Starting phenix.real_space_refine
on Sat Jun 14 22:03:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kjt_62375/06_2025/9kjt_62375.cif"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.021
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      72      5.16       5
     C   10359      2.51       5
     N    2820      2.21       5
     O    3162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16413
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
    Chain: "B"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
    Chain: "C"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
  Time building chain proxies: 12.28, per 1000 atoms: 0.75
  Number of scatterers: 16413
  At special positions: 0
  Unit cell: (107.9, 108.73, 136.12, 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      72     16.00
     O    3162      8.00
     N    2820      7.00
     C   10359      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: 5.04
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3960

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 15 sheets defined
      40.9% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 110
    Processing helix  chain 'A' and resid 124 through 139
    Processing helix  chain 'A' and resid 140 through 142
      No H-bonds generated for 'chain 'A' and resid 140 through 142'
    Processing helix  chain 'A' and resid 165 through 179
    Processing helix  chain 'A' and resid 205 through 212
    Processing helix  chain 'A' and resid 237 through 267
      removed outlier: 3.808A  pdb=" N   PHE A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN A 254 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 301
      removed outlier: 6.479A  pdb=" N   GLU A 293 " --> pdb=" O   LYS A 289 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ARG A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 328
    Processing helix  chain 'A' and resid 332 through 356
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 3.672A  pdb=" N   ILE A 406 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.580A  pdb=" N   THR A 413 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
    Processing helix  chain 'A' and resid 444 through 459
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 482 through 499
    Processing helix  chain 'A' and resid 534 through 541
    Processing helix  chain 'A' and resid 567 through 593
      removed outlier: 3.622A  pdb=" N   VAL A 571 " --> pdb=" O   PRO A 567 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 593 " --> pdb=" O   MET A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 622
      removed outlier: 3.930A  pdb=" N   ALA A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LYS A 619 " --> pdb=" O   SER A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 636
    Processing helix  chain 'A' and resid 653 through 671
      removed outlier: 3.975A  pdb=" N   ASP A 671 " --> pdb=" O   ILE A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 713
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 749 through 752
    Processing helix  chain 'B' and resid 105 through 110
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 140 through 142
      No H-bonds generated for 'chain 'B' and resid 140 through 142'
    Processing helix  chain 'B' and resid 165 through 179
    Processing helix  chain 'B' and resid 205 through 210
      removed outlier: 4.242A  pdb=" N   SER B 210 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 267
      removed outlier: 3.905A  pdb=" N   GLN B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 301
      removed outlier: 6.116A  pdb=" N   GLU B 293 " --> pdb=" O   LYS B 289 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ARG B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 328
    Processing helix  chain 'B' and resid 332 through 356
    Processing helix  chain 'B' and resid 401 through 406
      removed outlier: 3.624A  pdb=" N   ILE B 406 " --> pdb=" O   GLU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.788A  pdb=" N   THR B 413 " --> pdb=" O   ASP B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 435
    Processing helix  chain 'B' and resid 444 through 459
    Processing helix  chain 'B' and resid 460 through 462
      No H-bonds generated for 'chain 'B' and resid 460 through 462'
    Processing helix  chain 'B' and resid 482 through 499
    Processing helix  chain 'B' and resid 534 through 541
    Processing helix  chain 'B' and resid 567 through 593
      removed outlier: 3.667A  pdb=" N   VAL B 571 " --> pdb=" O   PRO B 567 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL B 580 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LYS B 591 " --> pdb=" O   GLN B 587 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR B 592 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE B 593 " --> pdb=" O   MET B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 622
      removed outlier: 4.339A  pdb=" N   ALA B 618 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   LYS B 619 " --> pdb=" O   SER B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 636
    Processing helix  chain 'B' and resid 653 through 671
      removed outlier: 4.350A  pdb=" N   ASP B 671 " --> pdb=" O   ILE B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 712
      No H-bonds generated for 'chain 'B' and resid 710 through 712'
    Processing helix  chain 'B' and resid 719 through 724
    Processing helix  chain 'C' and resid 124 through 139
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'C' and resid 165 through 179
    Processing helix  chain 'C' and resid 205 through 212
    Processing helix  chain 'C' and resid 237 through 267
      removed outlier: 3.660A  pdb=" N   PHE C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLN C 254 " --> pdb=" O   LYS C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 301
      removed outlier: 5.463A  pdb=" N   GLU C 293 " --> pdb=" O   LYS C 289 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   ARG C 294 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP C 301 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 328
    Processing helix  chain 'C' and resid 332 through 356
    Processing helix  chain 'C' and resid 401 through 406
      removed outlier: 3.784A  pdb=" N   ILE C 406 " --> pdb=" O   GLU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 416
      removed outlier: 4.105A  pdb=" N   THR C 413 " --> pdb=" O   ASP C 409 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 430 through 435
    Processing helix  chain 'C' and resid 444 through 459
    Processing helix  chain 'C' and resid 460 through 462
      No H-bonds generated for 'chain 'C' and resid 460 through 462'
    Processing helix  chain 'C' and resid 482 through 499
    Processing helix  chain 'C' and resid 534 through 541
    Processing helix  chain 'C' and resid 567 through 593
