 538 " --> pdb=" O   PHE B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 580
      removed outlier: 3.586A  pdb=" N   ALA B 560 " --> pdb=" O   SER B 556 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE B 565 " --> pdb=" O   ALA B 561 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   MET B 570 " --> pdb=" O   ALA B 566 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU B 571 " --> pdb=" O   THR B 567 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 574 " --> pdb=" O   MET B 570 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ILE B 575 " --> pdb=" O   LEU B 571 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA B 576 " --> pdb=" O   ASN B 572 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET B 577 " --> pdb=" O   LEU B 573 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP B 580 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 607
      removed outlier: 3.881A  pdb=" N   GLU B 588 " --> pdb=" O   ARG B 584 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ASP B 590 " --> pdb=" O   ALA B 586 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   GLU B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE B 597 " --> pdb=" O   TRP B 593 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 47
      removed outlier: 4.034A  pdb=" N   ARG C  33 " --> pdb=" O   TRP C  29 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP C  34 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLN C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 55
    Processing helix  chain 'C' and resid 57 through 67
      removed outlier: 3.710A  pdb=" N   LYS C  63 " --> pdb=" O   GLN C  59 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU C  65 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR C  67 " --> pdb=" O   LYS C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 89
    Processing helix  chain 'C' and resid 91 through 102
      removed outlier: 3.580A  pdb=" N   ALA C  95 " --> pdb=" O   ASN C  91 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL C  97 " --> pdb=" O   GLU C  93 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLU C 100 " --> pdb=" O   MET C  96 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 127
      removed outlier: 3.861A  pdb=" N   ILE C 123 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN C 127 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 139
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'C' and resid 165 through 173
      removed outlier: 3.556A  pdb=" N   VAL C 173 " --> pdb=" O   PHE C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 184
    Processing helix  chain 'C' and resid 198 through 205
      removed outlier: 3.790A  pdb=" N   ILE C 202 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU C 203 " --> pdb=" O   VAL C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 211
      No H-bonds generated for 'chain 'C' and resid 209 through 211'
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 4.157A  pdb=" N   TYR C 216 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN C 217 " --> pdb=" O   CYS C 213 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU C 220 " --> pdb=" O   TYR C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 250
    Processing helix  chain 'C' and resid 252 through 261
      removed outlier: 3.625A  pdb=" N   GLN C 261 " --> pdb=" O   GLN C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 298
      removed outlier: 3.756A  pdb=" N   ILE C 297 " --> pdb=" O   LEU C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 309
      removed outlier: 3.500A  pdb=" N   ILE C 307 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C 308 " --> pdb=" O   ARG C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 323
      removed outlier: 3.807A  pdb=" N   LEU C 316 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 349
      removed outlier: 3.649A  pdb=" N   ILE C 335 " --> pdb=" O   MET C 331 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR C 336 " --> pdb=" O   LEU C 332 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   CYS C 346 " --> pdb=" O   CYS C 342 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR C 349 " --> pdb=" O   MET C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 403
      removed outlier: 4.012A  pdb=" N   ILE C 384 " --> pdb=" O   PRO C 380 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 386 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR C 392 " --> pdb=" O   GLY C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 446
      removed outlier: 3.529A  pdb=" N   ALA C 433 " --> pdb=" O   ILE C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 464
      removed outlier: 3.559A  pdb=" N   MET C 454 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE C 456 " --> pdb=" O   VAL C 452 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY C 461 " --> pdb=" O   ALA C 457 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN C 464 " --> pdb=" O   LEU C 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 465 through 467
      No H-bonds generated for 'chain 'C' and resid 465 through 467'
    Processing helix  chain 'C' and resid 468 through 473
    Processing helix  chain 'C' and resid 480 through 486
      removed outlier: 3.773A  pdb=" N   MET C 485 " --> pdb=" O   MET C 481 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 489 through 512
      removed outlier: 4.489A  pdb=" N   TRP C 495 " --> pdb=" O   MET C 491 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU C 496 " --> pdb=" O   ARG C 492 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL C 500 " --> pdb=" O   LEU C 496 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA C 505 " --> pdb=" O   ILE C 501 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER C 506 " --> pdb=" O   LEU C 502 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 524
      removed outlier: 3.661A  pdb=" N   PHE C 523 " --> pdb=" O   LEU C 520 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   TYR C 524 " --> pdb=" O   GLY C 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 520 through 524'
    Processing helix  chain 'C' and resid 525 through 538
      removed outlier: 3.663A  pdb=" N   LEU C 530 " --> pdb=" O   TYR C 526 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE C 531 " --> pdb=" O   PRO C 527 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C 536 " --> pdb=" O   SER C 532 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU C 538 " --> pdb=" O   PHE C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 554 through 580
      removed outlier: 3.586A  pdb=" N   ALA C 560 " --> pdb=" O   SER C 556 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE C 565 " --> pdb=" O   ALA C 561 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   MET C 570 " --> pdb=" O   ALA C 566 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU C 571 " --> pdb=" O   THR C 567 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU C 574 " --> pdb=" O   MET C 570 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE C 575 " --> pdb=" O   LEU C 571 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA C 576 " --> pdb=" O   ASN C 572 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   MET C 577 " --> pdb=" O   LEU C 573 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP C 580 " --> pdb=" O   ALA C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 607
      removed outlier: 3.882A  pdb=" N   GLU C 588 " --> pdb=" O   ARG C 584 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ASP C 590 " --> pdb=" O   ALA C 586 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   GLU C 591 " --> pdb=" O   HIS C 587 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE C 597 " --> pdb=" O   TRP C 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 47
      removed outlier: 4.033A  pdb=" N   ARG D  33 " --> pdb=" O   TRP D  29 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP D  34 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN D  36 " --> pdb=" O   SER D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 55
    Processing helix  chain 'D' and resid 57 through 67
      removed outlier: 3.710A  pdb=" N   LYS D  63 " --> pdb=" O   GLN D  59 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU D  65 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR D  67 " --> pdb=" O   LYS D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 89
    Processing helix  chain 'D' and resid 91 through 102
      removed outlier: 3.580A  pdb=" N   ALA D  95 " --> pdb=" O   ASN D  91 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL D  97 " --> pdb=" O   GLU D  93 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU D 100 " --> pdb=" O   MET D  96 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA D 101 " --> pdb=" O   VAL D  97 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 127
      removed outlier: 3.861A  pdb=" N   ILE D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN D 127 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 139
    Processing helix  chain 'D' and resid 149 through 153
    Processing helix  chain 'D' and resid 165 through 173
      removed outlier: 3.557A  pdb=" N   VAL D 173 " --> pdb=" O   PHE D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 184
    Processing helix  chain 'D' and resid 198 through 205
      removed outlier: 3.790A  pdb=" N   ILE D 202 " --> pdb=" O   THR D 198 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU D 203 " --> pdb=" O   VAL D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 211
      No H-bonds generated for 'chain 'D' and resid 209 through 211'
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 4.158A  pdb=" N   TYR D 216 " --> pdb=" O   ALA D 212 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN D 217 " --> pdb=" O   CYS D 213 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU D 220 " --> pdb=" O   TYR D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 250
    Processing helix  chain 'D' and resid 252 through 261
      removed outlier: 3.626A  pdb=" N   GLN D 261 " --> pdb=" O   GLN D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 298
      removed outlier: 3.755A  pdb=" N   ILE D 297 " --> pdb=" O   LEU D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 309
      removed outlier: 3.500A  pdb=" N   ILE D 307 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU D 308 " --> pdb=" O   ARG D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 323
      removed outlier: 3.806A  pdb=" N   LEU D 316 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG D 323 " --> pdb=" O   LEU D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 349
      removed outlier: 3.649A  pdb=" N   ILE D 335 " --> pdb=" O   MET D 331 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR D 336 " --> pdb=" O   LEU D 332 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   CYS D 346 " --> pdb=" O   CYS D 342 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR D 349 " --> pdb=" O   MET D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 403
      removed outlier: 4.012A  pdb=" N   ILE D 384 " --> pdb=" O   PRO D 380 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 390 " --> pdb=" O   LEU D 386 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 425 through 446
      removed outlier: 3.529A  pdb=" N   ALA D 433 " --> pdb=" O   ILE D 429 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 450 through 464
      removed outlier: 3.559A  pdb=" N   MET D 454 " --> pdb=" O   GLU D 450 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE D 456 " --> pdb=" O   VAL D 452 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY D 461 " --> pdb=" O   ALA D 457 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN D 464 " --> pdb=" O   LEU D 460 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 465 through 467
      No H-bonds generated for 'chain 'D' and resid 465 through 467'
    Processing helix  chain 'D' and resid 468 through 473
    Processing helix  chain 'D' and resid 480 through 486
      removed outlier: 3.774A  pdb=" N   MET D 485 " --> pdb=" O   MET D 481 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 512
      removed outlier: 4.489A  pdb=" N   TRP D 495 " --> pdb=" O   MET D 491 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU D 496 " --> pdb=" O   ARG D 492 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL D 500 " --> pdb=" O   LEU D 496 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA D 505 " --> pdb=" O   ILE D 501 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER D 506 " --> pdb=" O   LEU D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 520 through 524
      removed outlier: 3.661A  pdb=" N   PHE D 523 " --> pdb=" O   LEU D 520 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   TYR D 524 " --> pdb=" O   GLY D 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 520 through 524'
    Processing helix  chain 'D' and resid 525 through 538
      removed outlier: 3.662A  pdb=" N   LEU D 530 " --> pdb=" O   TYR D 526 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE D 531 " --> pdb=" O   PRO D 527 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU D 536 " --> pdb=" O   SER D 532 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU D 538 " --> pdb=" O   PHE D 534 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 580
      removed outlier: 3.586A  pdb=" N   ALA D 560 " --> pdb=" O   SER D 556 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE D 565 " --> pdb=" O   ALA D 561 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   MET D 570 " --> pdb=" O   ALA D 566 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LEU D 571 " --> pdb=" O   THR D 567 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   LEU D 574 " --> pdb=" O   MET D 570 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ILE D 575 " --> pdb=" O   LEU D 571 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA D 576 " --> pdb=" O   ASN D 572 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET D 577 " --> pdb=" O   LEU D 573 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP D 580 " --> pdb=" O   ALA D 576 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 607
      removed outlier: 3.882A  pdb=" N   GLU D 588 " --> pdb=" O   ARG D 584 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ASP D 590 " --> pdb=" O   ALA D 586 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   GLU D 591 " --> pdb=" O   HIS D 587 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE D 597 " --> pdb=" O   TRP D 593 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270
      removed outlier: 3.586A  pdb=" N   LEU A 631 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270
      removed outlier: 3.585A  pdb=" N   LEU B 631 " --> pdb=" O   TYR B 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270
      removed outlier: 3.586A  pdb=" N   LEU C 631 " --> pdb=" O   TYR C 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270
      removed outlier: 3.585A  pdb=" N   LEU D 631 " --> pdb=" O   TYR D 278 " (cutoff:3.500A)

    793 hydrogen bonds defined for protein.
