Starting phenix.real_space_refine
on Wed Jul 30 04:16:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rfh_19121/07_2025/8rfh_19121.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      58      5.16       5
     C    7550      2.51       5
     N    2032      2.21       5
     O    2158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11802
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 730, 5874
          Classifications: {'peptide': 730}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 730, 5874
          Classifications: {'peptide': 730}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.50, per 1000 atoms: 0.64
  Number of scatterers: 11802
  At special positions: 0
  Unit cell: (141.588, 78.66, 91.908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P       4     15.00
     O    2158      8.00
     N    2032      7.00
     C    7550      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: 2.88
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 12 sheets defined
      43.6% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 157 through 170
    Processing helix  chain 'A' and resid 187 through 198
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.575A  pdb=" N   LYS A 229 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.662A  pdb=" N   HIS A 238 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 256
      removed outlier: 3.559A  pdb=" N   GLY A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 277
      removed outlier: 3.520A  pdb=" N   TRP A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE A 277 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 301
      removed outlier: 4.287A  pdb=" N   ALA A 298 " --> pdb=" O   ASP A 294 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 328
      removed outlier: 3.550A  pdb=" N   ILE A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 4.111A  pdb=" N   LEU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   SER A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 366
    Processing helix  chain 'A' and resid 368 through 382
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 3.763A  pdb=" N   ASN A 393 " --> pdb=" O   PRO A 389 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LYS A 394 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 395 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.688A  pdb=" N   GLY A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 445 through 460
    Processing helix  chain 'A' and resid 480 through 494
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 526 through 534
      removed outlier: 3.534A  pdb=" N   LYS A 534 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 565
    Processing helix  chain 'A' and resid 583 through 588
    Processing helix  chain 'A' and resid 605 through 611
    Processing helix  chain 'A' and resid 674 through 678
    Processing helix  chain 'A' and resid 679 through 685
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 3.862A  pdb=" N   LEU A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 715
      removed outlier: 3.878A  pdb=" N   VAL A 712 " --> pdb=" O   LEU A 708 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS A 714 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A 715 " --> pdb=" O   ASN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 742
    Processing helix  chain 'A' and resid 757 through 759
      No H-bonds generated for 'chain 'A' and resid 757 through 759'
    Processing helix  chain 'A' and resid 760 through 767
      removed outlier: 3.640A  pdb=" N   LEU A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   MET A 767 " --> pdb=" O   ILE A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 838
    Processing helix  chain 'A' and resid 850 through 871
    Processing helix  chain 'B' and resid 157 through 170
    Processing helix  chain 'B' and resid 187 through 198
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 218 through 229
      removed outlier: 3.575A  pdb=" N   LYS B 229 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.661A  pdb=" N   HIS B 238 " --> pdb=" O   LYS B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 256
      removed outlier: 3.559A  pdb=" N   GLY B 256 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 277
      removed outlier: 3.520A  pdb=" N   TRP B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE B 277 " --> pdb=" O   GLU B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 301
      removed outlier: 4.288A  pdb=" N   ALA B 298 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS B 301 " --> pdb=" O   VAL B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 334 through 348
      removed outlier: 4.111A  pdb=" N   LEU B 339 " --> pdb=" O   PRO B 335 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   SER B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 366
    Processing helix  chain 'B' and resid 368 through 382
    Processing helix  chain 'B' and resid 389 through 401
      removed outlier: 3.763A  pdb=" N   ASN B 393 " --> pdb=" O   PRO B 389 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS B 394 " --> pdb=" O   GLU B 390 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 395 " --> pdb=" O   ASN B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 415
      removed outlier: 3.687A  pdb=" N   GLY B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 436
    Processing helix  chain 'B' and resid 445 through 460
    Processing helix  chain 'B' and resid 480 through 494
    Processing helix  chain 'B' and resid 511 through 516
    Processing helix  chain 'B' and resid 526 through 534
      removed outlier: 3.533A  pdb=" N   LYS B 534 " --> pdb=" O   PHE B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 583 through 588
    Processing helix  chain 'B' and resid 605 through 611
    Processing helix  chain 'B' and resid 674 through 678
    Processing helix  chain 'B' and resid 679 through 685
    Processing helix  chain 'B' and resid 697 through 702
      removed outlier: 3.861A  pdb=" N   LEU B 701 " --> pdb=" O   LYS B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 715
      removed outlier: 3.879A  pdb=" N   VAL B 712 " --> pdb=" O   LEU B 708 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS B 714 " --> pdb=" O   LYS B 710 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 715 " --> pdb=" O   ASN B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 742
    Processing helix  chain 'B' and resid 757 through 759
