Starting phenix.real_space_refine
on Sun May 11 19:20:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd9_17607/05_2025/8pd9_17607.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      41      5.16       5
     C    5289      2.51       5
     N    1346      2.21       5
     O    1430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8107
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1024, 8085
          Classifications: {'peptide': 1024}
          Link IDs: {'PTRANS': 30, 'TRANS': 993}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 5.29, per 1000 atoms: 0.65
  Number of scatterers: 8107
  At special positions: 0
  Unit cell: (81.76, 115.486, 125.706, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P       1     15.00
     O    1430      8.00
     N    1346      7.00
     C    5289      6.00
    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=0, symmetry=0
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 882.5 milliseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      77.0% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 4.245A  pdb=" N   LYS A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 4.096A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 4.012A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   HIS A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.656A  pdb=" N   LEU A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 153
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 210 through 220
      removed outlier: 3.528A  pdb=" N   ALA A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 3.603A  pdb=" N   LYS A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 317
      removed outlier: 3.607A  pdb=" N   THR A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
      removed outlier: 3.523A  pdb=" N   ALA A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 376
    Processing helix  chain 'A' and resid 377 through 380
    Processing helix  chain 'A' and resid 381 through 411
      removed outlier: 3.886A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 428
      removed outlier: 3.598A  pdb=" N   VAL A 423 " --> pdb=" O   TRP A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.676A  pdb=" N   LEU A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 4.049A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 5.127A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 513
      removed outlier: 3.516A  pdb=" N   LYS A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 531
    Processing helix  chain 'A' and resid 571 through 600
      removed outlier: 3.688A  pdb=" N   ASP A 577 " --> pdb=" O   ARG A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 620
      removed outlier: 3.902A  pdb=" N   ASP A 620 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 4.096A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   SER A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TRP A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 653
      removed outlier: 3.613A  pdb=" N   ASP A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 651 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 706
      removed outlier: 4.117A  pdb=" N   ILE A 684 " --> pdb=" O   PHE A 680 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 3.797A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   LYS A 704 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 755
      removed outlier: 4.005A  pdb=" N   ILE A 734 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.670A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 783
    Processing helix  chain 'A' and resid 798 through 803
    Processing helix  chain 'A' and resid 803 through 812
      removed outlier: 4.035A  pdb=" N   MET A 810 " --> pdb=" O   ARG A 806 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 811 " --> pdb=" O   GLY A 807 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 858
      removed outlier: 3.992A  pdb=" N   LEU A 817 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ARG A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.515A  pdb=" N   LEU A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 920
    Processing helix  chain 'A' and resid 925 through 942
      removed outlier: 3.614A  pdb=" N   LYS A 929 " --> pdb=" O   MET A 925 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   MET A 942 " --> pdb=" O   MET A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 960
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 1043 through 1049
      removed outlier: 3.992A  pdb=" N   VAL A1047 " --> pdb=" O   GLY A1043 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A1048 " --> pdb=" O   GLU A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1108
      removed outlier: 3.657A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1123
      removed outlier: 3.709A  pdb=" N   ARG A1123 " --> pdb=" O   LEU A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1179 through 1183
      removed outlier: 4.066A  pdb=" N   GLU A1182 " --> pdb=" O   THR A1179 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A1183 " --> pdb=" O   ALA A1180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1179 through 1183'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 981
      removed outlier: 6.277A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.743A  pdb=" N   VAL A1057 " --> pdb=" O   ILE A 988 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 6.781A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136

    577 hydrogen bonds defined for protein.
    1701 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: 2.58

  Time building geometry restraints manager: 2.40 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: 2536
        1.34 -     1.46: 1089
        1.46 -     1.58: 4564
        1.58 -     1.70: 2
        1.70 -     1.81: 76
  Bond restraints: 8267
  Sorted by residual:
  bond pdb=" C4  CMP A1401 "
       pdb=" C5  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.349  0.141 2.00e-02 2.50e+03 4.97e+01
  bond pdb=" C5  CMP A1401 "
       pdb=" C6  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.389  0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" C8  CMP A1401 "
       pdb=" N9  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.337  1.400 -0.063 2.00e-02 2.50e+03 9.83e+00
  bond pdb=" C1' CMP A1401 "
       pdb=" O4' CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.412  1.456 -0.044 1.50e-02 4.44e+03 8.50e+00
  bond pdb=" O2P CMP A1401 "
       pdb=" P   CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.510  1.565 -0.055 2.00e-02 2.50e+03 7.47e+00
  ... (remaining 8262 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10736
        1.62 -     3.24: 379
        3.24 -     4.87: 84
        4.87 -     6.49: 15
        6.49 -     8.11: 4
  Bond angle restraints: 11218
  Sorted by residual:
  angle pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
        pdb=" C   TYR A 743 "
      ideal   model   delta    sigma   weight residual
     110.97  105.77    5.20 1.09e+00 8.42e-01 2.27e+01
  angle pdb=" OD1 ASN A1040 "
        pdb=" CG  ASN A1040 "
        pdb=" ND2 ASN A1040 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle pdb=" N   GLY A1010 "
