Starting phenix.real_space_refine
on Wed Feb 12 11:43:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7v_32349/02_2025/7w7v_32349.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4984      2.51       5
     N    1305      2.21       5
     O    1471      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7823
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1012, 7818
          Classifications: {'peptide': 1012}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 966}
          Chain breaks: 2
          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: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.60, per 1000 atoms: 0.59
  Number of scatterers: 7823
  At special positions: 0
  Unit cell: (88.395, 98.355, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1471      8.00
     N    1305      7.00
     C    4984      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.21
  Conformation dependent library (CDL) restraints added in 893.7 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      54.6% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.623A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 48 through 56
    Processing helix  chain 'A' and resid 59 through 79
    Processing helix  chain 'A' and resid 84 through 87
      removed outlier: 3.854A  pdb=" N   ALA A  87 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 87'
    Processing helix  chain 'A' and resid 88 through 117
      removed outlier: 3.935A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 230 through 242
    Processing helix  chain 'A' and resid 247 through 276
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.009A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP A 281 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 277 through 281'
    Processing helix  chain 'A' and resid 291 through 307
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 403 through 406
      removed outlier: 3.656A  pdb=" N   GLN A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 406'
    Processing helix  chain 'A' and resid 407 through 421
      removed outlier: 3.942A  pdb=" N   ASN A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.059A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 478
      removed outlier: 3.534A  pdb=" N   SER A 473 " --> pdb=" O   ASN A 469 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 3.630A  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 554
      removed outlier: 3.710A  pdb=" N   LYS A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 586
      removed outlier: 4.090A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.609A  pdb=" N   SER A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 660
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.916A  pdb=" N   ASP A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 692
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 730
    Processing helix  chain 'A' and resid 740 through 781
    Processing helix  chain 'A' and resid 787 through 807
      removed outlier: 4.331A  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
    Processing helix  chain 'A' and resid 887 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.546A  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 948
      removed outlier: 3.575A  pdb=" N   VAL A 933 " --> pdb=" O   ASN A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 956
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.861A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1031
      removed outlier: 3.589A  pdb=" N   LEU A1021 " --> pdb=" O   PRO A1017 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
      removed outlier: 4.690A  pdb=" N   TRP A1028 " --> pdb=" O   PRO A1024 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A1031 " --> pdb=" O   ILE A1027 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 141
      removed outlier: 6.159A  pdb=" N   SER A 136 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   ARG A 131 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   ILE A 163 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.594A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.387A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.166A  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: 7.470A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 595 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.347A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.417A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET A 598 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER A 493 " --> pdb=" O   PHE A 487 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE A 487 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.123A  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: 7.470A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 595 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.347A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.417A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.738A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.134A  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 428