      No H-bonds generated for 'chain 'B' and resid 757 through 759'
    Processing helix  chain 'B' and resid 760 through 767
      removed outlier: 3.640A  pdb=" N   LEU B 764 " --> pdb=" O   ASP B 760 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   MET B 767 " --> pdb=" O   ILE B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 838
    Processing helix  chain 'B' and resid 850 through 871
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212
      removed outlier: 3.567A  pdb=" N   ILE A 209 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP A 265 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLU A 176 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU A 290 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   THR A 292 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   VAL A 180 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 424
      removed outlier: 3.609A  pdb=" N   GLN A 467 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ARG A 478 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   VAL A 465 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 6.818A  pdb=" N   PHE A 543 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLU A 574 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522
      removed outlier: 6.818A  pdb=" N   PHE A 543 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLU A 574 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
      removed outlier: 10.309A  pdb=" N   TYR A 593 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 9.393A  pdb=" N   GLU A 574 " --> pdb=" O   TYR A 593 " (cutoff:3.500A)
      removed outlier: 8.766A  pdb=" N   ALA A 595 " --> pdb=" O   GLU A 574 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE A 576 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE A 594 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   ASN A 620 " --> pdb=" O   ILE A 594 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   PHE A 596 " --> pdb=" O   ASN A 620 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   LEU A 641 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ILE A 673 " --> pdb=" O   LEU A 641 " (cutoff:3.500A)
      removed outlier: 9.614A  pdb=" N   THR A 643 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR A 669 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLY A 693 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   SER A 671 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   ARG A 695 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   ILE A 673 " --> pdb=" O   ARG A 695 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 752 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A 725 " --> pdb=" O   VAL A 752 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU A 749 " --> pdb=" O   LYS A 774 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   LYS A 776 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   LEU A 751 " --> pdb=" O   LYS A 776 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU A 845 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 822 " --> pdb=" O   GLU A 845 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604
    Processing sheet with id=AA6, first strand: chain 'A' and resid 784 through 786
      removed outlier: 6.691A  pdb=" N   TRP A 785 " --> pdb=" O   LYS A 808 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 212
      removed outlier: 3.567A  pdb=" N   ILE B 209 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP B 265 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLU B 176 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU B 290 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   THR B 292 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   VAL B 180 " --> pdb=" O   THR B 292 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 424
      removed outlier: 3.608A  pdb=" N   GLN B 467 " --> pdb=" O   THR B 476 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ARG B 478 " --> pdb=" O   VAL B 465 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   VAL B 465 " --> pdb=" O   ARG B 478 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 520 through 522
      removed outlier: 6.819A  pdb=" N   PHE B 543 " --> pdb=" O   ASP B 572 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   GLU B 574 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 522
      removed outlier: 6.819A  pdb=" N   PHE B 543 " --> pdb=" O   ASP B 572 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   GLU B 574 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
      removed outlier: 10.308A  pdb=" N   TYR B 593 " --> pdb=" O   ASP B 572 " (cutoff:3.500A)
      removed outlier: 9.393A  pdb=" N   GLU B 574 " --> pdb=" O   TYR B 593 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   ALA B 595 " --> pdb=" O   GLU B 574 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE B 576 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE B 594 " --> pdb=" O   ILE B 618 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ASN B 620 " --> pdb=" O   ILE B 594 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE B 596 " --> pdb=" O   ASN B 620 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU B 641 " --> pdb=" O   SER B 671 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   ILE B 673 " --> pdb=" O   LEU B 641 " (cutoff:3.500A)
      removed outlier: 9.821A  pdb=" N   THR B 643 " --> pdb=" O   ILE B 673 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR B 672 " --> pdb=" O   GLY B 693 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ARG B 695 " --> pdb=" O   THR B 672 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 752 " --> pdb=" O   LEU B 723 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN B 725 " --> pdb=" O   VAL B 752 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU B 749 " --> pdb=" O   LYS B 774 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   LYS B 776 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   LEU B 751 " --> pdb=" O   LYS B 776 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU B 845 " --> pdb=" O   LEU B 820 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 822 " --> pdb=" O   GLU B 845 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 603 through 604
    Processing sheet with id=AB3, first strand: chain 'B' and resid 784 through 786
      removed outlier: 6.690A  pdb=" N   TRP B 785 " --> pdb=" O   LYS B 808 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    458 hydrogen bonds defined for protein.