        pdb=" CA  GLY A1010 "
        pdb=" C   GLY A1010 "
      ideal   model   delta    sigma   weight residual
     110.38  116.39   -6.01 1.48e+00 4.57e-01 1.65e+01
  angle pdb=" N   ALA A 964 "
        pdb=" CA  ALA A 964 "
        pdb=" C   ALA A 964 "
      ideal   model   delta    sigma   weight residual
     111.71  116.14   -4.43 1.15e+00 7.56e-01 1.49e+01
  angle pdb=" C   ILE A 742 "
        pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
      ideal   model   delta    sigma   weight residual
     120.65  115.99    4.66 1.32e+00 5.74e-01 1.24e+01
  ... (remaining 11213 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.32: 4746
       25.32 -    50.64: 168
       50.64 -    75.96: 13
       75.96 -   101.28: 2
      101.28 -   126.61: 3
  Dihedral angle restraints: 4932
    sinusoidal: 1953
      harmonic: 2979
  Sorted by residual:
  dihedral pdb=" C3' CMP A1401 "
           pdb=" O3' CMP A1401 "
           pdb=" P   CMP A1401 "
           pdb=" O1P CMP A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  173.39  126.61     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" C5' CMP A1401 "
           pdb=" O5' CMP A1401 "
           pdb=" P   CMP A1401 "
           pdb=" O1P CMP A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00 -173.83 -126.17     1      2.00e+01 2.50e-03 3.82e+01
  dihedral pdb=" CA  LEU A 963 "
           pdb=" C   LEU A 963 "
           pdb=" N   ALA A 964 "
           pdb=" CA  ALA A 964 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1062
       0.048 -    0.097: 225
       0.097 -    0.145: 50
       0.145 -    0.194: 9
       0.194 -    0.242: 2
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CA  THR A1049 "
            pdb=" N   THR A1049 "
            pdb=" C   THR A1049 "
            pdb=" CB  THR A1049 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ARG A1097 "
            pdb=" N   ARG A1097 "
            pdb=" C   ARG A1097 "
            pdb=" CB  ARG A1097 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LYS A1050 "
            pdb=" N   LYS A1050 "
            pdb=" C   LYS A1050 "
            pdb=" CB  LYS A1050 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.82e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1009 "    0.069 2.00e-02 2.50e+03   3.48e-02 2.42e+01
        pdb=" CG  TYR A1009 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1009 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1009 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1009 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1009 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1009 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A1009 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' CMP A1401 "    0.049 2.00e-02 2.50e+03   2.51e-02 1.73e+01
        pdb=" C2  CMP A1401 "   -0.027 2.00e-02 2.50e+03
        pdb=" C4  CMP A1401 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5  CMP A1401 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6  CMP A1401 "    0.003 2.00e-02 2.50e+03
        pdb=" C8  CMP A1401 "   -0.038 2.00e-02 2.50e+03
        pdb=" N1  CMP A1401 "    0.001 2.00e-02 2.50e+03
        pdb=" N3  CMP A1401 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6  CMP A1401 "    0.044 2.00e-02 2.50e+03
        pdb=" N7  CMP A1401 "   -0.015 2.00e-02 2.50e+03
        pdb=" N9  CMP A1401 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 962 "    0.033 2.00e-02 2.50e+03   2.39e-02 1.43e+01
        pdb=" CG  TRP A 962 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 962 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 962 "   -0.042 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 962 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 962 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 962 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 962 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 962 "    0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 962 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 715
        2.74 -     3.28: 8674
        3.28 -     3.82: 13246
        3.82 -     4.36: 14645
        4.36 -     4.90: 25808
  Nonbonded interactions: 63088
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  81 "
            pdb=" OG  SER A  84 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OH  TYR A 743 "
            pdb=" OD2 ASP A 767 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OE2 GLU A 746 "
            pdb=" CD  LYS A 750 "
     model   vdw
     2.327 3.440
  nonbonded pdb=" O   ASP A1078 "
            pdb=" OD1 ASP A1078 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   ASP A 650 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.372 3.040
  ... (remaining 63083 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 group one per residue
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:             4.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.290
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
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      :  0.005   0.141   8267  Z= 0.258
  Angle     :  0.734   8.111  11218  Z= 0.449
  Chirality :  0.043   0.242   1348
  Planarity :  0.005   0.079   1378
  Dihedral  : 13.444 126.606   3000
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  7.84 %
    Favored  : 92.05 %
  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:  2.01 (0.27), residues: 1012
  helix:  1.91 (0.19), residues: 712
  sheet: -0.90 (0.63), residues: 61
  loop :  0.37 (0.44), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 962 
 HIS   0.002   0.000   HIS A 928 
 PHE   0.018   0.002   PHE A1032 
 TYR   0.069   0.002   TYR A1009 
 ARG   0.006   0.000   ARG A1053 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13208 (  577)
  hydrogen bonds       : angle       5.55728 ( 1701)
  covalent geometry    : bond        0.00469 ( 8267)
  covalent geometry    : angle       0.73356 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.6780 (mm) cc_final: 0.6556 (mt)
REVERT: A  134 ASP cc_start: 0.7521 (m-30) cc_final: 0.6518 (p0)
REVERT: A  149 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6673 (tm-30)
REVERT: A  155 ASP cc_start: 0.6515 (t0) cc_final: 0.6081 (t0)
REVERT: A  157 HIS cc_start: 0.6930 (m90) cc_final: 0.6287 (m-70)
REVERT: A  160 MET cc_start: 0.7443 (mmt) cc_final: 0.6873 (mmt)
REVERT: A  163 PHE cc_start: 0.7509 (t80) cc_final: 0.7250 (t80)
REVERT: A  209 ASP cc_start: 0.7282 (t0) cc_final: 0.6839 (t0)
REVERT: A  220 LEU cc_start: 0.7081 (mm) cc_final: 0.6809 (mt)
REVERT: A  288 PHE cc_start: 0.7585 (t80) cc_final: 0.7038 (t80)
REVERT: A  289 PHE cc_start: 0.7463 (m-80) cc_final: 0.7234 (m-10)
REVERT: A  483 MET cc_start: 0.7348 (mtp) cc_final: 0.7109 (mtm)
REVERT: A  485 ASP cc_start: 0.7754 (m-30) cc_final: 0.7395 (p0)
REVERT: A  486 ILE cc_start: 0.7593 (mt) cc_final: 0.7276 (tp)
REVERT: A  500 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7196 (tpp80)
REVERT: A  517 PHE cc_start: 0.6182 (m-80) cc_final: 0.5848 (m-80)
REVERT: A  579 MET cc_start: 0.7017 (tmm) cc_final: 0.6714 (tmm)
REVERT: A  580 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7568 (mm-30)