      removed outlier: 3.727A  pdb=" N   VAL C 571 " --> pdb=" O   PRO C 567 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LYS C 591 " --> pdb=" O   GLN C 587 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   THR C 592 " --> pdb=" O   ILE C 588 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE C 593 " --> pdb=" O   MET C 589 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 613 through 622
      removed outlier: 4.181A  pdb=" N   ALA C 618 " --> pdb=" O   LEU C 614 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   LYS C 619 " --> pdb=" O   SER C 615 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 625 through 635
    Processing helix  chain 'C' and resid 653 through 668
    Processing helix  chain 'C' and resid 719 through 724
    Processing helix  chain 'C' and resid 749 through 753
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51
      removed outlier: 6.602A  pdb=" N   ALA A  79 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   ASP A 149 " --> pdb=" O   LYS A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202
      removed outlier: 3.594A  pdb=" N   ILE A 195 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU A 214 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   MET A 228 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   ILE A 226 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ILE A 561 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU A 229 " --> pdb=" O   ALA A 559 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   THR A 555 " --> pdb=" O   ALA A 233 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ILE A 554 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   THR A 550 " --> pdb=" O   ILE A 554 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   MET A 543 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU A 513 " --> pdb=" O   MET A 543 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 526 " --> pdb=" O   LYS A 516 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374
      removed outlier: 6.232A  pdb=" N   GLN A 392 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   MET A 424 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   SER A 474 " --> pdb=" O   MET A 424 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   HIS A 426 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL A 476 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLU A 428 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   GLU A 478 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611
    Processing sheet with id=AA5, first strand: chain 'A' and resid 705 through 708
      removed outlier: 6.679A  pdb=" N   LYS A 697 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ILE A 686 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 748 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER A 748 " --> pdb=" O   LYS A 734 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   ARG A 746 " --> pdb=" O   PHE A 736 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   ARG A 738 " --> pdb=" O   ARG A 744 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ARG A 744 " --> pdb=" O   ARG A 738 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.504A  pdb=" N   ALA B  79 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 202
      removed outlier: 3.871A  pdb=" N   ILE B 195 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LEU B 214 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASN B 215 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ALA B 231 " --> pdb=" O   ASN B 215 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU B 229 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA B 219 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU B 229 " --> pdb=" O   ALA B 559 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   THR B 555 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   MET B 543 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU B 513 " --> pdb=" O   MET B 543 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 374
      removed outlier: 3.543A  pdb=" N   GLY B 382 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLN B 392 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611
    Processing sheet with id=AB1, first strand: chain 'B' and resid 705 through 708
      removed outlier: 7.671A  pdb=" N   GLY B 693 " --> pdb=" O   ILE B 689 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   ILE B 689 " --> pdb=" O   GLY B 693 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   MET B 695 " --> pdb=" O   THR B 687 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS B 734 " --> pdb=" O   SER B 748 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 51
      removed outlier: 6.544A  pdb=" N   ALA C  79 " --> pdb=" O   LEU C 157 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ARG C 103 " --> pdb=" O   CYS C 154 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU C 156 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202
      removed outlier: 3.612A  pdb=" N   ILE C 195 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LEU C 214 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   MET C 228 " --> pdb=" O   ALA C 219 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA C 221 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ILE C 226 " --> pdb=" O   ALA C 221 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 561 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ILE C 561 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU C 229 " --> pdb=" O   ALA C 559 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   THR C 555 " --> pdb=" O   ALA C 233 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   ILE C 554 " --> pdb=" O   THR C 550 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   THR C 550 " --> pdb=" O   ILE C 554 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   MET C 543 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU C 513 " --> pdb=" O   MET C 543 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP C 526 " --> pdb=" O   LYS C 516 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 370 through 374
      removed outlier: 3.584A  pdb=" N   GLY C 382 " --> pdb=" O   VAL C 397 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLN C 392 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   MET C 424 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   SER C 474 " --> pdb=" O   MET C 424 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   HIS C 426 " --> pdb=" O   SER C 474 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   VAL C 476 " --> pdb=" O   HIS C 426 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   GLU C 428 " --> pdb=" O   VAL C 476 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   GLU C 478 " --> pdb=" O   GLU C 428 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 606 through 611
    Processing sheet with id=AB6, first strand: chain 'C' and resid 705 through 708
      removed outlier: 6.956A  pdb=" N   GLY C 693 " --> pdb=" O   ILE C 689 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   ILE C 689 " --> pdb=" O   GLY C 693 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   MET C 695 " --> pdb=" O   THR C 687 " (cutoff:3.500A)

    911 hydrogen bonds defined for protein.
