Starting phenix.real_space_refine
on Wed Feb 12 11:39:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7u_32348/02_2025/7w7u_32348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7u_32348/02_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_32348/02_2025/7w7u_32348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7u_32348/02_2025/7w7u_32348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7u_32348/02_2025/7w7u_32348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7u_32348/02_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-5592/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: 4.87, per 1000 atoms: 0.62
  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: 2.05
  Conformation dependent library (CDL) restraints added in 953.9 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: 1.04
  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: 3.30

  Time building geometry restraints manager: 2.34 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:             0.280
  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:                     21.830
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.880
-------------------------------------------------------------------------------
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      :  0.003   0.084   7980  Z= 0.192
  Angle     :  0.559  12.976  10831  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 

*********************** 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  : 0.850 
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: 1.3177
  time to fit residues: 208.8436
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  : 0.811 
-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.172072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.132435 restraints weight = 8177.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.73
r_work: 0.3231 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
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   7980  Z= 0.204
  Angle     :  0.526   6.095  10831  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 

*********************** 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  : 0.869 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8438 (mttp) cc_final: 0.7804 (mtpt)
REVERT: A  134 ARG cc_start: 0.6815 (ptp-170) cc_final: 0.6376 (ptp-170)
REVERT: A  220 MET cc_start: 0.8518 (ttm) cc_final: 0.8241 (mtm)
REVERT: A  399 ASP cc_start: 0.7237 (m-30) cc_final: 0.6910 (t0)
REVERT: A  467 ARG cc_start: 0.7398 (tpt-90) cc_final: 0.6855 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6326 (tp40) cc_final: 0.5959 (mm110)
REVERT: A  480 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7086 (ptmt)
REVERT: A  482 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: A  536 MET cc_start: 0.6730 (tpt) cc_final: 0.6530 (tpt)
REVERT: A  756 MET cc_start: 0.8648 (ttm) cc_final: 0.8317 (ttm)
REVERT: A  839 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7248 (mt)
REVERT: A  917 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6869 (tp30)
  outliers start: 27
  outliers final: 13
  residues processed: 136
  average time/residue: 1.2402
  time to fit residues: 178.8033
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  : 0.860 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0670
   chunk 62 optimal weight:    0.4980
   chunk 13 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.0920

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.174344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.134059 restraints weight = 8236.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.63
r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7980  Z= 0.177
  Angle     :  0.489   5.556  10831  Z= 0.261
  Chirality :  0.042   0.169   1272
  Planarity :  0.004   0.064   1379
  Dihedral  :  3.938  17.219   1072
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.67 %
    Favored  : 82.97 %
  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:  1.02 (0.26), residues: 1009
  helix:  1.60 (0.23), residues: 520
  sheet: -0.06 (0.54), residues: 81
  loop : -0.31 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.005   0.000   ARG A 571 

*********************** 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
  149 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8434 (mttp) cc_final: 0.7764 (mtpt)
REVERT: A   90 GLU cc_start: 0.7057 (tp30) cc_final: 0.6802 (tp30)
REVERT: A  134 ARG cc_start: 0.6855 (ptp-170) cc_final: 0.6463 (ptp-170)
REVERT: A  169 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7529 (mttp)
REVERT: A  399 ASP cc_start: 0.7339 (m-30) cc_final: 0.7016 (t0)
REVERT: A  467 ARG cc_start: 0.7384 (tpt-90) cc_final: 0.6840 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6199 (tp40) cc_final: 0.5920 (mm110)
REVERT: A  480 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7185 (ptmt)
REVERT: A  482 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7757 (mm-30)
REVERT: A  536 MET cc_start: 0.6551 (tpt) cc_final: 0.6233 (tpt)
REVERT: A  732 MET cc_start: 0.8855 (ttm) cc_final: 0.8595 (ttm)
REVERT: A  756 MET cc_start: 0.8661 (ttm) cc_final: 0.8323 (ttm)
REVERT: A  839 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7269 (mt)
  outliers start: 29
  outliers final: 10
  residues processed: 137
  average time/residue: 1.1988
  time to fit residues: 174.3013
Evaluate side-chains
  116 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  524 CYS
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  836 TYR
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:    0.0010
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0470
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5286

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

Flipped N/Q/H residues before XYZ refinement:
A 396 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 = 0.3960 r_free = 0.3960 target = 0.179530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.142455 restraints weight = 8196.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.44
r_work: 0.3336 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7980  Z= 0.137
  Angle     :  0.467   5.919  10831  Z= 0.247
  Chirality :  0.040   0.172   1272
  Planarity :  0.004   0.060   1379
  Dihedral  :  3.773  16.912   1072
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.95 %
    Favored  : 82.27 %
  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:  1.16 (0.27), residues: 1009
  helix:  1.80 (0.23), residues: 519
  sheet: -0.06 (0.54), residues: 81
  loop : -0.35 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 294 
 ARG   0.002   0.000   ARG A 571 

