Starting phenix.real_space_refine
on Tue Apr 29 03:58:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd9_17607/04_2025/8pd9_17607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd9_17607/04_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_17607/04_2025/8pd9_17607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd9_17607/04_2025/8pd9_17607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd9_17607/04_2025/8pd9_17607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd9_17607/04_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): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.54, per 1000 atoms: 0.81
  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: 2.83
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.05
  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: 5.10

  Time building geometry restraints manager: 2.73 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:             178.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     27.220
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.060
  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:4.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  210.870
-------------------------------------------------------------------------------
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  : 1.334 
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: 0.2540
  time to fit residues: 101.1327
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  : 0.971 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112476 restraints weight = 12837.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.115801 restraints weight = 5912.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117929 restraints weight = 3440.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
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  :  8.262 143.578   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       4.40868 ( 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  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8336 (mm) cc_final: 0.7851 (mt)
REVERT: A  134 ASP cc_start: 0.7611 (m-30) cc_final: 0.7182 (p0)
REVERT: A  149 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6980 (tm-30)
REVERT: A  155 ASP cc_start: 0.6393 (t0) cc_final: 0.6030 (t0)
REVERT: A  160 MET cc_start: 0.6901 (mmt) cc_final: 0.6537 (mmt)
REVERT: A  174 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7096 (tp)
REVERT: A  209 ASP cc_start: 0.7358 (t0) cc_final: 0.7058 (t0)
REVERT: A  475 GLN cc_start: 0.7905 (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: 0.6301 (tmm) cc_final: 0.5539 (tmm)
REVERT: A  583 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7500 (ttp80)
REVERT: A  588 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7478 (ttpp)
REVERT: A  628 VAL cc_start: 0.8294 (p) cc_final: 0.6994 (m)
REVERT: A  648 LEU cc_start: 0.8349 (mp) cc_final: 0.8142 (mp)
REVERT: A  810 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5746 (mpp)
REVERT: A  812 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7844 (ttp80)
REVERT: A  863 ILE cc_start: 0.7315 (mm) cc_final: 0.6919 (mm)
REVERT: A  872 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6207 (mm-30)
REVERT: A  880 LYS cc_start: 0.8377 (tttt) cc_final: 0.8020 (ttpp)
REVERT: A  887 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7354 (mtp85)
REVERT: A  910 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8025 (ttm170)
REVERT: A  938 MET cc_start: 0.7795 (tpp) cc_final: 0.7281 (ttm)
REVERT: A  946 SER cc_start: 0.8054 (p) cc_final: 0.7724 (t)
REVERT: A  968 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7657 (mtmt)
REVERT: A 1058 THR cc_start: 0.8192 (m) cc_final: 0.7818 (p)
REVERT: A 1059 CYS cc_start: 0.7223 (m) cc_final: 0.6916 (m)
REVERT: A 1085 SER cc_start: 0.8436 (t) cc_final: 0.8076 (m)
REVERT: A 1093 VAL cc_start: 0.8875 (p) cc_final: 0.8665 (p)
REVERT: A 1096 ILE cc_start: 0.8878 (mm) cc_final: 0.8534 (mt)
REVERT: A 1098 ILE cc_start: 0.8669 (tp) cc_final: 0.8467 (tt)
REVERT: A 1144 ASP cc_start: 0.7521 (m-30) cc_final: 0.7299 (m-30)
REVERT: A 1168 SER cc_start: 0.8759 (t) cc_final: 0.8495 (p)
REVERT: A 1189 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7428 (m)
  outliers start: 18
  outliers final: 8
  residues processed: 271
  average time/residue: 0.2542
  time to fit residues: 89.2498
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  : 0.959 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 24 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 74 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.128115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110081 restraints weight = 13349.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.113368 restraints weight = 6058.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.115430 restraints weight = 3489.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8267  Z= 0.147
  Angle     :  0.556   8.807  11218  Z= 0.292
  Chirality :  0.039   0.174   1348
  Planarity :  0.004   0.039   1378
  Dihedral  :  8.222 143.653   1104
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.70 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.27), residues: 1012
  helix:  2.03 (0.19), residues: 713
  sheet: -0.53 (0.68), residues: 61
  loop :  0.38 (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   0.021   0.001   PHE A 739 
 TYR   0.009   0.001   TYR A1066 
 ARG   0.006   0.001   ARG A1185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  577)
  hydrogen bonds       : angle       4.23712 ( 1701)
  covalent geometry    : bond        0.00319 ( 8267)