    428 hydrogen bonds defined for protein.
    1239 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: 2.67

  Time building geometry restraints manager: 2.53 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: 2554
        1.34 -     1.46: 1500
        1.46 -     1.58: 3824
        1.58 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 7968
  Sorted by residual:
  bond pdb=" F2  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" F3  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.546 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" F1  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.534 -0.058 2.00e-02 2.50e+03 8.32e+00
  bond pdb=" C   MET A1023 "
       pdb=" N   PRO A1024 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.014 9.80e-03 1.04e+04 2.18e+00
  bond pdb=" CB  GLU A 748 "
       pdb=" CG  GLU A 748 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.79e-01
  ... (remaining 7963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 10745
        2.73 -     5.46: 63
        5.46 -     8.20: 3
        8.20 -    10.93: 1
       10.93 -    13.66: 1
  Bond angle restraints: 10813
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.30   13.66 3.00e+00 1.11e-01 2.07e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.90   10.22 3.00e+00 1.11e-01 1.16e+01
  angle pdb=" N   GLY A 291 "
        pdb=" CA  GLY A 291 "
        pdb=" C   GLY A 291 "
      ideal   model   delta    sigma   weight residual
     115.66  110.50    5.16 1.56e+00 4.11e-01 1.09e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F2  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.91  112.04    7.87 3.00e+00 1.11e-01 6.88e+00
  angle pdb=" C   GLN A 758 "
        pdb=" N   PHE A 759 "
        pdb=" CA  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     121.14  116.57    4.57 1.75e+00 3.27e-01 6.81e+00
  ... (remaining 10808 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 4388
       17.45 -    34.91: 365
       34.91 -    52.36: 54
       52.36 -    69.81: 8
       69.81 -    87.27: 10
  Dihedral angle restraints: 4825
    sinusoidal: 1901
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CA  MET A 536 "
           pdb=" C   MET A 536 "
           pdb=" N   THR A 537 "
           pdb=" CA  THR A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  GLU A 439 "
           pdb=" CG  GLU A 439 "
           pdb=" CD  GLU A 439 "
           pdb=" OE1 GLU A 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.67  -86.67     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CA  GLU A 950 "
           pdb=" C   GLU A 950 "
           pdb=" N   PRO A 951 "
           pdb=" CA  PRO A 951 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.86  -15.14     0      5.00e+00 4.00e-02 9.16e+00
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 862
       0.036 -    0.072: 288
       0.072 -    0.109: 95
       0.109 -    0.145: 22
       0.145 -    0.181: 2
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CA  GLU A  90 "
            pdb=" N   GLU A  90 "
            pdb=" C   GLU A  90 "
            pdb=" CB  GLU A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  LEU A 974 "
            pdb=" N   LEU A 974 "
            pdb=" C   LEU A 974 "
            pdb=" CB  LEU A 974 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1266 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 534 "   -0.065 5.00e-02 4.00e+02   9.88e-02 1.56e+01
        pdb=" N   PRO A 535 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.053 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   1.71e-02 2.94e+00
        pdb=" C   LEU A 796 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A 796 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 797 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 759 "   -0.011 2.00e-02 2.50e+03   1.04e-02 1.90e+00
