Starting phenix.real_space_refine
on Fri Jun  6 14:03:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7u_32348/06_2025/7w7u_32348.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4996      2.51       5
     N    1306      2.21       5
     O    1468      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7833
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1015, 7828
          Classifications: {'peptide': 1015}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 46, 'TRANS': 968}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.64, per 1000 atoms: 0.72
  Number of scatterers: 7833
  At special positions: 0
  Unit cell: (105.825, 85.905, 136.95, 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)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1468      8.00
     N    1306      7.00
     C    4996      6.00
     Be      1      4.00
    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=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.06
  Conformation dependent library (CDL) restraints added in 931.8 milliseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      54.5% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 3.552A  pdb=" N   ARG A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 78
      removed outlier: 3.614A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
      removed outlier: 3.634A  pdb=" N   PHE A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 117
      removed outlier: 3.594A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (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 200 through 204
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 230 through 242
    Processing helix  chain 'A' and resid 247 through 275
      removed outlier: 3.851A  pdb=" N   ASN A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 305
    Processing helix  chain 'A' and resid 310 through 329
      removed outlier: 3.640A  pdb=" N   LYS A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 344
      removed outlier: 4.686A  pdb=" N   LEU A 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 3.715A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.813A  pdb=" N   GLY A 554 " --> pdb=" O   GLU A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 587
      removed outlier: 3.645A  pdb=" N   GLU A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 616
    Processing helix  chain 'A' and resid 627 through 638
    Processing helix  chain 'A' and resid 654 through 659
      removed outlier: 3.928A  pdb=" N   GLU A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 672
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.688A  pdb=" N   PHE A 693 " --> pdb=" O   PHE A 689 " (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: 4.308A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 797
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 814 through 818
      removed outlier: 4.036A  pdb=" N   LYS A 818 " --> pdb=" O   ILE A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.709A  pdb=" N   LEU A 837 " --> pdb=" O   PHE A 833 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 882 through 890
      removed outlier: 3.616A  pdb=" N   ALA A 888 " --> pdb=" O   GLY A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.434A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 948
    Processing helix  chain 'A' and resid 951 through 956
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.801A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 141
      removed outlier: 6.028A  pdb=" N   SER A 136 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   ARG A 131 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 9.207A  pdb=" N   ILE A 214 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 9.793A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 11.203A  pdb=" N   ALA A 216 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   THR A 171 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   LYS A 218 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ILE A 163 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 141
      removed outlier: 6.028A  pdb=" N   SER A 136 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   ARG A 131 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 9.207A  pdb=" N   ILE A 214 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 9.793A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 11.203A  pdb=" N   ALA A 216 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   THR A 171 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   LYS A 218 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ILE A 163 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333
      removed outlier: 6.670A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.784A  pdb=" N   ARG A 371 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE A 384 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG A 365 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.090A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.692A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.333A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.784A  pdb=" N   ARG A 371 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE A 384 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG A 365 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.090A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.692A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.333A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 427

    449 hydrogen bonds defined for protein.
    1290 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: 3.85