    2292 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: 2.90

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6066
        1.34 -     1.46: 3998
        1.46 -     1.58: 9148
        1.58 -     1.70: 0
        1.70 -     1.81: 264
  Bond restraints: 19476
  Sorted by residual:
  bond pdb=" CA  HIS A 265 "
       pdb=" CB  HIS A 265 "
    ideal  model  delta    sigma   weight residual
    1.526  1.486  0.040 1.70e-02 3.46e+03 5.59e+00
  bond pdb=" CA  HIS B 265 "
       pdb=" CB  HIS B 265 "
    ideal  model  delta    sigma   weight residual
    1.526  1.486  0.040 1.70e-02 3.46e+03 5.59e+00
  bond pdb=" CA  HIS D 265 "
       pdb=" CB  HIS D 265 "
    ideal  model  delta    sigma   weight residual
    1.526  1.486  0.040 1.70e-02 3.46e+03 5.47e+00
  bond pdb=" CA  HIS C 265 "
       pdb=" CB  HIS C 265 "
    ideal  model  delta    sigma   weight residual
    1.526  1.486  0.040 1.70e-02 3.46e+03 5.44e+00
  bond pdb=" C   ARG D 350 "
       pdb=" N   PRO D 351 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.07e+00
  ... (remaining 19471 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 25958
        3.82 -     7.65: 390
        7.65 -    11.47: 76
       11.47 -    15.30: 0
       15.30 -    19.12: 8
  Bond angle restraints: 26432
  Sorted by residual:
  angle pdb=" N   MET C 554 "
        pdb=" CA  MET C 554 "
        pdb=" C   MET C 554 "
      ideal   model   delta    sigma   weight residual
     114.75  105.37    9.38 1.26e+00 6.30e-01 5.54e+01
  angle pdb=" N   MET D 554 "
        pdb=" CA  MET D 554 "
        pdb=" C   MET D 554 "
      ideal   model   delta    sigma   weight residual
     114.75  105.40    9.35 1.26e+00 6.30e-01 5.51e+01
  angle pdb=" N   MET A 554 "
        pdb=" CA  MET A 554 "
        pdb=" C   MET A 554 "
      ideal   model   delta    sigma   weight residual
     114.75  105.43    9.32 1.26e+00 6.30e-01 5.47e+01
  angle pdb=" N   MET B 554 "
        pdb=" CA  MET B 554 "
        pdb=" C   MET B 554 "
      ideal   model   delta    sigma   weight residual
     114.75  105.44    9.31 1.26e+00 6.30e-01 5.46e+01
  angle pdb=" N   LEU B 352 "
        pdb=" CA  LEU B 352 "
        pdb=" C   LEU B 352 "
      ideal   model   delta    sigma   weight residual
     110.91  119.41   -8.50 1.17e+00 7.31e-01 5.28e+01
  ... (remaining 26427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 10801
       16.00 -    32.01: 657
       32.01 -    48.01: 194
       48.01 -    64.02: 4
       64.02 -    80.02: 24
  Dihedral angle restraints: 11680
    sinusoidal: 4720
      harmonic: 6960
  Sorted by residual:
  dihedral pdb=" CA  GLY B 476 "
           pdb=" C   GLY B 476 "
           pdb=" N   PRO B 477 "
           pdb=" CA  PRO B 477 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.92  -41.08     0      5.00e+00 4.00e-02 6.75e+01
  dihedral pdb=" CA  GLY D 476 "
           pdb=" C   GLY D 476 "
           pdb=" N   PRO D 477 "
           pdb=" CA  PRO D 477 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -138.93  -41.07     0      5.00e+00 4.00e-02 6.75e+01
  dihedral pdb=" CA  GLY A 476 "
           pdb=" C   GLY A 476 "
           pdb=" N   PRO A 477 "
           pdb=" CA  PRO A 477 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.94  -41.06     0      5.00e+00 4.00e-02 6.74e+01
  ... (remaining 11677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 2266
       0.060 -    0.121: 610
       0.121 -    0.181: 96
       0.181 -    0.241: 24
       0.241 -    0.302: 16
  Chirality restraints: 3012
  Sorted by residual:
  chirality pdb=" CB  VAL D 452 "
            pdb=" CA  VAL D 452 "
            pdb=" CG1 VAL D 452 "
            pdb=" CG2 VAL D 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CB  VAL A 452 "
            pdb=" CA  VAL A 452 "
            pdb=" CG1 VAL A 452 "
            pdb=" CG2 VAL A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CB  VAL B 452 "
            pdb=" CA  VAL B 452 "
            pdb=" CG1 VAL B 452 "
            pdb=" CG2 VAL B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 3009 not shown)

  Planarity restraints: 3336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C 582 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.26e+00
        pdb=" C   HIS C 582 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   HIS C 582 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TRP C 583 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 582 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.25e+00
        pdb=" C   HIS B 582 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   HIS B 582 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TRP B 583 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D 582 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   HIS D 582 "    0.043 2.00e-02 2.50e+03
        pdb=" O   HIS D 582 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TRP D 583 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 3333 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 5598
        2.82 -     3.34: 17973
        3.34 -     3.86: 29160
        3.86 -     4.38: 33836
        4.38 -     4.90: 55257
  Nonbonded interactions: 141824
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 284 "
            pdb=" OG  SER A 291 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASP D 284 "
            pdb=" OG  SER D 291 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASP C 284 "
            pdb=" OG  SER C 291 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ASP B 284 "
            pdb=" OG  SER B 291 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR B 339 "
            pdb=" O   THR B 392 "
     model   vdw
     2.345 3.040
  ... (remaining 141819 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     17.150
  Find NCS groups from input model:        0.300
  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:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  19476  Z= 0.329
  Angle     :  1.289  19.123  26432  Z= 0.723
  Chirality :  0.060   0.302   3012
  Planarity :  0.008   0.061   3336
  Dihedral  : 11.912  80.021   7176
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  5.23 %
    Favored  : 93.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.53 %

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 are not related in a simple way.