    1254 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: 4.62

  Time building geometry restraints manager: 3.26 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: 3588
        1.34 -     1.45: 1609
        1.45 -     1.57: 6771
        1.57 -     1.69: 6
        1.69 -     1.81: 82
  Bond restraints: 12056
  Sorted by residual:
  bond pdb=" N   THR A 315 "
       pdb=" CA  THR A 315 "
    ideal  model  delta    sigma   weight residual
    1.453  1.496 -0.043 1.31e-02 5.83e+03 1.08e+01
  bond pdb=" N   ILE A 673 "
       pdb=" CA  ILE A 673 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.14e-02 7.69e+03 1.05e+01
  bond pdb=" N   THR B 315 "
       pdb=" CA  THR B 315 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.042 1.34e-02 5.57e+03 9.89e+00
  bond pdb=" N   LEU A 314 "
       pdb=" CA  LEU A 314 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   ILE A 433 "
       pdb=" CA  ILE A 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.15e+00
  ... (remaining 12051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 15920
        2.22 -     4.45: 277
        4.45 -     6.67: 68
        6.67 -     8.89: 14
        8.89 -    11.12: 7
  Bond angle restraints: 16286
  Sorted by residual:
  angle pdb=" C   SER A 671 "
        pdb=" N   THR A 672 "
        pdb=" CA  THR A 672 "
      ideal   model   delta    sigma   weight residual
     122.30  114.12    8.18 1.35e+00 5.49e-01 3.67e+01
  angle pdb=" C   THR A 672 "
        pdb=" CA  THR A 672 "
        pdb=" CB  THR A 672 "
      ideal   model   delta    sigma   weight residual
     110.22  120.17   -9.95 1.67e+00 3.59e-01 3.55e+01
  angle pdb=" N   ASP B 317 "
        pdb=" CA  ASP B 317 "
        pdb=" C   ASP B 317 "
      ideal   model   delta    sigma   weight residual
     111.28  105.88    5.40 1.09e+00 8.42e-01 2.46e+01
  angle pdb=" N   ASP A 317 "
        pdb=" CA  ASP A 317 "
        pdb=" C   ASP A 317 "
      ideal   model   delta    sigma   weight residual
     111.28  106.71    4.57 1.09e+00 8.42e-01 1.76e+01
  angle pdb=" C   GLU A 316 "
        pdb=" CA  GLU A 316 "
        pdb=" CB  GLU A 316 "
      ideal   model   delta    sigma   weight residual
     110.79  105.33    5.46 1.66e+00 3.63e-01 1.08e+01
  ... (remaining 16281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 7135
       34.69 -    69.38: 185
       69.38 -   104.07: 12
      104.07 -   138.76: 0
      138.76 -   173.45: 2
  Dihedral angle restraints: 7334
    sinusoidal: 3096
      harmonic: 4238
  Sorted by residual:
  dihedral pdb=" C5' ADP B1001 "
           pdb=" O5' ADP B1001 "
           pdb=" PA  ADP B1001 "
           pdb=" O2A ADP B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.45 -173.45     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C5' ADP A1001 "
           pdb=" O5' ADP A1001 "
           pdb=" PA  ADP A1001 "
           pdb=" O2A ADP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.42 -173.42     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" CA  SER A 671 "
           pdb=" C   SER A 671 "
           pdb=" N   THR A 672 "
           pdb=" CA  THR A 672 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.32  -29.68     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 7331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1622
       0.078 -    0.156: 182
       0.156 -    0.234: 7
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" CA  THR A 672 "
            pdb=" N   THR A 672 "
            pdb=" C   THR A 672 "
            pdb=" CB  THR A 672 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.14    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  GLU A 316 "
            pdb=" N   GLU A 316 "
            pdb=" C   GLU A 316 "
            pdb=" CB  GLU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE B 673 "
            pdb=" N   ILE B 673 "
            pdb=" C   ILE B 673 "
            pdb=" CB  ILE B 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1809 not shown)

  Planarity restraints: 2060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 670 "    0.021 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   LEU A 670 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   LEU A 670 "    0.028 2.00e-02 2.50e+03
        pdb=" N   SER A 671 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 670 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.49e+00
        pdb=" C   LEU B 670 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B 670 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 671 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 671 "    0.014 2.00e-02 2.50e+03   2.76e-02 7.61e+00
        pdb=" C   SER A 671 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   SER A 671 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR A 672 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2057 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 859
        2.74 -     3.28: 12589
        3.28 -     3.82: 20182
        3.82 -     4.36: 23810
        4.36 -     4.90: 38512
  Nonbonded interactions: 95952
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 469 "
            pdb=" OD1 ASP B 471 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG1 THR A 469 "
