Starting phenix.real_space_refine
on Mon Nov 17 19:14:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ln5_0924/11_2025/6ln5_0924.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    4988      2.51       5
     N    1311      2.21       5
     O    1478      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7840
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1011, 7806
          Classifications: {'peptide': 1011}
          Link IDs: {'PTRANS': 46, 'TRANS': 964}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.89, per 1000 atoms: 0.24
  Number of scatterers: 7840
  At special positions: 0
  Unit cell: (103.335, 79.68, 138.195, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      2     19.99
     S      57     16.00
     P       3     15.00
     Mg      1     11.99
     O    1478      8.00
     N    1311      7.00
     C    4988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.02

  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: 0.80
  Conformation dependent library (CDL) restraints added in 319.8 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      53.3% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 3.686A  pdb=" N   VAL A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 55
    Processing helix  chain 'A' and resid 56 through 58
      No H-bonds generated for 'chain 'A' and resid 56 through 58'
    Processing helix  chain 'A' and resid 59 through 78
      removed outlier: 3.955A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 118
      removed outlier: 3.500A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.731A  pdb=" N   THR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 275
      removed outlier: 3.545A  pdb=" N   LYS A 252 " --> pdb=" O   PRO A 248 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASN A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 279
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
    Processing helix  chain 'A' and resid 310 through 329
      removed outlier: 3.614A  pdb=" N   THR A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 343
      removed outlier: 4.405A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   GLU A 340 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 406
      removed outlier: 3.828A  pdb=" N   GLN A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 406'
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 439 through 453
      removed outlier: 3.833A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.556A  pdb=" N   LYS A 543 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.539A  pdb=" N   TYR A 586 " --> pdb=" O   ASN A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 616
      removed outlier: 4.322A  pdb=" N   ALA A 607 " --> pdb=" O   ARG A 603 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   SER A 608 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 670
      removed outlier: 3.732A  pdb=" N   ASP A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 665 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A 670 " --> pdb=" O   ARG A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 692
      removed outlier: 3.626A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 4.252A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 753 " --> pdb=" O   GLY A 749 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASN A 767 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 799
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.637A  pdb=" N   TYR A 842 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 851 " --> pdb=" O   THR A 847 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
      removed outlier: 3.601A  pdb=" N   CYS A 875 " --> pdb=" O   PHE A 872 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 872 through 875'
    Processing helix  chain 'A' and resid 888 through 891
      removed outlier: 3.585A  pdb=" N   GLU A 891 " --> pdb=" O   ALA A 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 888 through 891'
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.447A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN A 913 " --> pdb=" O   CYS A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
    Processing helix  chain 'A' and resid 951 through 957
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.791A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1031
      Proline residue:  A1024  - end of helix
      removed outlier: 3.593A  pdb=" N   TRP A1028 " --> pdb=" O   PRO A1024 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141
      removed outlier: 4.366A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   ILE A 163 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.700A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP A 176 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ILE A 214 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.121A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.597A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 19.868A  pdb=" N   CYS A 524 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 17.601A  pdb=" N   PHE A 367 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 14.859A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   LEU A 369 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ARG A 528 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ARG A 371 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.597A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 19.868A  pdb=" N   CYS A 524 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 17.601A  pdb=" N   PHE A 367 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 14.859A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   LEU A 369 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ARG A 528 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ARG A 371 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.597A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.110A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.554A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.501A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428

    433 hydrogen bonds defined for protein.