  whole: -5.87 (0.11), residues: 2356
  helix: -4.01 (0.07), residues: 1344
  sheet: -4.97 (0.27), residues: 76
  loop : -3.34 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 615 
 TYR   0.019   0.003   TYR B 270 
 PHE   0.039   0.003   PHE B 162 
 TRP   0.031   0.004   TRP D 629 
 HIS   0.015   0.002   HIS D 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00712 (19476)
  covalent geometry    : angle       1.28868 (26432)
  hydrogen bonds       : bond        0.33153 (  793)
  hydrogen bonds       : angle      10.18384 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  782 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 746
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ARG cc_start: 0.8200 (mmt90) cc_final: 0.7941 (mmt90)
REVERT: A   96 MET cc_start: 0.8724 (mmm) cc_final: 0.8485 (mpp)
REVERT: A  168 SER cc_start: 0.9510 (m) cc_final: 0.9302 (p)
REVERT: A  178 ILE cc_start: 0.9214 (mp) cc_final: 0.8429 (mm)
REVERT: A  197 ASN cc_start: 0.9080 (m-40) cc_final: 0.8747 (m110)
REVERT: A  250 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8634 (mm-30)
REVERT: A  332 LEU cc_start: 0.9373 (tp) cc_final: 0.9038 (tt)
REVERT: A  434 PHE cc_start: 0.8502 (t80) cc_final: 0.8168 (t80)
REVERT: A  437 LEU cc_start: 0.9191 (mp) cc_final: 0.8311 (mp)
REVERT: A  453 PRO cc_start: 0.9560 (Cg_exo) cc_final: 0.9209 (Cg_endo)
REVERT: A  539 THR cc_start: 0.9079 (m) cc_final: 0.8842 (p)
REVERT: A  578 MET cc_start: 0.9186 (tpp) cc_final: 0.8938 (tpp)
REVERT: A  603 MET cc_start: 0.8089 (ttp) cc_final: 0.7846 (ttt)
REVERT: A  607 LYS cc_start: 0.8652 (mttp) cc_final: 0.8416 (mtmt)
REVERT: B   75 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7766 (mmt90)
REVERT: B   96 MET cc_start: 0.8709 (mmm) cc_final: 0.8402 (mmm)
REVERT: B  168 SER cc_start: 0.9523 (m) cc_final: 0.9161 (p)
REVERT: B  197 ASN cc_start: 0.9145 (m-40) cc_final: 0.8770 (m110)
REVERT: B  250 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8641 (mm-30)
REVERT: B  294 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7981 (mp0)
REVERT: B  316 LEU cc_start: 0.9407 (tp) cc_final: 0.9197 (tt)
REVERT: B  331 MET cc_start: 0.7263 (tmm) cc_final: 0.6787 (tmm)
REVERT: B  332 LEU cc_start: 0.9196 (tp) cc_final: 0.8891 (tt)
REVERT: B  339 TYR cc_start: 0.8633 (t80) cc_final: 0.8034 (t80)
REVERT: B  347 CYS cc_start: 0.8155 (t) cc_final: 0.7335 (t)
REVERT: B  389 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7099 (tp30)
REVERT: B  394 ILE cc_start: 0.9434 (mt) cc_final: 0.9194 (pt)
REVERT: B  432 TYR cc_start: 0.9495 (t80) cc_final: 0.9212 (t80)
REVERT: B  434 PHE cc_start: 0.8494 (t80) cc_final: 0.8154 (t80)
REVERT: B  479 THR cc_start: 0.4269 (OUTLIER) cc_final: 0.3921 (t)
REVERT: B  559 TYR cc_start: 0.9232 (t80) cc_final: 0.8962 (t80)
REVERT: B  628 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8385 (mtm-85)
REVERT: C   75 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7879 (mmt90)
REVERT: C   96 MET cc_start: 0.8799 (mmm) cc_final: 0.8506 (mmm)
REVERT: C  150 THR cc_start: 0.8972 (m) cc_final: 0.8747 (t)
REVERT: C  168 SER cc_start: 0.9508 (m) cc_final: 0.9123 (p)
REVERT: C  197 ASN cc_start: 0.9178 (m-40) cc_final: 0.8805 (m110)
REVERT: C  294 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7835 (mp0)
REVERT: C  297 ILE cc_start: 0.9231 (pp) cc_final: 0.8962 (mm)
REVERT: C  331 MET cc_start: 0.7201 (tmm) cc_final: 0.6953 (tmm)
REVERT: C  332 LEU cc_start: 0.9292 (tp) cc_final: 0.8998 (tt)
REVERT: C  339 TYR cc_start: 0.8576 (t80) cc_final: 0.7998 (t80)
REVERT: C  347 CYS cc_start: 0.8074 (t) cc_final: 0.7379 (t)
REVERT: C  389 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7058 (tp30)
REVERT: C  434 PHE cc_start: 0.8305 (t80) cc_final: 0.8082 (t80)
REVERT: C  456 PHE cc_start: 0.8655 (m-10) cc_final: 0.8296 (m-10)
REVERT: C  607 LYS cc_start: 0.8747 (mttp) cc_final: 0.8454 (mtmt)
REVERT: C  628 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8315 (mtm-85)
REVERT: D   96 MET cc_start: 0.8838 (mmm) cc_final: 0.8540 (mmm)
REVERT: D  197 ASN cc_start: 0.9142 (m-40) cc_final: 0.8701 (m110)
REVERT: D  250 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: D  294 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8023 (mp0)
REVERT: D  306 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8847 (tp40)
REVERT: D  332 LEU cc_start: 0.9277 (tp) cc_final: 0.9019 (tt)
REVERT: D  336 TYR cc_start: 0.8936 (t80) cc_final: 0.8505 (t80)
REVERT: D  342 CYS cc_start: 0.9165 (t) cc_final: 0.8873 (t)
REVERT: D  347 CYS cc_start: 0.8225 (t) cc_final: 0.7547 (t)
REVERT: D  394 ILE cc_start: 0.9396 (mt) cc_final: 0.9184 (pt)
REVERT: D  434 PHE cc_start: 0.8345 (t80) cc_final: 0.7983 (t80)
REVERT: D  456 PHE cc_start: 0.8888 (m-10) cc_final: 0.8589 (m-10)
REVERT: D  578 MET cc_start: 0.9287 (tpp) cc_final: 0.8746 (tpp)
REVERT: D  607 LYS cc_start: 0.8658 (mttp) cc_final: 0.8281 (mtmt)
  outliers start: 36
  outliers final: 10
  residues processed: 762
  average time/residue: 0.1322
  time to fit residues: 154.0141
Evaluate side-chains
  459 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 448
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 216 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    4.9990
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 235 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 HIS
B 174 ASN
B 357 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 582 HIS
C 174 ASN
C 357 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 582 HIS
D 174 ASN
D 206 GLN
D 357 ASN
D 464 ASN
D 582 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.089544 restraints weight = 46894.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.091941 restraints weight = 28779.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.093601 restraints weight = 20846.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.094614 restraints weight = 16903.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.095382 restraints weight = 14811.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  19476  Z= 0.198
  Angle     :  0.831  14.439  26432  Z= 0.420
  Chirality :  0.046   0.190   3012
  Planarity :  0.005   0.040   3336
  Dihedral  :  6.310  31.657   2592
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 10.02 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.14 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -3.52 (0.15), residues: 2356
  helix: -1.78 (0.12), residues: 1352
  sheet: -4.64 (0.31), residues: 76
  loop : -2.85 (0.19), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 385 
 TYR   0.012   0.002   TYR D 524 
 PHE   0.023   0.002   PHE A 472 
 TRP   0.017   0.002   TRP B 583 
 HIS   0.003   0.001   HIS A 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (19476)
  covalent geometry    : angle       0.83149 (26432)
  hydrogen bonds       : bond        0.04328 (  793)
  hydrogen bonds       : angle       5.21978 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  577 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 567
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8814 (tp) cc_final: 0.8528 (tp)
REVERT: A   61 LEU cc_start: 0.8272 (mt) cc_final: 0.7937 (mt)
REVERT: A   96 MET cc_start: 0.8394 (mmm) cc_final: 0.8042 (mmm)
REVERT: A  204 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9384 (mp)
REVERT: A  211 PHE cc_start: 0.8142 (t80) cc_final: 0.7707 (t80)
REVERT: A  260 MET cc_start: 0.8659 (tpp) cc_final: 0.8423 (tpt)
REVERT: A  363 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8254 (mtp180)
REVERT: A  434 PHE cc_start: 0.8372 (t80) cc_final: 0.7978 (t80)
REVERT: A  437 LEU cc_start: 0.9282 (mp) cc_final: 0.8969 (tt)
REVERT: A  442 MET cc_start: 0.8547 (ttm) cc_final: 0.8322 (ttm)
REVERT: A  497 MET cc_start: 0.8431 (ptp) cc_final: 0.8146 (ttp)
REVERT: A  501 ILE cc_start: 0.9551 (tt) cc_final: 0.9226 (tp)
REVERT: A  515 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: A  539 THR cc_start: 0.9081 (m) cc_final: 0.8762 (p)
REVERT: A  578 MET cc_start: 0.9076 (tpp) cc_final: 0.8713 (tpp)
REVERT: A  602 VAL cc_start: 0.9248 (t) cc_final: 0.8864 (p)
REVERT: A  607 LYS cc_start: 0.8524 (mttp) cc_final: 0.8082 (mtmt)
REVERT: A  629 TRP cc_start: 0.6993 (m-10) cc_final: 0.6759 (m-10)
REVERT: B   35 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8605 (mp0)
REVERT: B   38 LEU cc_start: 0.8746 (tp) cc_final: 0.8480 (tp)
REVERT: B   96 MET cc_start: 0.8410 (mmm) cc_final: 0.8112 (mmm)
REVERT: B  204 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9275 (mp)
REVERT: B  211 PHE cc_start: 0.8106 (t80) cc_final: 0.7645 (t80)
REVERT: B  294 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8119 (mp0)
REVERT: B  331 MET cc_start: 0.7020 (tmm) cc_final: 0.6744 (tmm)
REVERT: B  332 LEU cc_start: 0.9158 (tp) cc_final: 0.8763 (tt)
REVERT: B  339 TYR cc_start: 0.8738 (t80) cc_final: 0.8229 (t80)
REVERT: B  432 TYR cc_start: 0.9395 (t80) cc_final: 0.9006 (t80)
REVERT: B  442 MET cc_start: 0.8353 (ttm) cc_final: 0.8140 (ttm)
REVERT: B  501 ILE cc_start: 0.9386 (tt) cc_final: 0.9096 (tp)
REVERT: B  578 MET cc_start: 0.8546 (tpp) cc_final: 0.8216 (tpp)
REVERT: B  607 LYS cc_start: 0.8685 (mttp) cc_final: 0.8381 (mtmt)
