Starting phenix.real_space_refine
on Fri Jun  6 14:29:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7w_32350/06_2025/7w7w_32350.cif"
  }
  resolution = 3.2
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      58      5.16       5
     C    5011      2.51       5
     N    1315      2.21       5
     O    1480      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7870
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1018, 7864
          Classifications: {'peptide': 1018}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 971}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.01, per 1000 atoms: 0.64
  Number of scatterers: 7870
  At special positions: 0
  Unit cell: (99.935, 92.345, 136.62, 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
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1480      8.00
     N    1315      7.00
     C    5011      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 991.6 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:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 6 sheets defined
      53.1% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.617A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 3.833A  pdb=" N   LYS A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 79
      removed outlier: 3.615A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
    Processing helix  chain 'A' and resid 88 through 110
    Processing helix  chain 'A' and resid 141 through 145
      removed outlier: 3.865A  pdb=" N   ASP A 144 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ILE A 145 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 141 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 230 through 241
    Processing helix  chain 'A' and resid 247 through 279
      removed outlier: 3.778A  pdb=" N   GLY A 277 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 307
      removed outlier: 4.071A  pdb=" N   ALA A 292 " --> pdb=" O   TRP A 288 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ILE A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 329
      removed outlier: 4.661A  pdb=" N   ALA A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 343
    Processing helix  chain 'A' and resid 407 through 420
      removed outlier: 3.617A  pdb=" N   VAL A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 3.592A  pdb=" N   MET A 452 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 3.717A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 478
      removed outlier: 3.624A  pdb=" N   LEU A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 553
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.946A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.727A  pdb=" N   SER A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
    Processing helix  chain 'A' and resid 654 through 659
      removed outlier: 3.675A  pdb=" N   GLU A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.958A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.658A  pdb=" N   PHE A 693 " --> pdb=" O   PHE A 689 " (cutoff:3.500A)
    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: 4.103A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 808
      removed outlier: 3.810A  pdb=" N   THR A 798 " --> pdb=" O   VAL A 794 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ASP A 799 " --> pdb=" O   ASN A 795 " (cutoff:3.500A)
      Proline residue:  A 802  - end of helix
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.530A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 870
    Processing helix  chain 'A' and resid 886 through 891
      removed outlier: 3.575A  pdb=" N   ILE A 889 " --> pdb=" O   ASP A 886 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 890 " --> pdb=" O   CYS A 887 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU A 891 " --> pdb=" O   ALA A 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 886 through 891'
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.287A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
      removed outlier: 3.743A  pdb=" N   VAL A 933 " --> pdb=" O   ASN A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 956
      removed outlier: 3.935A  pdb=" N   ILE A 955 " --> pdb=" O   PRO A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 989
      removed outlier: 4.044A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1031
      removed outlier: 3.626A  pdb=" N   ILE A1022 " --> pdb=" O   PHE A1018 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   MET A1023 " --> pdb=" O   VAL A1019 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
      removed outlier: 3.536A  pdb=" N   ILE A1027 " --> pdb=" O   MET A1023 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TRP A1028 " --> pdb=" O   PRO A1024 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 153
      removed outlier: 7.037A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188
      removed outlier: 6.183A  pdb=" N   ASP A 176 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   ILE A 214 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.577A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE A 348 " --> pdb=" O   ILE A 621 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ILE A 623 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   SER A 350 " --> pdb=" O   ILE A 623 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 3.782A  pdb=" N   ARG A 371 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 384 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   ARG A 365 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.294A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.747A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 594 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   PHE A 483 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 3.782A  pdb=" N   ARG A 371 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 384 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   ARG A 365 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.294A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.747A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   CYS A 524 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE A 592 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.099A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 12.822A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 427
      removed outlier: 3.562A  pdb=" N   ASP A 426 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1191 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: 3.05