    2532 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: 6.39

  Time building geometry restraints manager: 5.86 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: 5496
        1.34 -     1.46: 3349
        1.46 -     1.58: 7709
        1.58 -     1.70: 0
        1.70 -     1.82: 123
  Bond restraints: 16677
  Sorted by residual:
  bond pdb=" CA  PHE A 545 "
       pdb=" CB  PHE A 545 "
    ideal  model  delta    sigma   weight residual
    1.526  1.495  0.032 1.70e-02 3.46e+03 3.45e+00
  bond pdb=" C   ALA B 651 "
       pdb=" N   PRO B 652 "
    ideal  model  delta    sigma   weight residual
    1.336  1.315  0.021 1.20e-02 6.94e+03 2.95e+00
  bond pdb=" C   PRO C  90 "
       pdb=" N   SER C  91 "
    ideal  model  delta    sigma   weight residual
    1.339  1.260  0.079 5.57e-02 3.22e+02 2.01e+00
  bond pdb=" C   MET A  96 "
       pdb=" N   PRO A  97 "
    ideal  model  delta    sigma   weight residual
    1.339  1.292  0.047 3.40e-02 8.65e+02 1.93e+00
  bond pdb=" C   MET B  96 "
       pdb=" N   PRO B  97 "
    ideal  model  delta    sigma   weight residual
    1.340  1.302  0.038 2.76e-02 1.31e+03 1.90e+00
  ... (remaining 16672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 22268
        2.36 -     4.73: 256
        4.73 -     7.09: 38
        7.09 -     9.46: 7
        9.46 -    11.82: 3
  Bond angle restraints: 22572
  Sorted by residual:
  angle pdb=" CB  MET C 657 "
        pdb=" CG  MET C 657 "
        pdb=" SD  MET C 657 "
      ideal   model   delta    sigma   weight residual
     112.70  124.52  -11.82 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CB  MET A 424 "
        pdb=" CG  MET A 424 "
        pdb=" SD  MET A 424 "
      ideal   model   delta    sigma   weight residual
     112.70  123.30  -10.60 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" CB  MET A 657 "
        pdb=" CG  MET A 657 "
        pdb=" SD  MET A 657 "
      ideal   model   delta    sigma   weight residual
     112.70  122.47   -9.77 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" CB  MET A 292 "
        pdb=" CG  MET A 292 "
        pdb=" SD  MET A 292 "
      ideal   model   delta    sigma   weight residual
     112.70  122.04   -9.34 3.00e+00 1.11e-01 9.70e+00
  angle pdb=" CB  MET B 228 "
        pdb=" CG  MET B 228 "
        pdb=" SD  MET B 228 "
      ideal   model   delta    sigma   weight residual
     112.70  121.83   -9.13 3.00e+00 1.11e-01 9.26e+00
  ... (remaining 22567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 8978
       17.88 -    35.77: 985
       35.77 -    53.65: 222
       53.65 -    71.53: 48
       71.53 -    89.42: 45
  Dihedral angle restraints: 10278
    sinusoidal: 4131
      harmonic: 6147
  Sorted by residual:
  dihedral pdb=" CA  LYS A 718 "
           pdb=" C   LYS A 718 "
           pdb=" N   HIS A 719 "
           pdb=" CA  HIS A 719 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.36   17.64     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASP C 518 "
           pdb=" CB  ASP C 518 "
           pdb=" CG  ASP C 518 "
           pdb=" OD1 ASP C 518 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.88   57.88     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  ASP B 135 "
           pdb=" CB  ASP B 135 "
           pdb=" CG  ASP B 135 "
           pdb=" OD1 ASP B 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.58   57.58     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 10275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1735
       0.034 -    0.067: 574
       0.067 -    0.101: 256
       0.101 -    0.134: 62
       0.134 -    0.168: 7
  Chirality restraints: 2634
  Sorted by residual:
  chirality pdb=" CB  THR A 205 "
            pdb=" CA  THR A 205 "
            pdb=" OG1 THR A 205 "
            pdb=" CG2 THR A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CB  THR C 703 "
            pdb=" CA  THR C 703 "
            pdb=" OG1 THR C 703 "
            pdb=" CG2 THR C 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CB  THR B 665 "
            pdb=" CA  THR B 665 "
            pdb=" OG1 THR B 665 "
            pdb=" CG2 THR B 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.97e-01
  ... (remaining 2631 not shown)

  Planarity restraints: 2931
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 683 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.92e+00
        pdb=" C   THR C 683 "    0.024 2.00e-02 2.50e+03
        pdb=" O   THR C 683 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA C 684 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 203 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO B 204 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 204 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 204 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 221 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO B 222 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 222 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 222 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2928 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 2034
        2.74 -     3.28: 17653
        3.28 -     3.82: 28072
        3.82 -     4.36: 32174
        4.36 -     4.90: 54336
  Nonbonded interactions: 134269
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 283 "
            pdb=" OG1 THR A 287 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER C  60 "
            pdb=" O   SER C  70 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" N   GLU A 520 "
            pdb=" OE1 GLU A 520 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR B  78 "
            pdb=" OD1 ASP B 160 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OE1 GLN B 387 "
            pdb=" NE2 GLN B 392 "
     model   vdw
     2.209 3.120