  Time building geometry restraints manager: 4.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2555
        1.34 -     1.46: 1611
        1.46 -     1.58: 3724
        1.58 -     1.70: 0
        1.70 -     1.81: 90
  Bond restraints: 7980
  Sorted by residual:
  bond pdb=" F2  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" F3  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.548 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" F1  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.532 -0.056 2.00e-02 2.50e+03 7.75e+00
  bond pdb=" CB  PRO A 960 "
       pdb=" CG  PRO A 960 "
    ideal  model  delta    sigma   weight residual
    1.492  1.549 -0.057 5.00e-02 4.00e+02 1.30e+00
  bond pdb=" CA  ASP A 490 "
       pdb=" C   ASP A 490 "
    ideal  model  delta    sigma   weight residual
    1.523  1.510  0.012 1.41e-02 5.03e+03 7.39e-01
  ... (remaining 7975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 10760
        2.60 -     5.19: 65
        5.19 -     7.79: 3
        7.79 -    10.38: 1
       10.38 -    12.98: 2
  Bond angle restraints: 10831
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.98   12.98 3.00e+00 1.11e-01 1.87e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.70   10.42 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F2  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.91  111.64    8.27 3.00e+00 1.11e-01 7.61e+00
  angle pdb=" C   ARG A 835 "
        pdb=" N   TYR A 836 "
        pdb=" CA  TYR A 836 "
      ideal   model   delta    sigma   weight residual
     120.72  116.41    4.31 1.67e+00 3.59e-01 6.65e+00
  angle pdb=" C   GLN A 758 "
        pdb=" N   PHE A 759 "
        pdb=" CA  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     121.14  117.16    3.98 1.75e+00 3.27e-01 5.17e+00
  ... (remaining 10826 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 4423
       17.06 -    34.12: 333
       34.12 -    51.18: 60
       51.18 -    68.23: 12
       68.23 -    85.29: 5
  Dihedral angle restraints: 4833
    sinusoidal: 1900
      harmonic: 2933
  Sorted by residual:
  dihedral pdb=" CB  CYS A 875 "
           pdb=" SG  CYS A 875 "
           pdb=" SG  CYS A 887 "
           pdb=" CB  CYS A 887 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.87   44.87     1      1.00e+01 1.00e-02 2.80e+01
  dihedral pdb=" CA  ARG A 571 "
           pdb=" C   ARG A 571 "
           pdb=" N   ARG A 572 "
           pdb=" CA  ARG A 572 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.68  -20.32     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" SG  CYS A 875 "
           pdb=" CB  CYS A 887 "
           pdb=" SG  CYS A 887 "
           pdb=" CA  CYS A 887 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    8.78   70.22     1      2.00e+01 2.50e-03 1.59e+01
  ... (remaining 4830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 821
       0.032 -    0.063: 293
       0.063 -    0.095: 100
       0.095 -    0.127: 54
       0.127 -    0.158: 4
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  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    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1269 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 959 "    0.065 5.00e-02 4.00e+02   9.82e-02 1.54e+01
        pdb=" N   PRO A 960 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 960 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 960 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 759 "   -0.012 2.00e-02 2.50e+03   1.24e-02 2.71e+00
        pdb=" CG  PHE A 759 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 759 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 759 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 759 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 534 "   -0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO A 535 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 42
        2.55 -     3.14: 6261
        3.14 -     3.73: 12574
        3.73 -     4.31: 16904
        4.31 -     4.90: 28477
  Nonbonded interactions: 64258
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     1.966 2.170
  nonbonded pdb=" F3  BEF A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     2.078 2.120
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.086 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.129 2.170
  nonbonded pdb=" OG  SER A 555 "
            pdb=" OE1 GLN A 643 "
     model   vdw
     2.281 3.040
  ... (remaining 64253 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:             8.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     29.310
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:132.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  170.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.555   7982  Z= 0.635
  Angle     :  0.559  12.976  10833  Z= 0.295
  Chirality :  0.041   0.158   1272
  Planarity :  0.005   0.098   1379
  Dihedral  : 12.540  85.292   2928
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1009
  helix:  1.37 (0.23), residues: 505
  sheet: -0.49 (0.52), residues: 100
  loop : -0.21 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 966 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 294 
 ARG   0.005   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15494 (  427)
  hydrogen bonds       : angle       5.98699 ( 1290)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.26955 (    2)
  covalent geometry    : bond        0.00283 ( 7980)
  covalent geometry    : angle       0.55869 (10831)
  Misc. bond           : bond        0.55456 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6800 (ptp-170) cc_final: 0.6591 (ptp-170)