            pdb=" OD1 ASP A 471 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER A 268 "
            pdb=" OD1 ASP A 270 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER B 268 "
            pdb=" OD1 ASP B 270 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   VAL A 653 "
            pdb=" NH2 ARG A 685 "
     model   vdw
     2.293 3.120
  ... (remaining 95947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.740
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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      :  0.003   0.043  12056  Z= 0.190
  Angle     :  0.760  11.116  16286  Z= 0.383
  Chirality :  0.048   0.389   1812
  Planarity :  0.004   0.043   2060
  Dihedral  : 15.836 173.446   4582
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.69 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.35 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.66 (0.23), residues: 1452
  helix:  0.50 (0.23), residues: 518
  sheet:  0.20 (0.37), residues: 212
  loop :  0.67 (0.24), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 798 
 HIS   0.004   0.001   HIS A 524 
 PHE   0.010   0.001   PHE B 571 
 TYR   0.006   0.001   TYR B 413 
 ARG   0.007   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21346 (  454)
  hydrogen bonds       : angle       7.65969 ( 1254)
  covalent geometry    : bond        0.00311 (12056)
  covalent geometry    : angle       0.75997 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 1.454 
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  351 LEU cc_start: 0.7900 (tt) cc_final: 0.7248 (tp)
REVERT: A  456 ASP cc_start: 0.8905 (m-30) cc_final: 0.8319 (t70)
REVERT: A  692 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tp)
REVERT: A  844 MET cc_start: 0.7277 (tmm) cc_final: 0.7032 (tmm)
REVERT: B  351 LEU cc_start: 0.7779 (tt) cc_final: 0.7215 (tp)
REVERT: B  432 TRP cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-90)
REVERT: B  456 ASP cc_start: 0.8881 (m-30) cc_final: 0.8274 (t70)
REVERT: B  671 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6842 (p)
REVERT: B  672 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6154 (p)
REVERT: B  692 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp)
REVERT: B  844 MET cc_start: 0.7143 (tmm) cc_final: 0.6898 (tmm)
  outliers start: 19
  outliers final: 3
  residues processed: 194
  average time/residue: 0.2047
  time to fit residues: 59.9457
Evaluate side-chains
  172 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  672 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:   30.0000
   chunk 110 optimal weight:    0.8980
   chunk 61 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 114 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0060
   chunk 132 optimal weight:    3.9990
   overall best weight:    1.5800

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
A 668 GLN
B 309 HIS
B 349 ASN
B 668 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.107037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.079063 restraints weight = 33923.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.082226 restraints weight = 18678.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.084391 restraints weight = 12554.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12056  Z= 0.134
  Angle     :  0.674   9.693  16286  Z= 0.325
  Chirality :  0.045   0.157   1812
  Planarity :  0.004   0.043   2060
  Dihedral  :  7.256 147.309   1586
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.24 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.56 (0.23), residues: 1452
  helix:  0.59 (0.23), residues: 530
  sheet: -0.08 (0.36), residues: 228
  loop :  0.57 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 432 
 HIS   0.004   0.001   HIS A 382 
 PHE   0.017   0.001   PHE A 585 
 TYR   0.012   0.001   TYR A 259 
 ARG   0.006   0.000   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  454)
  hydrogen bonds       : angle       5.52684 ( 1254)
  covalent geometry    : bond        0.00301 (12056)
  covalent geometry    : angle       0.67435 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 177
  time to evaluate  : 1.418 
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  407 LEU cc_start: 0.9570 (tp) cc_final: 0.9366 (tp)
REVERT: A  456 ASP cc_start: 0.8917 (m-30) cc_final: 0.8429 (t70)
REVERT: A  671 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7361 (p)
REVERT: A  722 LYS cc_start: 0.8760 (tptp) cc_final: 0.8250 (mttt)
REVERT: B  407 LEU cc_start: 0.9524 (tp) cc_final: 0.9317 (tp)
REVERT: B  432 TRP cc_start: 0.8468 (m-10) cc_final: 0.7995 (m-90)
REVERT: B  456 ASP cc_start: 0.8897 (m-30) cc_final: 0.8414 (t70)
REVERT: B  635 MET cc_start: 0.7623 (tpt) cc_final: 0.7419 (tpt)
REVERT: B  671 SER cc_start: 0.8009 (t) cc_final: 0.7622 (p)
REVERT: B  844 MET cc_start: 0.7429 (tmm) cc_final: 0.7209 (tmm)
  outliers start: 39
  outliers final: 23
  residues processed: 191
  average time/residue: 0.1892
  time to fit residues: 56.3537
Evaluate side-chains
  190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 1.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 130 optimal weight:    0.0970