    1257 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2575
        1.35 -     1.48: 1793
        1.48 -     1.61: 3523
        1.61 -     1.73: 4
        1.73 -     1.86: 90
  Bond restraints: 7985
  Sorted by residual:
  bond pdb=" C1' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.390  1.618 -0.228 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C1' ACP A2001 "
       pdb=" C2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.527  1.307  0.220 2.00e-02 2.50e+03 1.21e+02
  bond pdb=" C4' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.428  1.302  0.126 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C6  ACP A2001 "
       pdb=" N6  ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.449 -0.114 2.00e-02 2.50e+03 3.27e+01
  bond pdb=" C2' ACP A2001 "
       pdb=" O2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.401  1.493 -0.092 2.00e-02 2.50e+03 2.13e+01
  ... (remaining 7980 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 10792
        3.11 -     6.22: 43
        6.22 -     9.33: 3
        9.33 -    12.44: 5
       12.44 -    15.54: 1
  Bond angle restraints: 10844
  Sorted by residual:
  angle pdb=" O3A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O5' ACP A2001 "
      ideal   model   delta    sigma   weight residual
      93.75  109.29  -15.54 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" C3B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O3A ACP A2001 "
      ideal   model   delta    sigma   weight residual
      98.05  110.00  -11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" N1  ACP A2001 "
        pdb=" C6  ACP A2001 "
        pdb=" N6  ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.32  108.11   11.21 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" O1B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O2B ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.60  109.01   10.59 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" O1A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O2A ACP A2001 "
      ideal   model   delta    sigma   weight residual
     118.95  108.61   10.34 3.00e+00 1.11e-01 1.19e+01
  ... (remaining 10839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.94: 4614
       21.94 -    43.89: 215
       43.89 -    65.83: 16
       65.83 -    87.78: 14
       87.78 -   109.72: 2
  Dihedral angle restraints: 4861
    sinusoidal: 1941
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" CA  CYS A 887 "
           pdb=" C   CYS A 887 "
           pdb=" N   ALA A 888 "
           pdb=" CA  ALA A 888 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.97   21.03     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" O1A ACP A2001 "
           pdb=" O3A ACP A2001 "
           pdb=" PA  ACP A2001 "
           pdb=" PB  ACP A2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -48.75   60.97 -109.72     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" CA  PRO A 951 "
           pdb=" C   PRO A 951 "
           pdb=" N   LEU A 952 "
           pdb=" CA  LEU A 952 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1177
       0.077 -    0.154: 95
       0.154 -    0.231: 0
       0.231 -    0.308: 0
       0.308 -    0.385: 1
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" C2' ACP A2001 "
            pdb=" C1' ACP A2001 "
            pdb=" C3' ACP A2001 "
            pdb=" O2' ACP A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.37   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CA  ILE A 623 "
            pdb=" N   ILE A 623 "
            pdb=" C   ILE A 623 "
            pdb=" CB  ILE A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  VAL A 437 "
            pdb=" N   VAL A 437 "
            pdb=" C   VAL A 437 "
            pdb=" CB  VAL A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.59e-01
  ... (remaining 1270 not shown)

  Planarity restraints: 1377
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A1016 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A1017 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A1017 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A1017 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO A 975 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 787 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 788 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 788 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 788 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1374 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 74
        2.60 -     3.18: 6618
        3.18 -     3.75: 12044
        3.75 -     4.33: 17696
        4.33 -     4.90: 29002
  Nonbonded interactions: 65434
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.027 2.170
  nonbonded pdb=" OE2 GLU A 309 "
            pdb=" OD1 ASN A 795 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.172 2.170
  nonbonded pdb=" NH1 ARG A 491 "
            pdb=" OE2 GLU A 587 "
     model   vdw
     2.212 3.120