REVERT: A  467 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.6975 (tpt-90)
REVERT: A  477 GLN cc_start: 0.5667 (tp40) cc_final: 0.5370 (mm110)
REVERT: A  650 LYS cc_start: 0.8185 (mttp) cc_final: 0.7981 (mtmt)
REVERT: A  756 MET cc_start: 0.7879 (ttm) cc_final: 0.7495 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 1.9446
  time to fit residues: 308.7370
Evaluate side-chains
  107 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    7.9990
   chunk 58 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.171871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.131370 restraints weight = 8181.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.72
r_work: 0.3235 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7982  Z= 0.138
  Angle     :  0.526   6.095  10833  Z= 0.280
  Chirality :  0.042   0.169   1272
  Planarity :  0.005   0.072   1379
  Dihedral  :  3.981  17.040   1072
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 10.78 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1009
  helix:  1.49 (0.23), residues: 520
  sheet: -0.17 (0.55), residues: 85
  loop : -0.26 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.013   0.002   TYR A 842 
 ARG   0.005   0.000   ARG A 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  427)
  hydrogen bonds       : angle       4.28993 ( 1290)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.28120 (    2)
  covalent geometry    : bond        0.00314 ( 7980)
  covalent geometry    : angle       0.52593 (10831)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8417 (mttp) cc_final: 0.7776 (mtpt)
REVERT: A  134 ARG cc_start: 0.6801 (ptp-170) cc_final: 0.6363 (ptp-170)
REVERT: A  220 MET cc_start: 0.8501 (ttm) cc_final: 0.8216 (mtm)
REVERT: A  399 ASP cc_start: 0.7238 (m-30) cc_final: 0.6904 (t0)
REVERT: A  467 ARG cc_start: 0.7392 (tpt-90) cc_final: 0.6848 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6325 (tp40) cc_final: 0.5960 (mm110)
REVERT: A  480 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7080 (ptmt)
REVERT: A  482 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: A  756 MET cc_start: 0.8648 (ttm) cc_final: 0.8314 (ttm)
REVERT: A  839 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7235 (mt)
REVERT: A  917 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6852 (tp30)
  outliers start: 27
  outliers final: 13
  residues processed: 136
  average time/residue: 1.1859
  time to fit residues: 171.2036
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 28 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0470
   chunk 13 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 100 optimal weight:    0.3980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 396 HIS
A 919 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.175341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.138867 restraints weight = 8339.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.65
r_work: 0.3286 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7982  Z= 0.102
  Angle     :  0.466   5.476  10833  Z= 0.249
  Chirality :  0.041   0.161   1272
  Planarity :  0.004   0.065   1379
  Dihedral  :  3.805  17.495   1072
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.44 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1009
  helix:  1.72 (0.23), residues: 521
  sheet: -0.06 (0.54), residues: 81
  loop : -0.26 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 871 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  427)
  hydrogen bonds       : angle       3.91534 ( 1290)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.32577 (    2)
  covalent geometry    : bond        0.00219 ( 7980)
  covalent geometry    : angle       0.46619 (10831)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8410 (mttp) cc_final: 0.7729 (mtpt)
REVERT: A   90 GLU cc_start: 0.7100 (tp30) cc_final: 0.6872 (tp30)
REVERT: A  134 ARG cc_start: 0.6927 (ptp-170) cc_final: 0.6571 (ptp-170)
REVERT: A  169 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7547 (mttp)
REVERT: A  466 GLU cc_start: 0.7688 (pt0) cc_final: 0.6925 (tp30)
REVERT: A  467 ARG cc_start: 0.7437 (tpt-90) cc_final: 0.6814 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6192 (tp40) cc_final: 0.5929 (mm110)
REVERT: A  480 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7212 (ptmt)
REVERT: A  756 MET cc_start: 0.8501 (ttm) cc_final: 0.8134 (ttm)
REVERT: A  839 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7261 (mt)
REVERT: A  908 MET cc_start: 0.7363 (mpp) cc_final: 0.7138 (mmm)
  outliers start: 27
  outliers final: 7
  residues processed: 137
  average time/residue: 1.3045
  time to fit residues: 190.7285
Evaluate side-chains
  115 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.172942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.133795 restraints weight = 8184.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.70
r_work: 0.3245 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7982  Z= 0.113
  Angle     :  0.484   7.068  10833  Z= 0.255
  Chirality :  0.041   0.175   1272
  Planarity :  0.004   0.060   1379
  Dihedral  :  3.826  16.498   1072
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.72 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1009
  helix:  1.76 (0.23), residues: 519
  sheet: -0.09 (0.53), residues: 81
  loop : -0.37 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  427)
  hydrogen bonds       : angle       3.87072 ( 1290)
  SS BOND              : bond        0.00082 (    1)
  SS BOND              : angle       0.23809 (    2)
  covalent geometry    : bond        0.00254 ( 7980)