        pdb=" CG  PHE A 759 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 759 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 759 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 759 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 69
        2.59 -     3.17: 6785
        3.17 -     3.74: 12824
        3.74 -     4.32: 16942
        4.32 -     4.90: 27900
  Nonbonded interactions: 64520
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb=" F3  BEF A2001 "
     model   vdw
     2.010 2.990
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.076 2.170
  nonbonded pdb=" OE2 GLU A 373 "
            pdb=" OG1 THR A 376 "
     model   vdw
     2.130 3.040
  ... (remaining 64515 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:             0.260
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.150
  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:12.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   7968  Z= 0.171
  Angle     :  0.555  13.660  10813  Z= 0.299
  Chirality :  0.041   0.181   1269
  Planarity :  0.004   0.099   1378
  Dihedral  : 13.316  87.266   2929
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  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:  0.63 (0.27), residues: 1006
  helix:  1.34 (0.24), residues: 483
  sheet: -0.15 (0.51), residues: 97
  loop : -0.44 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 831 
 HIS   0.009   0.001   HIS A 278 
 PHE   0.024   0.001   PHE A 759 
 TYR   0.007   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 THR cc_start: 0.7687 (p) cc_final: 0.7479 (t)
REVERT: A  207 MET cc_start: 0.8443 (mmm) cc_final: 0.7943 (mmm)
REVERT: A  218 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7872 (ttmt)
REVERT: A  238 GLU cc_start: 0.6968 (tt0) cc_final: 0.6700 (tt0)
REVERT: A  259 GLN cc_start: 0.5474 (mt0) cc_final: 0.5268 (mt0)
REVERT: A  361 MET cc_start: 0.8148 (tpp) cc_final: 0.7754 (tpp)
REVERT: A  437 VAL cc_start: 0.6945 (m) cc_final: 0.6724 (t)
REVERT: A  452 MET cc_start: 0.8382 (ptt) cc_final: 0.8095 (ptt)
REVERT: A  466 GLU cc_start: 0.6981 (pm20) cc_final: 0.6280 (tp30)
REVERT: A  487 PHE cc_start: 0.6587 (t80) cc_final: 0.6231 (t80)
REVERT: A  508 MET cc_start: 0.5266 (tmm) cc_final: 0.3693 (tpp)
REVERT: A  536 MET cc_start: 0.3243 (mmp) cc_final: 0.2114 (tpp)
REVERT: A  670 LEU cc_start: 0.7702 (mm) cc_final: 0.7441 (mt)
REVERT: A  699 MET cc_start: 0.8088 (tpt) cc_final: 0.5974 (tpt)
REVERT: A  824 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6570 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 1.2745
  time to fit residues: 222.4588
Evaluate side-chains
  112 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN
A 380 ASN
A 428 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.201761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157854 restraints weight = 8226.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.66
r_work: 0.3611 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7968  Z= 0.197
  Angle     :  0.552  10.712  10813  Z= 0.288
  Chirality :  0.043   0.172   1269
  Planarity :  0.005   0.076   1378
  Dihedral  :  3.981  19.857   1070
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.88 %
    Favored  : 86.57 %
  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:  0.59 (0.27), residues: 1006
  helix:  1.23 (0.24), residues: 504
  sheet: -0.53 (0.51), residues: 93
  loop : -0.34 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 927 
 HIS   0.006   0.001   HIS A 405 
 PHE   0.030   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.005   0.001   ARG A 324 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7378 (pm20)
REVERT: A   33 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7038 (tptp)
REVERT: A  157 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7298 (m-30)
REVERT: A  218 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7912 (ttmt)
REVERT: A  238 GLU cc_start: 0.7551 (tt0) cc_final: 0.7276 (tt0)
REVERT: A  259 GLN cc_start: 0.5989 (mt0) cc_final: 0.5626 (mt0)
REVERT: A  361 MET cc_start: 0.8545 (tpp) cc_final: 0.8200 (tpp)
REVERT: A  399 ASP cc_start: 0.7624 (m-30) cc_final: 0.7382 (m-30)
REVERT: A  413 LEU cc_start: 0.8175 (tp) cc_final: 0.7669 (tt)
REVERT: A  437 VAL cc_start: 0.7140 (m) cc_final: 0.6867 (t)
REVERT: A  439 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7033 (tm-30)
REVERT: A  466 GLU cc_start: 0.7478 (pm20) cc_final: 0.6462 (tp30)
REVERT: A  487 PHE cc_start: 0.6549 (t80) cc_final: 0.6175 (t80)
REVERT: A  508 MET cc_start: 0.5105 (tmm) cc_final: 0.3404 (tpp)
REVERT: A  536 MET cc_start: 0.4251 (mmp) cc_final: 0.2980 (tpp)