  ... (remaining 65429 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.880
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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      :  0.005   0.228   7986  Z= 0.258
  Angle     :  0.630  15.544  10846  Z= 0.335
  Chirality :  0.042   0.385   1273
  Planarity :  0.004   0.039   1377
  Dihedral  : 12.833 109.724   2966
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.12 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (0.20), residues: 1007
  helix: -3.50 (0.13), residues: 500
  sheet: -1.77 (0.40), residues: 132
  loop : -1.65 (0.27), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 467 
 TYR   0.007   0.001   TYR A 295 
 PHE   0.011   0.001   PHE A 367 
 TRP   0.006   0.001   TRP A 793 
 HIS   0.006   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 7985)
  covalent geometry    : angle       0.63001 (10844)
  SS BOND              : bond        0.00729 (    1)
  SS BOND              : angle       0.52288 (    2)
  hydrogen bonds       : bond        0.26214 (  399)
  hydrogen bonds       : angle       8.91264 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7435 (tttm)
REVERT: A   31 LYS cc_start: 0.7380 (mttt) cc_final: 0.7128 (mmtp)
REVERT: A   33 LYS cc_start: 0.7988 (tptm) cc_final: 0.7734 (tppt)
REVERT: A  135 LYS cc_start: 0.7602 (pttt) cc_final: 0.7264 (mmtp)
REVERT: A  143 LYS cc_start: 0.8190 (pttt) cc_final: 0.7820 (ptmt)
REVERT: A  153 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8281 (tt)
REVERT: A  259 GLN cc_start: 0.8079 (mt0) cc_final: 0.7770 (mt0)
REVERT: A  365 ARG cc_start: 0.8105 (ptp-170) cc_final: 0.7899 (ptm160)
REVERT: A  371 ARG cc_start: 0.6508 (ptp-110) cc_final: 0.6069 (ptp90)
REVERT: A  379 LEU cc_start: 0.8347 (mt) cc_final: 0.8115 (mp)
REVERT: A  387 SER cc_start: 0.8261 (p) cc_final: 0.8047 (p)
REVERT: A  397 LYS cc_start: 0.7505 (tptp) cc_final: 0.7238 (tmtt)
REVERT: A  431 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8139 (mttp)
REVERT: A  433 VAL cc_start: 0.8698 (p) cc_final: 0.8447 (m)
REVERT: A  510 LYS cc_start: 0.8237 (mttt) cc_final: 0.8031 (mtpp)
REVERT: A  541 LYS cc_start: 0.8815 (tttt) cc_final: 0.8578 (ttmt)
REVERT: A  549 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6561 (mtm110)
REVERT: A  568 ASN cc_start: 0.8016 (m110) cc_final: 0.7636 (m-40)
REVERT: A  582 ASN cc_start: 0.7674 (m-40) cc_final: 0.7113 (m-40)
REVERT: A  585 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7734 (mttt)
REVERT: A  719 MET cc_start: 0.8879 (mmm) cc_final: 0.8209 (mmt)
REVERT: A  896 MET cc_start: 0.8490 (mtp) cc_final: 0.8008 (mtm)
REVERT: A  968 MET cc_start: 0.8225 (tpt) cc_final: 0.7933 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 167
  average time/residue: 0.6648
  time to fit residues: 116.2519
Evaluate side-chains
  127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  153 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
A   3 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 HIS
A 469 ASN
A 643 GLN
A 874 GLN
A 913 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.134754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.105241 restraints weight = 9039.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.67
r_work: 0.2989 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7986  Z= 0.120
  Angle     :  0.511   6.052  10846  Z= 0.268
  Chirality :  0.041   0.130   1273
  Planarity :  0.005   0.040   1377
  Dihedral  :  8.338 149.139   1107
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  9.84 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.24), residues: 1007
  helix: -0.67 (0.21), residues: 509
  sheet: -1.00 (0.45), residues: 122
  loop : -1.06 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 174 
 TYR   0.011   0.001   TYR A 842 
 PHE   0.012   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A1016 
 HIS   0.002   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7985)
  covalent geometry    : angle       0.51092 (10844)
  SS BOND              : bond        0.00572 (    1)
  SS BOND              : angle       0.70640 (    2)
  hydrogen bonds       : bond        0.04538 (  399)
  hydrogen bonds       : angle       4.69405 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7926 (pt0) cc_final: 0.7705 (pt0)
REVERT: A   31 LYS cc_start: 0.7621 (mttt) cc_final: 0.7136 (mmtp)
REVERT: A   77 TRP cc_start: 0.7946 (t60) cc_final: 0.7721 (t-100)
REVERT: A  135 LYS cc_start: 0.7886 (pttt) cc_final: 0.7301 (mmtp)
REVERT: A  174 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7804 (mtt-85)
REVERT: A  239 MET cc_start: 0.5344 (mtt) cc_final: 0.4141 (tpt)
REVERT: A  370 ASP cc_start: 0.6774 (t0) cc_final: 0.6481 (t0)
REVERT: A  371 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6116 (ptp90)
REVERT: A  397 LYS cc_start: 0.7789 (tptp) cc_final: 0.7488 (tmtt)
REVERT: A  431 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8368 (mttp)
REVERT: A  510 LYS cc_start: 0.8388 (mttt) cc_final: 0.8104 (mtpp)
REVERT: A  518 GLU cc_start: 0.8064 (mp0) cc_final: 0.7700 (mp0)