REVERT: A  583 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6800 (ttp80)
REVERT: A  591 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7521 (mttt)
REVERT: A  606 GLU cc_start: 0.7031 (tp30) cc_final: 0.6538 (tp30)
REVERT: A  609 ARG cc_start: 0.7824 (tpp80) cc_final: 0.6690 (tpp80)
REVERT: A  613 GLN cc_start: 0.8122 (tt0) cc_final: 0.7559 (mt0)
REVERT: A  616 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6686 (mt-10)
REVERT: A  621 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6029 (mt-10)
REVERT: A  632 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7523 (mttt)
REVERT: A  810 MET cc_start: 0.6128 (mpp) cc_final: 0.5425 (mpp)
REVERT: A  828 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6955 (tppt)
REVERT: A  859 ASP cc_start: 0.7459 (m-30) cc_final: 0.7176 (t0)
REVERT: A  863 ILE cc_start: 0.6277 (mm) cc_final: 0.6042 (mm)
REVERT: A  867 LEU cc_start: 0.6398 (mp) cc_final: 0.6078 (mt)
REVERT: A  870 ILE cc_start: 0.6404 (mt) cc_final: 0.6084 (mm)
REVERT: A  876 LEU cc_start: 0.6779 (mp) cc_final: 0.6568 (mm)
REVERT: A  880 LYS cc_start: 0.7402 (tttt) cc_final: 0.7056 (ttpt)
REVERT: A  887 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6969 (mtp85)
REVERT: A  915 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7009 (mt-10)
REVERT: A  926 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6769 (tt0)
REVERT: A  938 MET cc_start: 0.7635 (tpp) cc_final: 0.7285 (ttt)
REVERT: A  940 ARG cc_start: 0.7090 (mtt-85) cc_final: 0.6863 (mtm-85)
REVERT: A  954 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7116 (mt-10)
REVERT: A  966 ASP cc_start: 0.7310 (t0) cc_final: 0.6857 (p0)
REVERT: A  967 MET cc_start: 0.7773 (mtm) cc_final: 0.7338 (mtm)
REVERT: A  969 LEU cc_start: 0.8429 (tp) cc_final: 0.7889 (tp)
REVERT: A  993 ASP cc_start: 0.6845 (m-30) cc_final: 0.6495 (t70)
REVERT: A  994 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7590 (mt-10)
REVERT: A  998 LEU cc_start: 0.6575 (mp) cc_final: 0.6345 (mp)
REVERT: A  999 PHE cc_start: 0.7263 (m-80) cc_final: 0.7019 (m-80)
REVERT: A 1033 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6429 (mt-10)
REVERT: A 1035 TYR cc_start: 0.7867 (m-80) cc_final: 0.7454 (m-80)
REVERT: A 1037 THR cc_start: 0.7432 (t) cc_final: 0.7070 (t)
REVERT: A 1040 ASN cc_start: 0.7447 (m110) cc_final: 0.7100 (m110)
REVERT: A 1042 ILE cc_start: 0.6463 (mt) cc_final: 0.6186 (tt)
REVERT: A 1045 MET cc_start: 0.6961 (mtp) cc_final: 0.6721 (mtp)
REVERT: A 1050 LYS cc_start: 0.7830 (mttt) cc_final: 0.7613 (mmmt)
REVERT: A 1051 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7737 (ttmm)
REVERT: A 1059 CYS cc_start: 0.6908 (m) cc_final: 0.6495 (m)
REVERT: A 1061 THR cc_start: 0.7606 (p) cc_final: 0.7166 (p)
REVERT: A 1071 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: A 1073 MET cc_start: 0.7923 (mmm) cc_final: 0.7547 (mmp)
REVERT: A 1085 SER cc_start: 0.8246 (t) cc_final: 0.7872 (m)
REVERT: A 1098 ILE cc_start: 0.7594 (tp) cc_final: 0.7322 (tt)
REVERT: A 1122 GLU cc_start: 0.7721 (tp30) cc_final: 0.7521 (mm-30)
REVERT: A 1168 SER cc_start: 0.7593 (t) cc_final: 0.7248 (p)
REVERT: A 1183 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7077 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2330
  time to fit residues: 92.6340
Evaluate side-chains
  264 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0970
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0040
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 889 HIS
A 900 GLN
A1054 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.130867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112461 restraints weight = 12837.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.115766 restraints weight = 5937.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117889 restraints weight = 3456.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8267  Z= 0.143
  Angle     :  0.571   8.988  11218  Z= 0.297
  Chirality :  0.040   0.155   1348
  Planarity :  0.004   0.037   1378
  Dihedral  :  8.262 143.579   1104
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.66 %
    Favored  : 83.30 %
  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:  2.37 (0.27), residues: 1012
  helix:  2.12 (0.19), residues: 711
  sheet: -0.73 (0.64), residues: 61
  loop :  0.69 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A 600 
 PHE   0.025   0.002   PHE A 739 
 TYR   0.018   0.001   TYR A 984 
 ARG   0.007   0.001   ARG A 856 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04845 (  577)
  hydrogen bonds       : angle       4.40867 ( 1701)
  covalent geometry    : bond        0.00304 ( 8267)
  covalent geometry    : angle       0.57076 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 264
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8344 (mm) cc_final: 0.7858 (mt)
REVERT: A  134 ASP cc_start: 0.7609 (m-30) cc_final: 0.7182 (p0)
REVERT: A  149 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6977 (tm-30)
REVERT: A  155 ASP cc_start: 0.6393 (t0) cc_final: 0.6029 (t0)
REVERT: A  160 MET cc_start: 0.6900 (mmt) cc_final: 0.6538 (mmt)
REVERT: A  174 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (tp)
REVERT: A  209 ASP cc_start: 0.7356 (t0) cc_final: 0.7055 (t0)
REVERT: A  475 GLN cc_start: 0.7904 (tp40) cc_final: 0.7673 (tp-100)
REVERT: A  500 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7320 (tpp80)
REVERT: A  579 MET cc_start: 0.6292 (tmm) cc_final: 0.5529 (tmm)
REVERT: A  583 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7500 (ttp80)
REVERT: A  588 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7475 (ttpp)
REVERT: A  628 VAL cc_start: 0.8292 (p) cc_final: 0.6987 (m)
REVERT: A  648 LEU cc_start: 0.8350 (mp) cc_final: 0.8143 (mp)
REVERT: A  810 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5749 (mpp)
REVERT: A  812 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7844 (ttp80)
REVERT: A  863 ILE cc_start: 0.7317 (mm) cc_final: 0.6920 (mm)
REVERT: A  872 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6203 (mm-30)
REVERT: A  880 LYS cc_start: 0.8377 (tttt) cc_final: 0.8022 (ttpp)
REVERT: A  887 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7353 (mtp85)
REVERT: A  910 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8024 (ttm170)
REVERT: A  938 MET cc_start: 0.7792 (tpp) cc_final: 0.7278 (ttm)
REVERT: A  946 SER cc_start: 0.8053 (p) cc_final: 0.7724 (t)
REVERT: A  968 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7656 (mtmt)
REVERT: A 1058 THR cc_start: 0.8191 (m) cc_final: 0.7818 (p)
REVERT: A 1059 CYS cc_start: 0.7229 (m) cc_final: 0.6919 (m)
REVERT: A 1085 SER cc_start: 0.8436 (t) cc_final: 0.8077 (m)
REVERT: A 1093 VAL cc_start: 0.8879 (p) cc_final: 0.8668 (p)
REVERT: A 1096 ILE cc_start: 0.8881 (mm) cc_final: 0.8536 (mt)
REVERT: A 1098 ILE cc_start: 0.8670 (tp) cc_final: 0.8467 (tt)
REVERT: A 1144 ASP cc_start: 0.7519 (m-30) cc_final: 0.7294 (m-30)
REVERT: A 1168 SER cc_start: 0.8762 (t) cc_final: 0.8500 (p)
REVERT: A 1189 VAL cc_start: 0.7762 (OUTLIER) cc_final: 0.7427 (m)
  outliers start: 18
  outliers final: 8
  residues processed: 271
  average time/residue: 0.2470
  time to fit residues: 85.9670