  ... (remaining 134264 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             3.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     46.600
  Find NCS groups from input model:        0.630
  Set up NCS constraints:                  0.090
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
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      :  0.006   0.079  16677  Z= 0.285
  Angle     :  0.659  11.824  22572  Z= 0.325
  Chirality :  0.042   0.168   2634
  Planarity :  0.003   0.034   2931
  Dihedral  : 16.584  89.419   6318
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 24.06 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.19), residues: 2124
  helix:  1.91 (0.19), residues: 748
  sheet:  0.86 (0.24), residues: 507
  loop : -0.52 (0.23), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 184 
 HIS   0.007   0.001   HIS A 426 
 PHE   0.013   0.001   PHE A 650 
 TYR   0.012   0.001   TYR C 699 
 ARG   0.004   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20304 (  911)
  hydrogen bonds       : angle       7.97201 ( 2532)
  covalent geometry    : bond        0.00596 (16677)
  covalent geometry    : angle       0.65850 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 1.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8915 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 61
  average time/residue: 0.2543
  time to fit residues: 26.3933
Evaluate side-chains
  60 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 1.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  540 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 179 optimal weight:   20.0000
   chunk 161 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 86 optimal weight:    0.3980
   chunk 166 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 124 optimal weight:    7.9990
   chunk 193 optimal weight:    5.9990
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 387 GLN
C 392 GLN
** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 753 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.061128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.035144 restraints weight = 100056.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.036162 restraints weight = 69519.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.036815 restraints weight = 56451.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  16677  Z= 0.262
  Angle     :  0.599   8.809  22572  Z= 0.315
  Chirality :  0.044   0.173   2634
  Planarity :  0.004   0.031   2931
  Dihedral  :  3.994  38.598   2296
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.90 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.19), residues: 2124
  helix:  1.98 (0.19), residues: 756
  sheet:  0.88 (0.24), residues: 492
  loop : -0.65 (0.22), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.018   0.001   PHE A 650 
 TYR   0.012   0.001   TYR C 296 
 ARG   0.007   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05578 (  911)
  hydrogen bonds       : angle       5.56054 ( 2532)
  covalent geometry    : bond        0.00557 (16677)
  covalent geometry    : angle       0.59932 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 61
  time to evaluate  : 1.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.8999 (t60)
REVERT: A  209 MET cc_start: 0.8799 (mmm) cc_final: 0.8545 (mmm)
REVERT: A  424 MET cc_start: 0.8245 (ppp) cc_final: 0.7665 (ppp)
REVERT: B  376 MET cc_start: 0.8706 (mmm) cc_final: 0.8461 (mmp)
REVERT: B  424 MET cc_start: 0.7782 (tmm) cc_final: 0.7425 (tmm)
REVERT: C  184 TRP cc_start: 0.9303 (OUTLIER) cc_final: 0.7528 (t60)
REVERT: C  209 MET cc_start: 0.8802 (mmm) cc_final: 0.8576 (mmm)
REVERT: C  597 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8759 (mtm-85)
  outliers start: 35
  outliers final: 13
  residues processed: 93
  average time/residue: 0.3109
  time to fit residues: 44.8073
Evaluate side-chains
  74 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 1.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  597 ARG
Chi-restraints excluded: chain C residue  619 LYS
Chi-restraints excluded: chain C residue  718 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 178 optimal weight:    0.0010
   chunk 59 optimal weight:    0.9990
   chunk 143 optimal weight:    7.9990
   chunk 125 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.061835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.041360 restraints weight = 102869.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.042621 restraints weight = 65199.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.043475 restraints weight = 48480.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16677  Z= 0.118
  Angle     :  0.503   8.246  22572  Z= 0.262
  Chirality :  0.043   0.148   2634
  Planarity :  0.003   0.035   2931
  Dihedral  :  3.859  37.685   2294
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 22.13 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.19), residues: 2124
  helix:  2.29 (0.19), residues: 752
  sheet:  0.85 (0.24), residues: 497
  loop : -0.48 (0.22), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.011   0.001   PHE A 340 
 TYR   0.013   0.001   TYR B 334 
 ARG   0.005   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04453 (  911)
  hydrogen bonds       : angle       4.87568 ( 2532)
  covalent geometry    : bond        0.00252 (16677)
  covalent geometry    : angle       0.50315 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 63
  time to evaluate  : 1.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9294 (m)
REVERT: A  184 TRP cc_start: 0.9127 (OUTLIER) cc_final: 0.8818 (t60)
REVERT: A  209 MET cc_start: 0.8875 (mmm) cc_final: 0.8538 (mmm)
REVERT: A  424 MET cc_start: 0.8330 (ppp) cc_final: 0.7536 (ppp)
REVERT: A  543 MET cc_start: 0.9214 (ppp) cc_final: 0.8461 (ppp)