REVERT: C   35 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8641 (mp0)
REVERT: C   40 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8808 (tm-30)
REVERT: C   61 LEU cc_start: 0.8336 (mt) cc_final: 0.8030 (mt)
REVERT: C   96 MET cc_start: 0.8435 (mmm) cc_final: 0.8090 (mmm)
REVERT: C  204 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9338 (mp)
REVERT: C  305 ARG cc_start: 0.8689 (mmt180) cc_final: 0.8379 (mmt-90)
REVERT: C  331 MET cc_start: 0.7004 (tmm) cc_final: 0.6717 (tmm)
REVERT: C  332 LEU cc_start: 0.9128 (tp) cc_final: 0.8855 (tt)
REVERT: C  339 TYR cc_start: 0.8685 (t80) cc_final: 0.8217 (t80)
REVERT: C  342 CYS cc_start: 0.9033 (t) cc_final: 0.8719 (t)
REVERT: C  434 PHE cc_start: 0.8161 (t80) cc_final: 0.7920 (t80)
REVERT: C  454 MET cc_start: 0.9040 (mmm) cc_final: 0.8834 (mmm)
REVERT: C  497 MET cc_start: 0.7984 (ttp) cc_final: 0.7575 (ttm)
REVERT: C  501 ILE cc_start: 0.9270 (tt) cc_final: 0.9019 (tp)
REVERT: C  607 LYS cc_start: 0.8595 (mttp) cc_final: 0.8280 (mtmt)
REVERT: D   35 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8622 (mp0)
REVERT: D   40 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8778 (tm-30)
REVERT: D   61 LEU cc_start: 0.8305 (mt) cc_final: 0.8009 (mt)
REVERT: D   96 MET cc_start: 0.8550 (mmm) cc_final: 0.8194 (mmm)
REVERT: D  204 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9291 (mp)
REVERT: D  211 PHE cc_start: 0.8085 (t80) cc_final: 0.7630 (t80)
REVERT: D  331 MET cc_start: 0.6983 (tmm) cc_final: 0.6600 (tmm)
REVERT: D  339 TYR cc_start: 0.8639 (t80) cc_final: 0.8249 (t80)
REVERT: D  466 MET cc_start: 0.8065 (ttm) cc_final: 0.7635 (tmm)
REVERT: D  497 MET cc_start: 0.8226 (ttp) cc_final: 0.7809 (ttm)
REVERT: D  501 ILE cc_start: 0.9434 (tt) cc_final: 0.9155 (tp)
REVERT: D  607 LYS cc_start: 0.8477 (mttp) cc_final: 0.8118 (mtmt)
  outliers start: 10
  outliers final: 0
  residues processed: 569
  average time/residue: 0.1273
  time to fit residues: 112.7716
Evaluate side-chains
  423 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 419
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 164 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0370
   chunk 144 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 234 optimal weight:    9.9990
   chunk 218 optimal weight:    3.9990
   chunk 113 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.7464

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

Flipped N/Q/H residues before XYZ refinement:
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 464 ASN
C 464 ASN
D 174 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.090408 restraints weight = 47227.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.092840 restraints weight = 28549.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.094498 restraints weight = 20554.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.095422 restraints weight = 16636.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.096269 restraints weight = 14606.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  19476  Z= 0.160
  Angle     :  0.771  14.598  26432  Z= 0.380
  Chirality :  0.044   0.186   3012
  Planarity :  0.004   0.044   3336
  Dihedral  :  5.611  31.142   2592
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.84 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -2.44 (0.17), residues: 2356
  helix: -0.72 (0.14), residues: 1352
  sheet: -4.10 (0.37), residues: 76
  loop : -2.73 (0.20), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 628 
 TYR   0.016   0.001   TYR C 324 
 PHE   0.014   0.002   PHE C 162 
 TRP   0.021   0.002   TRP B 613 
 HIS   0.003   0.001   HIS D  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (19476)
  covalent geometry    : angle       0.77102 (26432)
  hydrogen bonds       : bond        0.03752 (  793)
  hydrogen bonds       : angle       4.48261 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  525 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 520
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8639 (mp0)
REVERT: A   38 LEU cc_start: 0.8686 (tp) cc_final: 0.8266 (tp)
REVERT: A   61 LEU cc_start: 0.8418 (mt) cc_final: 0.8046 (mt)
REVERT: A   96 MET cc_start: 0.8444 (mmm) cc_final: 0.8094 (mmm)
REVERT: A  204 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9418 (mp)
REVERT: A  363 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8246 (mtp180)
REVERT: A  434 PHE cc_start: 0.8350 (t80) cc_final: 0.7886 (t80)
REVERT: A  437 LEU cc_start: 0.9294 (mp) cc_final: 0.8936 (tt)
REVERT: A  442 MET cc_start: 0.8539 (ttm) cc_final: 0.8276 (ttm)
REVERT: A  520 LEU cc_start: 0.8755 (mt) cc_final: 0.8522 (mt)
REVERT: A  602 VAL cc_start: 0.9275 (t) cc_final: 0.8942 (p)
REVERT: A  603 MET cc_start: 0.8028 (ttt) cc_final: 0.7821 (ttt)
REVERT: A  607 LYS cc_start: 0.8505 (mttp) cc_final: 0.8192 (mtmt)
REVERT: A  629 TRP cc_start: 0.6992 (m-10) cc_final: 0.6781 (m-10)
REVERT: B   35 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8614 (mp0)
REVERT: B   38 LEU cc_start: 0.8625 (tp) cc_final: 0.8295 (tp)
REVERT: B  331 MET cc_start: 0.7086 (tmm) cc_final: 0.6704 (tmm)
REVERT: B  332 LEU cc_start: 0.9140 (tp) cc_final: 0.8842 (tt)
REVERT: B  339 TYR cc_start: 0.8781 (t80) cc_final: 0.8338 (t80)
REVERT: B  432 TYR cc_start: 0.9395 (t80) cc_final: 0.9013 (t80)
REVERT: B  472 PHE cc_start: 0.6424 (t80) cc_final: 0.6119 (t80)
REVERT: B  578 MET cc_start: 0.8606 (tpp) cc_final: 0.8344 (tpp)
REVERT: B  607 LYS cc_start: 0.8580 (mttp) cc_final: 0.8271 (mtmt)
REVERT: C   35 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8648 (mp0)
REVERT: C   40 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: C   61 LEU cc_start: 0.8369 (mt) cc_final: 0.8050 (mt)
REVERT: C   96 MET cc_start: 0.8413 (mmm) cc_final: 0.8158 (mmm)
REVERT: C  270 TYR cc_start: 0.9206 (t80) cc_final: 0.8954 (t80)
REVERT: C  305 ARG cc_start: 0.8692 (mmt180) cc_final: 0.8332 (mmt-90)
REVERT: C  331 MET cc_start: 0.7023 (tmm) cc_final: 0.6643 (tmm)
REVERT: C  332 LEU cc_start: 0.9108 (tp) cc_final: 0.8781 (tt)
REVERT: C  339 TYR cc_start: 0.8744 (t80) cc_final: 0.8291 (t80)
REVERT: C  342 CYS cc_start: 0.9092 (t) cc_final: 0.8804 (t)
REVERT: C  434 PHE cc_start: 0.8013 (t80) cc_final: 0.7806 (t80)
REVERT: C  472 PHE cc_start: 0.6498 (t80) cc_final: 0.6223 (t80)
REVERT: C  501 ILE cc_start: 0.9291 (tt) cc_final: 0.8975 (tp)
REVERT: C  607 LYS cc_start: 0.8620 (mttp) cc_final: 0.8302 (mtmt)
REVERT: D   35 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8660 (mp0)
REVERT: D   61 LEU cc_start: 0.8380 (mt) cc_final: 0.8057 (mt)
REVERT: D   96 MET cc_start: 0.8460 (mmm) cc_final: 0.8242 (mmm)
REVERT: D  204 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9366 (mp)
REVERT: D  339 TYR cc_start: 0.8771 (t80) cc_final: 0.8394 (t80)
REVERT: D  342 CYS cc_start: 0.9233 (t) cc_final: 0.9021 (t)
REVERT: D  466 MET cc_start: 0.7984 (ttm) cc_final: 0.7598 (tmm)
REVERT: D  607 LYS cc_start: 0.8561 (mttp) cc_final: 0.8176 (mtmt)
  outliers start: 5
  outliers final: 0
  residues processed: 521
  average time/residue: 0.1322
  time to fit residues: 106.5139
Evaluate side-chains
  415 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 413
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 89 optimal weight:    0.0870
   chunk 229 optimal weight:    5.9990
   chunk 157 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0170
   chunk 127 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 226 optimal weight:    1.9990
   chunk 211 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
B 464 ASN
C  91 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  91 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.115421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.093043 restraints weight = 47002.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.095519 restraints weight = 28252.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.097209 restraints weight = 20218.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098280 restraints weight = 16269.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.098659 restraints weight = 14174.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  19476  Z= 0.124
  Angle     :  0.722  14.289  26432  Z= 0.352
  Chirality :  0.042   0.183   3012
  Planarity :  0.004   0.044   3336
  Dihedral  :  5.190  31.198   2592
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  9.59 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.97 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -1.70 (0.17), residues: 2356
  helix: -0.13 (0.14), residues: 1300
  sheet: -3.52 (0.46), residues: 76
  loop : -2.30 (0.20), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 628 
 TYR   0.015   0.001   TYR B 270 
 PHE   0.019   0.001   PHE A 472 
 TRP   0.013   0.001   TRP C 629 
 HIS   0.003   0.001   HIS D 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (19476)
  covalent geometry    : angle       0.72172 (26432)
  hydrogen bonds       : bond        0.03256 (  793)
  hydrogen bonds       : angle       4.04193 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  536 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 532
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8635 (mp0)