Evaluate side-chains
  266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 255
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0050
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 900 GLN
A1120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109891 restraints weight = 13337.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.113152 restraints weight = 6071.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115193 restraints weight = 3515.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8267  Z= 0.161
  Angle     :  0.563   8.745  11218  Z= 0.296
  Chirality :  0.040   0.169   1348
  Planarity :  0.004   0.040   1378
  Dihedral  :  8.235 143.564   1104
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.59 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.27), residues: 1012
  helix:  1.96 (0.19), residues: 713
  sheet: -0.57 (0.68), residues: 61
  loop :  0.35 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 962 
 HIS   0.002   0.001   HIS A 869 
 PHE   0.022   0.001   PHE A 739 
 TYR   0.010   0.001   TYR A1066 
 ARG   0.007   0.001   ARG A1185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04754 (  577)
  hydrogen bonds       : angle       4.27155 ( 1701)
  covalent geometry    : bond        0.00351 ( 8267)
  covalent geometry    : angle       0.56271 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 261
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8360 (mm) cc_final: 0.7895 (mt)
REVERT: A  134 ASP cc_start: 0.7595 (m-30) cc_final: 0.7196 (p0)
REVERT: A  149 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6895 (tm-30)
REVERT: A  155 ASP cc_start: 0.6355 (t0) cc_final: 0.5911 (t0)
REVERT: A  160 MET cc_start: 0.6894 (mmt) cc_final: 0.6632 (mmt)
REVERT: A  199 MET cc_start: 0.7830 (mmm) cc_final: 0.7531 (mmm)
REVERT: A  205 MET cc_start: 0.7914 (tpp) cc_final: 0.7085 (mmm)
REVERT: A  209 ASP cc_start: 0.7379 (t0) cc_final: 0.6918 (t70)
REVERT: A  216 LEU cc_start: 0.8777 (mt) cc_final: 0.8428 (mp)
REVERT: A  233 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6503 (tt0)
REVERT: A  367 MET cc_start: 0.7244 (mtp) cc_final: 0.6881 (mtm)
REVERT: A  383 MET cc_start: 0.8042 (mmm) cc_final: 0.7515 (tpp)
REVERT: A  475 GLN cc_start: 0.7841 (tp40) cc_final: 0.7403 (tp-100)
REVERT: A  490 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8002 (mtmt)
REVERT: A  500 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7297 (tpp80)
REVERT: A  588 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7552 (ttpp)
REVERT: A  644 LEU cc_start: 0.8060 (mt) cc_final: 0.7678 (mm)
REVERT: A  705 MET cc_start: 0.5453 (mmt) cc_final: 0.4409 (mmm)
REVERT: A  810 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5835 (mpp)
REVERT: A  823 LEU cc_start: 0.8311 (mt) cc_final: 0.8052 (mt)
REVERT: A  835 LEU cc_start: 0.8714 (tp) cc_final: 0.8432 (tt)
REVERT: A  856 ARG cc_start: 0.6922 (ptp90) cc_final: 0.6633 (ptt-90)
REVERT: A  863 ILE cc_start: 0.7454 (mm) cc_final: 0.7131 (mm)
REVERT: A  872 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6306 (mm-30)
REVERT: A  878 VAL cc_start: 0.8481 (p) cc_final: 0.8225 (t)
REVERT: A  880 LYS cc_start: 0.8396 (tttt) cc_final: 0.7978 (ttpt)
REVERT: A  887 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7306 (mtp85)
REVERT: A  938 MET cc_start: 0.7749 (tpp) cc_final: 0.7330 (ttm)
REVERT: A  946 SER cc_start: 0.8046 (p) cc_final: 0.7716 (t)
REVERT: A  970 ILE cc_start: 0.8836 (tp) cc_final: 0.8617 (tp)
REVERT: A  986 GLU cc_start: 0.6998 (tt0) cc_final: 0.6415 (tt0)
REVERT: A 1035 TYR cc_start: 0.7988 (m-80) cc_final: 0.7762 (m-10)
REVERT: A 1058 THR cc_start: 0.8198 (m) cc_final: 0.7867 (p)
REVERT: A 1059 CYS cc_start: 0.7247 (m) cc_final: 0.7036 (m)
REVERT: A 1073 MET cc_start: 0.7914 (mmm) cc_final: 0.7630 (mmp)
REVERT: A 1085 SER cc_start: 0.8408 (t) cc_final: 0.8121 (p)
REVERT: A 1098 ILE cc_start: 0.8719 (tp) cc_final: 0.8506 (tp)
REVERT: A 1118 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8210 (mttp)
REVERT: A 1145 VAL cc_start: 0.8566 (t) cc_final: 0.8216 (p)
REVERT: A 1189 VAL cc_start: 0.7768 (m) cc_final: 0.7557 (m)
  outliers start: 29
  outliers final: 20
  residues processed: 268
  average time/residue: 0.2288
  time to fit residues: 79.6192
Evaluate side-chains
  268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 247
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1127 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 101 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0870
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 157 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.110033 restraints weight = 13153.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.113185 restraints weight = 6035.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.115276 restraints weight = 3512.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8267  Z= 0.145
  Angle     :  0.549   8.827  11218  Z= 0.285
  Chirality :  0.040   0.178   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.210 143.570   1104
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.84 %
    Favored  : 78.64 %
  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:  2.06 (0.27), residues: 1012
  helix:  1.96 (0.19), residues: 714
  sheet: -0.43 (0.73), residues: 54
  loop :  0.11 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 962 
 HIS   0.005   0.001   HIS A 132 
 PHE   0.017   0.001   PHE A 972 
 TYR   0.016   0.001   TYR A 984 
 ARG   0.004   0.000   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04493 (  577)
  hydrogen bonds       : angle       4.17439 ( 1701)
  covalent geometry    : bond        0.00316 ( 8267)
  covalent geometry    : angle       0.54850 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 250
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  108 ILE cc_start: 0.8374 (mm) cc_final: 0.7907 (mt)
REVERT: A  134 ASP cc_start: 0.7557 (m-30) cc_final: 0.7160 (p0)
REVERT: A  149 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6836 (tm-30)
REVERT: A  155 ASP cc_start: 0.6337 (t0) cc_final: 0.5827 (t0)
REVERT: A  157 HIS cc_start: 0.6504 (m-70) cc_final: 0.5763 (m90)
REVERT: A  160 MET cc_start: 0.6898 (mmt) cc_final: 0.6606 (mmt)
REVERT: A  199 MET cc_start: 0.7784 (mmm) cc_final: 0.7482 (mmm)
REVERT: A  205 MET cc_start: 0.7785 (tpp) cc_final: 0.7068 (mmm)
REVERT: A  216 LEU cc_start: 0.8783 (mt) cc_final: 0.8472 (mp)
REVERT: A  233 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6478 (tt0)
REVERT: A  367 MET cc_start: 0.7106 (mtp) cc_final: 0.6729 (mtm)
REVERT: A  383 MET cc_start: 0.7947 (mmm) cc_final: 0.7554 (tpp)
REVERT: A  443 GLU cc_start: 0.7469 (tp30) cc_final: 0.7245 (tp30)
REVERT: A  475 GLN cc_start: 0.7749 (tp40) cc_final: 0.7359 (tp-100)
REVERT: A  500 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7285 (tpp80)
REVERT: A  579 MET cc_start: 0.6050 (tmm) cc_final: 0.5669 (tmm)
REVERT: A  583 ARG cc_start: 0.7744 (tmm-80) cc_final: 0.7315 (ttp80)
REVERT: A  588 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7465 (ttpp)
REVERT: A  599 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7257 (mt-10)
REVERT: A  648 LEU cc_start: 0.8363 (mp) cc_final: 0.8153 (mp)