REVERT: B  209 MET cc_start: 0.8890 (mmm) cc_final: 0.8687 (mmm)
REVERT: B  376 MET cc_start: 0.8645 (mmm) cc_final: 0.8431 (mmp)
REVERT: B  424 MET cc_start: 0.7551 (tmm) cc_final: 0.7061 (tmm)
REVERT: B  702 MET cc_start: 0.0976 (mtt) cc_final: 0.0467 (mtt)
REVERT: C   81 MET cc_start: 0.8838 (tmm) cc_final: 0.8453 (tmm)
REVERT: C  209 MET cc_start: 0.8853 (mmm) cc_final: 0.8526 (mmm)
REVERT: C  323 GLN cc_start: 0.9589 (OUTLIER) cc_final: 0.9363 (mp10)
REVERT: C  485 MET cc_start: 0.9279 (mmp) cc_final: 0.9061 (mmp)
REVERT: C  543 MET cc_start: 0.9032 (ppp) cc_final: 0.8150 (ppp)
REVERT: C  745 MET cc_start: -0.6821 (ptp) cc_final: -0.7059 (ptp)
  outliers start: 31
  outliers final: 17
  residues processed: 92
  average time/residue: 0.2701
  time to fit residues: 39.9023
Evaluate side-chains
  81 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 1.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  323 GLN
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  718 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 200 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 165 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 99 optimal weight:    0.0770
   overall best weight:    3.4146

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 ASN
C 225 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.061350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035736 restraints weight = 98926.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.036873 restraints weight = 69236.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.037284 restraints weight = 55948.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  16677  Z= 0.226
  Angle     :  0.548   8.725  22572  Z= 0.281
  Chirality :  0.042   0.143   2634
  Planarity :  0.003   0.033   2931
  Dihedral  :  3.877  38.836   2294
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.85 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.19), residues: 2124
  helix:  2.14 (0.19), residues: 754
  sheet:  0.79 (0.24), residues: 498
  loop : -0.50 (0.22), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.019   0.001   PHE A 650 
 TYR   0.014   0.001   TYR B 334 
 ARG   0.005   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04246 (  911)
  hydrogen bonds       : angle       4.86948 ( 2532)
  covalent geometry    : bond        0.00486 (16677)
  covalent geometry    : angle       0.54805 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 59
  time to evaluate  : 3.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.9524 (OUTLIER) cc_final: 0.9320 (m)
REVERT: A  184 TRP cc_start: 0.9248 (OUTLIER) cc_final: 0.8952 (t60)
REVERT: A  209 MET cc_start: 0.8973 (mmm) cc_final: 0.8597 (mmm)
REVERT: A  424 MET cc_start: 0.8239 (ppp) cc_final: 0.7480 (ppp)
REVERT: A  543 MET cc_start: 0.9296 (ppp) cc_final: 0.8524 (ppp)
REVERT: B  376 MET cc_start: 0.8719 (mmm) cc_final: 0.8508 (mmp)
REVERT: B  424 MET cc_start: 0.7536 (tmm) cc_final: 0.7064 (tmm)
REVERT: B  543 MET cc_start: 0.8969 (ppp) cc_final: 0.8021 (ppp)
REVERT: C   81 MET cc_start: 0.8883 (tmm) cc_final: 0.8505 (tmm)
REVERT: C  184 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.7816 (t60)
REVERT: C  209 MET cc_start: 0.8894 (mmm) cc_final: 0.8545 (mmm)
REVERT: C  323 GLN cc_start: 0.9589 (OUTLIER) cc_final: 0.9360 (mp10)
REVERT: C  485 MET cc_start: 0.9366 (mmp) cc_final: 0.9083 (mmp)
REVERT: C  543 MET cc_start: 0.9036 (ppp) cc_final: 0.8794 (ppp)
  outliers start: 53
  outliers final: 31
  residues processed: 109
  average time/residue: 0.3272
  time to fit residues: 55.1786
Evaluate side-chains
  94 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 59
  time to evaluate  : 1.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  323 GLN
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  547 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 158 optimal weight:    8.9990
   chunk 135 optimal weight:   50.0000
   chunk 26 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 118 optimal weight:    5.9990
   chunk 180 optimal weight:    7.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 392 GLN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.061675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.041991 restraints weight = 105192.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.043231 restraints weight = 66123.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.044064 restraints weight = 48584.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  16677  Z= 0.211
  Angle     :  0.551   9.620  22572  Z= 0.280
  Chirality :  0.043   0.145   2634
  Planarity :  0.003   0.034   2931
  Dihedral  :  3.905  39.347   2294
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.41 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.19), residues: 2124
  helix:  2.12 (0.19), residues: 759
  sheet:  0.74 (0.24), residues: 494
  loop : -0.49 (0.22), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.018   0.001   PHE A 650 
 TYR   0.014   0.001   TYR B 334 
 ARG   0.007   0.000   ARG B 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  911)
  hydrogen bonds       : angle       4.77508 ( 2532)
  covalent geometry    : bond        0.00451 (16677)
  covalent geometry    : angle       0.55074 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 60
  time to evaluate  : 1.994 
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   47 VAL cc_start: 0.9502 (OUTLIER) cc_final: 0.9276 (m)
REVERT: A  184 TRP cc_start: 0.9229 (OUTLIER) cc_final: 0.8954 (t60)
REVERT: A  209 MET cc_start: 0.9040 (mmm) cc_final: 0.8667 (mmm)
REVERT: A  424 MET cc_start: 0.8283 (ppp) cc_final: 0.7573 (ppp)
REVERT: A  543 MET cc_start: 0.9278 (ppp) cc_final: 0.8449 (ppp)
REVERT: B  376 MET cc_start: 0.8724 (mmm) cc_final: 0.8515 (mmp)
REVERT: B  424 MET cc_start: 0.7582 (tmm) cc_final: 0.7077 (tmm)
