Starting phenix.real_space_refine
on Sat Dec 28 05:40:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7w_32350/12_2024/7w7w_32350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7w_32350/12_2024/7w7w_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_32350/12_2024/7w7w_32350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7w_32350/12_2024/7w7w_32350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7w_32350/12_2024/7w7w_32350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7w_32350/12_2024/7w7w_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-5532/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: 4.93, per 1000 atoms: 0.63
  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: 2.20
  Conformation dependent library (CDL) restraints added in 867.5 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  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: 1.03
  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: 2.88

  Time building geometry restraints manager: 2.51 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.000
  Set scattering table:                    0.050
  Process input model:                     21.180
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.630
-------------------------------------------------------------------------------
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      :  0.003   0.099   8017  Z= 0.216
  Angle     :  1.162  71.002  10882  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 

*********************** 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  : 0.909 
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: 0.2024
  time to fit residues: 34.4719
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  : 0.945 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
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   8017  Z= 0.240
  Angle     :  0.841  30.847  10882  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 

*********************** 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  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 MET cc_start: 0.6762 (ptt) cc_final: 0.6162 (ptt)
REVERT: A  527 ILE cc_start: 0.8583 (mm) cc_final: 0.8292 (mm)
REVERT: A  557 THR cc_start: 0.8009 (p) cc_final: 0.7679 (p)
REVERT: A  758 GLN cc_start: 0.7348 (mt0) cc_final: 0.6476 (mm110)
REVERT: A  784 GLU cc_start: 0.5642 (mm-30) cc_final: 0.4741 (mm-30)
REVERT: A 1023 MET cc_start: 0.1873 (mmt) cc_final: 0.1127 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1897
  time to fit residues: 29.5334
Evaluate side-chains
  103 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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 50 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0770
   chunk 25 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 90 optimal weight:    0.8980
   overall best weight:    1.0942

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8017  Z= 0.192
  Angle     :  0.815  30.375  10882  Z= 0.344
  Chirality :  0.042   0.165   1276
  Planarity :  0.004   0.045   1387
  Dihedral  :  4.162  15.271   1078
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.03 %
    Favored  : 87.59 %
  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:  0.59 (0.26), residues: 1014
  helix:  1.49 (0.24), residues: 498
  sheet: -0.36 (0.51), residues: 96
  loop : -0.72 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.030   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 491 

*********************** 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
  114 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 PHE cc_start: 0.7672 (m-10) cc_final: 0.7450 (m-80)
REVERT: A  452 MET cc_start: 0.6802 (ptt) cc_final: 0.6416 (ptt)
REVERT: A  715 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7651 (tp)
REVERT: A  758 GLN cc_start: 0.7344 (mt0) cc_final: 0.6718 (tp40)
REVERT: A  784 GLU cc_start: 0.5642 (mm-30) cc_final: 0.4696 (mm-30)
REVERT: A 1023 MET cc_start: 0.1816 (mmt) cc_final: 0.1098 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1890
  time to fit residues: 29.6359
Evaluate side-chains
  106 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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  494 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  715 ILE
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 69 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0070
   chunk 92 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.6600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8017  Z= 0.159
  Angle     :  0.801  29.789  10882  Z= 0.333
  Chirality :  0.041   0.161   1276
  Planarity :  0.004   0.045   1387
  Dihedral  :  4.005  15.310   1078
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.30 %
    Favored  : 86.21 %
  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:  0.71 (0.26), residues: 1014
  helix:  1.63 (0.24), residues: 498
  sheet: -0.38 (0.51), residues: 98
  loop : -0.71 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.030   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.002   0.000   ARG A 491 

*********************** 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
  121 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.6150 (t60) cc_final: 0.5839 (t60)
REVERT: A  373 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4748 (mm-30)
REVERT: A  452 MET cc_start: 0.6668 (ptt) cc_final: 0.6150 (ptt)
REVERT: A  536 MET cc_start: 0.7530 (tpt) cc_final: 0.6513 (tpt)
REVERT: A  758 GLN cc_start: 0.7351 (mt0) cc_final: 0.6929 (tp40)
REVERT: A  784 GLU cc_start: 0.5614 (mm-30) cc_final: 0.4625 (mm-30)
REVERT: A 1023 MET cc_start: 0.1790 (mmt) cc_final: 0.1055 (mmt)
  outliers start: 13
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1812
  time to fit residues: 29.9542
Evaluate side-chains
  111 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  222 VAL
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   8017  Z= 0.362
  Angle     :  0.881  34.086  10882  Z= 0.389
  Chirality :  0.046   0.212   1276
  Planarity :  0.005   0.050   1387
  Dihedral  :  4.580  16.398   1078
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.33 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1014
  helix:  1.16 (0.23), residues: 492
  sheet: -0.97 (0.52), residues: 93
  loop : -0.86 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  36 
 HIS   0.005   0.001   HIS A 566 
 PHE   0.029   0.002   PHE A 759 
 TYR   0.016   0.002   TYR A 434 
 ARG   0.005   0.001   ARG A 164 