*********************** 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: 24
    poor density    : 115
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8441 (mttp) cc_final: 0.7835 (mtpt)
REVERT: A   90 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6814 (tm-30)
REVERT: A  120 LYS cc_start: 0.6376 (mmtt) cc_final: 0.6130 (mmtp)
REVERT: A  134 ARG cc_start: 0.6962 (ptp-170) cc_final: 0.6624 (ptp-170)
REVERT: A  466 GLU cc_start: 0.7620 (pt0) cc_final: 0.6956 (tp30)
REVERT: A  467 ARG cc_start: 0.7476 (tpt-90) cc_final: 0.6937 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6243 (tp40) cc_final: 0.5990 (mm110)
REVERT: A  480 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7215 (ptmt)
REVERT: A  482 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: A  536 MET cc_start: 0.6239 (tpt) cc_final: 0.5951 (tpt)
REVERT: A  732 MET cc_start: 0.8819 (ttm) cc_final: 0.8578 (ttm)
REVERT: A  756 MET cc_start: 0.8491 (ttm) cc_final: 0.8126 (ttm)
REVERT: A  796 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8083 (mm)
REVERT: A  839 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7296 (mt)
REVERT: A  917 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6805 (tp30)
  outliers start: 24
  outliers final: 10
  residues processed: 127
  average time/residue: 1.1960
  time to fit residues: 161.1906
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  479 MET
Chi-restraints excluded: chain A residue  524 CYS
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  796 LEU
Chi-restraints excluded: chain A residue  839 ILE
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:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 30 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0030
   chunk 19 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.4794

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.171554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.132318 restraints weight = 8118.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.74
r_work: 0.3209 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7980  Z= 0.211
  Angle     :  0.514   5.828  10831  Z= 0.272
  Chirality :  0.043   0.177   1272
  Planarity :  0.004   0.058   1379
  Dihedral  :  3.958  15.615   1072
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.41 %
    Favored  : 81.00 %
  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:  1.01 (0.26), residues: 1009
  helix:  1.67 (0.23), residues: 519
  sheet: -0.17 (0.52), residues: 81
  loop : -0.40 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 571 

*********************** 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
  139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8441 (mttp) cc_final: 0.7736 (mtpt)
REVERT: A   90 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6845 (tm-30)
REVERT: A  120 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6058 (mmtp)
REVERT: A  134 ARG cc_start: 0.6804 (ptp-170) cc_final: 0.6423 (ptp-170)
REVERT: A  399 ASP cc_start: 0.7223 (m-30) cc_final: 0.6945 (t0)
REVERT: A  400 LYS cc_start: 0.6862 (pptt) cc_final: 0.6353 (pmtt)
REVERT: A  467 ARG cc_start: 0.7336 (tpt-90) cc_final: 0.6801 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6428 (tp40) cc_final: 0.6189 (mm110)
REVERT: A  480 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7134 (ptmt)
REVERT: A  482 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7809 (mm-30)
REVERT: A  536 MET cc_start: 0.6440 (tpt) cc_final: 0.6116 (tpt)
REVERT: A  714 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8140 (mp0)
REVERT: A  732 MET cc_start: 0.8954 (ttm) cc_final: 0.8688 (ttm)
REVERT: A  756 MET cc_start: 0.8748 (ttm) cc_final: 0.8434 (ttm)
REVERT: A  839 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7294 (mt)
REVERT: A  917 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6833 (tp30)
  outliers start: 31
  outliers final: 16
  residues processed: 127
  average time/residue: 1.2449
  time to fit residues: 168.0237
Evaluate side-chains
  124 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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  323 THR
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
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  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0040
   chunk 65 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5352

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.177596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.139592 restraints weight = 8184.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.65
r_work: 0.3285 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7980  Z= 0.140
  Angle     :  0.470   6.102  10831  Z= 0.249
  Chirality :  0.040   0.188   1272
  Planarity :  0.004   0.057   1379
  Dihedral  :  3.802  15.623   1072
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.61 %
    Favored  : 79.84 %
  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:  1.80 (0.23), residues: 520
  sheet: -0.11 (0.53), residues: 81
  loop : -0.41 (0.30), residues: 408

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   0.003   0.000   ARG A 571 