   chunk 27 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 145 optimal weight:    8.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    3.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.101702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.073783 restraints weight = 35307.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.076643 restraints weight = 19805.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.078523 restraints weight = 13611.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12056  Z= 0.222
  Angle     :  0.727   9.151  16286  Z= 0.359
  Chirality :  0.047   0.161   1812
  Planarity :  0.005   0.045   2060
  Dihedral  :  7.046 128.164   1583
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 17.33 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.47 (0.23), residues: 1452
  helix:  0.64 (0.23), residues: 516
  sheet: -0.45 (0.35), residues: 224
  loop :  0.53 (0.25), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 432 
 HIS   0.005   0.001   HIS B 309 
 PHE   0.020   0.002   PHE A 530 
 TYR   0.016   0.002   TYR A 413 
 ARG   0.004   0.001   ARG B 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04137 (  454)
  hydrogen bonds       : angle       5.52267 ( 1254)
  covalent geometry    : bond        0.00484 (12056)
  covalent geometry    : angle       0.72731 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 169
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 ILE cc_start: 0.9297 (pp) cc_final: 0.9057 (pp)
REVERT: A  432 TRP cc_start: 0.8377 (m-10) cc_final: 0.8168 (m-90)
REVERT: A  522 CYS cc_start: 0.7704 (p) cc_final: 0.7343 (p)
REVERT: A  635 MET cc_start: 0.7762 (tpt) cc_final: 0.7549 (tpt)
REVERT: A  671 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7740 (p)
REVERT: A  722 LYS cc_start: 0.8804 (tptp) cc_final: 0.8373 (mttt)
REVERT: B  313 PHE cc_start: 0.7838 (m-80) cc_final: 0.7486 (m-80)
REVERT: B  432 TRP cc_start: 0.8491 (m-10) cc_final: 0.8022 (m-90)
REVERT: B  522 CYS cc_start: 0.7537 (p) cc_final: 0.7101 (p)
REVERT: B  671 SER cc_start: 0.8289 (t) cc_final: 0.8085 (p)
REVERT: B  722 LYS cc_start: 0.8772 (tptp) cc_final: 0.8258 (mttt)
REVERT: B  844 MET cc_start: 0.7592 (tmm) cc_final: 0.7344 (tmm)
  outliers start: 60
  outliers final: 43
  residues processed: 197
  average time/residue: 0.1948
  time to fit residues: 59.7529
Evaluate side-chains
  211 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 167
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 132 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 80 optimal weight:    0.4980
   chunk 100 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
** A 640 HIS ** 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 = 0.4013 r_free = 0.4013 target = 0.104202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.075934 restraints weight = 34273.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.078959 restraints weight = 18858.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.080916 restraints weight = 12839.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12056  Z= 0.125
  Angle     :  0.684  10.315  16286  Z= 0.324
  Chirality :  0.045   0.171   1812
  Planarity :  0.004   0.046   2060
  Dihedral  :  6.357 101.397   1582
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.00 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.48 (0.23), residues: 1452
  helix:  0.70 (0.23), residues: 518
  sheet: -0.47 (0.34), residues: 224
  loop :  0.50 (0.25), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 432 
 HIS   0.004   0.001   HIS B 524 
 PHE   0.020   0.001   PHE A 571 
 TYR   0.015   0.001   TYR A 212 
 ARG   0.003   0.000   ARG B 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  454)
  hydrogen bonds       : angle       5.21488 ( 1254)
  covalent geometry    : bond        0.00284 (12056)
  covalent geometry    : angle       0.68448 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 175
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 CYS cc_start: 0.7588 (p) cc_final: 0.7098 (p)
REVERT: A  722 LYS cc_start: 0.8780 (tptp) cc_final: 0.8464 (mttt)
REVERT: B  313 PHE cc_start: 0.7852 (m-80) cc_final: 0.7429 (m-80)
REVERT: B  351 LEU cc_start: 0.8122 (tt) cc_final: 0.7464 (tp)
REVERT: B  403 LEU cc_start: 0.8644 (tp) cc_final: 0.8253 (tt)
REVERT: B  432 TRP cc_start: 0.8461 (m-10) cc_final: 0.8101 (m-90)
REVERT: B  522 CYS cc_start: 0.7614 (p) cc_final: 0.7221 (p)
REVERT: B  671 SER cc_start: 0.8318 (t) cc_final: 0.8099 (p)
REVERT: B  722 LYS cc_start: 0.8740 (tptp) cc_final: 0.8333 (mttt)
REVERT: B  844 MET cc_start: 0.7649 (tmm) cc_final: 0.7435 (tmm)
REVERT: B  879 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8473 (tt)
  outliers start: 46
  outliers final: 26
  residues processed: 194
  average time/residue: 0.1955
  time to fit residues: 58.2876
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 55 optimal weight:    0.0000
   chunk 9 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   chunk 71 optimal weight:   20.0000
   chunk 129 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 74 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 107 optimal weight:    0.1980
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 539 HIS