REVERT: A  810 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5773 (mpp)
REVERT: A  812 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7694 (ttp80)
REVERT: A  815 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8117 (ttpp)
REVERT: A  823 LEU cc_start: 0.8291 (mt) cc_final: 0.8058 (mt)
REVERT: A  835 LEU cc_start: 0.8674 (tp) cc_final: 0.8405 (tt)
REVERT: A  863 ILE cc_start: 0.7318 (mm) cc_final: 0.6733 (mm)
REVERT: A  872 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6225 (mm-30)
REVERT: A  878 VAL cc_start: 0.8515 (p) cc_final: 0.8287 (t)
REVERT: A  880 LYS cc_start: 0.8411 (tttt) cc_final: 0.8039 (ttpt)
REVERT: A  887 ARG cc_start: 0.7636 (mmm-85) cc_final: 0.7322 (mtp85)
REVERT: A  938 MET cc_start: 0.7784 (tpp) cc_final: 0.7314 (ttm)
REVERT: A  946 SER cc_start: 0.8060 (p) cc_final: 0.7714 (t)
REVERT: A  986 GLU cc_start: 0.7028 (tt0) cc_final: 0.6181 (tt0)
REVERT: A  993 ASP cc_start: 0.7893 (m-30) cc_final: 0.7421 (m-30)
REVERT: A  994 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7462 (tm-30)
REVERT: A 1058 THR cc_start: 0.8198 (m) cc_final: 0.7930 (p)
REVERT: A 1059 CYS cc_start: 0.7253 (m) cc_final: 0.7003 (m)
REVERT: A 1085 SER cc_start: 0.8395 (t) cc_final: 0.8077 (p)
REVERT: A 1086 LEU cc_start: 0.8697 (tt) cc_final: 0.8440 (tp)
REVERT: A 1098 ILE cc_start: 0.8739 (tp) cc_final: 0.8502 (tp)
REVERT: A 1145 VAL cc_start: 0.8587 (t) cc_final: 0.8267 (p)
REVERT: A 1189 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7560 (m)
  outliers start: 31
  outliers final: 24
  residues processed: 260
  average time/residue: 0.2329
  time to fit residues: 79.1406
Evaluate side-chains
  268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   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 132 HIS
A 877 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.128329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.110380 restraints weight = 12992.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.113662 restraints weight = 5975.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115690 restraints weight = 3453.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8267  Z= 0.177
  Angle     :  0.560   8.734  11218  Z= 0.296
  Chirality :  0.040   0.140   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.260 144.446   1104
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 17.50 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.27), residues: 1012
  helix:  1.79 (0.19), residues: 715
  sheet: -0.49 (0.75), residues: 54
  loop : -0.04 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 962 
 HIS   0.010   0.001   HIS A 132 
 PHE   0.023   0.002   PHE A 598 
 TYR   0.013   0.001   TYR A 984 
 ARG   0.006   0.001   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  577)
  hydrogen bonds       : angle       4.21003 ( 1701)
  covalent geometry    : bond        0.00388 ( 8267)
  covalent geometry    : angle       0.56000 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 246
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8363 (mm) cc_final: 0.7917 (mt)
REVERT: A  134 ASP cc_start: 0.7569 (m-30) cc_final: 0.7350 (p0)
REVERT: A  149 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6842 (tm-30)
REVERT: A  155 ASP cc_start: 0.6391 (t0) cc_final: 0.5941 (t0)
REVERT: A  160 MET cc_start: 0.7007 (mmt) cc_final: 0.6749 (mmt)
REVERT: A  164 SER cc_start: 0.8444 (m) cc_final: 0.8178 (p)
REVERT: A  199 MET cc_start: 0.7763 (mmm) cc_final: 0.7518 (mmm)
REVERT: A  205 MET cc_start: 0.7715 (tpp) cc_final: 0.7111 (mmm)
REVERT: A  216 LEU cc_start: 0.8753 (mt) cc_final: 0.8425 (mp)
REVERT: A  233 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6460 (tt0)
REVERT: A  373 THR cc_start: 0.7582 (m) cc_final: 0.7367 (m)
REVERT: A  383 MET cc_start: 0.7962 (mmm) cc_final: 0.7583 (tpp)
REVERT: A  424 ILE cc_start: 0.8080 (mm) cc_final: 0.7796 (tp)
REVERT: A  443 GLU cc_start: 0.7496 (tp30) cc_final: 0.7195 (tp30)
REVERT: A  475 GLN cc_start: 0.7758 (tp40) cc_final: 0.7492 (tp40)
REVERT: A  500 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7280 (tpp80)
REVERT: A  534 ASP cc_start: 0.7466 (t0) cc_final: 0.7033 (t0)
REVERT: A  579 MET cc_start: 0.6059 (tmm) cc_final: 0.5664 (tmm)
REVERT: A  588 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7575 (ttpp)
REVERT: A  705 MET cc_start: 0.5097 (mmt) cc_final: 0.3947 (mmm)
REVERT: A  810 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5973 (mpp)
REVERT: A  815 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8132 (ttpp)
REVERT: A  823 LEU cc_start: 0.8287 (mt) cc_final: 0.8074 (mt)
REVERT: A  835 LEU cc_start: 0.8650 (tp) cc_final: 0.8343 (tt)
REVERT: A  856 ARG cc_start: 0.6933 (ptp90) cc_final: 0.6661 (ptt180)
REVERT: A  863 ILE cc_start: 0.7133 (mm) cc_final: 0.6712 (mm)
REVERT: A  872 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6284 (mm-30)
REVERT: A  878 VAL cc_start: 0.8432 (p) cc_final: 0.8219 (t)
REVERT: A  880 LYS cc_start: 0.8456 (tttt) cc_final: 0.8011 (ttpt)
REVERT: A  938 MET cc_start: 0.7777 (tpp) cc_final: 0.7341 (ttm)
REVERT: A  946 SER cc_start: 0.8096 (p) cc_final: 0.7719 (t)
REVERT: A  986 GLU cc_start: 0.7141 (tt0) cc_final: 0.6326 (tt0)
REVERT: A 1033 GLU cc_start: 0.7005 (tp30) cc_final: 0.6790 (tp30)
REVERT: A 1035 TYR cc_start: 0.7997 (m-80) cc_final: 0.7721 (m-10)
REVERT: A 1058 THR cc_start: 0.8249 (m) cc_final: 0.7925 (p)
REVERT: A 1059 CYS cc_start: 0.7302 (m) cc_final: 0.7026 (m)
REVERT: A 1082 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6980 (tt)
REVERT: A 1085 SER cc_start: 0.8382 (t) cc_final: 0.8095 (p)
REVERT: A 1098 ILE cc_start: 0.8803 (tp) cc_final: 0.8546 (tp)
REVERT: A 1105 GLU cc_start: 0.7206 (pp20) cc_final: 0.6929 (pp20)
REVERT: A 1145 VAL cc_start: 0.8587 (t) cc_final: 0.8277 (p)
REVERT: A 1189 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7571 (m)
  outliers start: 41
  outliers final: 31
  residues processed: 258
  average time/residue: 0.2228
  time to fit residues: 75.4250
Evaluate side-chains
  276 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 241
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1147 LEU
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0980
   chunk 54 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 877 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.111014 restraints weight = 13103.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.114342 restraints weight = 5971.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.116422 restraints weight = 3436.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8267  Z= 0.147
  Angle     :  0.566   8.677  11218  Z= 0.295
  Chirality :  0.039   0.166   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.268 145.311   1104
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.52 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.27), residues: 1012
  helix:  1.92 (0.19), residues: 706
  sheet: -0.41 (0.75), residues: 54
  loop : -0.05 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 595 
 HIS   0.006   0.001   HIS A 132 
 PHE   0.017   0.001   PHE A 598 
 TYR   0.014   0.001   TYR A 984 
 ARG   0.008   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  577)