  covalent geometry    : angle       0.48452 (10831)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8424 (mttp) cc_final: 0.7778 (mtpt)
REVERT: A   90 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6824 (tm-30)
REVERT: A  120 LYS cc_start: 0.6308 (mmtt) cc_final: 0.6075 (mmtp)
REVERT: A  134 ARG cc_start: 0.6856 (ptp-170) cc_final: 0.6478 (ptp-170)
REVERT: A  169 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7597 (mttp)
REVERT: A  328 LYS cc_start: 0.8327 (tmmt) cc_final: 0.8103 (ttmt)
REVERT: A  467 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.6808 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6241 (tp40) cc_final: 0.5974 (mm110)
REVERT: A  480 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7149 (ptmt)
REVERT: A  482 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7791 (mm-30)
REVERT: A  732 MET cc_start: 0.8942 (ttm) cc_final: 0.8627 (ttm)
REVERT: A  756 MET cc_start: 0.8647 (ttm) cc_final: 0.8291 (ttm)
REVERT: A  839 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7246 (mt)
REVERT: A  908 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7040 (mmm)
REVERT: A  917 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6801 (tp30)
  outliers start: 28
  outliers final: 11
  residues processed: 127
  average time/residue: 1.1493
  time to fit residues: 155.3260
Evaluate side-chains
  121 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0030
   chunk 78 optimal weight:    0.0870
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5970

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

Flipped N/Q/H residues before XYZ refinement:
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.179553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.141478 restraints weight = 8155.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.63
r_work: 0.3304 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7982  Z= 0.100
  Angle     :  0.468   5.539  10833  Z= 0.248
  Chirality :  0.041   0.176   1272
  Planarity :  0.004   0.058   1379
  Dihedral  :  3.758  16.153   1072
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.34 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 1009
  helix:  1.86 (0.23), residues: 519
  sheet:  0.01 (0.54), residues: 80
  loop : -0.34 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  427)
  hydrogen bonds       : angle       3.76814 ( 1290)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.23100 (    2)
  covalent geometry    : bond        0.00217 ( 7980)
  covalent geometry    : angle       0.46844 (10831)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8386 (mttp) cc_final: 0.7769 (mtpt)
REVERT: A   90 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6822 (tm-30)
REVERT: A  120 LYS cc_start: 0.6413 (mmtt) cc_final: 0.6197 (mmtp)
REVERT: A  134 ARG cc_start: 0.6853 (ptp-170) cc_final: 0.6498 (ptp-170)
REVERT: A  466 GLU cc_start: 0.7604 (pt0) cc_final: 0.6885 (tp30)
REVERT: A  467 ARG cc_start: 0.7328 (tpt-90) cc_final: 0.6854 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6234 (tp40) cc_final: 0.5967 (mm110)
REVERT: A  480 LYS cc_start: 0.7712 (mtmt) cc_final: 0.7152 (ptmt)
REVERT: A  482 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: A  732 MET cc_start: 0.8892 (ttm) cc_final: 0.8572 (ttm)
REVERT: A  756 MET cc_start: 0.8527 (ttm) cc_final: 0.8164 (ttm)
REVERT: A  839 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7143 (mt)
REVERT: A  908 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7126 (mmm)
REVERT: A  940 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6892 (mmt)
  outliers start: 25
  outliers final: 10
  residues processed: 120
  average time/residue: 1.2004
  time to fit residues: 152.8391
Evaluate side-chains
  115 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  940 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 28 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 526 HIS
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.177786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.138457 restraints weight = 8075.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.72
r_work: 0.3268 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7982  Z= 0.114
  Angle     :  0.482   5.289  10833  Z= 0.255
  Chirality :  0.041   0.184   1272
  Planarity :  0.004   0.057   1379
  Dihedral  :  3.829  15.605   1072
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.45 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.26), residues: 1009
  helix:  1.79 (0.23), residues: 520
  sheet: -0.06 (0.53), residues: 81
  loop : -0.41 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.003   0.000   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  427)
  hydrogen bonds       : angle       3.78084 ( 1290)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.12648 (    2)
  covalent geometry    : bond        0.00260 ( 7980)
  covalent geometry    : angle       0.48160 (10831)
  Misc. bond           : bond        0.00072 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8362 (mttp) cc_final: 0.7643 (mtpt)
REVERT: A  120 LYS cc_start: 0.6209 (mmtt) cc_final: 0.5968 (mmtp)
REVERT: A  134 ARG cc_start: 0.6755 (ptp-170) cc_final: 0.6213 (ptp-170)
REVERT: A  466 GLU cc_start: 0.7657 (pt0) cc_final: 0.6865 (tp30)
REVERT: A  467 ARG cc_start: 0.7297 (tpt-90) cc_final: 0.6767 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7001 (ptmt)
REVERT: A  482 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: A  732 MET cc_start: 0.8957 (ttm) cc_final: 0.8601 (ttm)
REVERT: A  756 MET cc_start: 0.8683 (ttm) cc_final: 0.8345 (ttm)
REVERT: A  792 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6632 (tp)
REVERT: A  816 MET cc_start: 0.7975 (mmm) cc_final: 0.7691 (mmp)