REVERT: A  541 LYS cc_start: 0.8572 (tttt) cc_final: 0.8159 (ttmt)
REVERT: A  549 ARG cc_start: 0.7675 (mtt180) cc_final: 0.6891 (ttp-110)
REVERT: A  568 ASN cc_start: 0.8003 (m110) cc_final: 0.7702 (m-40)
REVERT: A  585 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7810 (mttt)
REVERT: A  719 MET cc_start: 0.9164 (mmm) cc_final: 0.8614 (mmt)
REVERT: A  797 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8134 (p)
REVERT: A  896 MET cc_start: 0.8970 (mtp) cc_final: 0.8536 (mtm)
REVERT: A  968 MET cc_start: 0.8310 (tpt) cc_final: 0.7896 (mmm)
  outliers start: 22
  outliers final: 8
  residues processed: 147
  average time/residue: 0.6788
  time to fit residues: 104.8340
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  797 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 GLN
A 874 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.105509 restraints weight = 8881.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.55
r_work: 0.3034 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7986  Z= 0.149
  Angle     :  0.526   5.806  10846  Z= 0.271
  Chirality :  0.043   0.134   1273
  Planarity :  0.004   0.036   1377
  Dihedral  :  8.594 157.823   1107
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.54 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.25), residues: 1007
  helix:  0.36 (0.23), residues: 510
  sheet: -0.95 (0.46), residues: 119
  loop : -0.75 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 491 
 TYR   0.014   0.002   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.010   0.001   TRP A1016 
 HIS   0.003   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7985)
  covalent geometry    : angle       0.52544 (10844)
  SS BOND              : bond        0.00803 (    1)
  SS BOND              : angle       0.98021 (    2)
  hydrogen bonds       : bond        0.04527 (  399)
  hydrogen bonds       : angle       4.39293 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7242 (tp30)
REVERT: A  135 LYS cc_start: 0.7804 (pttt) cc_final: 0.7231 (mmtp)
REVERT: A  239 MET cc_start: 0.5290 (mtt) cc_final: 0.4081 (tpt)
REVERT: A  370 ASP cc_start: 0.6787 (t0) cc_final: 0.6503 (t0)
REVERT: A  371 ARG cc_start: 0.6650 (ptp-110) cc_final: 0.6014 (ptp90)
REVERT: A  397 LYS cc_start: 0.7927 (tptp) cc_final: 0.7445 (tmtt)
REVERT: A  431 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8453 (mttp)
REVERT: A  510 LYS cc_start: 0.8452 (mttt) cc_final: 0.8196 (mtpp)
REVERT: A  528 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8388 (tpp-160)
REVERT: A  541 LYS cc_start: 0.8638 (tttt) cc_final: 0.8378 (ttmt)
REVERT: A  549 ARG cc_start: 0.7719 (mtt180) cc_final: 0.6984 (ttp-110)
REVERT: A  568 ASN cc_start: 0.8004 (m110) cc_final: 0.7681 (m-40)
REVERT: A  585 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7962 (mttt)
REVERT: A  714 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7227 (mp0)
REVERT: A  719 MET cc_start: 0.9187 (mmm) cc_final: 0.8641 (mmt)
REVERT: A  797 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8278 (p)
REVERT: A  896 MET cc_start: 0.8925 (mtp) cc_final: 0.8521 (mtm)
REVERT: A  908 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8379 (mpp)
REVERT: A  989 ASN cc_start: 0.8080 (m-40) cc_final: 0.7866 (m-40)
  outliers start: 25
  outliers final: 13
  residues processed: 140
  average time/residue: 0.6483
  time to fit residues: 95.4527
Evaluate side-chains
  134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  908 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 GLN
A 874 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.102475 restraints weight = 9043.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.54
r_work: 0.2978 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   7986  Z= 0.226
  Angle     :  0.604   6.234  10846  Z= 0.309
  Chirality :  0.046   0.142   1273
  Planarity :  0.005   0.044   1377
  Dihedral  :  9.251 171.457   1107
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 13.43 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.26), residues: 1007
  helix:  0.60 (0.23), residues: 509
  sheet: -0.77 (0.43), residues: 130
  loop : -0.69 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 491 
 TYR   0.016   0.002   TYR A 295 
 PHE   0.016   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A1016 
 HIS   0.004   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 7985)
  covalent geometry    : angle       0.60368 (10844)
  SS BOND              : bond        0.01164 (    1)
  SS BOND              : angle       1.36706 (    2)
  hydrogen bonds       : bond        0.05131 (  399)
  hydrogen bonds       : angle       4.50889 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7309 (tp30)
REVERT: A   65 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8290 (mp)
REVERT: A   75 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (mt)
REVERT: A  135 LYS cc_start: 0.7986 (pttt) cc_final: 0.7392 (mmtp)
REVERT: A  143 LYS cc_start: 0.8580 (pttt) cc_final: 0.8175 (ptmt)