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2561
        1.34 -     1.46: 1086
        1.46 -     1.58: 4276
        1.58 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 8017
  Sorted by residual:
  bond pdb=" F1  ALF A2001 "
       pdb="AL   ALF A2001 "
    ideal  model  delta    sigma   weight residual
    1.684  1.783 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" F2  ALF A2001 "
       pdb="AL   ALF A2001 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" F3  ALF A2001 "
       pdb="AL   ALF A2001 "
    ideal  model  delta    sigma   weight residual
    1.685  1.782 -0.097 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" F4  ALF A2001 "
       pdb="AL   ALF A2001 "
    ideal  model  delta    sigma   weight residual
    1.686  1.783 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" N   LEU A 796 "
       pdb=" CA  LEU A 796 "
    ideal  model  delta    sigma   weight residual
    1.468  1.455  0.014 1.24e-02 6.50e+03 1.20e+00
  ... (remaining 8012 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.20: 10876
       14.20 -    28.40: 4
       28.40 -    42.60: 0
       42.60 -    56.80: 0
       56.80 -    71.00: 2
  Bond angle restraints: 10882
  Sorted by residual:
  angle pdb=" F1  ALF A2001 "
        pdb="AL   ALF A2001 "
        pdb=" F2  ALF A2001 "
      ideal   model   delta    sigma   weight residual
     108.68  179.68  -71.00 3.00e+00 1.11e-01 5.60e+02
  angle pdb=" F3  ALF A2001 "
        pdb="AL   ALF A2001 "
        pdb=" F4  ALF A2001 "
      ideal   model   delta    sigma   weight residual
     109.63  179.93  -70.30 3.00e+00 1.11e-01 5.49e+02
  angle pdb=" F2  ALF A2001 "
        pdb="AL   ALF A2001 "
        pdb=" F4  ALF A2001 "
      ideal   model   delta    sigma   weight residual
     110.21   90.17   20.04 3.00e+00 1.11e-01 4.46e+01
  angle pdb=" F2  ALF A2001 "
        pdb="AL   ALF A2001 "
        pdb=" F3  ALF A2001 "
      ideal   model   delta    sigma   weight residual
     109.59   89.78   19.81 3.00e+00 1.11e-01 4.36e+01
  angle pdb=" F1  ALF A2001 "
        pdb="AL   ALF A2001 "
        pdb=" F3  ALF A2001 "
      ideal   model   delta    sigma   weight residual
     109.69   89.90   19.79 3.00e+00 1.11e-01 4.35e+01
  ... (remaining 10877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 4394
       18.01 -    36.03: 402
       36.03 -    54.04: 54
       54.04 -    72.06: 9
       72.06 -    90.07: 3
  Dihedral angle restraints: 4862
    sinusoidal: 1919
      harmonic: 2943
  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 -176.07   90.07     1      1.00e+01 1.00e-02 9.61e+01
  dihedral pdb=" CA  ASP A 157 "
           pdb=" CB  ASP A 157 "
           pdb=" CG  ASP A 157 "
           pdb=" OD1 ASP A 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.22   54.22     1      2.00e+01 2.50e-03 9.97e+00
  dihedral pdb=" CA  ILE A 116 "
           pdb=" C   ILE A 116 "
           pdb=" N   GLU A 117 "
           pdb=" CA  GLU A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.40  -15.60     0      5.00e+00 4.00e-02 9.74e+00
  ... (remaining 4859 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 880
       0.037 -    0.073: 276
       0.073 -    0.110: 103
       0.110 -    0.147: 15
       0.147 -    0.183: 2
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" CB  ILE A 715 "
            pdb=" CA  ILE A 715 "
            pdb=" CG1 ILE A 715 "
            pdb=" CG2 ILE A 715 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.41e-01
  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    2.36    0.15 2.00e-01 2.50e+01 5.97e-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 4.36e-01
  ... (remaining 1273 not shown)