REVERT: A   38 LEU cc_start: 0.8584 (tp) cc_final: 0.8232 (tp)
REVERT: A   61 LEU cc_start: 0.8521 (mt) cc_final: 0.8149 (mt)
REVERT: A   96 MET cc_start: 0.8422 (mmm) cc_final: 0.8075 (mmm)
REVERT: A  211 PHE cc_start: 0.7865 (t80) cc_final: 0.7555 (t80)
REVERT: A  434 PHE cc_start: 0.8317 (t80) cc_final: 0.7920 (t80)
REVERT: A  520 LEU cc_start: 0.8593 (mt) cc_final: 0.8385 (mt)
REVERT: A  530 LEU cc_start: 0.9549 (mt) cc_final: 0.9264 (mp)
REVERT: A  589 ARG cc_start: 0.7113 (mmt180) cc_final: 0.6763 (mmt180)
REVERT: A  602 VAL cc_start: 0.9284 (t) cc_final: 0.8998 (p)
REVERT: A  607 LYS cc_start: 0.8444 (mttp) cc_final: 0.8005 (mtmt)
REVERT: B   35 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8615 (mp0)
REVERT: B   96 MET cc_start: 0.8484 (mmm) cc_final: 0.8124 (mmm)
REVERT: B  331 MET cc_start: 0.7033 (tmm) cc_final: 0.6617 (tmm)
REVERT: B  332 LEU cc_start: 0.9101 (tp) cc_final: 0.8747 (tt)
REVERT: B  339 TYR cc_start: 0.8837 (t80) cc_final: 0.8373 (t80)
REVERT: B  428 LEU cc_start: 0.8554 (pp) cc_final: 0.7958 (pp)
REVERT: B  432 TYR cc_start: 0.9398 (t80) cc_final: 0.9089 (t80)
REVERT: B  442 MET cc_start: 0.8422 (ttm) cc_final: 0.8210 (ttm)
REVERT: B  472 PHE cc_start: 0.6370 (t80) cc_final: 0.6069 (t80)
REVERT: B  481 MET cc_start: 0.8042 (tpp) cc_final: 0.7722 (tpt)
REVERT: B  497 MET cc_start: 0.7879 (ttp) cc_final: 0.7291 (ttm)
REVERT: B  501 ILE cc_start: 0.9390 (tt) cc_final: 0.9080 (tp)
REVERT: B  559 TYR cc_start: 0.8986 (t80) cc_final: 0.8660 (t80)
REVERT: B  607 LYS cc_start: 0.8621 (mttp) cc_final: 0.8333 (mtmt)
REVERT: C   35 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8623 (mp0)
REVERT: C   40 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8685 (tm-30)
REVERT: C   61 LEU cc_start: 0.8388 (mt) cc_final: 0.8023 (mt)
REVERT: C   96 MET cc_start: 0.8398 (mmm) cc_final: 0.7979 (mmm)
REVERT: C  279 ASP cc_start: 0.8405 (t70) cc_final: 0.8085 (t70)
REVERT: C  305 ARG cc_start: 0.8719 (mmt180) cc_final: 0.8337 (mmt-90)
REVERT: C  331 MET cc_start: 0.7077 (tmm) cc_final: 0.6684 (tmm)
REVERT: C  339 TYR cc_start: 0.8756 (t80) cc_final: 0.8335 (t80)
REVERT: C  501 ILE cc_start: 0.9258 (tt) cc_final: 0.8973 (tp)
REVERT: C  550 ASP cc_start: 0.8481 (m-30) cc_final: 0.8229 (m-30)
REVERT: C  607 LYS cc_start: 0.8613 (mttp) cc_final: 0.8295 (mtmt)
REVERT: D   35 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8658 (mp0)
REVERT: D   44 ILE cc_start: 0.9231 (pt) cc_final: 0.9025 (tp)
REVERT: D   61 LEU cc_start: 0.8453 (mt) cc_final: 0.8112 (mt)
REVERT: D   96 MET cc_start: 0.8428 (mmm) cc_final: 0.8055 (mmm)
REVERT: D  339 TYR cc_start: 0.8793 (t80) cc_final: 0.8493 (t80)
REVERT: D  466 MET cc_start: 0.7961 (ttm) cc_final: 0.7702 (tmm)
REVERT: D  472 PHE cc_start: 0.6841 (t80) cc_final: 0.6547 (t80)
REVERT: D  501 ILE cc_start: 0.9378 (tt) cc_final: 0.9084 (tp)
REVERT: D  607 LYS cc_start: 0.8559 (mttp) cc_final: 0.8128 (mtmt)
  outliers start: 4
  outliers final: 0
  residues processed: 533
  average time/residue: 0.1255
  time to fit residues: 104.9068
Evaluate side-chains
  421 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 421
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 142 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 129 optimal weight:   20.0000
   chunk 181 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 202 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 134 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 135 optimal weight:    7.9990
   chunk 164 optimal weight:    0.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 174 ASN
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 ASN
C 118 GLN
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  91 ASN
D 174 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.110941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.087962 restraints weight = 47826.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.090378 restraints weight = 28500.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.092018 restraints weight = 20374.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.093036 restraints weight = 16400.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.093678 restraints weight = 14336.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  19476  Z= 0.206
  Angle     :  0.788  15.241  26432  Z= 0.386
  Chirality :  0.046   0.184   3012
  Planarity :  0.004   0.048   3336
  Dihedral  :  5.160  29.775   2592
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.15 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.18), residues: 2356
  helix:  0.24 (0.15), residues: 1280
  sheet: -3.45 (0.49), residues: 76
  loop : -2.30 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 615 
 TYR   0.023   0.002   TYR C 115 
 PHE   0.013   0.002   PHE D 478 
 TRP   0.022   0.002   TRP A 629 
 HIS   0.004   0.001   HIS C 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (19476)
  covalent geometry    : angle       0.78768 (26432)
  hydrogen bonds       : bond        0.03460 (  793)
  hydrogen bonds       : angle       4.28913 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 479
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8625 (mp0)
REVERT: A   38 LEU cc_start: 0.8659 (tp) cc_final: 0.8271 (tp)
REVERT: A   61 LEU cc_start: 0.8581 (mt) cc_final: 0.8120 (mt)
REVERT: A   96 MET cc_start: 0.8503 (mmm) cc_final: 0.8134 (mmm)
REVERT: A  434 PHE cc_start: 0.8385 (t80) cc_final: 0.8002 (t80)
REVERT: A  442 MET cc_start: 0.8550 (ttm) cc_final: 0.8333 (ttm)
REVERT: A  589 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6890 (mmt180)
REVERT: A  602 VAL cc_start: 0.9378 (t) cc_final: 0.9054 (p)
REVERT: A  607 LYS cc_start: 0.8569 (mttp) cc_final: 0.8264 (mtmt)
REVERT: B   35 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8623 (mp0)
REVERT: B   96 MET cc_start: 0.8537 (mmm) cc_final: 0.8192 (mmm)
REVERT: B  305 ARG cc_start: 0.8738 (mmt180) cc_final: 0.8365 (mmt-90)
REVERT: B  339 TYR cc_start: 0.8822 (t80) cc_final: 0.8394 (t80)
REVERT: B  472 PHE cc_start: 0.6652 (t80) cc_final: 0.6323 (t80)
REVERT: B  497 MET cc_start: 0.8204 (ttp) cc_final: 0.7715 (ttm)
REVERT: B  501 ILE cc_start: 0.9442 (tt) cc_final: 0.9174 (tp)
REVERT: B  602 VAL cc_start: 0.9457 (t) cc_final: 0.9157 (p)
REVERT: B  607 LYS cc_start: 0.8652 (mttp) cc_final: 0.8336 (mtmt)
REVERT: C   35 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8637 (mp0)
REVERT: C   61 LEU cc_start: 0.8535 (mt) cc_final: 0.8120 (mt)
REVERT: C   96 MET cc_start: 0.8481 (mmm) cc_final: 0.8049 (mmm)
REVERT: C  305 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8322 (mmt-90)
REVERT: C  339 TYR cc_start: 0.8740 (t80) cc_final: 0.8364 (t80)
REVERT: C  472 PHE cc_start: 0.6670 (t80) cc_final: 0.6188 (t80)
REVERT: C  550 ASP cc_start: 0.8677 (m-30) cc_final: 0.8340 (m-30)
REVERT: C  559 TYR cc_start: 0.9367 (t80) cc_final: 0.9055 (t80)
REVERT: C  602 VAL cc_start: 0.9481 (t) cc_final: 0.9230 (p)
REVERT: C  607 LYS cc_start: 0.8681 (mttp) cc_final: 0.8362 (mtmt)
REVERT: D   35 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8618 (mp0)
REVERT: D   38 LEU cc_start: 0.8747 (tp) cc_final: 0.8503 (tp)
REVERT: D   61 LEU cc_start: 0.8517 (mt) cc_final: 0.8118 (mt)
REVERT: D   96 MET cc_start: 0.8471 (mmm) cc_final: 0.8006 (mmm)
REVERT: D  385 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8264 (ttt180)
REVERT: D  459 VAL cc_start: 0.9510 (t) cc_final: 0.9302 (p)
REVERT: D  466 MET cc_start: 0.8115 (ttm) cc_final: 0.7763 (tmm)
REVERT: D  501 ILE cc_start: 0.9501 (tt) cc_final: 0.9213 (tp)
REVERT: D  559 TYR cc_start: 0.9316 (t80) cc_final: 0.8997 (t80)
REVERT: D  602 VAL cc_start: 0.9404 (t) cc_final: 0.9037 (p)
REVERT: D  607 LYS cc_start: 0.8619 (mttp) cc_final: 0.8172 (mtmt)
  outliers start: 4
  outliers final: 0
  residues processed: 483
  average time/residue: 0.1298
  time to fit residues: 97.6556
Evaluate side-chains
  395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 395
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 214 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 134 optimal weight:    6.9990
   chunk 147 optimal weight:    0.7980
   chunk 204 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
A 206 GLN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 GLN
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 ASN
** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.092756 restraints weight = 46219.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.095156 restraints weight = 27980.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.096681 restraints weight = 20124.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.097793 restraints weight = 16405.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098502 restraints weight = 14311.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  19476  Z= 0.124
  Angle     :  0.725  14.024  26432  Z= 0.350
  Chirality :  0.043   0.180   3012
  Planarity :  0.004   0.046   3336
  Dihedral  :  4.956  30.797   2592
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.23 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.00 %
    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 are not related in a simple way.