REVERT: A  839 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7083 (mt)
REVERT: A  908 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7086 (mmm)
REVERT: A  917 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6857 (tp30)
REVERT: A  940 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6968 (mmt)
  outliers start: 28
  outliers final: 13
  residues processed: 125
  average time/residue: 1.2196
  time to fit residues: 161.8741
Evaluate side-chains
  120 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  940 MET
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.176632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.140005 restraints weight = 8162.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.53
r_work: 0.3271 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7982  Z= 0.104
  Angle     :  0.464   5.229  10833  Z= 0.246
  Chirality :  0.041   0.185   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.769  15.417   1072
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.84 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1009
  helix:  1.88 (0.23), residues: 520
  sheet: -0.07 (0.53), residues: 81
  loop : -0.41 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  427)
  hydrogen bonds       : angle       3.73913 ( 1290)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.14179 (    2)
  covalent geometry    : bond        0.00231 ( 7980)
  covalent geometry    : angle       0.46427 (10831)
  Misc. bond           : bond        0.00049 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8378 (mttp) cc_final: 0.7682 (mtpt)
REVERT: A  120 LYS cc_start: 0.6345 (mmtt) cc_final: 0.6120 (mmtp)
REVERT: A  134 ARG cc_start: 0.6758 (ptp-170) cc_final: 0.6330 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6817 (pptt) cc_final: 0.6402 (pmtt)
REVERT: A  467 ARG cc_start: 0.7344 (tpt-90) cc_final: 0.6780 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7571 (mtmt) cc_final: 0.7058 (ptmt)
REVERT: A  482 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7720 (mm-30)
REVERT: A  714 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8096 (mp0)
REVERT: A  732 MET cc_start: 0.8952 (ttm) cc_final: 0.8626 (ttm)
REVERT: A  756 MET cc_start: 0.8679 (ttm) cc_final: 0.8335 (ttm)
REVERT: A  792 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6711 (tp)
REVERT: A  816 MET cc_start: 0.8158 (mmm) cc_final: 0.7824 (mmp)
REVERT: A  839 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7050 (mt)
REVERT: A  908 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7148 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 117
  average time/residue: 1.2385
  time to fit residues: 153.6417
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0270
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.3644

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.174414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.136047 restraints weight = 8223.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.54
r_work: 0.3262 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7982  Z= 0.131
  Angle     :  0.497   5.309  10833  Z= 0.264
  Chirality :  0.042   0.193   1272
  Planarity :  0.004   0.055   1379
  Dihedral  :  3.920  14.752   1072
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.96 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.26), residues: 1009
  helix:  1.79 (0.23), residues: 519
  sheet: -0.23 (0.52), residues: 81
  loop : -0.48 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.008   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  427)
  hydrogen bonds       : angle       3.82174 ( 1290)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.06260 (    2)
  covalent geometry    : bond        0.00308 ( 7980)
  covalent geometry    : angle       0.49706 (10831)
  Misc. bond           : bond        0.00105 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8413 (mttp) cc_final: 0.7730 (mtpt)
REVERT: A   19 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7710 (t0)
REVERT: A  120 LYS cc_start: 0.6254 (mmtt) cc_final: 0.6024 (mmtp)
REVERT: A  134 ARG cc_start: 0.6796 (ptp-170) cc_final: 0.6372 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6893 (pptt) cc_final: 0.6411 (pmtt)
REVERT: A  466 GLU cc_start: 0.7650 (pt0) cc_final: 0.7036 (tp30)
REVERT: A  480 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7083 (ptmt)
REVERT: A  482 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7751 (mm-30)
REVERT: A  714 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8042 (mp0)
REVERT: A  732 MET cc_start: 0.8934 (ttm) cc_final: 0.8589 (ttm)
REVERT: A  756 MET cc_start: 0.8683 (ttm) cc_final: 0.8340 (ttm)
REVERT: A  792 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6760 (tp)
REVERT: A  816 MET cc_start: 0.8169 (mmm) cc_final: 0.7836 (mmp)
REVERT: A  839 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7190 (mt)
REVERT: A  908 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7203 (mmm)
REVERT: A  917 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6771 (tp30)
  outliers start: 26
  outliers final: 12
  residues processed: 121
  average time/residue: 1.1970
  time to fit residues: 153.9943
Evaluate side-chains
  122 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0000
   chunk 75 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.176737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.139041 restraints weight = 8278.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.53
r_work: 0.3287 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7982  Z= 0.103
  Angle     :  0.482   9.674  10833  Z= 0.252
