Starting phenix.real_space_refine
on Wed Feb 12 11:50:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e7s_31003/02_2025/7e7s_31003.cif"
  }
  resolution = 3.3
  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=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      58      5.16       5
     C    5027      2.51       5
     N    1314      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7884
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1020, 7882
          Classifications: {'peptide': 1020}
          Link IDs: {'PTRANS': 46, 'TRANS': 973}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.68, per 1000 atoms: 0.59
  Number of scatterers: 7884
  At special positions: 0
  Unit cell: (78.435, 84.66, 150.645, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      58     16.00
     O    1483      8.00
     N    1314      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.03

  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=0, symmetry=0
  Time building additional restraints: 2.11
  Conformation dependent library (CDL) restraints added in 967.5 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      55.0% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.599A  pdb=" N   THR A   6 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A   7 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3 through 7'
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.588A  pdb=" N   GLU A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 76
    Processing helix  chain 'A' and resid 88 through 123
      removed outlier: 3.509A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 123 " --> pdb=" O   LEU A 119 " (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 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.976A  pdb=" N   ASN A 229 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.748A  pdb=" N   HIS A 278 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.631A  pdb=" N   PHE A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.690A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 407 through 420
      removed outlier: 3.745A  pdb=" N   VAL A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.106A  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: 3.622A  pdb=" N   GLN A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 3.859A  pdb=" N   PHE A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.502A  pdb=" N   ASN A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.868A  pdb=" N   LYS A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 729
      removed outlier: 3.639A  pdb=" N   LYS A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 3.705A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 800
      removed outlier: 3.676A  pdb=" N   GLY A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 858
      removed outlier: 3.557A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 858 " --> pdb=" O   TRP A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.425A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 946
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.621A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.632A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153
      removed outlier: 6.861A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 163 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176
      removed outlier: 6.552A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 653
      removed outlier: 8.069A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 734 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 515 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 564 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   CYS A 524 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 592 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.026A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428

    413 hydrogen bonds defined for protein.
    1185 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: 3.13