*********************** 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
  131 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A  296 PHE cc_start: 0.8018 (m-80) cc_final: 0.7766 (m-10)
REVERT: A  373 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.4749 (mm-30)
REVERT: A  452 MET cc_start: 0.7066 (ptt) cc_final: 0.6740 (ptt)
REVERT: A  536 MET cc_start: 0.7389 (tpt) cc_final: 0.6268 (tpt)
REVERT: A  715 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7597 (tp)
REVERT: A  784 GLU cc_start: 0.5774 (mm-30) cc_final: 0.4751 (mm-30)
REVERT: A  940 MET cc_start: 0.6980 (tpp) cc_final: 0.6670 (mmm)
REVERT: A 1023 MET cc_start: 0.1779 (mmt) cc_final: 0.1020 (mmt)
  outliers start: 29
  outliers final: 19
  residues processed: 120
  average time/residue: 0.1807
  time to fit residues: 31.1157
Evaluate side-chains
  119 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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  508 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  595 CYS
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  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 87 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   8017  Z= 0.294
  Angle     :  0.854  31.716  10882  Z= 0.371
  Chirality :  0.044   0.175   1276
  Planarity :  0.005   0.052   1387
  Dihedral  :  4.487  16.348   1078
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.98 %
    Favored  : 81.38 %
  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:  1.19 (0.23), residues: 490
  sheet: -1.03 (0.50), residues: 104
  loop : -0.84 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.028   0.002   PHE A 759 
 TYR   0.014   0.002   TYR A 122 
 ARG   0.004   0.000   ARG A 164 

*********************** 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
  129 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4976 (mm-30)
REVERT: A  452 MET cc_start: 0.6935 (ptt) cc_final: 0.6597 (ptt)
REVERT: A  492 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7617 (mtpt)
REVERT: A  599 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7387 (pt)
REVERT: A  715 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7580 (tp)
REVERT: A  784 GLU cc_start: 0.5712 (mm-30) cc_final: 0.4686 (mm-30)
REVERT: A  940 MET cc_start: 0.6892 (tpp) cc_final: 0.6612 (mmm)
REVERT: A 1023 MET cc_start: 0.1583 (mmt) cc_final: 0.1023 (mmt)
  outliers start: 23
  outliers final: 18
  residues processed: 121
  average time/residue: 0.1945
  time to fit residues: 33.2586
Evaluate side-chains
  122 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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  508 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  595 CYS
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  916 SER
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8017  Z= 0.230
  Angle     :  0.833  30.971  10882  Z= 0.355
  Chirality :  0.043   0.170   1276
  Planarity :  0.005   0.051   1387
  Dihedral  :  4.330  16.181   1078
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.67 %
    Favored  : 80.57 %
  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:  0.24 (0.26), residues: 1014
  helix:  1.19 (0.23), residues: 503
  sheet: -0.97 (0.50), residues: 102
  loop : -0.78 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 831 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 122 
 ARG   0.003   0.000   ARG A 491 

*********************** 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
  129 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7607 (mtpt)
REVERT: A  536 MET cc_start: 0.7448 (tpt) cc_final: 0.6328 (tpt)
REVERT: A  599 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7406 (pt)
REVERT: A  715 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7578 (tp)
REVERT: A  784 GLU cc_start: 0.5720 (mm-30) cc_final: 0.4677 (mm-30)
REVERT: A  940 MET cc_start: 0.6818 (tpp) cc_final: 0.6588 (mmm)
REVERT: A 1023 MET cc_start: 0.1606 (mmt) cc_final: 0.0666 (mtp)
  outliers start: 24
  outliers final: 19
  residues processed: 121
  average time/residue: 0.2018
  time to fit residues: 33.9995
Evaluate side-chains
  124 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
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  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  595 CYS
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  916 SER
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 29 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8017  Z= 0.201
  Angle     :  0.822  30.504  10882  Z= 0.348
  Chirality :  0.042   0.167   1276
  Planarity :  0.004   0.051   1387
  Dihedral  :  4.227  18.694   1078
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.78 %
    Favored  : 80.69 %
  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:  0.27 (0.26), residues: 1014
  helix:  1.30 (0.23), residues: 504
  sheet: -0.86 (0.51), residues: 99
  loop : -0.92 (0.29), 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   0.027   0.001   PHE A 759 
 TYR   0.014   0.001   TYR A 295 
 ARG   0.002   0.000   ARG A 491 