  Planarity restraints: 1387
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 534 "   -0.036 5.00e-02 4.00e+02   5.51e-02 4.85e+00
        pdb=" N   PRO A 535 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 796 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   LEU A 796 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LEU A 796 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 797 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 959 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO A 960 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 960 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 960 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1384 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 55
        2.62 -     3.19: 7143
        3.19 -     3.76: 12450
        3.76 -     4.33: 16583
        4.33 -     4.90: 27875
  Nonbonded interactions: 64106
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.051 2.170
  nonbonded pdb=" F3  ALF A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     2.055 2.120
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.071 2.170
  nonbonded pdb=" NH2 ARG A 131 "
            pdb=" OE1 GLU A 152 "
     model   vdw
     2.167 3.120
  ... (remaining 64101 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:             0.270
  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:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.570
  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:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
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      :  0.006   0.437   8019  Z= 0.516
  Angle     :  1.162  71.002  10884  Z= 0.455
  Chirality :  0.041   0.183   1276
  Planarity :  0.004   0.055   1387
  Dihedral  : 13.443  75.289   2951
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  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:  0.82 (0.26), residues: 1014
  helix:  1.66 (0.24), residues: 489
  sheet: -0.03 (0.50), residues: 105
  loop : -0.62 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 831 
 HIS   0.002   0.001   HIS A 943 
 PHE   0.019   0.001   PHE A 759 
 TYR   0.025   0.001   TYR A 586 
 ARG   0.005   0.000   ARG A 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15321 (  402)
  hydrogen bonds       : angle       6.23727 ( 1191)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.64530 (    2)
  covalent geometry    : bond        0.00342 ( 8017)
  covalent geometry    : angle       1.16235 (10882)
  Misc. bond           : bond        0.43727 (    1)

*********************** 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
  123 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 MET cc_start: 0.6826 (ptt) cc_final: 0.6150 (ptt)
REVERT: A  557 THR cc_start: 0.7993 (p) cc_final: 0.7663 (p)
REVERT: A  784 GLU cc_start: 0.5533 (mm-30) cc_final: 0.4672 (mm-30)
REVERT: A 1023 MET cc_start: 0.1857 (mmt) cc_final: 0.1158 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2581
  time to fit residues: 45.1856
Evaluate side-chains
  98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0770
   overall best weight:    1.5542

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 738 ASN
A 879 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.179664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.144270 restraints weight = 8674.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 1.78
r_work: 0.3538 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.1062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8019  Z= 0.149
  Angle     :  0.841  30.847  10884  Z= 0.362
  Chirality :  0.044   0.175   1276
  Planarity :  0.005   0.044   1387
  Dihedral  :  4.302  15.287   1078
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.47 %
    Favored  : 91.49 %
  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:  0.58 (0.26), residues: 1014
  helix:  1.44 (0.23), residues: 497
  sheet: -0.19 (0.52), residues: 96
  loop : -0.72 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.032   0.002   PHE A 759 
 TYR   0.012   0.001   TYR A 434 
 ARG   0.003   0.000   ARG A 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  402)
  hydrogen bonds       : angle       5.10985 ( 1191)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.50116 (    2)
  covalent geometry    : bond        0.00356 ( 8017)
  covalent geometry    : angle       0.84129 (10882)
  Misc. bond           : bond        0.00123 (    1)

*********************** 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
  113 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 MET cc_start: 0.7103 (ptt) cc_final: 0.6525 (ptt)
REVERT: A  536 MET cc_start: 0.7778 (tpp) cc_final: 0.7504 (tpt)
REVERT: A  557 THR cc_start: 0.8070 (p) cc_final: 0.7744 (p)
REVERT: A  758 GLN cc_start: 0.7614 (mt0) cc_final: 0.6540 (mm110)
REVERT: A  784 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5135 (mm-30)
REVERT: A  940 MET cc_start: 0.7382 (tpp) cc_final: 0.7123 (mmm)
REVERT: A 1023 MET cc_start: 0.1859 (mmt) cc_final: 0.1129 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1870
  time to fit residues: 29.0124
Evaluate side-chains
  102 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  738 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 92 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.171250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135293 restraints weight = 8902.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.81
r_work: 0.3424 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.134   8019  Z= 0.291
  Angle     :  0.943  36.456  10884  Z= 0.429
  Chirality :  0.050   0.269   1276
  Planarity :  0.006   0.055   1387
  Dihedral  :  4.943  18.378   1078
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.41 %
    Favored  : 85.52 %
  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: -0.16 (0.26), residues: 1014
  helix:  0.77 (0.23), residues: 492
  sheet: -0.96 (0.49), residues: 98
  loop : -0.86 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  36 
 HIS   0.006   0.002   HIS A 566 
 PHE   0.032   0.003   PHE A 759 
 TYR   0.021   0.003   TYR A 434 
 ARG   0.009   0.001   ARG A 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05717 (  402)
  hydrogen bonds       : angle       5.37309 ( 1191)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       0.85950 (    2)
  covalent geometry    : bond        0.00726 ( 8017)
  covalent geometry    : angle       0.94299 (10882)
  Misc. bond           : bond        0.00010 (    1)