REVERT: A  575 MET cc_start: 0.3904 (mmp) cc_final: 0.3226 (mmt)
REVERT: A  650 LYS cc_start: 0.8412 (mttt) cc_final: 0.8204 (mtpp)
REVERT: A  670 LEU cc_start: 0.7618 (mm) cc_final: 0.7143 (mt)
REVERT: A  699 MET cc_start: 0.8549 (tpt) cc_final: 0.6361 (tpt)
REVERT: A  731 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7265 (mt-10)
REVERT: A  756 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7510 (mmt)
REVERT: A  824 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6660 (mmpt)
REVERT: A 1023 MET cc_start: 0.3288 (tmt) cc_final: 0.2459 (ptt)
  outliers start: 22
  outliers final: 9
  residues processed: 137
  average time/residue: 1.1937
  time to fit residues: 173.6396
Evaluate side-chains
  117 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0170
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0470
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.2674

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
A 380 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.204303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.160024 restraints weight = 8357.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.67
r_work: 0.3633 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7968  Z= 0.136
  Angle     :  0.480   6.790  10813  Z= 0.253
  Chirality :  0.041   0.164   1269
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.773  16.852   1070
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.89 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 1006
  helix:  1.70 (0.24), residues: 485
  sheet: -0.73 (0.50), residues: 93
  loop : -0.30 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 497 
 ARG   0.004   0.000   ARG A 324 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6186 (tpp) cc_final: 0.5953 (tpp)
REVERT: A    2 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7346 (pm20)
REVERT: A   33 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7080 (tptp)
REVERT: A  205 LYS cc_start: 0.8699 (mttm) cc_final: 0.8420 (mtpp)
REVERT: A  218 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7997 (ttmm)
REVERT: A  228 VAL cc_start: 0.8130 (t) cc_final: 0.7874 (m)
REVERT: A  238 GLU cc_start: 0.7539 (tt0) cc_final: 0.7255 (tt0)
REVERT: A  259 GLN cc_start: 0.5927 (mt0) cc_final: 0.5603 (mt0)
REVERT: A  399 ASP cc_start: 0.7609 (m-30) cc_final: 0.7370 (m-30)
REVERT: A  413 LEU cc_start: 0.8026 (tp) cc_final: 0.7547 (tt)
REVERT: A  437 VAL cc_start: 0.7219 (m) cc_final: 0.6971 (t)
REVERT: A  439 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6915 (tm-30)
REVERT: A  466 GLU cc_start: 0.7508 (pm20) cc_final: 0.6460 (tp30)
REVERT: A  487 PHE cc_start: 0.6644 (t80) cc_final: 0.6232 (t80)
REVERT: A  508 MET cc_start: 0.5131 (tmm) cc_final: 0.3439 (tpp)
REVERT: A  518 GLU cc_start: 0.6465 (pm20) cc_final: 0.5947 (mm-30)
REVERT: A  536 MET cc_start: 0.4145 (mmp) cc_final: 0.3107 (tpt)
REVERT: A  559 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7436 (mtm110)
REVERT: A  575 MET cc_start: 0.3788 (mmp) cc_final: 0.2397 (ppp)
REVERT: A  699 MET cc_start: 0.8552 (tpt) cc_final: 0.6309 (tpt)
REVERT: A  731 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7210 (mt-10)
REVERT: A  824 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6664 (mmpt)
REVERT: A 1023 MET cc_start: 0.3530 (tmt) cc_final: 0.2533 (ptm)
  outliers start: 21
  outliers final: 7
  residues processed: 138
  average time/residue: 1.1909
  time to fit residues: 174.5316
Evaluate side-chains
  122 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A   3 ASN
A 250 GLN
A 380 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.195876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.152918 restraints weight = 8314.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.77
r_work: 0.3489 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7968  Z= 0.283
  Angle     :  0.567   6.218  10813  Z= 0.300
  Chirality :  0.045   0.180   1269
  Planarity :  0.005   0.056   1378
  Dihedral  :  4.178  23.423   1070
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.81 %
    Favored  : 81.60 %
  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:  0.52 (0.26), residues: 1006
  helix:  1.23 (0.24), residues: 493
  sheet: -0.58 (0.49), residues: 95
  loop : -0.41 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.031   0.002   PHE A 367 
 TYR   0.013   0.002   TYR A 762 
 ARG   0.003   0.001   ARG A 619 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6239 (tpp) cc_final: 0.5880 (tpp)
REVERT: A   10 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7356 (mm-30)