*********************** 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
  128 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  536 MET cc_start: 0.7436 (tpt) cc_final: 0.6623 (tpt)
REVERT: A  585 LYS cc_start: 0.8028 (mptt) cc_final: 0.7670 (mtpp)
REVERT: A  599 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7383 (pt)
REVERT: A  715 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7641 (tp)
REVERT: A  731 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7364 (mt-10)
REVERT: A  784 GLU cc_start: 0.5746 (mm-30) cc_final: 0.4678 (mm-30)
REVERT: A  940 MET cc_start: 0.6782 (tpp) cc_final: 0.6566 (mmm)
REVERT: A 1023 MET cc_start: 0.1600 (mmt) cc_final: 0.0657 (mtp)
  outliers start: 22
  outliers final: 19
  residues processed: 119
  average time/residue: 0.1984
  time to fit residues: 33.2993
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  : 0.822 
-------------------------------------------------------------------------------
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  473 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  508 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  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  916 SER
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 90 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0070
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0040
   chunk 85 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0870
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8017  Z= 0.150
  Angle     :  0.811  29.623  10882  Z= 0.338
  Chirality :  0.041   0.162   1276
  Planarity :  0.004   0.050   1387
  Dihedral  :  4.026  21.131   1078
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.70 %
    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:  0.57 (0.27), residues: 1014
  helix:  1.63 (0.24), residues: 498
  sheet: -0.52 (0.52), residues: 98
  loop : -0.92 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 295 
 ARG   0.002   0.000   ARG A 246 

*********************** 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
  125 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  452 MET cc_start: 0.6568 (ptt) cc_final: 0.6000 (ptt)
REVERT: A  536 MET cc_start: 0.7176 (tpt) cc_final: 0.6651 (tpt)
REVERT: A  585 LYS cc_start: 0.8104 (mptt) cc_final: 0.7700 (mtpp)
REVERT: A  599 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7354 (pt)
REVERT: A  715 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7684 (tp)
REVERT: A  758 GLN cc_start: 0.7421 (mt0) cc_final: 0.6815 (mm110)
REVERT: A  784 GLU cc_start: 0.5758 (mm-30) cc_final: 0.4673 (mm-30)
REVERT: A 1023 MET cc_start: 0.1652 (mmt) cc_final: 0.0648 (mtp)
  outliers start: 17
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1937
  time to fit residues: 32.4785
Evaluate side-chains
  121 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  473 SER
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  599 LEU
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  916 SER
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 45 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0030
   chunk 80 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   chunk 61 optimal weight:    0.0000
   chunk 49 optimal weight:   10.0000
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.3572

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8017  Z= 0.148
  Angle     :  0.809  29.670  10882  Z= 0.334
  Chirality :  0.041   0.160   1276
  Planarity :  0.004   0.050   1387
  Dihedral  :  3.834  15.422   1078
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.70 %
    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:  0.73 (0.27), residues: 1014
  helix:  1.72 (0.24), residues: 499
  sheet: -0.22 (0.53), residues: 98
  loop : -0.86 (0.30), residues: 417

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   0.029   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 295 
 ARG   0.002   0.000   ARG A 491 

********************** 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
  127 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.6977 (mtp) cc_final: 0.6696 (ttm)
REVERT: A  452 MET cc_start: 0.6298 (ptt) cc_final: 0.5711 (ptt)
REVERT: A  536 MET cc_start: 0.7046 (tpt) cc_final: 0.6662 (tpt)
REVERT: A  585 LYS cc_start: 0.8088 (mptt) cc_final: 0.7674 (mtpp)
REVERT: A  599 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7357 (pt)
REVERT: A  715 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7642 (tp)
REVERT: A  758 GLN cc_start: 0.7393 (mt0) cc_final: 0.6898 (tp40)
REVERT: A  784 GLU cc_start: 0.5801 (mm-30) cc_final: 0.4718 (mm-30)
REVERT: A  940 MET cc_start: 0.6645 (mmm) cc_final: 0.6413 (mmm)
REVERT: A 1023 MET cc_start: 0.1857 (mmt) cc_final: 0.0750 (mtp)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1939
  time to fit residues: 32.0504
Evaluate side-chains
  120 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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  473 SER
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  599 LEU
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  916 SER
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 73 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0040
   chunk 22 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0060
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.3408

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

Flipped N/Q/H residues before XYZ refinement:
A 767 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.183192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148329 restraints weight = 8727.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.79
r_work: 0.3589 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8017  Z= 0.144
  Angle     :  0.807  29.590  10882  Z= 0.333
  Chirality :  0.041   0.161   1276
  Planarity :  0.004   0.049   1387
  Dihedral  :  3.794  17.996   1078
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.82 %
    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:  0.86 (0.27), residues: 1014
  helix:  1.80 (0.24), residues: 499
  sheet: -0.01 (0.53), residues: 98
  loop : -0.80 (0.30), residues: 417

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   0.029   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 295 
 ARG   0.003   0.000   ARG A 164 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1831.51 seconds
wall clock time: 34 minutes 9.04 seconds (2049.04 seconds total)