REVERT: B  543 MET cc_start: 0.8991 (ppp) cc_final: 0.8028 (ppp)
REVERT: C   81 MET cc_start: 0.8882 (tmm) cc_final: 0.8494 (tmm)
REVERT: C  184 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.7949 (t60)
REVERT: C  209 MET cc_start: 0.8920 (mmm) cc_final: 0.8521 (mmm)
REVERT: C  323 GLN cc_start: 0.9588 (OUTLIER) cc_final: 0.9348 (mp10)
REVERT: C  543 MET cc_start: 0.9089 (ppp) cc_final: 0.8121 (ppp)
  outliers start: 56
  outliers final: 39
  residues processed: 112
  average time/residue: 0.3068
  time to fit residues: 55.9892
Evaluate side-chains
  103 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 60
  time to evaluate  : 2.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  323 GLN
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  619 LYS
Chi-restraints excluded: chain C residue  669 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 154 optimal weight:    2.9990
   chunk 190 optimal weight:    3.9990
   chunk 186 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 203 optimal weight:    0.8980
   chunk 138 optimal weight:    7.9990
   chunk 167 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.061254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.041023 restraints weight = 106428.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.042279 restraints weight = 67100.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.043085 restraints weight = 49592.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16677  Z= 0.157
  Angle     :  0.516  10.431  22572  Z= 0.263
  Chirality :  0.043   0.155   2634
  Planarity :  0.003   0.036   2931
  Dihedral  :  3.853  39.272   2294
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.12 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.19), residues: 2124
  helix:  2.24 (0.19), residues: 759
  sheet:  0.79 (0.24), residues: 494
  loop : -0.44 (0.22), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.014   0.001   PHE A 650 
 TYR   0.013   0.001   TYR B 334 
 ARG   0.004   0.000   ARG B 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03928 (  911)
  hydrogen bonds       : angle       4.61192 ( 2532)
  covalent geometry    : bond        0.00337 (16677)
  covalent geometry    : angle       0.51562 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 61
  time to evaluate  : 1.910 
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   47 VAL cc_start: 0.9491 (OUTLIER) cc_final: 0.9256 (m)
REVERT: A  184 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8808 (t60)
REVERT: A  209 MET cc_start: 0.9119 (mmm) cc_final: 0.8736 (mmm)
REVERT: A  424 MET cc_start: 0.8270 (ppp) cc_final: 0.7549 (ppp)
REVERT: A  543 MET cc_start: 0.9264 (ppp) cc_final: 0.8425 (ppp)
REVERT: B  184 TRP cc_start: 0.9143 (OUTLIER) cc_final: 0.8844 (t60)
REVERT: B  376 MET cc_start: 0.8682 (mmm) cc_final: 0.8472 (mmp)
REVERT: B  424 MET cc_start: 0.7505 (tmm) cc_final: 0.6985 (tmm)
REVERT: B  543 MET cc_start: 0.8990 (ppp) cc_final: 0.8005 (ppp)
REVERT: C  184 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.7873 (t60)
REVERT: C  209 MET cc_start: 0.8938 (mmm) cc_final: 0.8503 (mmm)
REVERT: C  323 GLN cc_start: 0.9584 (OUTLIER) cc_final: 0.9362 (mp10)
REVERT: C  485 MET cc_start: 0.9368 (mmp) cc_final: 0.9012 (mmp)
REVERT: C  543 MET cc_start: 0.9100 (ppp) cc_final: 0.8137 (ppp)
  outliers start: 47
  outliers final: 33
  residues processed: 104
  average time/residue: 0.2586
  time to fit residues: 44.0931
Evaluate side-chains
  98 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 60
  time to evaluate  : 1.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  184 TRP
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  323 GLN
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  547 ILE
Chi-restraints excluded: chain C residue  669 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 104 optimal weight:    0.0870
   chunk 125 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 162 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 201 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 212 optimal weight:   30.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.061895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.041743 restraints weight = 102841.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.043005 restraints weight = 64412.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.043857 restraints weight = 47477.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16677  Z= 0.117
  Angle     :  0.507  11.071  22572  Z= 0.255
  Chirality :  0.043   0.145   2634
  Planarity :  0.003   0.038   2931
  Dihedral  :  3.813  38.842   2294
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 24.06 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.19), residues: 2124
  helix:  2.38 (0.19), residues: 757
  sheet:  0.85 (0.24), residues: 494
  loop : -0.36 (0.23), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 184 
 HIS   0.003   0.000   HIS A 708 
 PHE   0.010   0.001   PHE A 650 
 TYR   0.013   0.001   TYR B 334 
 ARG   0.009   0.000   ARG A 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  911)
  hydrogen bonds       : angle       4.45889 ( 2532)
  covalent geometry    : bond        0.00253 (16677)
  covalent geometry    : angle       0.50703 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 64
  time to evaluate  : 2.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9246 (m)
REVERT: A  184 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8766 (t60)
REVERT: A  209 MET cc_start: 0.9181 (mmm) cc_final: 0.8787 (mmm)
REVERT: A  424 MET cc_start: 0.8274 (ppp) cc_final: 0.7576 (ppp)
REVERT: A  496 MET cc_start: 0.9419 (tpt) cc_final: 0.9169 (tpt)
REVERT: A  543 MET cc_start: 0.9239 (ppp) cc_final: 0.8382 (ppp)
REVERT: B  376 MET cc_start: 0.8667 (mmm) cc_final: 0.8460 (mmp)