REVERT: A   33 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7168 (tptp)
REVERT: A  157 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7268 (m-30)
REVERT: A  179 ILE cc_start: 0.7875 (mp) cc_final: 0.7534 (mp)
REVERT: A  205 LYS cc_start: 0.8595 (mttm) cc_final: 0.8356 (mtpp)
REVERT: A  207 MET cc_start: 0.8587 (mmm) cc_final: 0.8161 (mmm)
REVERT: A  218 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7851 (ttmm)
REVERT: A  228 VAL cc_start: 0.8352 (t) cc_final: 0.8146 (m)
REVERT: A  238 GLU cc_start: 0.7502 (tt0) cc_final: 0.7224 (tt0)
REVERT: A  259 GLN cc_start: 0.6069 (mt0) cc_final: 0.5777 (mt0)
REVERT: A  384 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7889 (mm)
REVERT: A  399 ASP cc_start: 0.7618 (m-30) cc_final: 0.7392 (m-30)
REVERT: A  413 LEU cc_start: 0.8011 (tp) cc_final: 0.7542 (tt)
REVERT: A  435 GLU cc_start: 0.7605 (mp0) cc_final: 0.6767 (mp0)
REVERT: A  439 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7225 (tm-30)
REVERT: A  466 GLU cc_start: 0.7681 (pm20) cc_final: 0.6501 (tp30)
REVERT: A  487 PHE cc_start: 0.6548 (t80) cc_final: 0.6121 (t80)
REVERT: A  508 MET cc_start: 0.5010 (tmm) cc_final: 0.3181 (tpp)
REVERT: A  536 MET cc_start: 0.4496 (mmp) cc_final: 0.3486 (tpt)
REVERT: A  559 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7550 (mtm110)
REVERT: A  575 MET cc_start: 0.3500 (mmp) cc_final: 0.2883 (mmt)
REVERT: A  731 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7140 (mt-10)
REVERT: A  756 MET cc_start: 0.7951 (mtp) cc_final: 0.7260 (mtp)
REVERT: A  824 LYS cc_start: 0.7345 (mmtt) cc_final: 0.6741 (mmpt)
REVERT: A  970 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7536 (mp)
REVERT: A 1023 MET cc_start: 0.3857 (tmt) cc_final: 0.2831 (ptt)
  outliers start: 31
  outliers final: 16
  residues processed: 141
  average time/residue: 1.2088
  time to fit residues: 180.9355
Evaluate side-chains
  134 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 918 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.198697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.154465 restraints weight = 8217.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 1.67
r_work: 0.3583 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7968  Z= 0.171
  Angle     :  0.504   6.570  10813  Z= 0.265
  Chirality :  0.042   0.167   1269
  Planarity :  0.004   0.054   1378
  Dihedral  :  3.980  20.631   1070
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.20 %
    Favored  : 80.67 %
  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 (0.27), residues: 1006
  helix:  1.55 (0.24), residues: 488
  sheet: -1.07 (0.48), residues: 88
  loop : -0.37 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 762 
 ARG   0.003   0.000   ARG A 324 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6015 (tpp) cc_final: 0.5770 (tpp)
REVERT: A    2 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7302 (pm20)
REVERT: A   33 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7133 (tptp)
REVERT: A  179 ILE cc_start: 0.7694 (mp) cc_final: 0.7478 (mp)
REVERT: A  205 LYS cc_start: 0.8609 (mttm) cc_final: 0.8403 (mtpp)
REVERT: A  218 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7865 (ttmm)
REVERT: A  238 GLU cc_start: 0.7513 (tt0) cc_final: 0.7251 (tt0)
REVERT: A  259 GLN cc_start: 0.5944 (mt0) cc_final: 0.5652 (mt0)
REVERT: A  399 ASP cc_start: 0.7626 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  413 LEU cc_start: 0.8081 (tp) cc_final: 0.7627 (tt)
REVERT: A  435 GLU cc_start: 0.7477 (mp0) cc_final: 0.6817 (mp0)
REVERT: A  466 GLU cc_start: 0.7690 (pm20) cc_final: 0.6529 (tp30)
REVERT: A  487 PHE cc_start: 0.6555 (t80) cc_final: 0.6092 (t80)
REVERT: A  508 MET cc_start: 0.5001 (tmm) cc_final: 0.3117 (tpp)
REVERT: A  518 GLU cc_start: 0.6245 (pm20) cc_final: 0.5739 (mm-30)
REVERT: A  536 MET cc_start: 0.4092 (mmp) cc_final: 0.3233 (tpt)
REVERT: A  559 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7537 (mtm110)
REVERT: A  575 MET cc_start: 0.3512 (mmp) cc_final: 0.2267 (ppp)
REVERT: A  731 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7295 (mt-10)
REVERT: A  756 MET cc_start: 0.7884 (mtp) cc_final: 0.7623 (mtp)
REVERT: A  824 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6671 (mmpt)
REVERT: A 1023 MET cc_start: 0.3783 (tmt) cc_final: 0.2779 (ptt)
REVERT: A 1039 MET cc_start: 0.3233 (mmm) cc_final: 0.2886 (mmm)
  outliers start: 27
  outliers final: 13
  residues processed: 139
  average time/residue: 1.2315
  time to fit residues: 181.8504
Evaluate side-chains