  hydrogen bonds       : angle       4.14057 ( 1701)
  covalent geometry    : bond        0.00319 ( 8267)
  covalent geometry    : angle       0.56579 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 242
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7083 (mptt) cc_final: 0.6859 (mppt)
REVERT: A  108 ILE cc_start: 0.8336 (mm) cc_final: 0.7894 (mt)
REVERT: A  149 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6831 (tm-30)
REVERT: A  155 ASP cc_start: 0.6383 (t0) cc_final: 0.5900 (t0)
REVERT: A  160 MET cc_start: 0.7002 (mmt) cc_final: 0.6731 (mmt)
REVERT: A  164 SER cc_start: 0.8429 (m) cc_final: 0.8192 (p)
REVERT: A  199 MET cc_start: 0.7735 (mmm) cc_final: 0.7517 (mmm)
REVERT: A  205 MET cc_start: 0.7643 (tpp) cc_final: 0.7037 (mmm)
REVERT: A  216 LEU cc_start: 0.8734 (mt) cc_final: 0.8427 (mp)
REVERT: A  233 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6424 (tt0)
REVERT: A  373 THR cc_start: 0.7530 (m) cc_final: 0.7319 (m)
REVERT: A  383 MET cc_start: 0.7922 (mmm) cc_final: 0.7577 (tpp)
REVERT: A  443 GLU cc_start: 0.7503 (tp30) cc_final: 0.7183 (tp30)
REVERT: A  475 GLN cc_start: 0.7731 (tp40) cc_final: 0.7498 (tp40)
REVERT: A  500 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7213 (tpp80)
REVERT: A  534 ASP cc_start: 0.7469 (t0) cc_final: 0.7117 (t0)
REVERT: A  579 MET cc_start: 0.5969 (tmm) cc_final: 0.5649 (tmm)
REVERT: A  583 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7428 (ttp-170)
REVERT: A  586 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6847 (ttp)
REVERT: A  588 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7469 (ttpp)
REVERT: A  628 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7878 (p)
REVERT: A  644 LEU cc_start: 0.8133 (mt) cc_final: 0.7599 (mm)
REVERT: A  648 LEU cc_start: 0.8393 (mp) cc_final: 0.8171 (mp)
REVERT: A  705 MET cc_start: 0.5165 (mmt) cc_final: 0.4132 (mmt)
REVERT: A  810 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5914 (mpp)
REVERT: A  811 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6152 (mm)
REVERT: A  815 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8199 (ttpp)
REVERT: A  823 LEU cc_start: 0.8254 (mt) cc_final: 0.8038 (mt)
REVERT: A  835 LEU cc_start: 0.8562 (tp) cc_final: 0.8328 (tt)
REVERT: A  863 ILE cc_start: 0.7059 (mm) cc_final: 0.6621 (mm)
REVERT: A  872 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6242 (mm-30)
REVERT: A  878 VAL cc_start: 0.8444 (p) cc_final: 0.8183 (t)
REVERT: A  880 LYS cc_start: 0.8395 (tttt) cc_final: 0.7965 (ttpt)
REVERT: A  887 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7632 (mtp85)
REVERT: A  938 MET cc_start: 0.7792 (tpp) cc_final: 0.7372 (ttm)
REVERT: A  946 SER cc_start: 0.8132 (p) cc_final: 0.7714 (t)
REVERT: A  986 GLU cc_start: 0.7117 (tt0) cc_final: 0.6288 (tt0)
REVERT: A 1035 TYR cc_start: 0.7964 (m-80) cc_final: 0.7718 (m-10)
REVERT: A 1058 THR cc_start: 0.8228 (m) cc_final: 0.7922 (p)
REVERT: A 1059 CYS cc_start: 0.7297 (m) cc_final: 0.7005 (m)
REVERT: A 1082 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6971 (tt)
REVERT: A 1085 SER cc_start: 0.8342 (t) cc_final: 0.8064 (p)
REVERT: A 1098 ILE cc_start: 0.8767 (tp) cc_final: 0.8520 (tp)
REVERT: A 1105 GLU cc_start: 0.7156 (pp20) cc_final: 0.6867 (pp20)
REVERT: A 1145 VAL cc_start: 0.8557 (t) cc_final: 0.8272 (p)
REVERT: A 1189 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7539 (m)
  outliers start: 36
  outliers final: 22
  residues processed: 258
  average time/residue: 0.2062
  time to fit residues: 70.2527
Evaluate side-chains
  266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 237
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110950 restraints weight = 13117.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.114240 restraints weight = 5965.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116327 restraints weight = 3430.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8267  Z= 0.161
  Angle     :  0.581   9.280  11218  Z= 0.304
  Chirality :  0.041   0.338   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.276 145.592   1104
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.43 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 1012
  helix:  1.87 (0.20), residues: 706
  sheet: -0.54 (0.73), residues: 54
  loop : -0.02 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 595 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 598 
 TYR   0.013   0.001   TYR A 984 
 ARG   0.009   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  577)
  hydrogen bonds       : angle       4.16241 ( 1701)
  covalent geometry    : bond        0.00363 ( 8267)
  covalent geometry    : angle       0.58082 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 240
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7098 (mptt) cc_final: 0.6890 (mppt)
REVERT: A  108 ILE cc_start: 0.8334 (mm) cc_final: 0.7885 (mt)
REVERT: A  149 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6829 (tm-30)
REVERT: A  155 ASP cc_start: 0.6434 (t0) cc_final: 0.5977 (t0)
REVERT: A  160 MET cc_start: 0.7002 (mmt) cc_final: 0.6706 (mmt)
REVERT: A  164 SER cc_start: 0.8433 (m) cc_final: 0.8199 (p)
REVERT: A  199 MET cc_start: 0.7725 (mmm) cc_final: 0.7482 (mmm)
REVERT: A  205 MET cc_start: 0.7554 (tpp) cc_final: 0.7309 (mmm)
REVERT: A  216 LEU cc_start: 0.8712 (mt) cc_final: 0.8431 (mp)
REVERT: A  233 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6468 (tt0)
REVERT: A  373 THR cc_start: 0.7533 (m) cc_final: 0.7315 (m)
REVERT: A  383 MET cc_start: 0.7944 (mmm) cc_final: 0.7607 (tpp)
REVERT: A  424 ILE cc_start: 0.8259 (tp) cc_final: 0.7964 (tp)
REVERT: A  443 GLU cc_start: 0.7511 (tp30) cc_final: 0.7209 (tp30)
REVERT: A  500 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7223 (tpp80)
REVERT: A  534 ASP cc_start: 0.7477 (t0) cc_final: 0.7131 (t0)
REVERT: A  579 MET cc_start: 0.6003 (tmm) cc_final: 0.5659 (tmm)
REVERT: A  583 ARG cc_start: 0.7796 (tmm-80) cc_final: 0.7242 (ttp-170)
REVERT: A  588 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7478 (ttpp)
REVERT: A  624 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7301 (tp40)
REVERT: A  628 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7760 (p)
REVERT: A  705 MET cc_start: 0.5168 (mmt) cc_final: 0.4135 (mmt)
REVERT: A  810 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5786 (mpp)
REVERT: A  811 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6260 (mm)
REVERT: A  815 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8234 (ttpp)
REVERT: A  835 LEU cc_start: 0.8537 (tp) cc_final: 0.8318 (tt)
REVERT: A  863 ILE cc_start: 0.7069 (mm) cc_final: 0.6615 (mm)
REVERT: A  872 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6221 (mm-30)
REVERT: A  878 VAL cc_start: 0.8425 (p) cc_final: 0.8174 (t)
REVERT: A  880 LYS cc_start: 0.8378 (tttt) cc_final: 0.7955 (ttpt)
REVERT: A  887 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7637 (mtp85)
REVERT: A  938 MET cc_start: 0.7787 (tpp) cc_final: 0.7368 (ttm)
REVERT: A  946 SER cc_start: 0.8173 (p) cc_final: 0.7733 (t)
REVERT: A  960 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7794 (p)
REVERT: A  986 GLU cc_start: 0.7125 (tt0) cc_final: 0.6322 (tt0)