  Time building geometry restraints manager: 2.41 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: 2577
        1.34 -     1.46: 1658
        1.46 -     1.58: 3706
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 8031
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" CB  VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.72e-01
  bond pdb=" CG  LEU A 806 "
       pdb=" CD1 LEU A 806 "
    ideal  model  delta    sigma   weight residual
    1.521  1.498  0.023 3.30e-02 9.18e+02 4.87e-01
  bond pdb=" N   PRO A 819 "
       pdb=" CA  PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.31e-02 5.83e+03 4.68e-01
  bond pdb=" C   PRO A 819 "
       pdb=" O   PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.246  1.240  0.005 8.50e-03 1.38e+04 4.18e-01
  bond pdb=" CG  PRO A 312 "
       pdb=" CD  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.14e-01
  ... (remaining 8026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 10771
        1.66 -     3.32: 94
        3.32 -     4.98: 26
        4.98 -     6.64: 7
        6.64 -     8.30: 1
  Bond angle restraints: 10899
  Sorted by residual:
  angle pdb=" CB  MET A 908 "
        pdb=" CG  MET A 908 "
        pdb=" SD  MET A 908 "
      ideal   model   delta    sigma   weight residual
     112.70  121.00   -8.30 3.00e+00 1.11e-01 7.65e+00
  angle pdb=" N   ILE A 232 "
        pdb=" CA  ILE A 232 "
        pdb=" C   ILE A 232 "
      ideal   model   delta    sigma   weight residual
     113.07  109.43    3.64 1.36e+00 5.41e-01 7.18e+00
  angle pdb=" C   VAL A 223 "
        pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
      ideal   model   delta    sigma   weight residual
     122.66  120.19    2.47 9.70e-01 1.06e+00 6.46e+00
  angle pdb=" CB  LYS A 541 "
        pdb=" CG  LYS A 541 "
        pdb=" CD  LYS A 541 "
      ideal   model   delta    sigma   weight residual
     111.30  116.95   -5.65 2.30e+00 1.89e-01 6.04e+00
  angle pdb=" N   LEU A 952 "
        pdb=" CA  LEU A 952 "
        pdb=" C   LEU A 952 "
      ideal   model   delta    sigma   weight residual
     109.81  115.21   -5.40 2.21e+00 2.05e-01 5.98e+00
  ... (remaining 10894 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4353
       17.73 -    35.45: 426
       35.45 -    53.18: 64
       53.18 -    70.91: 17
       70.91 -    88.63: 8
  Dihedral angle restraints: 4868
    sinusoidal: 1922
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASP A1038 "
           pdb=" CB  ASP A1038 "
           pdb=" CG  ASP A1038 "
           pdb=" OD1 ASP A1038 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.97   58.97     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CB  GLU A  79 "
           pdb=" CG  GLU A  79 "
           pdb=" CD  GLU A  79 "
           pdb=" OE1 GLU A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.63  -88.63     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 919
       0.036 -    0.072: 256
       0.072 -    0.108: 85
       0.108 -    0.144: 18
       0.144 -    0.180: 1
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" CB  ILE A 150 "
            pdb=" CA  ILE A 150 "
            pdb=" CG1 ILE A 150 "
            pdb=" CG2 ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-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   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  PRO A 788 "
            pdb=" N   PRO A 788 "
            pdb=" C   PRO A 788 "
            pdb=" CB  PRO A 788 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1276 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 400 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 401 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 401 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 401 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 247 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO A 248 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 892 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO A 893 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 893 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 893 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 222
        2.71 -     3.26: 8253
        3.26 -     3.81: 12642
        3.81 -     4.35: 15906
        4.35 -     4.90: 26753
  Nonbonded interactions: 63776
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 879 "
            pdb=" OD1 ASP A 881 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG A 619 "
            pdb=" O   CYS A 669 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   PHE A 209 "
            pdb=" OG1 THR A 212 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER A  38 "
            pdb=" O   LYS A 143 "
     model   vdw
     2.296 3.040
  ... (remaining 63771 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:             0.510
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.830
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
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   0.031   8031  Z= 0.171
  Angle     :  0.496   8.299  10899  Z= 0.261
  Chirality :  0.040   0.180   1279
  Planarity :  0.004   0.054   1389
  Dihedral  : 14.410  88.632   2955
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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: -0.13 (0.26), residues: 1014
  helix:  0.30 (0.23), residues: 482
  sheet: -1.14 (0.48), residues: 109
  loop : -0.03 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 272 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A1040 
 TYR   0.008   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7479 (mmm) cc_final: 0.7023 (tmm)
REVERT: A  399 ASP cc_start: 0.6887 (t70) cc_final: 0.6640 (t70)
REVERT: A  568 ASN cc_start: 0.7578 (t0) cc_final: 0.7082 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2078
  time to fit residues: 30.5161
Evaluate side-chains
  81 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.4980
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 403 ASN
A 691 GLN
A 913 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.185826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.116444 restraints weight = 8273.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.07
r_work: 0.3003 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8031  Z= 0.177
  Angle     :  0.539   7.275  10899  Z= 0.280
  Chirality :  0.042   0.177   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.887  21.640   1078
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.76 %
    Favored  : 92.90 %
  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:  0.69 (0.27), residues: 1014
  helix:  1.32 (0.23), residues: 500
  sheet: -1.18 (0.47), residues: 105
  loop : -0.03 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.009   0.001   PHE A 367 
 TYR   0.017   0.002   TYR A 842 
 ARG   0.003   0.000   ARG A 619 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A  467 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7430 (tpp-160)
REVERT: A  482 GLU cc_start: 0.6873 (mp0) cc_final: 0.6142 (mp0)
REVERT: A  568 ASN cc_start: 0.7835 (t0) cc_final: 0.7370 (p0)
REVERT: A  586 TYR cc_start: 0.6602 (m-10) cc_final: 0.6286 (m-10)
REVERT: A  714 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8425 (mm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2241
  time to fit residues: 31.8459
Evaluate side-chains
  84 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.185285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.115216 restraints weight = 8403.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.10
r_work: 0.3007 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8031  Z= 0.165
  Angle     :  0.501   6.420  10899  Z= 0.256
  Chirality :  0.041   0.145   1279
  Planarity :  0.004   0.045   1389
  Dihedral  :  3.768  23.140   1078
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.31 %
    Favored  : 89.00 %
  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:  0.97 (0.27), residues: 1014
  helix:  1.60 (0.23), residues: 501
  sheet: -0.71 (0.55), residues: 77
  loop : -0.15 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 405 
 PHE   0.013   0.001   PHE A1040 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 549 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A  482 GLU cc_start: 0.6775 (mp0) cc_final: 0.6301 (mp0)
REVERT: A  553 SER cc_start: 0.8106 (t) cc_final: 0.7790 (p)
REVERT: A  568 ASN cc_start: 0.7704 (t0) cc_final: 0.7283 (p0)
REVERT: A  586 TYR cc_start: 0.6623 (m-10) cc_final: 0.6366 (m-10)
REVERT: A  898 MET cc_start: 0.8983 (mmm) cc_final: 0.8705 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 99
  average time/residue: 0.2217
  time to fit residues: 29.9444
Evaluate side-chains
  91 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 88 optimal weight:    0.4980
   chunk 1 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.185725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113931 restraints weight = 8317.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.89
r_work: 0.3021 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.157
  Angle     :  0.490   6.092  10899  Z= 0.249
  Chirality :  0.041   0.134   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.731  22.995   1078
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.83 %
    Favored  : 86.37 %
  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:  1.11 (0.27), residues: 1014
  helix:  1.77 (0.23), residues: 501
  sheet: -0.42 (0.57), residues: 77
  loop : -0.20 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.012   0.001   PHE A1040 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  467 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7574 (tpp-160)
REVERT: A  479 MET cc_start: 0.7113 (tpt) cc_final: 0.6905 (tpt)
REVERT: A  482 GLU cc_start: 0.6603 (mp0) cc_final: 0.6164 (mp0)
REVERT: A  549 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6753 (mtm110)
REVERT: A  553 SER cc_start: 0.8097 (t) cc_final: 0.7784 (p)
REVERT: A  568 ASN cc_start: 0.7683 (t0) cc_final: 0.7307 (p0)
REVERT: A  586 TYR cc_start: 0.6671 (m-10) cc_final: 0.6453 (m-10)
REVERT: A  763 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8638 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 102
  average time/residue: 0.2200
  time to fit residues: 30.4562
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0570
   chunk 21 optimal weight:    7.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
A 879 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.181298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.106204 restraints weight = 8411.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.98
r_work: 0.3007 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8031  Z= 0.163
  Angle     :  0.490   6.608  10899  Z= 0.249
  Chirality :  0.041   0.173   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.726  23.326   1078
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.83 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1014
  helix:  1.81 (0.23), residues: 501
  sheet: -0.37 (0.58), residues: 77
  loop : -0.15 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.011   0.001   PHE A1040 
 TYR   0.016   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.4638 (OUTLIER) cc_final: 0.4378 (tp)
REVERT: A  467 ARG cc_start: 0.7733 (tpp80) cc_final: 0.7519 (tpp-160)
REVERT: A  482 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6093 (mp0)
REVERT: A  549 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.6732 (mtm110)
REVERT: A  553 SER cc_start: 0.8036 (t) cc_final: 0.7730 (p)
REVERT: A  568 ASN cc_start: 0.7705 (t0) cc_final: 0.7363 (p0)
REVERT: A  763 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8567 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2120
  time to fit residues: 30.7575
Evaluate side-chains
  104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0000
   overall best weight:    0.6584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.186833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.115204 restraints weight = 8318.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.90
r_work: 0.3027 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.161
  Angle     :  0.493   6.985  10899  Z= 0.249
  Chirality :  0.041   0.151   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.713  23.029   1078
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.09 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 1014
  helix:  1.87 (0.23), residues: 501
  sheet: -0.51 (0.58), residues: 67
  loop : -0.17 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.009   0.001   PHE A1040 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.4673 (OUTLIER) cc_final: 0.4466 (tp)
REVERT: A  479 MET cc_start: 0.6998 (tpt) cc_final: 0.6744 (tpt)
REVERT: A  482 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6031 (mp0)
REVERT: A  549 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.6808 (mtm110)
REVERT: A  553 SER cc_start: 0.8056 (t) cc_final: 0.7769 (p)
REVERT: A  568 ASN cc_start: 0.7656 (t0) cc_final: 0.7341 (p0)
REVERT: A  763 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8606 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 104
  average time/residue: 0.2184
  time to fit residues: 30.8565
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 98 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0030
   overall best weight:    0.8794