  129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 56 optimal weight:   20.0000
   chunk 58 optimal weight:    6.9990
   chunk 8 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 86 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 643 GLN
A 918 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.199019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.156793 restraints weight = 8277.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.78
r_work: 0.3603 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7968  Z= 0.190
  Angle     :  0.512   6.458  10813  Z= 0.269
  Chirality :  0.042   0.169   1269
  Planarity :  0.004   0.049   1378
  Dihedral  :  3.972  21.003   1070
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.86 %
    Favored  : 80.56 %
  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: 1006
  helix:  1.50 (0.24), residues: 494
  sheet: -0.89 (0.49), residues: 89
  loop : -0.35 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 666 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5992 (tpp) cc_final: 0.5653 (tpp)
REVERT: A   33 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7223 (tptp)
REVERT: A   88 PHE cc_start: 0.6008 (m-80) cc_final: 0.5703 (m-80)
REVERT: A  218 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8090 (ttmm)
REVERT: A  238 GLU cc_start: 0.7538 (tt0) cc_final: 0.7257 (tt0)
REVERT: A  259 GLN cc_start: 0.6129 (mt0) cc_final: 0.5794 (mt0)
REVERT: A  413 LEU cc_start: 0.8163 (tp) cc_final: 0.7728 (tt)
REVERT: A  435 GLU cc_start: 0.7648 (mp0) cc_final: 0.6972 (mp0)
REVERT: A  466 GLU cc_start: 0.7720 (pm20) cc_final: 0.6576 (tp30)
REVERT: A  487 PHE cc_start: 0.6634 (t80) cc_final: 0.6170 (t80)
REVERT: A  508 MET cc_start: 0.5128 (tmm) cc_final: 0.3229 (tpp)
REVERT: A  518 GLU cc_start: 0.6268 (pm20) cc_final: 0.5775 (mm-30)
REVERT: A  536 MET cc_start: 0.3988 (mmp) cc_final: 0.3285 (tpt)
REVERT: A  559 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7655 (mtm110)
REVERT: A  575 MET cc_start: 0.3462 (mmp) cc_final: 0.2265 (ppp)
REVERT: A  731 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7320 (mt-10)
REVERT: A  824 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6794 (mmpt)
REVERT: A 1023 MET cc_start: 0.3610 (tmt) cc_final: 0.2593 (ptt)
REVERT: A 1039 MET cc_start: 0.3519 (mmm) cc_final: 0.3238 (mmm)
  outliers start: 31
  outliers final: 15
  residues processed: 138
  average time/residue: 1.2318
  time to fit residues: 180.2387
Evaluate side-chains
  124 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.199432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.155709 restraints weight = 8312.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.75
r_work: 0.3569 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7968  Z= 0.201
  Angle     :  0.527   6.363  10813  Z= 0.276
  Chirality :  0.042   0.170   1269
  Planarity :  0.004   0.047   1378
  Dihedral  :  4.011  21.657   1070
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.13 %
    Favored  : 79.63 %
  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:  0.63 (0.26), residues: 1006
  helix:  1.41 (0.24), residues: 496
  sheet: -0.93 (0.49), residues: 89
  loop : -0.38 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 761 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5768 (tpp) cc_final: 0.5539 (tpp)
REVERT: A   33 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7157 (tptp)
REVERT: A   88 PHE cc_start: 0.5948 (m-80) cc_final: 0.5598 (m-80)
REVERT: A  218 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8008 (ttmm)
REVERT: A  238 GLU cc_start: 0.7494 (tt0) cc_final: 0.7204 (tt0)
REVERT: A  259 GLN cc_start: 0.6107 (mt0) cc_final: 0.5756 (mt0)
REVERT: A  384 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7653 (mm)
REVERT: A  413 LEU cc_start: 0.8041 (tp) cc_final: 0.7611 (tt)
REVERT: A  435 GLU cc_start: 0.7604 (mp0) cc_final: 0.6886 (mp0)
REVERT: A  439 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7307 (tm-30)
REVERT: A  466 GLU cc_start: 0.7686 (pm20) cc_final: 0.6600 (tp30)
REVERT: A  487 PHE cc_start: 0.6634 (t80) cc_final: 0.6154 (t80)
REVERT: A  508 MET cc_start: 0.5035 (tmm) cc_final: 0.3028 (tpp)
REVERT: A  518 GLU cc_start: 0.6362 (pm20) cc_final: 0.5865 (mm-30)
REVERT: A  559 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7613 (mtm110)
REVERT: A  575 MET cc_start: 0.3389 (mmp) cc_final: 0.2907 (mmt)
REVERT: A  702 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.6829 (p0)
REVERT: A  731 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7317 (mt-10)