*********************** 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
  127 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6939 (mm-30)
REVERT: A  439 GLU cc_start: 0.7576 (tp30) cc_final: 0.7316 (mm-30)
REVERT: A  452 MET cc_start: 0.7384 (ptt) cc_final: 0.7131 (ptt)
REVERT: A  575 MET cc_start: 0.6669 (mmm) cc_final: 0.6378 (tpp)
REVERT: A  784 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5234 (mm-30)
REVERT: A  792 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7729 (mm)
REVERT: A  836 TYR cc_start: 0.7806 (m-80) cc_final: 0.7555 (m-80)
REVERT: A 1023 MET cc_start: 0.1350 (mmt) cc_final: 0.0586 (mmt)
  outliers start: 18
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1775
  time to fit residues: 29.7267
Evaluate side-chains
  119 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.175711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140213 restraints weight = 8720.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.79
r_work: 0.3483 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8019  Z= 0.132
  Angle     :  0.828  30.632  10884  Z= 0.354
  Chirality :  0.043   0.167   1276
  Planarity :  0.005   0.051   1387
  Dihedral  :  4.434  16.415   1078
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.25 %
    Favored  : 83.45 %
  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:  0.21 (0.26), residues: 1014
  helix:  1.23 (0.24), residues: 491
  sheet: -0.90 (0.52), residues: 97
  loop : -0.86 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 831 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 122 
 ARG   0.002   0.000   ARG A 491 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  402)
  hydrogen bonds       : angle       4.94894 ( 1191)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.26007 (    2)
  covalent geometry    : bond        0.00307 ( 8017)
  covalent geometry    : angle       0.82781 (10882)
  Misc. bond           : bond        0.00005 (    1)

*********************** 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
  123 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A  373 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5117 (mm-30)
REVERT: A  439 GLU cc_start: 0.7459 (tp30) cc_final: 0.7211 (mm-30)
REVERT: A  452 MET cc_start: 0.7397 (ptt) cc_final: 0.7186 (ptt)
REVERT: A  492 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7622 (mtpt)
REVERT: A  599 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7266 (pt)
REVERT: A  715 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: A  784 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5117 (mm-30)
REVERT: A 1023 MET cc_start: 0.1644 (mmt) cc_final: 0.0935 (mmt)
  outliers start: 20
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1724
  time to fit residues: 28.7718
Evaluate side-chains
  114 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.178540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.143146 restraints weight = 8709.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.79
r_work: 0.3521 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8019  Z= 0.113
  Angle     :  0.811  30.205  10884  Z= 0.342
  Chirality :  0.042   0.163   1276
  Planarity :  0.004   0.051   1387
  Dihedral  :  4.146  15.785   1078
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.63 %
    Favored  : 82.07 %
  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:  0.36 (0.27), residues: 1014
  helix:  1.37 (0.24), residues: 497
  sheet: -0.80 (0.50), residues: 104
  loop : -0.85 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 831 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.046   0.002   TYR A 586 
 ARG   0.002   0.000   ARG A 491 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  402)
  hydrogen bonds       : angle       4.69454 ( 1191)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.16130 (    2)
  covalent geometry    : bond        0.00259 ( 8017)
  covalent geometry    : angle       0.81091 (10882)
  Misc. bond           : bond        0.00017 (    1)