REVERT: A  239 MET cc_start: 0.5333 (mtt) cc_final: 0.4069 (tpt)
REVERT: A  259 GLN cc_start: 0.8123 (mt0) cc_final: 0.7778 (mt0)
REVERT: A  361 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8260 (mtm)
REVERT: A  370 ASP cc_start: 0.6971 (t0) cc_final: 0.6648 (t0)
REVERT: A  371 ARG cc_start: 0.6543 (ptp-110) cc_final: 0.5907 (ptp90)
REVERT: A  397 LYS cc_start: 0.7979 (tptp) cc_final: 0.7548 (tmtt)
REVERT: A  431 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8390 (mttp)
REVERT: A  510 LYS cc_start: 0.8343 (mttt) cc_final: 0.8103 (mtpp)
REVERT: A  529 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8216 (m)
REVERT: A  541 LYS cc_start: 0.8655 (tttt) cc_final: 0.8356 (ttmt)
REVERT: A  549 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7131 (ttp-110)
REVERT: A  568 ASN cc_start: 0.8086 (m110) cc_final: 0.7757 (m-40)
REVERT: A  585 LYS cc_start: 0.8455 (mtpp) cc_final: 0.7929 (mttt)
REVERT: A  604 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (mm)
REVERT: A  623 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8557 (mm)
REVERT: A  714 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: A  719 MET cc_start: 0.9281 (mmm) cc_final: 0.8855 (mmt)
REVERT: A  797 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8365 (p)
REVERT: A  812 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7414 (m-30)
REVERT: A  891 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (mp0)
REVERT: A  896 MET cc_start: 0.8980 (mtp) cc_final: 0.8600 (mtm)
REVERT: A  989 ASN cc_start: 0.8138 (m-40) cc_final: 0.7885 (m-40)
  outliers start: 36
  outliers final: 16
  residues processed: 138
  average time/residue: 0.6952
  time to fit residues: 100.6835
Evaluate side-chains
  140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  891 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0970
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 874 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.107286 restraints weight = 8937.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.54
r_work: 0.2984 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7986  Z= 0.102
  Angle     :  0.490   5.708  10846  Z= 0.252
  Chirality :  0.041   0.123   1273
  Planarity :  0.004   0.033   1377
  Dihedral  :  8.797 170.863   1107
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.74 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.27), residues: 1007
  helix:  1.19 (0.24), residues: 509
  sheet: -0.74 (0.46), residues: 119
  loop : -0.35 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 923 
 TYR   0.012   0.001   TYR A 295 
 PHE   0.015   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 7985)
  covalent geometry    : angle       0.49031 (10844)
  SS BOND              : bond        0.00785 (    1)
  SS BOND              : angle       0.49069 (    2)
  hydrogen bonds       : bond        0.03581 (  399)
  hydrogen bonds       : angle       4.06213 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  135 LYS cc_start: 0.7914 (pttt) cc_final: 0.7341 (mmtp)
REVERT: A  239 MET cc_start: 0.5194 (mtt) cc_final: 0.4024 (tpt)
REVERT: A  328 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7311 (mptm)
REVERT: A  370 ASP cc_start: 0.6665 (t0) cc_final: 0.6462 (t0)
REVERT: A  371 ARG cc_start: 0.6398 (ptp-110) cc_final: 0.5674 (ptp90)
REVERT: A  397 LYS cc_start: 0.7962 (tptp) cc_final: 0.7488 (tmtt)
REVERT: A  431 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8475 (mttp)
REVERT: A  510 LYS cc_start: 0.8283 (mttt) cc_final: 0.8049 (mtpp)
REVERT: A  528 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8191 (tpp-160)
REVERT: A  541 LYS cc_start: 0.8590 (tttt) cc_final: 0.8343 (ttmt)
REVERT: A  549 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7027 (mtp180)
REVERT: A  585 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7813 (mttt)
REVERT: A  604 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8047 (mm)
REVERT: A  719 MET cc_start: 0.9135 (mmm) cc_final: 0.8634 (mmp)
REVERT: A  797 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8161 (p)
REVERT: A  896 MET cc_start: 0.8921 (mtp) cc_final: 0.8592 (mtm)
REVERT: A  989 ASN cc_start: 0.8081 (m-40) cc_final: 0.7858 (m-40)
  outliers start: 24
  outliers final: 10
  residues processed: 128
  average time/residue: 0.6477
  time to fit residues: 87.3725
Evaluate side-chains
  118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0670
   chunk 76 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0470
   chunk 79 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A 874 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.137704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.109959 restraints weight = 8910.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.52
r_work: 0.3024 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7986  Z= 0.093
  Angle     :  0.482   5.971  10846  Z= 0.245
  Chirality :  0.040   0.125   1273
  Planarity :  0.004   0.033   1377
  Dihedral  :  8.535 166.189   1107