REVERT: A  824 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6738 (mmpt)
REVERT: A  916 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8203 (m)
REVERT: A 1023 MET cc_start: 0.3554 (tmt) cc_final: 0.2565 (ptt)
  outliers start: 28
  outliers final: 14
  residues processed: 131
  average time/residue: 1.1916
  time to fit residues: 165.9643
Evaluate side-chains
  129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0770
   chunk 2 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0770
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.199713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.157008 restraints weight = 8347.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.61
r_work: 0.3630 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7968  Z= 0.155
  Angle     :  0.518  11.038  10813  Z= 0.267
  Chirality :  0.042   0.167   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.883  19.481   1070
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.94 %
    Favored  : 79.40 %
  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:  0.79 (0.27), residues: 1006
  helix:  1.59 (0.24), residues: 495
  sheet: -0.89 (0.50), residues: 89
  loop : -0.39 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 324 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5754 (tpp) cc_final: 0.5408 (tpp)
REVERT: A   33 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7169 (tptp)
REVERT: A   88 PHE cc_start: 0.6007 (m-80) cc_final: 0.5719 (m-80)
REVERT: A  203 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8306 (m-30)
REVERT: A  218 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7999 (ttmm)
REVERT: A  238 GLU cc_start: 0.7457 (tt0) cc_final: 0.7206 (tt0)
REVERT: A  259 GLN cc_start: 0.6160 (mt0) cc_final: 0.5807 (mt0)
REVERT: A  413 LEU cc_start: 0.8245 (tp) cc_final: 0.7745 (tt)
REVERT: A  435 GLU cc_start: 0.7605 (mp0) cc_final: 0.6882 (mp0)
REVERT: A  466 GLU cc_start: 0.7690 (pm20) cc_final: 0.6570 (tp30)
REVERT: A  487 PHE cc_start: 0.6722 (t80) cc_final: 0.6273 (t80)
REVERT: A  508 MET cc_start: 0.4614 (tmm) cc_final: 0.3314 (tpp)
REVERT: A  518 GLU cc_start: 0.6219 (pm20) cc_final: 0.5767 (mm-30)
REVERT: A  559 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7610 (mtm110)
REVERT: A  575 MET cc_start: 0.3413 (mmp) cc_final: 0.2943 (mmt)
REVERT: A  731 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6954 (mt-10)
REVERT: A  824 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6787 (mmpt)
REVERT: A  916 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8075 (m)
REVERT: A 1023 MET cc_start: 0.3872 (tmt) cc_final: 0.2923 (ptt)
  outliers start: 23
  outliers final: 15
  residues processed: 131
  average time/residue: 1.1991
  time to fit residues: 167.0373
Evaluate side-chains
  131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 85 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.200944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.155419 restraints weight = 8334.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 1.77
r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7968  Z= 0.147
  Angle     :  0.505   7.444  10813  Z= 0.262
  Chirality :  0.041   0.165   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.822  18.988   1070
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.71 %
    Favored  : 79.40 %
  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:  0.88 (0.27), residues: 1006
  helix:  1.68 (0.24), residues: 494
  sheet: -0.85 (0.50), residues: 89
  loop : -0.35 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 405 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.008   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 324 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5737 (tpp) cc_final: 0.5455 (tpp)
REVERT: A   10 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7250 (mp0)
REVERT: A   33 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7142 (tptp)
REVERT: A   88 PHE cc_start: 0.5917 (m-80) cc_final: 0.5683 (m-80)
REVERT: A  113 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7110 (mm-30)
REVERT: A  138 GLN cc_start: 0.7146 (pm20) cc_final: 0.6891 (tt0)
REVERT: A  218 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7842 (ttmm)
REVERT: A  238 GLU cc_start: 0.7542 (tt0) cc_final: 0.7289 (tt0)
REVERT: A  259 GLN cc_start: 0.6110 (mt0) cc_final: 0.5780 (mt0)
REVERT: A  400 LYS cc_start: 0.7700 (pttm) cc_final: 0.7485 (pttt)
REVERT: A  413 LEU cc_start: 0.8098 (tp) cc_final: 0.7642 (tt)
REVERT: A  435 GLU cc_start: 0.7488 (mp0) cc_final: 0.6767 (mp0)