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 875 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.105641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.077570 restraints weight = 34181.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.080630 restraints weight = 18717.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.082683 restraints weight = 12731.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12056  Z= 0.114
  Angle     :  0.702  12.373  16286  Z= 0.326
  Chirality :  0.045   0.208   1812
  Planarity :  0.004   0.048   2060
  Dihedral  :  5.968  85.851   1582
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.97 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.56 (0.23), residues: 1452
  helix:  0.74 (0.23), residues: 520
  sheet: -0.35 (0.33), residues: 250
  loop :  0.59 (0.26), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 432 
 HIS   0.005   0.001   HIS A 819 
 PHE   0.015   0.001   PHE B 571 
 TYR   0.014   0.001   TYR B 740 
 ARG   0.005   0.000   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03213 (  454)
  hydrogen bonds       : angle       5.09174 ( 1254)
  covalent geometry    : bond        0.00258 (12056)
  covalent geometry    : angle       0.70246 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 175
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 LEU cc_start: 0.8576 (tp) cc_final: 0.8210 (tt)
REVERT: A  522 CYS cc_start: 0.7633 (p) cc_final: 0.7223 (p)
REVERT: A  722 LYS cc_start: 0.8759 (tptp) cc_final: 0.8462 (mttt)
REVERT: B  403 LEU cc_start: 0.8575 (tp) cc_final: 0.8226 (tt)
REVERT: B  522 CYS cc_start: 0.7576 (p) cc_final: 0.7211 (p)
REVERT: B  671 SER cc_start: 0.8279 (t) cc_final: 0.8047 (p)
REVERT: B  722 LYS cc_start: 0.8786 (tptp) cc_final: 0.8387 (mttt)
REVERT: B  841 PHE cc_start: 0.8682 (t80) cc_final: 0.8469 (t80)
REVERT: B  844 MET cc_start: 0.7666 (tmm) cc_final: 0.7341 (tmm)
REVERT: B  879 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8388 (tt)
  outliers start: 31
  outliers final: 24
  residues processed: 189
  average time/residue: 0.2158
  time to fit residues: 61.2003
Evaluate side-chains
  187 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 144 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 145 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 122 optimal weight:    9.9990
   chunk 127 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:   30.0000
   chunk 70 optimal weight:    5.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 778 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.099845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.072205 restraints weight = 35695.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.074997 restraints weight = 20095.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.076855 restraints weight = 13850.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  12056  Z= 0.242
  Angle     :  0.788  14.048  16286  Z= 0.383
  Chirality :  0.049   0.193   1812
  Planarity :  0.005   0.073   2060
  Dihedral  :  6.332  90.222   1582
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.35 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.25 (0.23), residues: 1452
  helix:  0.65 (0.23), residues: 516
  sheet: -0.64 (0.34), residues: 218
  loop :  0.24 (0.25), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.003   TRP A 432 
 HIS   0.008   0.002   HIS A 309 
 PHE   0.019   0.002   PHE A 530 
 TYR   0.015   0.002   TYR B 593 
 ARG   0.009   0.001   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  454)
  hydrogen bonds       : angle       5.39925 ( 1254)
  covalent geometry    : bond        0.00532 (12056)
  covalent geometry    : angle       0.78846 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 161
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: A  323 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8698 (pp)
REVERT: A  403 LEU cc_start: 0.8595 (tp) cc_final: 0.8280 (tt)
REVERT: A  429 ILE cc_start: 0.9272 (pp) cc_final: 0.8743 (pp)
REVERT: A  432 TRP cc_start: 0.8308 (m-90) cc_final: 0.7788 (m-90)
REVERT: A  522 CYS cc_start: 0.7628 (p) cc_final: 0.7120 (p)
REVERT: A  722 LYS cc_start: 0.8809 (tptp) cc_final: 0.8457 (mttt)
REVERT: B  522 CYS cc_start: 0.7527 (p) cc_final: 0.6952 (p)
REVERT: B  722 LYS cc_start: 0.8812 (tptp) cc_final: 0.8412 (mttt)
REVERT: B  844 MET cc_start: 0.7691 (tmm) cc_final: 0.7388 (tmm)
REVERT: B  879 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8537 (tt)
  outliers start: 47
  outliers final: 32
  residues processed: 183
  average time/residue: 0.2000
  time to fit residues: 56.4284
Evaluate side-chains
  190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  778 ASN
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 120 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 134 optimal weight:   20.0000
   chunk 34 optimal weight:    0.0040
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 875 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.103862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.076181 restraints weight = 34064.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.079259 restraints weight = 18331.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.081311 restraints weight = 12296.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12056  Z= 0.114