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.20 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.27), residues: 1007
  helix:  1.46 (0.24), residues: 510
  sheet: -0.47 (0.46), residues: 124
  loop : -0.15 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 923 
 TYR   0.011   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7985)
  covalent geometry    : angle       0.48176 (10844)
  SS BOND              : bond        0.00478 (    1)
  SS BOND              : angle       0.52037 (    2)
  hydrogen bonds       : bond        0.03324 (  399)
  hydrogen bonds       : angle       3.88743 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7454 (mmtp)
REVERT: A  135 LYS cc_start: 0.7887 (pttt) cc_final: 0.7298 (mmtp)
REVERT: A  174 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7899 (mtp180)
REVERT: A  239 MET cc_start: 0.5162 (mtt) cc_final: 0.4049 (tpt)
REVERT: A  328 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7298 (mptm)
REVERT: A  371 ARG cc_start: 0.6403 (ptp-110) cc_final: 0.5856 (ptp90)
REVERT: A  397 LYS cc_start: 0.7947 (tptp) cc_final: 0.7481 (tmtt)
REVERT: A  431 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8504 (mttp)
REVERT: A  506 THR cc_start: 0.2919 (OUTLIER) cc_final: 0.2679 (t)
REVERT: A  510 LYS cc_start: 0.8287 (mttt) cc_final: 0.8036 (mtpp)
REVERT: A  528 ARG cc_start: 0.8658 (tpp-160) cc_final: 0.8152 (tpp-160)
REVERT: A  549 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7054 (mtm110)
REVERT: A  585 LYS cc_start: 0.8450 (mtpp) cc_final: 0.7861 (mttt)
REVERT: A  719 MET cc_start: 0.9125 (mmm) cc_final: 0.8620 (mmp)
REVERT: A  797 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8179 (p)
REVERT: A  896 MET cc_start: 0.8919 (mtp) cc_final: 0.8602 (mtm)
REVERT: A  917 GLU cc_start: 0.8458 (tt0) cc_final: 0.7971 (tp30)
REVERT: A  989 ASN cc_start: 0.8121 (m-40) cc_final: 0.7891 (m-40)
  outliers start: 23
  outliers final: 8
  residues processed: 129
  average time/residue: 0.6763
  time to fit residues: 91.8027
Evaluate side-chains
  120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0010
   chunk 16 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 874 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.135845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.107542 restraints weight = 8933.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.56
r_work: 0.2992 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7986  Z= 0.109
  Angle     :  0.503   8.025  10846  Z= 0.253
  Chirality :  0.041   0.126   1273
  Planarity :  0.004   0.033   1377
  Dihedral  :  8.521 163.239   1107
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.20 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.27), residues: 1007
  helix:  1.47 (0.24), residues: 514
  sheet: -0.26 (0.45), residues: 134
  loop : -0.17 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 923 
 TYR   0.013   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7985)
  covalent geometry    : angle       0.50257 (10844)
  SS BOND              : bond        0.00576 (    1)
  SS BOND              : angle       0.37562 (    2)
  hydrogen bonds       : bond        0.03587 (  399)
  hydrogen bonds       : angle       3.93382 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7144 (tp30)
REVERT: A   31 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7415 (mmtp)
REVERT: A   65 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: A  135 LYS cc_start: 0.7861 (pttt) cc_final: 0.7365 (mmtp)
REVERT: A  239 MET cc_start: 0.5185 (mtt) cc_final: 0.4044 (tpt)
REVERT: A  290 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7596 (mtp85)
REVERT: A  328 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7479 (mptm)
REVERT: A  371 ARG cc_start: 0.6421 (ptp-110) cc_final: 0.5906 (ptp90)
REVERT: A  397 LYS cc_start: 0.7961 (tptp) cc_final: 0.7526 (tmtt)
REVERT: A  431 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8519 (mttp)
REVERT: A  506 THR cc_start: 0.2949 (OUTLIER) cc_final: 0.2704 (t)
REVERT: A  510 LYS cc_start: 0.8275 (mttt) cc_final: 0.8019 (mtpp)
REVERT: A  528 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8180 (tpp-160)
REVERT: A  549 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7035 (mtm110)
REVERT: A  585 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7808 (mttt)
REVERT: A  719 MET cc_start: 0.9169 (mmm) cc_final: 0.8684 (mmp)
REVERT: A  797 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8224 (p)
REVERT: A  896 MET cc_start: 0.8927 (mtp) cc_final: 0.8630 (mtm)
REVERT: A  917 GLU cc_start: 0.8442 (tt0) cc_final: 0.7935 (tp30)
REVERT: A  989 ASN cc_start: 0.8160 (m-40) cc_final: 0.7897 (m-40)
  outliers start: 27
  outliers final: 12
  residues processed: 129
  average time/residue: 0.6691
  time to fit residues: 90.9402
Evaluate side-chains
  124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
A 874 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.134855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.106362 restraints weight = 9010.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.56