*********************** 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
  130 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8402 (mttp) cc_final: 0.7687 (mtpt)
REVERT: A  120 LYS cc_start: 0.6315 (mmtt) cc_final: 0.6068 (mmtp)
REVERT: A  134 ARG cc_start: 0.6870 (ptp-170) cc_final: 0.6359 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6966 (pptt) cc_final: 0.6449 (pmtt)
REVERT: A  466 GLU cc_start: 0.7691 (pt0) cc_final: 0.6974 (tp30)
REVERT: A  467 ARG cc_start: 0.7406 (tpt-90) cc_final: 0.6863 (tpt-90)
REVERT: A  477 GLN cc_start: 0.6297 (tp40) cc_final: 0.6043 (mm110)
REVERT: A  480 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7112 (ptmt)
REVERT: A  482 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: A  529 VAL cc_start: 0.7891 (t) cc_final: 0.7568 (m)
REVERT: A  536 MET cc_start: 0.6425 (tpt) cc_final: 0.6086 (tpt)
REVERT: A  732 MET cc_start: 0.8893 (ttm) cc_final: 0.8621 (ttm)
REVERT: A  756 MET cc_start: 0.8618 (ttm) cc_final: 0.8269 (ttm)
REVERT: A  839 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7266 (mt)
  outliers start: 22
  outliers final: 12
  residues processed: 123
  average time/residue: 1.2413
  time to fit residues: 162.0056
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
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  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
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  869 LEU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3891 r_free = 0.3891 target = 0.172613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.133424 restraints weight = 8221.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.76
r_work: 0.3238 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7980  Z= 0.155
  Angle     :  0.469   5.241  10831  Z= 0.248
  Chirality :  0.041   0.194   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.789  15.055   1072
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.61 %
    Favored  : 79.61 %
  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:  1.14 (0.26), residues: 1009
  helix:  1.81 (0.23), residues: 520
  sheet: -0.14 (0.53), residues: 81
  loop : -0.40 (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   0.002   0.000   ARG A 139 

*********************** 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
  132 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8410 (mttp) cc_final: 0.7720 (mtpt)
REVERT: A  120 LYS cc_start: 0.6260 (mmtt) cc_final: 0.5995 (mmtp)
REVERT: A  134 ARG cc_start: 0.6749 (ptp-170) cc_final: 0.6333 (ptp-170)
REVERT: A  400 LYS cc_start: 0.6900 (pptt) cc_final: 0.6383 (pmtt)
REVERT: A  480 LYS cc_start: 0.7560 (mtmt) cc_final: 0.7023 (ptmt)
REVERT: A  482 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: A  529 VAL cc_start: 0.7883 (t) cc_final: 0.7557 (m)
REVERT: A  536 MET cc_start: 0.6434 (tpt) cc_final: 0.6090 (tpt)
REVERT: A  732 MET cc_start: 0.8952 (ttm) cc_final: 0.8669 (ttm)
REVERT: A  756 MET cc_start: 0.8714 (ttm) cc_final: 0.8382 (ttm)
REVERT: A  792 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6763 (tp)
REVERT: A  839 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7106 (mt)
REVERT: A  917 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6943 (tp30)
  outliers start: 24
  outliers final: 12
  residues processed: 120
  average time/residue: 1.2053
  time to fit residues: 153.7216
Evaluate side-chains
  120 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
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  479 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
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  869 LEU
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.0970
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 48 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.178286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.139831 restraints weight = 8295.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.63
r_work: 0.3317 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7980  Z= 0.132
  Angle     :  0.453   5.342  10831  Z= 0.241
  Chirality :  0.040   0.203   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.710  14.732   1072
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.54 %
    Favored  : 79.37 %
  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:  1.28 (0.27), residues: 1009
  helix:  1.92 (0.23), residues: 520
  sheet:  0.00 (0.53), residues: 80
  loop : -0.33 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 107 
 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   0.004   0.000   ARG A 467 