  Angle     :  0.737  15.353  16286  Z= 0.337
  Chirality :  0.047   0.357   1812
  Planarity :  0.004   0.064   2060
  Dihedral  :  5.820  70.732   1582
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.34 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.42 (0.23), residues: 1452
  helix:  0.72 (0.23), residues: 516
  sheet: -0.49 (0.33), residues: 240
  loop :  0.42 (0.25), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.002   TRP A 432 
 HIS   0.005   0.001   HIS A 819 
 PHE   0.025   0.001   PHE B 841 
 TYR   0.011   0.001   TYR B 740 
 ARG   0.009   0.000   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03183 (  454)
  hydrogen bonds       : angle       5.08315 ( 1254)
  covalent geometry    : bond        0.00262 (12056)
  covalent geometry    : angle       0.73750 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 1.418 
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  323 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8664 (pp)
REVERT: A  351 LEU cc_start: 0.8048 (tt) cc_final: 0.7374 (tp)
REVERT: A  403 LEU cc_start: 0.8608 (tp) cc_final: 0.8260 (tt)
REVERT: A  522 CYS cc_start: 0.7589 (p) cc_final: 0.7136 (p)
REVERT: A  722 LYS cc_start: 0.8821 (tptp) cc_final: 0.8512 (mttt)
REVERT: A  844 MET cc_start: 0.7229 (tmm) cc_final: 0.7017 (tmm)
REVERT: B  277 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7870 (tp)
REVERT: B  522 CYS cc_start: 0.7554 (p) cc_final: 0.7083 (p)
REVERT: B  722 LYS cc_start: 0.8809 (tptp) cc_final: 0.8485 (mttt)
REVERT: B  844 MET cc_start: 0.7733 (tmm) cc_final: 0.7350 (tmm)
REVERT: B  879 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8443 (tt)
  outliers start: 36
  outliers final: 21
  residues processed: 191
  average time/residue: 0.2094
  time to fit residues: 60.2636
Evaluate side-chains
  191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 12 optimal weight:    0.0010
   chunk 60 optimal weight:    9.9990
   chunk 82 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 105 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 137 optimal weight:   10.0000
   chunk 132 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** 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 = 0.3999 r_free = 0.3999 target = 0.103501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.076137 restraints weight = 33583.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.079177 restraints weight = 18291.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.081144 restraints weight = 12281.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12056  Z= 0.122
  Angle     :  0.750  15.728  16286  Z= 0.340
  Chirality :  0.047   0.342   1812
  Planarity :  0.004   0.076   2060
  Dihedral  :  5.708  64.963   1580
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.10 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.46 (0.23), residues: 1452
  helix:  0.75 (0.23), residues: 518
  sheet: -0.39 (0.33), residues: 240
  loop :  0.42 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 432 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.018   0.001   PHE A 841 
 TYR   0.016   0.001   TYR B 740 
 ARG   0.009   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  454)
  hydrogen bonds       : angle       5.00360 ( 1254)
  covalent geometry    : bond        0.00282 (12056)
  covalent geometry    : angle       0.74970 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8659 (pp)
REVERT: A  403 LEU cc_start: 0.8604 (tp) cc_final: 0.8283 (tt)
REVERT: A  432 TRP cc_start: 0.8287 (m-10) cc_final: 0.7852 (m-90)
REVERT: A  522 CYS cc_start: 0.7671 (p) cc_final: 0.7142 (p)
REVERT: A  722 LYS cc_start: 0.8834 (tptp) cc_final: 0.8521 (mttt)
REVERT: A  844 MET cc_start: 0.7279 (tmm) cc_final: 0.6990 (tmm)
REVERT: B  351 LEU cc_start: 0.7700 (tt) cc_final: 0.7208 (tp)
REVERT: B  522 CYS cc_start: 0.7643 (p) cc_final: 0.7154 (p)
REVERT: B  722 LYS cc_start: 0.8835 (tptp) cc_final: 0.8479 (mttt)
REVERT: B  844 MET cc_start: 0.7774 (tmm) cc_final: 0.7355 (tmm)
REVERT: B  879 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8457 (tt)
  outliers start: 33
  outliers final: 25
  residues processed: 182
  average time/residue: 0.2073
  time to fit residues: 56.9918
Evaluate side-chains
  188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 130 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0870
   chunk 131 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0470
   chunk 141 optimal weight:    5.9990
   chunk 133 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    1.2176

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** 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 = 0.4004 r_free = 0.4004 target = 0.104039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.076857 restraints weight = 33419.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.079944 restraints weight = 18109.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.082022 restraints weight = 12106.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12056  Z= 0.118
  Angle     :  0.748  15.973  16286  Z= 0.338
  Chirality :  0.046   0.365   1812
  Planarity :  0.004   0.075   2060
  Dihedral  :  5.647  59.228   1580