REVERT: B  424 MET cc_start: 0.7461 (tmm) cc_final: 0.6933 (tmm)
REVERT: B  543 MET cc_start: 0.8991 (ppp) cc_final: 0.8009 (ppp)
REVERT: C   81 MET cc_start: 0.8795 (tmm) cc_final: 0.8518 (tmm)
REVERT: C  209 MET cc_start: 0.8914 (mmm) cc_final: 0.8462 (mmm)
REVERT: C  485 MET cc_start: 0.9363 (mmp) cc_final: 0.9022 (mmp)
REVERT: C  543 MET cc_start: 0.9122 (ppp) cc_final: 0.8169 (ppp)
  outliers start: 36
  outliers final: 27
  residues processed: 98
  average time/residue: 0.3363
  time to fit residues: 54.9495
Evaluate side-chains
  90 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 2.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  545 PHE
Chi-restraints excluded: chain C residue  547 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 65 optimal weight:   30.0000
   chunk 169 optimal weight:    4.9990
   chunk 193 optimal weight:    7.9990
   chunk 208 optimal weight:   10.0000
   chunk 119 optimal weight:    6.9990
   chunk 191 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 172 optimal weight:    0.9990
   chunk 111 optimal weight:    7.9990
   chunk 198 optimal weight:    0.0060
   chunk 95 optimal weight:    7.9990
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.061313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.041178 restraints weight = 103806.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.042401 restraints weight = 65820.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.043246 restraints weight = 48736.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16677  Z= 0.200
  Angle     :  0.559  11.828  22572  Z= 0.278
  Chirality :  0.042   0.142   2634
  Planarity :  0.003   0.039   2931
  Dihedral  :  3.826  39.499   2294
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.51 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.19), residues: 2124
  helix:  2.27 (0.19), residues: 757
  sheet:  0.81 (0.24), residues: 494
  loop : -0.40 (0.23), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 184 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.017   0.001   PHE A 650 
 TYR   0.014   0.001   TYR B 334 
 ARG   0.005   0.000   ARG B 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03750 (  911)
  hydrogen bonds       : angle       4.55131 ( 2532)
  covalent geometry    : bond        0.00430 (16677)
  covalent geometry    : angle       0.55937 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 59
  time to evaluate  : 1.980 
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: A   47 VAL cc_start: 0.9495 (OUTLIER) cc_final: 0.9261 (m)
REVERT: A  184 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8810 (t60)
REVERT: A  209 MET cc_start: 0.9176 (mmm) cc_final: 0.8794 (mmm)
REVERT: A  424 MET cc_start: 0.8239 (ppp) cc_final: 0.7583 (ppp)
REVERT: A  543 MET cc_start: 0.9243 (ppp) cc_final: 0.8334 (ppp)
REVERT: B  376 MET cc_start: 0.8708 (mmm) cc_final: 0.8501 (mmp)
REVERT: B  424 MET cc_start: 0.7513 (tmm) cc_final: 0.6963 (tmm)
REVERT: B  543 MET cc_start: 0.8969 (ppp) cc_final: 0.7955 (ppp)
REVERT: C   81 MET cc_start: 0.8823 (tmm) cc_final: 0.8523 (tmm)
REVERT: C  184 TRP cc_start: 0.9257 (OUTLIER) cc_final: 0.7879 (t60)
REVERT: C  209 MET cc_start: 0.8946 (mmm) cc_final: 0.8504 (mmm)
REVERT: C  485 MET cc_start: 0.9388 (mmp) cc_final: 0.9067 (mmp)
REVERT: C  543 MET cc_start: 0.9100 (ppp) cc_final: 0.8109 (ppp)
  outliers start: 48
  outliers final: 41
  residues processed: 104
  average time/residue: 0.2870
  time to fit residues: 48.2362
Evaluate side-chains
  103 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 59
  time to evaluate  : 1.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  547 ILE
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  669 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 104 optimal weight:    0.0470
   chunk 28 optimal weight:    0.3980
   chunk 91 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 115 optimal weight:    9.9990
   chunk 101 optimal weight:    0.8980
   chunk 125 optimal weight:    0.5980
   chunk 204 optimal weight:   20.0000
   chunk 170 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 672 GLN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 627 ASN
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.062113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.041640 restraints weight = 104019.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.042925 restraints weight = 65298.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.043765 restraints weight = 48275.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  16677  Z= 0.097
  Angle     :  0.522  12.474  22572  Z= 0.259
  Chirality :  0.043   0.145   2634
  Planarity :  0.003   0.039   2931
  Dihedral  :  3.761  38.703   2294
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.90 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.19), residues: 2124
  helix:  2.30 (0.19), residues: 769
  sheet:  0.88 (0.24), residues: 489
  loop : -0.33 (0.22), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 184 
 HIS   0.003   0.000   HIS A 708 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.013   0.001   TYR B 334 
 ARG   0.005   0.000   ARG C 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  911)
  hydrogen bonds       : angle       4.36224 ( 2532)
  covalent geometry    : bond        0.00209 (16677)
  covalent geometry    : angle       0.52164 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 63
  time to evaluate  : 1.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9230 (m)
REVERT: A  184 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8685 (t60)
REVERT: A  209 MET cc_start: 0.9184 (mmm) cc_final: 0.8774 (mmm)
REVERT: A  424 MET cc_start: 0.8322 (ppp) cc_final: 0.7633 (ppp)
REVERT: A  543 MET cc_start: 0.9222 (ppp) cc_final: 0.8372 (ppp)
REVERT: B  376 MET cc_start: 0.8599 (mmm) cc_final: 0.8399 (mmp)