  whole: -1.09 (0.18), residues: 2356
  helix:  0.43 (0.15), residues: 1288
  sheet: -3.06 (0.53), residues: 76
  loop : -2.11 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 589 
 TYR   0.016   0.001   TYR B 270 
 PHE   0.020   0.001   PHE C 434 
 TRP   0.010   0.001   TRP C 495 
 HIS   0.002   0.000   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (19476)
  covalent geometry    : angle       0.72520 (26432)
  hydrogen bonds       : bond        0.03067 (  793)
  hydrogen bonds       : angle       3.87931 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  517 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 515
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8549 (tp) cc_final: 0.8166 (tp)
REVERT: A   44 ILE cc_start: 0.8973 (pt) cc_final: 0.8767 (tp)
REVERT: A   61 LEU cc_start: 0.8606 (mt) cc_final: 0.8206 (mt)
REVERT: A   92 LEU cc_start: 0.8652 (pt) cc_final: 0.8258 (pt)
REVERT: A  113 GLU cc_start: 0.7958 (mp0) cc_final: 0.7683 (mp0)
REVERT: A  130 MET cc_start: 0.8236 (tpt) cc_final: 0.7411 (tpp)
REVERT: A  217 ASN cc_start: 0.8988 (t0) cc_final: 0.8744 (t0)
REVERT: A  434 PHE cc_start: 0.8252 (t80) cc_final: 0.7928 (t80)
REVERT: A  442 MET cc_start: 0.8449 (ttm) cc_final: 0.8217 (ttm)
REVERT: A  570 MET cc_start: 0.8236 (ttm) cc_final: 0.8018 (tpp)
REVERT: A  602 VAL cc_start: 0.9304 (t) cc_final: 0.8972 (p)
REVERT: A  607 LYS cc_start: 0.8443 (mttp) cc_final: 0.8035 (mtmt)
REVERT: B   35 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8525 (mp0)
REVERT: B   55 ASP cc_start: 0.8234 (t70) cc_final: 0.7605 (t70)
REVERT: B   78 MET cc_start: 0.8306 (ptp) cc_final: 0.8015 (mtm)
REVERT: B   92 LEU cc_start: 0.8711 (pt) cc_final: 0.8469 (pt)
REVERT: B  116 GLU cc_start: 0.7593 (mp0) cc_final: 0.7190 (mp0)
REVERT: B  130 MET cc_start: 0.8187 (tpt) cc_final: 0.7293 (tpp)
REVERT: B  216 TYR cc_start: 0.8826 (t80) cc_final: 0.8507 (t80)
REVERT: B  339 TYR cc_start: 0.8808 (t80) cc_final: 0.8467 (t80)
REVERT: B  472 PHE cc_start: 0.6477 (t80) cc_final: 0.6137 (t80)
REVERT: B  497 MET cc_start: 0.7948 (ttp) cc_final: 0.7553 (ttm)
REVERT: B  501 ILE cc_start: 0.9335 (tt) cc_final: 0.9077 (tp)
REVERT: B  570 MET cc_start: 0.8206 (ttm) cc_final: 0.7820 (tpp)
REVERT: B  602 VAL cc_start: 0.9405 (t) cc_final: 0.9112 (p)
REVERT: B  607 LYS cc_start: 0.8634 (mttp) cc_final: 0.8284 (mtmt)
REVERT: C   35 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8609 (mp0)
REVERT: C   61 LEU cc_start: 0.8595 (mt) cc_final: 0.8192 (mt)
REVERT: C   92 LEU cc_start: 0.8730 (tp) cc_final: 0.8515 (pp)
REVERT: C  113 GLU cc_start: 0.7797 (mp0) cc_final: 0.7511 (mp0)
REVERT: C  130 MET cc_start: 0.8216 (tpt) cc_final: 0.7435 (tpp)
REVERT: C  217 ASN cc_start: 0.8947 (t0) cc_final: 0.8701 (t0)
REVERT: C  305 ARG cc_start: 0.8707 (mmt180) cc_final: 0.8347 (mmt-90)
REVERT: C  331 MET cc_start: 0.7151 (tmm) cc_final: 0.6917 (tmm)
REVERT: C  339 TYR cc_start: 0.8772 (t80) cc_final: 0.8402 (t80)
REVERT: C  454 MET cc_start: 0.9224 (tpt) cc_final: 0.8986 (tpt)
REVERT: C  481 MET cc_start: 0.7439 (tpp) cc_final: 0.7137 (tpt)
REVERT: C  539 THR cc_start: 0.9113 (m) cc_final: 0.8901 (p)
REVERT: C  550 ASP cc_start: 0.8570 (m-30) cc_final: 0.8308 (m-30)
REVERT: C  593 TRP cc_start: 0.8707 (t60) cc_final: 0.8214 (t60)
REVERT: C  602 VAL cc_start: 0.9402 (t) cc_final: 0.9167 (p)
REVERT: C  607 LYS cc_start: 0.8650 (mttp) cc_final: 0.8310 (mtmt)
REVERT: D   35 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8577 (mp0)
REVERT: D   61 LEU cc_start: 0.8594 (mt) cc_final: 0.8169 (mt)
REVERT: D  279 ASP cc_start: 0.8502 (t70) cc_final: 0.8228 (t70)
REVERT: D  385 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8033 (ttt180)
REVERT: D  501 ILE cc_start: 0.9466 (tt) cc_final: 0.9210 (tp)
REVERT: D  602 VAL cc_start: 0.9344 (t) cc_final: 0.9075 (p)
REVERT: D  607 LYS cc_start: 0.8575 (mttp) cc_final: 0.8123 (mtmt)
  outliers start: 2
  outliers final: 0
  residues processed: 517
  average time/residue: 0.1295
  time to fit residues: 103.9243
Evaluate side-chains
  422 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 422
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 150 optimal weight:    4.9990
   chunk 193 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 158 optimal weight:    8.9990
   chunk 138 optimal weight:    7.9990
   chunk 123 optimal weight:    4.9990
   chunk 142 optimal weight:    3.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 206 GLN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.114885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.091604 restraints weight = 45906.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.094169 restraints weight = 26784.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.095893 restraints weight = 18858.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.097012 restraints weight = 15026.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.097748 restraints weight = 13044.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.5540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  19476  Z= 0.140
  Angle     :  0.729  15.240  26432  Z= 0.352
  Chirality :  0.043   0.178   3012
  Planarity :  0.004   0.046   3336
  Dihedral  :  4.877  30.766   2592
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.62 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -0.98 (0.18), residues: 2356
  helix:  0.54 (0.15), residues: 1304
  sheet: -3.04 (0.53), residues: 76
  loop : -2.13 (0.21), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 153 
 TYR   0.014   0.001   TYR A 336 
 PHE   0.019   0.001   PHE C 434 
 TRP   0.010   0.001   TRP D 583 
 HIS   0.002   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (19476)
  covalent geometry    : angle       0.72944 (26432)
  hydrogen bonds       : bond        0.03143 (  793)
  hydrogen bonds       : angle       4.00278 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  496 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 494
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8590 (mp0)
REVERT: A   38 LEU cc_start: 0.8609 (tp) cc_final: 0.8249 (tp)
REVERT: A   44 ILE cc_start: 0.8994 (pt) cc_final: 0.8762 (tp)
REVERT: A   61 LEU cc_start: 0.8627 (mt) cc_final: 0.8204 (mt)
REVERT: A   96 MET cc_start: 0.8659 (mmm) cc_final: 0.8113 (mmt)
REVERT: A  130 MET cc_start: 0.8277 (tpt) cc_final: 0.7456 (tpp)
REVERT: A  217 ASN cc_start: 0.8938 (t0) cc_final: 0.8653 (t0)
REVERT: A  434 PHE cc_start: 0.8316 (t80) cc_final: 0.7991 (t80)
REVERT: A  442 MET cc_start: 0.8478 (ttm) cc_final: 0.8227 (ttm)
REVERT: A  559 TYR cc_start: 0.8995 (t80) cc_final: 0.8658 (t80)
REVERT: A  570 MET cc_start: 0.8182 (ttm) cc_final: 0.7938 (tpp)
REVERT: A  602 VAL cc_start: 0.9295 (t) cc_final: 0.8964 (p)
REVERT: A  607 LYS cc_start: 0.8505 (mttp) cc_final: 0.8136 (mtmt)
REVERT: B   35 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8529 (mp0)
REVERT: B   92 LEU cc_start: 0.8743 (pt) cc_final: 0.8406 (pt)
REVERT: B   96 MET cc_start: 0.8426 (mmm) cc_final: 0.8095 (mmm)
REVERT: B  130 MET cc_start: 0.8087 (tpt) cc_final: 0.7158 (tpp)
REVERT: B  216 TYR cc_start: 0.8924 (t80) cc_final: 0.8601 (t80)
REVERT: B  472 PHE cc_start: 0.6661 (t80) cc_final: 0.6340 (t80)
REVERT: B  497 MET cc_start: 0.7909 (ttp) cc_final: 0.7474 (ttm)
REVERT: B  607 LYS cc_start: 0.8681 (mttp) cc_final: 0.8336 (mtmt)
REVERT: C   35 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8603 (mp0)
REVERT: C   61 LEU cc_start: 0.8630 (mt) cc_final: 0.8199 (mt)
REVERT: C  130 MET cc_start: 0.8062 (tpt) cc_final: 0.7218 (tpp)
REVERT: C  217 ASN cc_start: 0.9021 (t0) cc_final: 0.8773 (t0)
REVERT: C  305 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8396 (mmt-90)
REVERT: C  454 MET cc_start: 0.9169 (tpt) cc_final: 0.8902 (tpp)
REVERT: C  472 PHE cc_start: 0.6533 (t80) cc_final: 0.6223 (t80)
REVERT: C  530 LEU cc_start: 0.9540 (mp) cc_final: 0.9326 (mp)
REVERT: C  550 ASP cc_start: 0.8584 (m-30) cc_final: 0.8312 (m-30)
REVERT: C  593 TRP cc_start: 0.8858 (t60) cc_final: 0.8319 (t60)
REVERT: C  607 LYS cc_start: 0.8678 (mttp) cc_final: 0.8321 (mtmt)
REVERT: D   35 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8584 (mp0)
REVERT: D   61 LEU cc_start: 0.8594 (mt) cc_final: 0.8161 (mt)
REVERT: D   96 MET cc_start: 0.8746 (mmp) cc_final: 0.8037 (mmm)
REVERT: D  130 MET cc_start: 0.8183 (tpt) cc_final: 0.7547 (tpp)
REVERT: D  279 ASP cc_start: 0.8492 (t70) cc_final: 0.8211 (t70)
REVERT: D  385 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8009 (ttt180)
REVERT: D  602 VAL cc_start: 0.9369 (t) cc_final: 0.9044 (p)
REVERT: D  607 LYS cc_start: 0.8607 (mttp) cc_final: 0.8196 (mtmt)
  outliers start: 2
  outliers final: 0
  residues processed: 496
  average time/residue: 0.1281
  time to fit residues: 99.2390
Evaluate side-chains
  408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 408
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 179 optimal weight:    4.9990
   chunk 182 optimal weight:    8.9990
   chunk 214 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 202 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 185 optimal weight:    0.0050