r_work: 0.2975 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7986  Z= 0.122
  Angle     :  0.520   8.341  10846  Z= 0.262
  Chirality :  0.042   0.129   1273
  Planarity :  0.004   0.033   1377
  Dihedral  :  8.598 163.292   1107
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.01 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.27), residues: 1007
  helix:  1.49 (0.24), residues: 510
  sheet: -0.25 (0.45), residues: 134
  loop : -0.14 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 923 
 TYR   0.014   0.001   TYR A 842 
 PHE   0.015   0.001   PHE A  73 
 TRP   0.008   0.001   TRP A1016 
 HIS   0.002   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7985)
  covalent geometry    : angle       0.52030 (10844)
  SS BOND              : bond        0.00634 (    1)
  SS BOND              : angle       0.39709 (    2)
  hydrogen bonds       : bond        0.03786 (  399)
  hydrogen bonds       : angle       3.99337 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7196 (tp30)
REVERT: A   31 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7437 (mmtp)
REVERT: A   65 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: A  135 LYS cc_start: 0.7860 (pttt) cc_final: 0.7372 (mmtp)
REVERT: A  239 MET cc_start: 0.5169 (mtt) cc_final: 0.4034 (tpt)
REVERT: A  290 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7623 (mtp85)
REVERT: A  328 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7334 (mptm)
REVERT: A  371 ARG cc_start: 0.6392 (ptp-110) cc_final: 0.5889 (ptp90)
REVERT: A  397 LYS cc_start: 0.7967 (tptp) cc_final: 0.7539 (tmtt)
REVERT: A  431 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8523 (mttp)
REVERT: A  462 LEU cc_start: 0.8092 (mt) cc_final: 0.7838 (mt)
REVERT: A  506 THR cc_start: 0.2880 (OUTLIER) cc_final: 0.2677 (t)
REVERT: A  510 LYS cc_start: 0.8306 (mttt) cc_final: 0.8049 (mtpp)
REVERT: A  528 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8140 (tpp-160)
REVERT: A  549 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7056 (mtm110)
REVERT: A  585 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7867 (mttt)
REVERT: A  604 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8069 (mm)
REVERT: A  719 MET cc_start: 0.9201 (mmm) cc_final: 0.8653 (mmt)
REVERT: A  797 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8238 (p)
REVERT: A  896 MET cc_start: 0.8939 (mtp) cc_final: 0.8624 (mtm)
REVERT: A  989 ASN cc_start: 0.8160 (m-40) cc_final: 0.7893 (m-40)
  outliers start: 25
  outliers final: 13
  residues processed: 130
  average time/residue: 0.6394
  time to fit residues: 87.7321
Evaluate side-chains
  128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 76 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 822 ASN
A 874 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.136683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.108752 restraints weight = 8884.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.54
r_work: 0.3003 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7986  Z= 0.110
  Angle     :  0.516   9.109  10846  Z= 0.257
  Chirality :  0.041   0.127   1273
  Planarity :  0.004   0.032   1377
  Dihedral  :  8.520 162.435   1107
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.36 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.27), residues: 1007
  helix:  1.52 (0.24), residues: 514
  sheet: -0.25 (0.45), residues: 134
  loop : -0.10 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 923 
 TYR   0.012   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7985)
  covalent geometry    : angle       0.51605 (10844)
  SS BOND              : bond        0.00573 (    1)
  SS BOND              : angle       0.41462 (    2)
  hydrogen bonds       : bond        0.03579 (  399)
  hydrogen bonds       : angle       3.95043 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7187 (tp30)
REVERT: A   31 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7448 (mmtp)
REVERT: A   65 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: A  135 LYS cc_start: 0.7876 (pttt) cc_final: 0.7465 (mmtp)
REVERT: A  174 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7972 (mtp180)
REVERT: A  239 MET cc_start: 0.5158 (mtt) cc_final: 0.4039 (tpt)
REVERT: A  290 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7627 (mtp85)
REVERT: A  328 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7333 (mptm)
REVERT: A  371 ARG cc_start: 0.6424 (ptp-110) cc_final: 0.5977 (ptp90)
REVERT: A  397 LYS cc_start: 0.7981 (tptp) cc_final: 0.7767 (tmtt)
REVERT: A  431 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8540 (mttp)
REVERT: A  462 LEU cc_start: 0.8116 (mt) cc_final: 0.7856 (mt)
REVERT: A  506 THR cc_start: 0.2574 (OUTLIER) cc_final: 0.2332 (t)
REVERT: A  510 LYS cc_start: 0.8324 (mttt) cc_final: 0.8070 (mtpp)
REVERT: A  528 ARG cc_start: 0.8805 (tpp-160) cc_final: 0.8257 (tpp-160)
REVERT: A  549 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7065 (mtm110)