REVERT: A  439 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7070 (tm-30)
REVERT: A  466 GLU cc_start: 0.7649 (pm20) cc_final: 0.6512 (tp30)
REVERT: A  487 PHE cc_start: 0.6719 (t80) cc_final: 0.6274 (t80)
REVERT: A  518 GLU cc_start: 0.6147 (pm20) cc_final: 0.5692 (mm-30)
REVERT: A  559 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7577 (mtm110)
REVERT: A  575 MET cc_start: 0.3459 (mmp) cc_final: 0.2991 (mmt)
REVERT: A  598 MET cc_start: 0.8499 (ptp) cc_final: 0.7588 (ptp)
REVERT: A  731 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7060 (mt-10)
REVERT: A  756 MET cc_start: 0.7745 (mtp) cc_final: 0.7502 (mtm)
REVERT: A  824 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6731 (mmpt)
REVERT: A  916 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7998 (m)
REVERT: A 1023 MET cc_start: 0.3813 (tmt) cc_final: 0.2900 (ptt)
  outliers start: 25
  outliers final: 15
  residues processed: 133
  average time/residue: 1.2086
  time to fit residues: 170.5576
Evaluate side-chains
  129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.198867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.153206 restraints weight = 8354.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.77
r_work: 0.3512 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7968  Z= 0.174
  Angle     :  0.520   7.833  10813  Z= 0.270
  Chirality :  0.042   0.170   1269
  Planarity :  0.004   0.044   1378
  Dihedral  :  3.859  20.344   1070
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.40 %
    Favored  : 78.82 %
  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: 1006
  helix:  1.58 (0.24), residues: 497
  sheet: -0.77 (0.50), residues: 90
  loop : -0.36 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 405 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 990 
 ARG   0.008   0.000   ARG A 334 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5683 (tpp) cc_final: 0.5434 (tpp)
REVERT: A   33 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7165 (tptp)
REVERT: A   88 PHE cc_start: 0.5527 (m-80) cc_final: 0.5242 (m-80)
REVERT: A  113 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7063 (mm-30)
REVERT: A  218 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7833 (ttmm)
REVERT: A  238 GLU cc_start: 0.7522 (tt0) cc_final: 0.7268 (tt0)
REVERT: A  259 GLN cc_start: 0.6087 (mt0) cc_final: 0.5773 (mt0)
REVERT: A  413 LEU cc_start: 0.8081 (tp) cc_final: 0.7606 (tt)
REVERT: A  435 GLU cc_start: 0.7534 (mp0) cc_final: 0.6800 (mp0)
REVERT: A  439 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7104 (tm-30)
REVERT: A  466 GLU cc_start: 0.7654 (pm20) cc_final: 0.6498 (tp30)
REVERT: A  487 PHE cc_start: 0.6663 (t80) cc_final: 0.6246 (t80)
REVERT: A  518 GLU cc_start: 0.6488 (pm20) cc_final: 0.5981 (mm-30)
REVERT: A  559 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7623 (mtm110)
REVERT: A  575 MET cc_start: 0.3515 (mmp) cc_final: 0.3051 (mmt)
REVERT: A  598 MET cc_start: 0.8511 (ptp) cc_final: 0.7580 (ptp)
REVERT: A  731 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6892 (mt-10)
REVERT: A  756 MET cc_start: 0.7788 (mtp) cc_final: 0.7564 (mtm)
REVERT: A  824 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6717 (mmpt)
REVERT: A  916 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8011 (m)
REVERT: A 1023 MET cc_start: 0.3690 (tmt) cc_final: 0.2792 (ptt)
  outliers start: 24
  outliers final: 17
  residues processed: 129
  average time/residue: 1.2489
  time to fit residues: 170.8856
Evaluate side-chains
  129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 64 optimal weight:    0.1980
   chunk 46 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.199647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.153965 restraints weight = 8283.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.77
r_work: 0.3520 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7968  Z= 0.163
  Angle     :  0.516   7.878  10813  Z= 0.267
  Chirality :  0.042   0.168   1269
  Planarity :  0.004   0.044   1378
  Dihedral  :  3.839  19.855   1070
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.40 %
    Favored  : 78.94 %
  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 (0.26), residues: 1006
  helix:  1.61 (0.24), residues: 498
  sheet: -0.72 (0.50), residues: 90
  loop : -0.34 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 405 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 761 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6393.50 seconds
wall clock time: 113 minutes 28.86 seconds (6808.86 seconds total)