REVERT: A 1035 TYR cc_start: 0.7945 (m-80) cc_final: 0.7740 (m-10)
REVERT: A 1058 THR cc_start: 0.8223 (m) cc_final: 0.7900 (p)
REVERT: A 1059 CYS cc_start: 0.7258 (m) cc_final: 0.7016 (m)
REVERT: A 1082 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7055 (tt)
REVERT: A 1085 SER cc_start: 0.8395 (t) cc_final: 0.8113 (p)
REVERT: A 1098 ILE cc_start: 0.8785 (tp) cc_final: 0.8525 (tp)
REVERT: A 1105 GLU cc_start: 0.7083 (pp20) cc_final: 0.6772 (pp20)
REVERT: A 1145 VAL cc_start: 0.8558 (t) cc_final: 0.8261 (p)
REVERT: A 1189 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7548 (m)
  outliers start: 36
  outliers final: 24
  residues processed: 255
  average time/residue: 0.2156
  time to fit residues: 72.8376
Evaluate side-chains
  267 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 236
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0060
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0270
   chunk 51 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0040
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.2666

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 157 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.113079 restraints weight = 13148.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.116373 restraints weight = 5993.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118462 restraints weight = 3445.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8267  Z= 0.124
  Angle     :  0.570   8.987  11218  Z= 0.294
  Chirality :  0.040   0.249   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.282 146.730   1104
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.45 %
    Favored  : 76.02 %
  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:  2.09 (0.27), residues: 1012
  helix:  2.06 (0.20), residues: 706
  sheet: -0.41 (0.74), residues: 54
  loop : -0.06 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 595 
 HIS   0.004   0.001   HIS A 157 
 PHE   0.015   0.001   PHE A 598 
 TYR   0.017   0.001   TYR A 984 
 ARG   0.009   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  577)
  hydrogen bonds       : angle       4.04101 ( 1701)
  covalent geometry    : bond        0.00273 ( 8267)
  covalent geometry    : angle       0.56959 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 242
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7064 (mptt) cc_final: 0.6844 (mppt)
REVERT: A  108 ILE cc_start: 0.8324 (mm) cc_final: 0.7858 (mt)
REVERT: A  149 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6814 (tm-30)
REVERT: A  155 ASP cc_start: 0.6334 (t0) cc_final: 0.5912 (t0)
REVERT: A  160 MET cc_start: 0.6907 (mmt) cc_final: 0.6631 (mmt)
REVERT: A  164 SER cc_start: 0.8442 (m) cc_final: 0.8180 (p)
REVERT: A  199 MET cc_start: 0.7691 (mmm) cc_final: 0.7449 (mmm)
REVERT: A  216 LEU cc_start: 0.8660 (mt) cc_final: 0.8437 (mp)
REVERT: A  233 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6431 (tt0)
REVERT: A  383 MET cc_start: 0.7916 (mmm) cc_final: 0.7621 (tpp)
REVERT: A  424 ILE cc_start: 0.8290 (tp) cc_final: 0.8015 (tp)
REVERT: A  443 GLU cc_start: 0.7479 (tp30) cc_final: 0.7167 (tp30)
REVERT: A  500 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7203 (tpp80)
REVERT: A  534 ASP cc_start: 0.7463 (t0) cc_final: 0.7118 (t0)
REVERT: A  579 MET cc_start: 0.5848 (tmm) cc_final: 0.5543 (tmm)
REVERT: A  583 ARG cc_start: 0.7773 (tmm-80) cc_final: 0.7220 (ttp-170)
REVERT: A  586 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6751 (ttp)
REVERT: A  588 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7409 (ttpp)
REVERT: A  591 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8071 (mtpt)
REVERT: A  644 LEU cc_start: 0.8162 (mt) cc_final: 0.7900 (mm)
REVERT: A  705 MET cc_start: 0.5077 (mmt) cc_final: 0.3941 (mmt)
REVERT: A  810 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5527 (mpp)
REVERT: A  811 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6030 (mm)
REVERT: A  828 LYS cc_start: 0.8099 (tppt) cc_final: 0.7692 (mmtm)
REVERT: A  863 ILE cc_start: 0.6971 (mm) cc_final: 0.6611 (mm)
REVERT: A  872 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6164 (mm-30)
REVERT: A  880 LYS cc_start: 0.8439 (tttt) cc_final: 0.8016 (ttpt)
REVERT: A  887 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7607 (mtp85)
REVERT: A  938 MET cc_start: 0.7769 (tpp) cc_final: 0.7355 (ttm)
REVERT: A  946 SER cc_start: 0.8168 (p) cc_final: 0.7741 (t)
REVERT: A  970 ILE cc_start: 0.8937 (tt) cc_final: 0.8695 (tp)
REVERT: A 1035 TYR cc_start: 0.7902 (m-80) cc_final: 0.7690 (m-10)
REVERT: A 1058 THR cc_start: 0.8185 (m) cc_final: 0.7903 (p)
REVERT: A 1082 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6952 (tt)
REVERT: A 1085 SER cc_start: 0.8363 (t) cc_final: 0.8059 (p)
REVERT: A 1098 ILE cc_start: 0.8710 (tp) cc_final: 0.8454 (tp)
REVERT: A 1105 GLU cc_start: 0.7103 (pp20) cc_final: 0.6796 (pp20)
REVERT: A 1145 VAL cc_start: 0.8550 (t) cc_final: 0.8260 (p)
  outliers start: 31
  outliers final: 17
  residues processed: 255
  average time/residue: 0.2178
  time to fit residues: 73.2401
Evaluate side-chains
  252 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 231
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 HIS
A 928 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.129417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.111120 restraints weight = 13230.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.114397 restraints weight = 6061.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116461 restraints weight = 3495.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8267  Z= 0.174
  Angle     :  0.622  11.024  11218  Z= 0.320
  Chirality :  0.041   0.261   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.267 145.579   1104
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.84 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.27), residues: 1012
  helix:  1.80 (0.20), residues: 712
  sheet: -0.43 (0.75), residues: 54
  loop :  0.02 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 595 
 HIS   0.005   0.001   HIS A 157 
 PHE   0.015   0.002   PHE A 625 
 TYR   0.010   0.001   TYR A 984 
 ARG   0.008   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  577)
  hydrogen bonds       : angle       4.14387 ( 1701)
  covalent geometry    : bond        0.00392 ( 8267)
  covalent geometry    : angle       0.62226 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7100 (mptt) cc_final: 0.6882 (mppt)
REVERT: A  108 ILE cc_start: 0.8350 (mm) cc_final: 0.7897 (mt)
REVERT: A  149 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6813 (tm-30)
REVERT: A  158 THR cc_start: 0.8124 (p) cc_final: 0.7811 (m)
REVERT: A  160 MET cc_start: 0.6924 (mmt) cc_final: 0.6660 (mmt)
REVERT: A  168 ILE cc_start: 0.8324 (tt) cc_final: 0.7650 (pt)
REVERT: A  199 MET cc_start: 0.7728 (mmm) cc_final: 0.7494 (mmm)
REVERT: A  216 LEU cc_start: 0.8665 (mt) cc_final: 0.8409 (mp)
REVERT: A  233 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6565 (tt0)
REVERT: A  383 MET cc_start: 0.8025 (mmm) cc_final: 0.7710 (tpp)
REVERT: A  424 ILE cc_start: 0.8285 (tp) cc_final: 0.7954 (tp)
REVERT: A  443 GLU cc_start: 0.7436 (tp30) cc_final: 0.7129 (tp30)