   chunk 130 optimal weight:    5.9990
   chunk 161 optimal weight:    0.8980
   overall best weight:    1.7598

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  91 ASN
D 174 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.090732 restraints weight = 45728.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.093291 restraints weight = 26701.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.095007 restraints weight = 18816.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.096149 restraints weight = 15030.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.096834 restraints weight = 13019.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.5656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  19476  Z= 0.146
  Angle     :  0.740  15.042  26432  Z= 0.356
  Chirality :  0.043   0.179   3012
  Planarity :  0.004   0.046   3336
  Dihedral  :  4.851  30.988   2592
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.79 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -0.87 (0.18), residues: 2356
  helix:  0.69 (0.15), residues: 1304
  sheet: -2.90 (0.54), residues: 76
  loop : -2.19 (0.20), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.013   0.001   TYR A 336 
 PHE   0.021   0.001   PHE D 434 
 TRP   0.010   0.001   TRP A 629 
 HIS   0.002   0.001   HIS D 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (19476)
  covalent geometry    : angle       0.73959 (26432)
  hydrogen bonds       : bond        0.03144 (  793)
  hydrogen bonds       : angle       4.03696 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 489
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8584 (mp0)
REVERT: A   38 LEU cc_start: 0.8607 (tp) cc_final: 0.8250 (tp)
REVERT: A   44 ILE cc_start: 0.9012 (pt) cc_final: 0.8803 (tp)
REVERT: A   61 LEU cc_start: 0.8611 (mt) cc_final: 0.8183 (mt)
REVERT: A   96 MET cc_start: 0.8598 (mmm) cc_final: 0.8074 (mmt)
REVERT: A  130 MET cc_start: 0.8218 (tpt) cc_final: 0.7390 (tpp)
REVERT: A  217 ASN cc_start: 0.8935 (t0) cc_final: 0.8697 (t0)
REVERT: A  434 PHE cc_start: 0.8319 (t80) cc_final: 0.8027 (t80)
REVERT: A  515 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8502 (mm-30)
REVERT: A  559 TYR cc_start: 0.9032 (t80) cc_final: 0.8688 (t80)
REVERT: A  570 MET cc_start: 0.8303 (ttm) cc_final: 0.7991 (tpp)
REVERT: A  602 VAL cc_start: 0.9291 (t) cc_final: 0.8968 (p)
REVERT: A  607 LYS cc_start: 0.8501 (mttp) cc_final: 0.8142 (mtmt)
REVERT: B   35 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8527 (mp0)
REVERT: B   55 ASP cc_start: 0.8290 (t70) cc_final: 0.7665 (t70)
REVERT: B   62 ASN cc_start: 0.8622 (m-40) cc_final: 0.8270 (m-40)
REVERT: B   92 LEU cc_start: 0.8771 (pt) cc_final: 0.8505 (pt)
REVERT: B   96 MET cc_start: 0.8523 (mmm) cc_final: 0.8236 (mmm)
REVERT: B  130 MET cc_start: 0.8220 (tpt) cc_final: 0.7456 (tpp)
REVERT: B  437 LEU cc_start: 0.9011 (mp) cc_final: 0.8796 (tt)
REVERT: B  472 PHE cc_start: 0.6678 (t80) cc_final: 0.6406 (t80)
REVERT: B  497 MET cc_start: 0.7966 (ttp) cc_final: 0.7495 (ttm)
REVERT: B  602 VAL cc_start: 0.9482 (t) cc_final: 0.9201 (p)
REVERT: B  607 LYS cc_start: 0.8623 (mttp) cc_final: 0.8256 (mtmt)
REVERT: C   35 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8610 (mp0)
REVERT: C   61 LEU cc_start: 0.8597 (mt) cc_final: 0.8189 (mt)
REVERT: C  130 MET cc_start: 0.8268 (tpt) cc_final: 0.7501 (tpp)
REVERT: C  217 ASN cc_start: 0.8976 (t0) cc_final: 0.8711 (t0)
REVERT: C  279 ASP cc_start: 0.8365 (t70) cc_final: 0.8151 (t70)
REVERT: C  305 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8405 (mmt-90)
REVERT: C  437 LEU cc_start: 0.8937 (mp) cc_final: 0.8668 (tt)
REVERT: C  454 MET cc_start: 0.9172 (tpt) cc_final: 0.8956 (tpp)
REVERT: C  472 PHE cc_start: 0.6648 (t80) cc_final: 0.6345 (t80)
REVERT: C  550 ASP cc_start: 0.8595 (m-30) cc_final: 0.8320 (m-30)
REVERT: C  559 TYR cc_start: 0.8996 (t80) cc_final: 0.8481 (t80)
REVERT: C  577 MET cc_start: 0.8605 (ttm) cc_final: 0.8104 (ttm)
REVERT: C  593 TRP cc_start: 0.8712 (t60) cc_final: 0.8255 (t60)
REVERT: C  602 VAL cc_start: 0.9479 (t) cc_final: 0.9211 (p)
REVERT: C  607 LYS cc_start: 0.8703 (mttp) cc_final: 0.8296 (mtmt)
REVERT: D   35 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8588 (mp0)
REVERT: D   61 LEU cc_start: 0.8630 (mt) cc_final: 0.8207 (mt)
REVERT: D   92 LEU cc_start: 0.8586 (tp) cc_final: 0.8365 (tp)
REVERT: D   96 MET cc_start: 0.8724 (mmp) cc_final: 0.8005 (mmm)
REVERT: D  130 MET cc_start: 0.8161 (tpt) cc_final: 0.7512 (tpp)
REVERT: D  279 ASP cc_start: 0.8507 (t70) cc_final: 0.8238 (t70)
REVERT: D  385 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.8021 (ttt180)
REVERT: D  593 TRP cc_start: 0.8909 (t60) cc_final: 0.8263 (t60)
REVERT: D  602 VAL cc_start: 0.9400 (t) cc_final: 0.9089 (p)
REVERT: D  607 LYS cc_start: 0.8541 (mttp) cc_final: 0.8155 (mtmt)
  outliers start: 4
  outliers final: 0
  residues processed: 493
  average time/residue: 0.1270
  time to fit residues: 98.0126
Evaluate side-chains
  397 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 397
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 164 optimal weight:    0.9980
   chunk 235 optimal weight:    9.9990
   chunk 167 optimal weight:    1.9990
   chunk 106 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0980
   chunk 144 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 159 optimal weight:    0.9980
   chunk 132 optimal weight:    6.9990
   chunk 232 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
C 206 GLN
** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 ASN
** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.093896 restraints weight = 45379.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.096531 restraints weight = 26616.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.098308 restraints weight = 18773.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099484 restraints weight = 14982.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.100225 restraints weight = 12982.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  19476  Z= 0.121
  Angle     :  0.728  15.547  26432  Z= 0.348
  Chirality :  0.042   0.173   3012
  Planarity :  0.004   0.045   3336
  Dihedral  :  4.753  32.417   2592
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.07 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -0.70 (0.18), residues: 2356
  helix:  0.92 (0.15), residues: 1272
  sheet: -2.73 (0.55), residues: 76
  loop : -2.17 (0.20), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 153 
 TYR   0.013   0.001   TYR C 336 
 PHE   0.024   0.001   PHE C 434 
 TRP   0.011   0.001   TRP C 583 
 HIS   0.002   0.000   HIS A 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (19476)
  covalent geometry    : angle       0.72815 (26432)
  hydrogen bonds       : bond        0.02878 (  793)
  hydrogen bonds       : angle       3.87981 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  510 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 506
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8530 (mp0)
REVERT: A   38 LEU cc_start: 0.8523 (tp) cc_final: 0.8181 (tp)
REVERT: A   44 ILE cc_start: 0.9009 (pt) cc_final: 0.8792 (tp)
REVERT: A   61 LEU cc_start: 0.8542 (mt) cc_final: 0.8130 (mt)
REVERT: A   92 LEU cc_start: 0.8683 (pt) cc_final: 0.8145 (pt)
REVERT: A   96 MET cc_start: 0.8557 (mmm) cc_final: 0.8121 (mmm)
REVERT: A  116 GLU cc_start: 0.7427 (mp0) cc_final: 0.7089 (mp0)
REVERT: A  130 MET cc_start: 0.8130 (tpt) cc_final: 0.7302 (tpp)
REVERT: A  217 ASN cc_start: 0.8794 (t0) cc_final: 0.8548 (t0)
REVERT: A  331 MET cc_start: 0.7403 (tmm) cc_final: 0.7088 (tmm)
REVERT: A  434 PHE cc_start: 0.8242 (t80) cc_final: 0.7956 (t80)
REVERT: A  454 MET cc_start: 0.8976 (tpp) cc_final: 0.8744 (tpp)
REVERT: A  515 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8356 (mm-30)
REVERT: A  520 LEU cc_start: 0.8714 (mt) cc_final: 0.8431 (mt)
REVERT: A  602 VAL cc_start: 0.9333 (t) cc_final: 0.9060 (p)
REVERT: A  607 LYS cc_start: 0.8412 (mttp) cc_final: 0.8079 (mtmt)
REVERT: B   35 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8450 (mp0)
REVERT: B   55 ASP cc_start: 0.8392 (t70) cc_final: 0.7675 (t70)
REVERT: B   92 LEU cc_start: 0.8735 (pt) cc_final: 0.8487 (pt)
REVERT: B   96 MET cc_start: 0.8492 (mmm) cc_final: 0.8174 (mmm)
REVERT: B  116 GLU cc_start: 0.7486 (mp0) cc_final: 0.7196 (mp0)
REVERT: B  130 MET cc_start: 0.8089 (tpt) cc_final: 0.7557 (tpp)
REVERT: B  279 ASP cc_start: 0.8462 (t70) cc_final: 0.8151 (t70)
REVERT: B  385 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8448 (ttp-170)
REVERT: B  437 LEU cc_start: 0.9000 (mp) cc_final: 0.8791 (tt)
REVERT: B  454 MET cc_start: 0.8910 (tpp) cc_final: 0.8687 (tpp)
REVERT: B  497 MET cc_start: 0.7978 (ttp) cc_final: 0.7494 (ttm)
REVERT: B  570 MET cc_start: 0.8130 (ttm) cc_final: 0.7772 (tpp)
REVERT: B  593 TRP cc_start: 0.8620 (t60) cc_final: 0.8212 (t60)
REVERT: B  602 VAL cc_start: 0.9483 (t) cc_final: 0.9198 (p)
REVERT: B  607 LYS cc_start: 0.8576 (mttp) cc_final: 0.8158 (mtmt)
REVERT: C   35 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8587 (mp0)