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.186037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.114271 restraints weight = 8487.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.90
r_work: 0.3016 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8031  Z= 0.182
  Angle     :  0.505   7.507  10899  Z= 0.254
  Chirality :  0.041   0.177   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.744  23.511   1078
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.55 %
    Favored  : 84.31 %
  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:  1.19 (0.27), residues: 1014
  helix:  1.88 (0.23), residues: 501
  sheet: -0.50 (0.59), residues: 67
  loop : -0.20 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.009   0.001   PHE A 693 
 TYR   0.017   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.4507 (tp)
REVERT: A  479 MET cc_start: 0.7049 (tpt) cc_final: 0.6805 (tpt)
REVERT: A  482 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6097 (mp0)
REVERT: A  549 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.6817 (mtm110)
REVERT: A  553 SER cc_start: 0.8062 (t) cc_final: 0.7782 (p)
REVERT: A  568 ASN cc_start: 0.7719 (t0) cc_final: 0.7454 (p0)
REVERT: A  693 PHE cc_start: 0.7682 (m-80) cc_final: 0.7475 (m-80)
REVERT: A  763 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8645 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 99
  average time/residue: 0.2007
  time to fit residues: 27.4195
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 87 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 879 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.107541 restraints weight = 8541.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.97
r_work: 0.3013 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8031  Z= 0.165
  Angle     :  0.496   8.071  10899  Z= 0.250
  Chirality :  0.041   0.176   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.720  23.140   1078
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.66 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 1014
  helix:  1.91 (0.23), residues: 501
  sheet: -0.58 (0.67), residues: 57
  loop : -0.23 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.009   0.001   PHE A 367 
 TYR   0.016   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  479 MET cc_start: 0.6920 (tpt) cc_final: 0.6671 (tpt)
REVERT: A  482 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6066 (mp0)
REVERT: A  549 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.6679 (mtm110)
REVERT: A  553 SER cc_start: 0.8030 (t) cc_final: 0.7768 (p)
REVERT: A  568 ASN cc_start: 0.7693 (t0) cc_final: 0.7445 (p0)
REVERT: A  763 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 0.2066
  time to fit residues: 28.2078
Evaluate side-chains
  100 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 92 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0770
   overall best weight:    1.0942