REVERT: B  424 MET cc_start: 0.7439 (tmm) cc_final: 0.6900 (tmm)
REVERT: B  543 MET cc_start: 0.8978 (ppp) cc_final: 0.7993 (ppp)
REVERT: C   44 MET cc_start: 0.6093 (pmm) cc_final: 0.5738 (ptp)
REVERT: C   81 MET cc_start: 0.8779 (tmm) cc_final: 0.8534 (tmm)
REVERT: C  209 MET cc_start: 0.8935 (mmm) cc_final: 0.8493 (mmm)
REVERT: C  485 MET cc_start: 0.9352 (mmp) cc_final: 0.9045 (mmp)
REVERT: C  543 MET cc_start: 0.9094 (ppp) cc_final: 0.8139 (ppp)
  outliers start: 39
  outliers final: 36
  residues processed: 100
  average time/residue: 0.2558
  time to fit residues: 41.9697
Evaluate side-chains
  99 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 61
  time to evaluate  : 1.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  545 PHE
Chi-restraints excluded: chain C residue  547 ILE
Chi-restraints excluded: chain C residue  586 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 142 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 209 optimal weight:    7.9990
   chunk 147 optimal weight:    0.9980
   chunk 164 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 158 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.061641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.041417 restraints weight = 104087.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.042664 restraints weight = 65866.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.043527 restraints weight = 48673.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  16677  Z= 0.176
  Angle     :  0.557  12.812  22572  Z= 0.274
  Chirality :  0.042   0.146   2634
  Planarity :  0.003   0.043   2931
  Dihedral  :  3.760  39.312   2294
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.68 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.19), residues: 2124
  helix:  2.37 (0.19), residues: 757
  sheet:  0.87 (0.24), residues: 498
  loop : -0.35 (0.23), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 184 
 HIS   0.003   0.000   HIS A 708 
 PHE   0.015   0.001   PHE A 650 
 TYR   0.014   0.001   TYR B 334 
 ARG   0.004   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  911)
  hydrogen bonds       : angle       4.44153 ( 2532)
  covalent geometry    : bond        0.00383 (16677)
  covalent geometry    : angle       0.55732 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 60
  time to evaluate  : 1.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.9499 (OUTLIER) cc_final: 0.9268 (m)
REVERT: A  184 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.8770 (t60)
REVERT: A  209 MET cc_start: 0.9187 (mmm) cc_final: 0.8786 (mmm)
REVERT: A  285 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9269 (ptpp)
REVERT: A  424 MET cc_start: 0.8246 (ppp) cc_final: 0.7584 (ppp)
REVERT: A  543 MET cc_start: 0.9215 (ppp) cc_final: 0.8307 (ppp)
REVERT: B  184 TRP cc_start: 0.9150 (OUTLIER) cc_final: 0.8846 (t60)
REVERT: B  376 MET cc_start: 0.8690 (mmm) cc_final: 0.8485 (mmp)
REVERT: B  424 MET cc_start: 0.7511 (tmm) cc_final: 0.6967 (tmm)
REVERT: B  543 MET cc_start: 0.8984 (ppp) cc_final: 0.7981 (ppp)
REVERT: C   44 MET cc_start: 0.6091 (pmm) cc_final: 0.5800 (ptp)
REVERT: C   81 MET cc_start: 0.8804 (tmm) cc_final: 0.8517 (tmm)
REVERT: C  209 MET cc_start: 0.8935 (mmm) cc_final: 0.8487 (mmm)
REVERT: C  485 MET cc_start: 0.9372 (mmp) cc_final: 0.9051 (mmp)
REVERT: C  543 MET cc_start: 0.9112 (ppp) cc_final: 0.8135 (ppp)
  outliers start: 45
  outliers final: 41
  residues processed: 103
  average time/residue: 0.2563
  time to fit residues: 42.9239
Evaluate side-chains
  105 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 60
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  715 ARG
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain B residue  184 TRP
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  685 THR
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain B residue  696 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain C residue  545 PHE
Chi-restraints excluded: chain C residue  547 ILE
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  707 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 178 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    7.9990
   chunk 181 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 193 optimal weight:    1.9990
   chunk 166 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 141 optimal weight:   30.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 392 GLN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 714 GLN
** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.061888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.041455 restraints weight = 102927.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.042700 restraints weight = 66151.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.043541 restraints weight = 49108.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16677  Z= 0.145
  Angle     :  0.538  12.766  22572  Z= 0.266
  Chirality :  0.042   0.159   2634
  Planarity :  0.003   0.041   2931
  Dihedral  :  3.765  39.668   2294
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 23.79 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.19), residues: 2124
  helix:  2.28 (0.19), residues: 763
  sheet:  0.89 (0.24), residues: 494
  loop : -0.37 (0.23), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 184 
 HIS   0.003   0.000   HIS A 708 
 PHE   0.013   0.001   PHE A 650 
 TYR   0.014   0.001   TYR B 334 
 ARG   0.004   0.000   ARG C 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  911)
  hydrogen bonds       : angle       4.40211 ( 2532)
  covalent geometry    : bond        0.00319 (16677)
  covalent geometry    : angle       0.53825 (22572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4969.74 seconds
wall clock time: 89 minutes 33.58 seconds (5373.58 seconds total)