REVERT: C   61 LEU cc_start: 0.8585 (mt) cc_final: 0.8192 (mt)
REVERT: C   96 MET cc_start: 0.8446 (mmm) cc_final: 0.8213 (mmm)
REVERT: C  130 MET cc_start: 0.8137 (tpt) cc_final: 0.7350 (tpp)
REVERT: C  217 ASN cc_start: 0.8905 (t0) cc_final: 0.8676 (t0)
REVERT: C  279 ASP cc_start: 0.8308 (t70) cc_final: 0.8064 (t70)
REVERT: C  305 ARG cc_start: 0.8687 (mmt180) cc_final: 0.8407 (mmt-90)
REVERT: C  577 MET cc_start: 0.8551 (ttm) cc_final: 0.8282 (ttm)
REVERT: C  593 TRP cc_start: 0.8715 (t60) cc_final: 0.8222 (t60)
REVERT: C  602 VAL cc_start: 0.9467 (t) cc_final: 0.9252 (p)
REVERT: C  607 LYS cc_start: 0.8638 (mttp) cc_final: 0.8240 (mtmt)
REVERT: D   35 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8558 (mp0)
REVERT: D   61 LEU cc_start: 0.8602 (mt) cc_final: 0.8188 (mt)
REVERT: D   92 LEU cc_start: 0.8546 (tp) cc_final: 0.8248 (tp)
REVERT: D   96 MET cc_start: 0.8607 (mmp) cc_final: 0.7926 (mmm)
REVERT: D  130 MET cc_start: 0.8065 (tpt) cc_final: 0.7391 (tpp)
REVERT: D  279 ASP cc_start: 0.8461 (t70) cc_final: 0.8184 (t70)
REVERT: D  385 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8013 (ttt180)
REVERT: D  454 MET cc_start: 0.8975 (tpp) cc_final: 0.8719 (tpp)
REVERT: D  515 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7538 (tp30)
REVERT: D  593 TRP cc_start: 0.8815 (t60) cc_final: 0.8283 (t60)
REVERT: D  602 VAL cc_start: 0.9374 (t) cc_final: 0.9114 (p)
REVERT: D  607 LYS cc_start: 0.8472 (mttp) cc_final: 0.8115 (mtmt)
  outliers start: 4
  outliers final: 0
  residues processed: 510
  average time/residue: 0.1279
  time to fit residues: 101.4068
Evaluate side-chains
  399 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 399
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 159 optimal weight:    0.8980
   chunk 179 optimal weight:    8.9990
   chunk 204 optimal weight:    2.9990
   chunk 125 optimal weight:    9.9990
   chunk 181 optimal weight:    0.5980
   chunk 182 optimal weight:    8.9990
   chunk 225 optimal weight:    0.8980
   chunk 212 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
B 252 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 ASN
C 131 ASN
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 ASN
D 252 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.092040 restraints weight = 45719.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.094529 restraints weight = 26845.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.096319 restraints weight = 19111.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.097451 restraints weight = 15259.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.098174 restraints weight = 13228.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.5960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  19476  Z= 0.139
  Angle     :  0.752  15.650  26432  Z= 0.360
  Chirality :  0.043   0.179   3012
  Planarity :  0.004   0.044   3336
  Dihedral  :  4.747  32.199   2592
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.53 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -0.63 (0.18), residues: 2356
  helix:  0.96 (0.15), residues: 1272
  sheet: -2.67 (0.56), residues: 76
  loop : -2.12 (0.20), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 610 
 TYR   0.013   0.001   TYR A 270 
 PHE   0.024   0.001   PHE C 434 
 TRP   0.026   0.001   TRP A 583 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (19476)
  covalent geometry    : angle       0.75163 (26432)
  hydrogen bonds       : bond        0.02973 (  793)
  hydrogen bonds       : angle       3.96229 ( 2292)

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

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

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4712 Ramachandran restraints generated.
    2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 488
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8543 (mp0)
REVERT: A   38 LEU cc_start: 0.8583 (tp) cc_final: 0.8217 (tp)
REVERT: A   44 ILE cc_start: 0.9043 (pt) cc_final: 0.8830 (tp)
REVERT: A   61 LEU cc_start: 0.8569 (mt) cc_final: 0.8141 (mt)
REVERT: A   96 MET cc_start: 0.8566 (mmm) cc_final: 0.8131 (mmm)
REVERT: A  116 GLU cc_start: 0.7540 (mp0) cc_final: 0.7192 (mp0)
REVERT: A  217 ASN cc_start: 0.8865 (t0) cc_final: 0.8617 (t0)
REVERT: A  331 MET cc_start: 0.7460 (tmm) cc_final: 0.7169 (tmm)
REVERT: A  454 MET cc_start: 0.9048 (tpp) cc_final: 0.8788 (tpp)
REVERT: A  485 MET cc_start: 0.7450 (pmm) cc_final: 0.7232 (pmm)
REVERT: A  602 VAL cc_start: 0.9296 (t) cc_final: 0.8964 (p)
REVERT: A  607 LYS cc_start: 0.8449 (mttp) cc_final: 0.8151 (mtmt)
REVERT: B   35 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8477 (mp0)
REVERT: B   55 ASP cc_start: 0.8388 (t70) cc_final: 0.7726 (t70)
REVERT: B   92 LEU cc_start: 0.8709 (pt) cc_final: 0.8462 (pt)
REVERT: B   96 MET cc_start: 0.8504 (mmm) cc_final: 0.8176 (mmm)
REVERT: B  130 MET cc_start: 0.8024 (tpt) cc_final: 0.7551 (tpp)
REVERT: B  305 ARG cc_start: 0.8689 (mmt180) cc_final: 0.8462 (mmt-90)
REVERT: B  385 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8460 (ttp-170)
REVERT: B  437 LEU cc_start: 0.8961 (mp) cc_final: 0.8716 (tt)
REVERT: B  497 MET cc_start: 0.7976 (ttp) cc_final: 0.7449 (ttm)
REVERT: B  593 TRP cc_start: 0.8652 (t60) cc_final: 0.8231 (t60)
REVERT: B  602 VAL cc_start: 0.9487 (t) cc_final: 0.9205 (p)
REVERT: B  607 LYS cc_start: 0.8482 (mttp) cc_final: 0.8212 (mtmt)
REVERT: C   35 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8601 (mp0)
REVERT: C   61 LEU cc_start: 0.8621 (mt) cc_final: 0.8215 (mt)
REVERT: C   96 MET cc_start: 0.8424 (mmm) cc_final: 0.8120 (mmm)
REVERT: C  130 MET cc_start: 0.8244 (tpt) cc_final: 0.7448 (tpp)
REVERT: C  217 ASN cc_start: 0.8879 (t0) cc_final: 0.8624 (t0)
REVERT: C  279 ASP cc_start: 0.8282 (t70) cc_final: 0.8053 (t70)
REVERT: C  305 ARG cc_start: 0.8674 (mmt180) cc_final: 0.8357 (mmt-90)
REVERT: C  437 LEU cc_start: 0.9041 (mp) cc_final: 0.8788 (tt)
REVERT: C  472 PHE cc_start: 0.6740 (t80) cc_final: 0.6434 (t80)
REVERT: C  515 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7820 (tp30)
REVERT: C  559 TYR cc_start: 0.9002 (t80) cc_final: 0.8505 (t80)
REVERT: C  593 TRP cc_start: 0.8769 (t60) cc_final: 0.8283 (t60)
REVERT: C  602 VAL cc_start: 0.9482 (t) cc_final: 0.9217 (p)
REVERT: C  607 LYS cc_start: 0.8615 (mttp) cc_final: 0.8201 (mtmt)
REVERT: D   35 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8571 (mp0)
REVERT: D   61 LEU cc_start: 0.8643 (mt) cc_final: 0.8228 (mt)
REVERT: D   96 MET cc_start: 0.8612 (mmp) cc_final: 0.7952 (mmm)
REVERT: D  130 MET cc_start: 0.8157 (tpt) cc_final: 0.7539 (tpp)
REVERT: D  279 ASP cc_start: 0.8456 (t70) cc_final: 0.8178 (t70)
REVERT: D  385 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8045 (ttt180)
REVERT: D  454 MET cc_start: 0.9021 (tpp) cc_final: 0.8760 (tpp)
REVERT: D  593 TRP cc_start: 0.8817 (t60) cc_final: 0.8313 (t60)
REVERT: D  602 VAL cc_start: 0.9355 (t) cc_final: 0.9098 (p)
REVERT: D  607 LYS cc_start: 0.8472 (mttp) cc_final: 0.8146 (mtmt)
  outliers start: 5
  outliers final: 0
  residues processed: 493
  average time/residue: 0.1234
  time to fit residues: 94.8965
Evaluate side-chains
  395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 395
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 192 optimal weight:    3.9990
   chunk 157 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 211 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 126 optimal weight:    8.9990
   chunk 164 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 ASN
** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.116960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.094091 restraints weight = 45502.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.096621 restraints weight = 27270.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.098331 restraints weight = 19491.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.099432 restraints weight = 15697.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.100133 restraints weight = 13683.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.6116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  19476  Z= 0.122
  Angle     :  0.748  15.556  26432  Z= 0.355
  Chirality :  0.042   0.176   3012
  Planarity :  0.004   0.051   3336
  Dihedral  :  4.668  30.731   2592
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.39 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 are not related in a simple way.
  whole: -0.61 (0.18), residues: 2356
  helix:  0.94 (0.15), residues: 1288
  sheet: -2.59 (0.56), residues: 76
  loop : -2.10 (0.20), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.012   0.001   TYR A 270 
 PHE   0.026   0.001   PHE D 434 
 TRP   0.022   0.001   TRP D 583 
 HIS   0.004   0.000   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (19476)
  covalent geometry    : angle       0.74753 (26432)
  hydrogen bonds       : bond        0.02914 (  793)
  hydrogen bonds       : angle       3.89723 ( 2292)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3224.66 seconds
wall clock time: 56 minutes 29.84 seconds (3389.84 seconds total)