REVERT: A  500 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7213 (tpp80)
REVERT: A  534 ASP cc_start: 0.7468 (t0) cc_final: 0.7127 (t0)
REVERT: A  579 MET cc_start: 0.5948 (tmm) cc_final: 0.5634 (tmm)
REVERT: A  583 ARG cc_start: 0.7869 (tmm-80) cc_final: 0.7593 (ttt-90)
REVERT: A  588 LYS cc_start: 0.8009 (ttpp) cc_final: 0.7409 (ttpp)
REVERT: A  591 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8092 (mtpt)
REVERT: A  644 LEU cc_start: 0.8133 (mt) cc_final: 0.7758 (mm)
REVERT: A  705 MET cc_start: 0.5143 (mmt) cc_final: 0.4015 (mmt)
REVERT: A  810 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5852 (mpp)
REVERT: A  828 LYS cc_start: 0.8134 (tppt) cc_final: 0.7757 (mmtm)
REVERT: A  863 ILE cc_start: 0.7094 (mm) cc_final: 0.6755 (mm)
REVERT: A  872 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6241 (mm-30)
REVERT: A  878 VAL cc_start: 0.8424 (p) cc_final: 0.8217 (t)
REVERT: A  880 LYS cc_start: 0.8341 (tttt) cc_final: 0.7926 (ttpt)
REVERT: A  887 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7571 (mtp85)
REVERT: A  926 GLU cc_start: 0.6435 (tt0) cc_final: 0.6216 (tt0)
REVERT: A  938 MET cc_start: 0.7753 (tpp) cc_final: 0.7345 (ttm)
REVERT: A  946 SER cc_start: 0.8162 (p) cc_final: 0.7753 (t)
REVERT: A 1035 TYR cc_start: 0.7916 (m-80) cc_final: 0.7714 (m-10)
REVERT: A 1058 THR cc_start: 0.8200 (m) cc_final: 0.7871 (p)
REVERT: A 1059 CYS cc_start: 0.7203 (m) cc_final: 0.6965 (m)
REVERT: A 1082 LEU cc_start: 0.7399 (mm) cc_final: 0.7159 (tt)
REVERT: A 1085 SER cc_start: 0.8334 (t) cc_final: 0.8082 (p)
REVERT: A 1098 ILE cc_start: 0.8760 (tp) cc_final: 0.8492 (tp)
REVERT: A 1105 GLU cc_start: 0.6927 (pp20) cc_final: 0.6563 (pp20)
REVERT: A 1145 VAL cc_start: 0.8505 (t) cc_final: 0.8219 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 248
  average time/residue: 0.2228
  time to fit residues: 72.6804
Evaluate side-chains
  258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 238
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.130153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111932 restraints weight = 13063.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115211 restraints weight = 6040.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.117287 restraints weight = 3488.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8267  Z= 0.147
  Angle     :  0.609   9.299  11218  Z= 0.314
  Chirality :  0.040   0.209   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.301 146.331   1104
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.75 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 1012
  helix:  1.83 (0.20), residues: 712
  sheet: -0.30 (0.76), residues: 54
  loop : -0.02 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 595 
 HIS   0.005   0.001   HIS A 614 
 PHE   0.021   0.001   PHE A 625 
 TYR   0.019   0.001   TYR A 267 
 ARG   0.008   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04270 (  577)
  hydrogen bonds       : angle       4.11585 ( 1701)
  covalent geometry    : bond        0.00331 ( 8267)
  covalent geometry    : angle       0.60891 (11218)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 239
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7050 (mptt) cc_final: 0.6831 (mppt)
REVERT: A  108 ILE cc_start: 0.8317 (mm) cc_final: 0.7861 (mt)
REVERT: A  149 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6796 (tm-30)
REVERT: A  160 MET cc_start: 0.6893 (mmt) cc_final: 0.6585 (mmt)
REVERT: A  168 ILE cc_start: 0.8240 (tt) cc_final: 0.7645 (pt)
REVERT: A  199 MET cc_start: 0.7716 (mmm) cc_final: 0.7501 (mmm)
REVERT: A  209 ASP cc_start: 0.7255 (t0) cc_final: 0.6870 (t0)
REVERT: A  233 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6534 (tt0)
REVERT: A  383 MET cc_start: 0.7996 (mmm) cc_final: 0.7645 (tpp)
REVERT: A  424 ILE cc_start: 0.8353 (tp) cc_final: 0.7984 (tp)
REVERT: A  443 GLU cc_start: 0.7417 (tp30) cc_final: 0.7112 (tp30)
REVERT: A  500 ARG cc_start: 0.7585 (tpp80) cc_final: 0.7183 (tpp80)
REVERT: A  534 ASP cc_start: 0.7464 (t0) cc_final: 0.7126 (t0)
REVERT: A  579 MET cc_start: 0.5925 (tmm) cc_final: 0.5615 (tmm)
REVERT: A  586 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6789 (ttp)
REVERT: A  588 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7415 (ttpp)
REVERT: A  591 LYS cc_start: 0.8290 (mtpt) cc_final: 0.8032 (mtpt)
REVERT: A  609 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6558 (tpp80)
REVERT: A  633 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7900 (mtmm)
REVERT: A  644 LEU cc_start: 0.8113 (mt) cc_final: 0.7882 (mm)
REVERT: A  705 MET cc_start: 0.5086 (mmt) cc_final: 0.3983 (mmt)
REVERT: A  810 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5692 (mpp)
REVERT: A  828 LYS cc_start: 0.8124 (tppt) cc_final: 0.7599 (mmtp)
REVERT: A  863 ILE cc_start: 0.7006 (mm) cc_final: 0.6641 (mm)
REVERT: A  872 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6213 (mm-30)
REVERT: A  878 VAL cc_start: 0.8393 (p) cc_final: 0.8182 (t)
REVERT: A  880 LYS cc_start: 0.8339 (tttt) cc_final: 0.7933 (ttpt)
REVERT: A  887 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7573 (mtp85)
REVERT: A  938 MET cc_start: 0.7746 (tpp) cc_final: 0.7341 (ttm)
REVERT: A  946 SER cc_start: 0.8145 (p) cc_final: 0.7746 (t)
REVERT: A 1035 TYR cc_start: 0.7884 (m-80) cc_final: 0.7674 (m-10)
REVERT: A 1058 THR cc_start: 0.8176 (m) cc_final: 0.7889 (p)
REVERT: A 1082 LEU cc_start: 0.7336 (mm) cc_final: 0.7126 (tt)
REVERT: A 1085 SER cc_start: 0.8328 (t) cc_final: 0.8063 (p)
REVERT: A 1098 ILE cc_start: 0.8709 (tp) cc_final: 0.8459 (tp)
REVERT: A 1105 GLU cc_start: 0.6939 (pp20) cc_final: 0.6582 (pp20)
  outliers start: 20
  outliers final: 18
  residues processed: 247
  average time/residue: 0.2296
  time to fit residues: 74.3317
Evaluate side-chains
  254 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 234
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 94 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 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.111252 restraints weight = 13196.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.114535 restraints weight = 6087.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.116638 restraints weight = 3526.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8267  Z= 0.167
  Angle     :  0.632  10.120  11218  Z= 0.326
  Chirality :  0.041   0.210   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.301 146.196   1104
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.86 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.27), residues: 1012
  helix:  1.72 (0.20), residues: 712
  sheet: -0.28 (0.78), residues: 54
  loop : -0.03 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 595 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.016   0.001   PHE A 625 
 TYR   0.021   0.001   TYR A 267 
 ARG   0.007   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  577)
  hydrogen bonds       : angle       4.14532 ( 1701)
  covalent geometry    : bond        0.00376 ( 8267)
  covalent geometry    : angle       0.63245 (11218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2936.45 seconds
wall clock time: 52 minutes 9.16 seconds (3129.16 seconds total)