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.184648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.112600 restraints weight = 8530.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.90
r_work: 0.3004 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8031  Z= 0.206
  Angle     :  0.519   8.409  10899  Z= 0.261
  Chirality :  0.042   0.264   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.767  23.997   1078
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.32 %
    Favored  : 84.31 %
  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:  1.17 (0.27), residues: 1014
  helix:  1.85 (0.23), residues: 501
  sheet: -0.42 (0.62), residues: 67
  loop : -0.21 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.018   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.8273 (t70) cc_final: 0.7588 (t0)
REVERT: A  482 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6070 (mp0)
REVERT: A  549 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.6693 (mtm110)
REVERT: A  553 SER cc_start: 0.7969 (t) cc_final: 0.7698 (p)
REVERT: A  568 ASN cc_start: 0.7654 (t0) cc_final: 0.7427 (p0)
REVERT: A  763 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8619 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1907
  time to fit residues: 26.1872
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0670
   chunk 4 optimal weight:    0.0870
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.3096

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.182885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.109024 restraints weight = 8514.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.09
r_work: 0.3035 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.136
  Angle     :  0.494   8.585  10899  Z= 0.248
  Chirality :  0.041   0.199   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.664  22.028   1078
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.78 %
    Favored  : 84.19 %
  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:  1.33 (0.27), residues: 1014
  helix:  2.01 (0.24), residues: 500
  sheet: -0.21 (0.65), residues: 67
  loop : -0.19 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 793 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   58 GLU cc_start: 0.7942 (pp20) cc_final: 0.7690 (pp20)
REVERT: A  239 MET cc_start: 0.4489 (mmm) cc_final: 0.4159 (mmm)
REVERT: A  482 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6013 (mp0)
REVERT: A  549 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.6882 (mtt90)
REVERT: A  553 SER cc_start: 0.7865 (t) cc_final: 0.7629 (p)
REVERT: A  763 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8571 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1999
  time to fit residues: 27.7199
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 80 optimal weight:    0.3980
   chunk 19 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0040
   chunk 20 optimal weight:   20.0000
   chunk 63 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   overall best weight:    0.2710

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.183481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109677 restraints weight = 8469.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.12
r_work: 0.3040 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.139
  Angle     :  0.518   8.997  10899  Z= 0.258
  Chirality :  0.041   0.188   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.601  21.942   1078
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.01 %
    Favored  : 84.08 %
  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:  1.37 (0.27), residues: 1014
  helix:  2.05 (0.24), residues: 500
  sheet: -0.35 (0.62), residues: 69
  loop : -0.15 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 405 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5107.73 seconds
wall clock time: 91 minutes 5.89 seconds (5465.89 seconds total)