*********************** 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
  127 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A  373 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.5161 (mm-30)
REVERT: A  452 MET cc_start: 0.7294 (ptt) cc_final: 0.6950 (ptt)
REVERT: A  492 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7610 (mtpt)
REVERT: A  715 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7715 (tp)
REVERT: A  758 GLN cc_start: 0.7600 (mt0) cc_final: 0.6721 (tp40)
REVERT: A  784 GLU cc_start: 0.6142 (mm-30) cc_final: 0.5023 (mm-30)
REVERT: A  940 MET cc_start: 0.7282 (tpp) cc_final: 0.6946 (mmm)
REVERT: A 1023 MET cc_start: 0.1159 (mmt) cc_final: 0.0394 (mmt)
  outliers start: 20
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1807
  time to fit residues: 30.8870
Evaluate side-chains
  119 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 71 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.178906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143761 restraints weight = 8652.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.79
r_work: 0.3527 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8019  Z= 0.113
  Angle     :  0.809  30.310  10884  Z= 0.340
  Chirality :  0.041   0.163   1276
  Planarity :  0.004   0.050   1387
  Dihedral  :  4.042  15.615   1078
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.86 %
    Favored  : 81.15 %
  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:  0.47 (0.27), residues: 1014
  helix:  1.43 (0.24), residues: 504
  sheet: -0.74 (0.51), residues: 99
  loop : -0.78 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.037   0.002   TYR A 586 
 ARG   0.002   0.000   ARG A 491 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  402)
  hydrogen bonds       : angle       4.62116 ( 1191)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.21086 (    2)
  covalent geometry    : bond        0.00258 ( 8017)
  covalent geometry    : angle       0.80881 (10882)
  Misc. bond           : bond        0.00002 (    1)

*********************** 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
  133 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6867 (mm-30)
REVERT: A  373 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.5251 (mm-30)
REVERT: A  452 MET cc_start: 0.7205 (ptt) cc_final: 0.6856 (ptt)
REVERT: A  492 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7523 (mtpt)
REVERT: A  599 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7218 (pt)
REVERT: A  715 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7751 (tp)
REVERT: A  731 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7600 (mt-10)
REVERT: A  758 GLN cc_start: 0.7675 (mt0) cc_final: 0.6942 (tp40)
REVERT: A  784 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5053 (mm-30)
REVERT: A  940 MET cc_start: 0.7294 (tpp) cc_final: 0.6941 (mmm)
REVERT: A 1023 MET cc_start: 0.1751 (mmt) cc_final: 0.1115 (mmt)
  outliers start: 26
  outliers final: 16
  residues processed: 125
  average time/residue: 0.1896
  time to fit residues: 33.6720
Evaluate side-chains
  121 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 87 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 GLN
A 582 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.175011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139495 restraints weight = 8774.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 1.78
r_work: 0.3482 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8019  Z= 0.163
  Angle     :  0.840  31.542  10884  Z= 0.360
  Chirality :  0.043   0.172   1276
  Planarity :  0.005   0.065   1387
  Dihedral  :  4.300  16.255   1078
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.55 %
    Favored  : 80.34 %
  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:  0.31 (0.27), residues: 1014
  helix:  1.22 (0.24), residues: 503
  sheet: -0.85 (0.51), residues: 99
  loop : -0.73 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.028   0.002   PHE A 759 
 TYR   0.031   0.002   TYR A 586 
 ARG   0.004   0.000   ARG A 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04424 (  402)
  hydrogen bonds       : angle       4.75464 ( 1191)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.41919 (    2)
  covalent geometry    : bond        0.00398 ( 8017)
  covalent geometry    : angle       0.83973 (10882)
  Misc. bond           : bond        0.00007 (    1)