  Chirality :  0.041   0.202   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.815  14.952   1072
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.42 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1009
  helix:  1.91 (0.23), residues: 519
  sheet: -0.18 (0.53), residues: 81
  loop : -0.46 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 842 
 ARG   0.008   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  427)
  hydrogen bonds       : angle       3.73947 ( 1290)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.13958 (    2)
  covalent geometry    : bond        0.00225 ( 7980)
  covalent geometry    : angle       0.48229 (10831)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8386 (mttp) cc_final: 0.7733 (mtpt)
REVERT: A   19 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7693 (t0)
REVERT: A  134 ARG cc_start: 0.6855 (ptp-170) cc_final: 0.6367 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6971 (pptt) cc_final: 0.6474 (pmtt)
REVERT: A  466 GLU cc_start: 0.7655 (pt0) cc_final: 0.7020 (tp30)
REVERT: A  480 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6938 (ptmt)
REVERT: A  482 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7767 (mm-30)
REVERT: A  714 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7896 (mp0)
REVERT: A  732 MET cc_start: 0.8897 (ttm) cc_final: 0.8562 (ttm)
REVERT: A  756 MET cc_start: 0.8662 (ttm) cc_final: 0.8310 (ttm)
REVERT: A  792 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6755 (tp)
REVERT: A  816 MET cc_start: 0.8140 (mmm) cc_final: 0.7826 (mmp)
REVERT: A  839 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7079 (mt)
REVERT: A  908 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7230 (mmm)
REVERT: A  917 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6719 (tp30)
  outliers start: 22
  outliers final: 9
  residues processed: 119
  average time/residue: 1.2149
  time to fit residues: 153.7757
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  480 LYS
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.175886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.138978 restraints weight = 8209.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.55
r_work: 0.3257 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7982  Z= 0.112
  Angle     :  0.496   9.638  10833  Z= 0.260
  Chirality :  0.042   0.207   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.843  14.762   1072
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.24 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.26), residues: 1009
  helix:  1.88 (0.23), residues: 519
  sheet:  0.11 (0.52), residues: 91
  loop : -0.58 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.012   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  427)
  hydrogen bonds       : angle       3.75469 ( 1290)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.13149 (    2)
  covalent geometry    : bond        0.00256 ( 7980)
  covalent geometry    : angle       0.49588 (10831)
  Misc. bond           : bond        0.00068 (    1)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8372 (mttp) cc_final: 0.7699 (mtpt)
REVERT: A   19 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7561 (t0)
REVERT: A  134 ARG cc_start: 0.6834 (ptp-170) cc_final: 0.6409 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6933 (pptt) cc_final: 0.6442 (pmtt)
REVERT: A  466 GLU cc_start: 0.7664 (pt0) cc_final: 0.7008 (tp30)
REVERT: A  480 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6959 (ptmt)
REVERT: A  482 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: A  714 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7948 (mp0)
REVERT: A  732 MET cc_start: 0.8960 (ttm) cc_final: 0.8629 (ttm)
REVERT: A  756 MET cc_start: 0.8706 (ttm) cc_final: 0.8364 (ttm)
REVERT: A  792 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6720 (tp)
REVERT: A  816 MET cc_start: 0.8161 (mmm) cc_final: 0.7822 (mmp)
REVERT: A  839 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7092 (mt)
REVERT: A  908 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7226 (mmm)
REVERT: A  917 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6769 (tp30)
REVERT: A  922 LEU cc_start: 0.5709 (mt) cc_final: 0.5402 (mt)
  outliers start: 17
  outliers final: 9
  residues processed: 117
  average time/residue: 1.1982
  time to fit residues: 148.7358
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  480 LYS
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 81 optimal weight:    0.1980
   chunk 93 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.175210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.138204 restraints weight = 8200.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.61
r_work: 0.3258 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7982  Z= 0.113
  Angle     :  0.499   8.968  10833  Z= 0.262
  Chirality :  0.042   0.201   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.848  14.557   1072
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.24 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1009
  helix:  1.87 (0.23), residues: 519
  sheet: -0.27 (0.53), residues: 81
  loop : -0.53 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 842 
 ARG   0.009   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  427)
  hydrogen bonds       : angle       3.75811 ( 1290)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.14745 (    2)
  covalent geometry    : bond        0.00255 ( 7980)
  covalent geometry    : angle       0.49893 (10831)
  Misc. bond           : bond        0.00071 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6825.35 seconds
wall clock time: 118 minutes 42.51 seconds (7122.51 seconds total)