REVERT: A  585 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7837 (mttt)
REVERT: A  719 MET cc_start: 0.9178 (mmm) cc_final: 0.8645 (mmt)
REVERT: A  797 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (p)
REVERT: A  896 MET cc_start: 0.8939 (mtp) cc_final: 0.8662 (mtm)
REVERT: A  917 GLU cc_start: 0.8447 (tt0) cc_final: 0.7949 (tp30)
REVERT: A  989 ASN cc_start: 0.8141 (m-40) cc_final: 0.7879 (m-40)
  outliers start: 22
  outliers final: 13
  residues processed: 129
  average time/residue: 0.6592
  time to fit residues: 89.6587
Evaluate side-chains
  125 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 874 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.133928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.105879 restraints weight = 8862.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.51
r_work: 0.3042 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7986  Z= 0.149
  Angle     :  0.555   9.262  10846  Z= 0.277
  Chirality :  0.043   0.133   1273
  Planarity :  0.004   0.034   1377
  Dihedral  :  8.768 166.591   1107
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.59 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 1007
  helix:  1.40 (0.24), residues: 512
  sheet: -0.32 (0.44), residues: 134
  loop : -0.13 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 923 
 TYR   0.015   0.002   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A1016 
 HIS   0.003   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7985)
  covalent geometry    : angle       0.55540 (10844)
  SS BOND              : bond        0.00757 (    1)
  SS BOND              : angle       0.51091 (    2)
  hydrogen bonds       : bond        0.04108 (  399)
  hydrogen bonds       : angle       4.11159 ( 1257)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7266 (tp30)
REVERT: A   31 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7457 (mmtp)
REVERT: A   65 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: A  135 LYS cc_start: 0.7849 (pttt) cc_final: 0.7388 (mmtp)
REVERT: A  143 LYS cc_start: 0.8579 (pttt) cc_final: 0.8176 (ptmt)
REVERT: A  174 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.7930 (mtp180)
REVERT: A  239 MET cc_start: 0.5154 (mtt) cc_final: 0.4023 (tpt)
REVERT: A  290 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7634 (mtp85)
REVERT: A  328 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7551 (mptm)
REVERT: A  371 ARG cc_start: 0.6448 (ptp-110) cc_final: 0.5964 (ptp90)
REVERT: A  397 LYS cc_start: 0.8007 (tptp) cc_final: 0.7529 (tmtt)
REVERT: A  398 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6363 (m-30)
REVERT: A  431 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8530 (mttp)
REVERT: A  462 LEU cc_start: 0.8104 (mt) cc_final: 0.7829 (mt)
REVERT: A  506 THR cc_start: 0.2607 (OUTLIER) cc_final: 0.2382 (t)
REVERT: A  510 LYS cc_start: 0.8374 (mttt) cc_final: 0.8146 (mttm)
REVERT: A  528 ARG cc_start: 0.8835 (tpp-160) cc_final: 0.8286 (tpp-160)
REVERT: A  549 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7105 (mtm110)
REVERT: A  570 LEU cc_start: 0.7993 (mt) cc_final: 0.7715 (mt)
REVERT: A  585 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8050 (mttt)
REVERT: A  604 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: A  719 MET cc_start: 0.9205 (mmm) cc_final: 0.8675 (mmt)
REVERT: A  797 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8363 (p)
REVERT: A  896 MET cc_start: 0.8932 (mtp) cc_final: 0.8619 (mtm)
REVERT: A  989 ASN cc_start: 0.8105 (m-40) cc_final: 0.7874 (m-40)
  outliers start: 23
  outliers final: 14
  residues processed: 129
  average time/residue: 0.6450
  time to fit residues: 87.5686
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  812 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 874 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.103488 restraints weight = 8942.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.54
r_work: 0.3032 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7986  Z= 0.183
  Angle     :  0.590  10.209  10846  Z= 0.295
  Chirality :  0.045   0.137   1273
  Planarity :  0.004   0.032   1377
  Dihedral  :  9.075 172.461   1107
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.82 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.27), residues: 1007
  helix:  1.24 (0.23), residues: 511
  sheet: -0.35 (0.44), residues: 134
  loop : -0.17 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 923 
 TYR   0.017   0.002   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.010   0.001   TRP A1016 
 HIS   0.003   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7985)
  covalent geometry    : angle       0.59031 (10844)
  SS BOND              : bond        0.00985 (    1)
  SS BOND              : angle       0.57053 (    2)
  hydrogen bonds       : bond        0.04513 (  399)
  hydrogen bonds       : angle       4.26565 ( 1257)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3155.88 seconds
wall clock time: 54 minutes 26.74 seconds (3266.74 seconds total)