*********************** 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
  126 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6873 (mm-30)
REVERT: A  126 MET cc_start: 0.6309 (ttp) cc_final: 0.6096 (ttt)
REVERT: A  373 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.5343 (mm-30)
REVERT: A  452 MET cc_start: 0.7214 (ptt) cc_final: 0.6852 (ptt)
REVERT: A  492 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7545 (mtpt)
REVERT: A  599 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7207 (pt)
REVERT: A  715 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7296 (tp)
REVERT: A  731 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7543 (mt-10)
REVERT: A  784 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5110 (mm-30)
REVERT: A 1023 MET cc_start: 0.1470 (mmt) cc_final: 0.0522 (mtp)
  outliers start: 27
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1738
  time to fit residues: 29.9462
Evaluate side-chains
  119 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 81 optimal weight:    0.3980
   chunk 59 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.177232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141944 restraints weight = 8706.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.79
r_work: 0.3510 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8019  Z= 0.119
  Angle     :  0.814  30.101  10884  Z= 0.342
  Chirality :  0.042   0.165   1276
  Planarity :  0.005   0.050   1387
  Dihedral  :  4.096  15.580   1078
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.90 %
    Favored  : 80.11 %
  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:  0.45 (0.27), residues: 1014
  helix:  1.37 (0.24), residues: 504
  sheet: -0.70 (0.52), residues: 99
  loop : -0.74 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 831 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.030   0.001   TYR A 586 
 ARG   0.002   0.000   ARG A 491 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  402)
  hydrogen bonds       : angle       4.63092 ( 1191)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.19712 (    2)
  covalent geometry    : bond        0.00277 ( 8017)
  covalent geometry    : angle       0.81362 (10882)
  Misc. bond           : bond        0.00031 (    1)

*********************** 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
  133 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8109 (tp30) cc_final: 0.7902 (tp30)
REVERT: A  452 MET cc_start: 0.7169 (ptt) cc_final: 0.6688 (ptt)
REVERT: A  492 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7542 (mtpt)
REVERT: A  573 GLU cc_start: 0.6870 (pt0) cc_final: 0.6329 (pt0)
REVERT: A  599 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7202 (pt)
REVERT: A  715 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7733 (tp)
REVERT: A  731 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: A  758 GLN cc_start: 0.7667 (mt0) cc_final: 0.6954 (tp40)
REVERT: A  784 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5120 (mm-30)
REVERT: A 1023 MET cc_start: 0.1467 (mmt) cc_final: 0.0509 (mtp)
  outliers start: 26
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1638
  time to fit residues: 30.3456
Evaluate side-chains
  126 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0010
   chunk 73 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 89 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.179510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.144307 restraints weight = 8902.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 1.82
r_work: 0.3538 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8019  Z= 0.106
  Angle     :  0.812  29.685  10884  Z= 0.338
  Chirality :  0.041   0.162   1276
  Planarity :  0.004   0.050   1387
  Dihedral  :  3.925  15.348   1078
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.59 %
    Favored  : 80.23 %
  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:  0.61 (0.27), residues: 1014
  helix:  1.53 (0.24), residues: 504
  sheet: -0.48 (0.51), residues: 99
  loop : -0.75 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.030   0.001   TYR A 586 
 ARG   0.004   0.000   ARG A 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  402)
  hydrogen bonds       : angle       4.47238 ( 1191)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.12617 (    2)
  covalent geometry    : bond        0.00238 ( 8017)
  covalent geometry    : angle       0.81172 (10882)
  Misc. bond           : bond        0.00034 (    1)