*********************** 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
  126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8406 (mttp) cc_final: 0.7722 (mtpt)
REVERT: A  134 ARG cc_start: 0.6837 (ptp-170) cc_final: 0.6416 (ptp-170)
REVERT: A  466 GLU cc_start: 0.7589 (pt0) cc_final: 0.6893 (tp30)
REVERT: A  480 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6978 (ptmt)
REVERT: A  482 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7796 (mm-30)
REVERT: A  529 VAL cc_start: 0.7914 (t) cc_final: 0.7615 (m)
REVERT: A  536 MET cc_start: 0.6648 (tpt) cc_final: 0.6124 (tpt)
REVERT: A  714 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8124 (mp0)
REVERT: A  756 MET cc_start: 0.8559 (ttm) cc_final: 0.8054 (ttm)
REVERT: A  792 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6859 (tp)
REVERT: A  816 MET cc_start: 0.7977 (mmm) cc_final: 0.7724 (mmp)
REVERT: A  839 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7094 (mt)
REVERT: A  917 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6919 (tp30)
  outliers start: 18
  outliers final: 10
  residues processed: 120
  average time/residue: 1.2303
  time to fit residues: 156.5960
Evaluate side-chains
  117 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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  479 MET
Chi-restraints excluded: chain A residue  480 LYS
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
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  839 ILE
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 75 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 85 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.173630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.134092 restraints weight = 8352.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.81
r_work: 0.3256 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7980  Z= 0.140
  Angle     :  0.478  10.284  10831  Z= 0.249
  Chirality :  0.041   0.203   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.701  14.530   1072
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.31 %
    Favored  : 79.49 %
  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:  1.28 (0.27), residues: 1009
  helix:  1.95 (0.23), residues: 520
  sheet: -0.10 (0.53), residues: 81
  loop : -0.36 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 854 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.008   0.000   ARG A 139 

*********************** 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
  124 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8366 (mttp) cc_final: 0.7684 (mtpt)
REVERT: A  134 ARG cc_start: 0.6753 (ptp-170) cc_final: 0.6314 (ptp-170)
REVERT: A  480 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6902 (ptmt)
REVERT: A  529 VAL cc_start: 0.7904 (t) cc_final: 0.7602 (m)
REVERT: A  536 MET cc_start: 0.6677 (tpt) cc_final: 0.6152 (tpt)
REVERT: A  714 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7971 (mp0)
REVERT: A  756 MET cc_start: 0.8620 (ttm) cc_final: 0.8257 (ttm)
REVERT: A  792 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6797 (tp)
REVERT: A  816 MET cc_start: 0.8035 (mmm) cc_final: 0.7752 (mmp)
REVERT: A  917 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7009 (tp30)
REVERT: A  922 LEU cc_start: 0.5645 (mt) cc_final: 0.5359 (mt)
  outliers start: 19
  outliers final: 12
  residues processed: 117
  average time/residue: 1.1789
  time to fit residues: 146.4426
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  : 0.833 
-------------------------------------------------------------------------------
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  479 MET
Chi-restraints excluded: chain A residue  480 LYS
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
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  869 LEU
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:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 91 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.1594

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.172966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133596 restraints weight = 8260.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.71
r_work: 0.3241 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7980  Z= 0.183
  Angle     :  0.511  10.496  10831  Z= 0.264
  Chirality :  0.042   0.207   1272
  Planarity :  0.004   0.055   1379
  Dihedral  :  3.836  14.729   1072
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.31 %
    Favored  : 79.26 %
  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 (0.26), residues: 1009
  helix:  1.85 (0.23), residues: 520
  sheet: -0.24 (0.52), residues: 81
  loop : -0.42 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.011   0.001   ARG A 139 

********************** 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
  126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8387 (mttp) cc_final: 0.7729 (mtpt)
REVERT: A  134 ARG cc_start: 0.6784 (ptp-170) cc_final: 0.6364 (ptp-170)
REVERT: A  442 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7755 (mt-10)
REVERT: A  480 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (ptmt)
REVERT: A  529 VAL cc_start: 0.7889 (t) cc_final: 0.7578 (m)
REVERT: A  536 MET cc_start: 0.6778 (tpt) cc_final: 0.6266 (tpt)
REVERT: A  714 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8118 (mp0)
REVERT: A  756 MET cc_start: 0.8737 (ttm) cc_final: 0.8416 (ttm)
REVERT: A  792 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6742 (tp)
REVERT: A  816 MET cc_start: 0.8142 (mmm) cc_final: 0.7811 (mmp)
REVERT: A  917 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6821 (tp30)
  outliers start: 21
  outliers final: 11
  residues processed: 115
  average time/residue: 1.2624
  time to fit residues: 154.1727
Evaluate side-chains
  117 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  442 GLU
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  480 LYS
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  524 CYS
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  869 LEU
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:    0.0870
   chunk 57 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1562

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.171863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.131655 restraints weight = 8245.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.82
r_work: 0.3223 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7980  Z= 0.184
  Angle     :  0.510   9.674  10831  Z= 0.264
  Chirality :  0.042   0.198   1272
  Planarity :  0.004   0.055   1379
  Dihedral  :  3.867  14.770   1072
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.66 %
    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:  1.08 (0.26), residues: 1009
  helix:  1.80 (0.23), residues: 520
  sheet: -0.26 (0.53), residues: 81
  loop : -0.46 (0.30), residues: 408

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   0.009   0.001   ARG A 139 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6170.06 seconds
wall clock time: 109 minutes 23.12 seconds (6563.12 seconds total)