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.10 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.49 (0.23), residues: 1452
  helix:  0.76 (0.23), residues: 518
  sheet: -0.33 (0.33), residues: 240
  loop :  0.43 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 432 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.017   0.001   PHE B 841 
 TYR   0.007   0.001   TYR B 196 
 ARG   0.011   0.000   ARG B 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03105 (  454)
  hydrogen bonds       : angle       4.97432 ( 1254)
  covalent geometry    : bond        0.00277 (12056)
  covalent geometry    : angle       0.74788 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8030 (mp)
REVERT: A  403 LEU cc_start: 0.8616 (tp) cc_final: 0.8313 (tt)
REVERT: A  432 TRP cc_start: 0.8303 (m-10) cc_final: 0.8004 (m-90)
REVERT: A  522 CYS cc_start: 0.7632 (p) cc_final: 0.7074 (p)
REVERT: A  722 LYS cc_start: 0.8829 (tptp) cc_final: 0.8533 (mttt)
REVERT: A  844 MET cc_start: 0.7362 (tmm) cc_final: 0.7063 (tmm)
REVERT: B  522 CYS cc_start: 0.7633 (p) cc_final: 0.7102 (p)
REVERT: B  722 LYS cc_start: 0.8831 (tptp) cc_final: 0.8502 (mttt)
REVERT: B  844 MET cc_start: 0.7795 (tmm) cc_final: 0.7387 (tmm)
REVERT: B  879 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8477 (tt)
  outliers start: 31
  outliers final: 26
  residues processed: 185
  average time/residue: 0.2117
  time to fit residues: 59.9969
Evaluate side-chains
  185 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 144 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 126 optimal weight:   10.0000
   chunk 116 optimal weight:    0.0050
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.105057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.077592 restraints weight = 33230.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.080657 restraints weight = 17950.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.082754 restraints weight = 12072.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12056  Z= 0.111
  Angle     :  0.769  16.899  16286  Z= 0.345
  Chirality :  0.046   0.373   1812
  Planarity :  0.004   0.049   2060
  Dihedral  :  5.243  46.260   1580
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.56 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.49 (0.23), residues: 1452
  helix:  0.71 (0.23), residues: 520
  sheet: -0.30 (0.33), residues: 250
  loop :  0.48 (0.25), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 432 
 HIS   0.005   0.001   HIS A 819 
 PHE   0.019   0.001   PHE A 841 
 TYR   0.020   0.001   TYR A 212 
 ARG   0.009   0.000   ARG B 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (  454)
  hydrogen bonds       : angle       4.96080 ( 1254)
  covalent geometry    : bond        0.00255 (12056)
  covalent geometry    : angle       0.76865 (16286)

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: A  403 LEU cc_start: 0.8638 (tp) cc_final: 0.8341 (tt)
REVERT: A  522 CYS cc_start: 0.7641 (p) cc_final: 0.7122 (p)
REVERT: A  722 LYS cc_start: 0.8799 (tptp) cc_final: 0.8531 (mttt)
REVERT: B  351 LEU cc_start: 0.7437 (tp) cc_final: 0.7229 (tt)
REVERT: B  522 CYS cc_start: 0.7654 (p) cc_final: 0.7134 (p)
REVERT: B  722 LYS cc_start: 0.8801 (tptp) cc_final: 0.8506 (mttt)
REVERT: B  740 TYR cc_start: 0.8743 (p90) cc_final: 0.8535 (p90)
REVERT: B  844 MET cc_start: 0.7799 (tmm) cc_final: 0.7380 (tmm)
REVERT: B  879 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8529 (tt)
  outliers start: 28
  outliers final: 21
  residues processed: 177
  average time/residue: 0.1938
  time to fit residues: 52.9807
Evaluate side-chains
  181 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  433 ILE
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  879 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 64 optimal weight:   30.0000
   chunk 96 optimal weight:    0.0870
   chunk 92 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.105377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.077300 restraints weight = 34137.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.080415 restraints weight = 18501.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.082530 restraints weight = 12492.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12056  Z= 0.112
  Angle     :  0.766  16.919  16286  Z= 0.342
  Chirality :  0.046   0.364   1812
  Planarity :  0.004   0.047   2060
  Dihedral  :  4.913  47.471   1580
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 23.71 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.61 (0.23), residues: 1452
  helix:  0.74 (0.23), residues: 520
  sheet: -0.08 (0.34), residues: 242
  loop :  0.53 (0.25), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 432 
 HIS   0.011   0.001   HIS B 819 
 PHE   0.018   0.001   PHE B 841 
 TYR   0.022   0.001   TYR A 212 
 ARG   0.008   0.000   ARG B 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  454)
  hydrogen bonds       : angle       4.90572 ( 1254)
  covalent geometry    : bond        0.00262 (12056)
  covalent geometry    : angle       0.76607 (16286)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4056.23 seconds
wall clock time: 71 minutes 22.95 seconds (4282.95 seconds total)