*********************** 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
  128 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  467 ARG cc_start: 0.6520 (tmt170) cc_final: 0.6226 (tpt90)
REVERT: A  492 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7495 (mtpt)
REVERT: A  573 GLU cc_start: 0.6925 (pt0) cc_final: 0.6423 (pt0)
REVERT: A  599 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7210 (pt)
REVERT: A  715 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7655 (tp)
REVERT: A  758 GLN cc_start: 0.7665 (mt0) cc_final: 0.6807 (tp40)
REVERT: A  784 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5111 (mm-30)
REVERT: A  908 MET cc_start: 0.8524 (mmp) cc_final: 0.8019 (mmp)
REVERT: A  940 MET cc_start: 0.7315 (tpp) cc_final: 0.6960 (mmm)
REVERT: A 1023 MET cc_start: 0.1499 (mmt) cc_final: 0.0490 (mtp)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1700
  time to fit residues: 30.1495
Evaluate side-chains
  123 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  771 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0470
   chunk 43 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 100 optimal weight:    7.9990
   chunk 96 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.180632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.145860 restraints weight = 8746.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.79
r_work: 0.3558 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8019  Z= 0.105
  Angle     :  0.812  29.629  10884  Z= 0.339
  Chirality :  0.041   0.161   1276
  Planarity :  0.004   0.050   1387
  Dihedral  :  3.830  15.145   1078
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.74 %
    Favored  : 79.31 %
  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:  0.74 (0.27), residues: 1014
  helix:  1.60 (0.24), residues: 505
  sheet: -0.26 (0.53), residues: 97
  loop : -0.69 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.029   0.001   TYR A 586 
 ARG   0.004   0.000   ARG A 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  402)
  hydrogen bonds       : angle       4.42028 ( 1191)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.17027 (    2)
  covalent geometry    : bond        0.00234 ( 8017)
  covalent geometry    : angle       0.81183 (10882)
  Misc. bond           : bond        0.00032 (    1)

********************** 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
  125 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  132 GLN cc_start: 0.6326 (mt0) cc_final: 0.6037 (mt0)
REVERT: A  452 MET cc_start: 0.6914 (ptt) cc_final: 0.6392 (ptt)
REVERT: A  467 ARG cc_start: 0.6440 (tmt170) cc_final: 0.6215 (tpt90)
REVERT: A  492 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7491 (mtpt)
REVERT: A  536 MET cc_start: 0.6956 (tpt) cc_final: 0.6688 (tpt)
REVERT: A  573 GLU cc_start: 0.6765 (pt0) cc_final: 0.5991 (pt0)
REVERT: A  575 MET cc_start: 0.6187 (mmt) cc_final: 0.4506 (mmm)
REVERT: A  599 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7169 (pt)
REVERT: A  715 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7648 (tp)
REVERT: A  758 GLN cc_start: 0.7665 (mt0) cc_final: 0.6798 (tp40)
REVERT: A  784 GLU cc_start: 0.6245 (mm-30) cc_final: 0.5114 (mm-30)
REVERT: A  908 MET cc_start: 0.8524 (mmp) cc_final: 0.8051 (mmp)
REVERT: A  940 MET cc_start: 0.7247 (tpp) cc_final: 0.6942 (mmm)
REVERT: A 1023 MET cc_start: 0.1714 (mmt) cc_final: 0.0629 (mtp)
  outliers start: 17
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1823
  time to fit residues: 31.1245
Evaluate side-chains
  123 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  980 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.180857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146617 restraints weight = 8634.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.76
r_work: 0.3515 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8019  Z= 0.134
  Angle     :  0.831  31.127  10884  Z= 0.352
  Chirality :  0.042   0.168   1276
  Planarity :  0.005   0.051   1387
  Dihedral  :  4.029  15.603   1078
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.05 %
    Favored  : 79.31 %
  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:  0.61 (0.27), residues: 1014
  helix:  1.46 (0.24), residues: 504
  sheet: -0.62 (0.52), residues: 99
  loop : -0.59 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.039   0.002   TYR A 586 
 ARG   0.004   0.000   ARG A 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  402)
  hydrogen bonds       : angle       4.53358 ( 1191)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.36030 (    2)
  covalent geometry    : bond        0.00322 ( 8017)
  covalent geometry    : angle       0.83104 (10882)
  Misc. bond           : bond        0.00023 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4713.38 seconds
wall clock time: 82 minutes 12.37 seconds (4932.37 seconds total)