  covalent geometry    : angle       0.55630 (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
  285 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 256
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8349 (mm) cc_final: 0.7880 (mt)
REVERT: A  134 ASP cc_start: 0.7585 (m-30) cc_final: 0.7193 (p0)
REVERT: A  149 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6826 (tm-30)
REVERT: A  155 ASP cc_start: 0.6323 (t0) cc_final: 0.5856 (t0)
REVERT: A  160 MET cc_start: 0.6887 (mmt) cc_final: 0.6612 (mmt)
REVERT: A  199 MET cc_start: 0.7819 (mmm) cc_final: 0.7383 (tpt)
REVERT: A  205 MET cc_start: 0.7924 (tpp) cc_final: 0.7084 (mmm)
REVERT: A  209 ASP cc_start: 0.7355 (t0) cc_final: 0.6891 (t70)
REVERT: A  367 MET cc_start: 0.7240 (mtp) cc_final: 0.6849 (mtm)
REVERT: A  383 MET cc_start: 0.8030 (mmm) cc_final: 0.7511 (tpp)
REVERT: A  490 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7988 (mtmt)
REVERT: A  500 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7289 (tpp80)
REVERT: A  588 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7555 (ttpp)
REVERT: A  705 MET cc_start: 0.5448 (mmt) cc_final: 0.4401 (mmm)
REVERT: A  810 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5792 (mpp)
REVERT: A  823 LEU cc_start: 0.8299 (mt) cc_final: 0.8037 (mt)
REVERT: A  835 LEU cc_start: 0.8720 (tp) cc_final: 0.8431 (tt)
REVERT: A  863 ILE cc_start: 0.7417 (mm) cc_final: 0.7100 (mm)
REVERT: A  872 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6378 (mm-30)
REVERT: A  878 VAL cc_start: 0.8468 (p) cc_final: 0.8209 (t)
REVERT: A  880 LYS cc_start: 0.8393 (tttt) cc_final: 0.7950 (ttpt)
REVERT: A  887 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7300 (mtp85)
REVERT: A  938 MET cc_start: 0.7759 (tpp) cc_final: 0.7327 (ttm)
REVERT: A  946 SER cc_start: 0.8056 (p) cc_final: 0.7723 (t)
REVERT: A  970 ILE cc_start: 0.8832 (tp) cc_final: 0.8618 (tp)
REVERT: A  986 GLU cc_start: 0.7000 (tt0) cc_final: 0.6400 (tt0)
REVERT: A 1035 TYR cc_start: 0.7977 (m-80) cc_final: 0.7760 (m-10)
REVERT: A 1058 THR cc_start: 0.8185 (m) cc_final: 0.7865 (p)
REVERT: A 1059 CYS cc_start: 0.7231 (m) cc_final: 0.7014 (m)
REVERT: A 1073 MET cc_start: 0.7908 (mmm) cc_final: 0.7646 (mmp)
REVERT: A 1085 SER cc_start: 0.8403 (t) cc_final: 0.8125 (m)
REVERT: A 1086 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8382 (tp)
REVERT: A 1098 ILE cc_start: 0.8689 (tp) cc_final: 0.8486 (tp)
REVERT: A 1118 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8184 (mttp)
REVERT: A 1145 VAL cc_start: 0.8564 (t) cc_final: 0.8213 (p)
REVERT: A 1189 VAL cc_start: 0.7761 (m) cc_final: 0.7544 (m)
  outliers start: 29
  outliers final: 18
  residues processed: 263
  average time/residue: 0.2463
  time to fit residues: 83.9779
Evaluate side-chains
  268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 248
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
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 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:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.127959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.109466 restraints weight = 13100.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112782 restraints weight = 5954.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114943 restraints weight = 3461.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.3093

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= 0.175
  Angle     :  0.560   8.861  11218  Z= 0.293
  Chirality :  0.040   0.175   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.214 143.249   1104
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.50 %
    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:  1.91 (0.27), residues: 1012
  helix:  1.82 (0.19), residues: 721
  sheet: -0.44 (0.73), residues: 54
  loop :  0.10 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 962 
 HIS   0.005   0.001   HIS A 132 
 PHE   0.018   0.002   PHE A 739 
 TYR   0.014   0.001   TYR A 984 
 ARG   0.007   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04741 (  577)
  hydrogen bonds       : angle       4.23309 ( 1701)
  covalent geometry    : bond        0.00385 ( 8267)
  covalent geometry    : angle       0.56023 (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
  282 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 248
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8340 (mm) cc_final: 0.7888 (mt)
REVERT: A  133 MET cc_start: 0.6057 (mmm) cc_final: 0.5853 (mmm)
REVERT: A  134 ASP cc_start: 0.7578 (m-30) cc_final: 0.7153 (p0)
REVERT: A  149 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6840 (tm-30)
REVERT: A  155 ASP cc_start: 0.6400 (t0) cc_final: 0.5913 (t0)
REVERT: A  160 MET cc_start: 0.6975 (mmt) cc_final: 0.6682 (mmt)
REVERT: A  199 MET cc_start: 0.7786 (mmm) cc_final: 0.7488 (mmm)
REVERT: A  205 MET cc_start: 0.7775 (tpp) cc_final: 0.7078 (mmm)
REVERT: A  216 LEU cc_start: 0.8734 (mt) cc_final: 0.8454 (mp)
REVERT: A  233 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6483 (tt0)
REVERT: A  367 MET cc_start: 0.7153 (mtp) cc_final: 0.6811 (mtm)
REVERT: A  383 MET cc_start: 0.7994 (mmm) cc_final: 0.7594 (tpp)
REVERT: A  443 GLU cc_start: 0.7499 (tp30) cc_final: 0.7221 (tp30)
REVERT: A  500 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7320 (tpp80)
REVERT: A  579 MET cc_start: 0.6118 (tmm) cc_final: 0.5752 (tmm)
REVERT: A  583 ARG cc_start: 0.7726 (tmm-80) cc_final: 0.7321 (ttp80)
REVERT: A  585 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6956 (ttp-110)
REVERT: A  588 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7561 (ttpp)
REVERT: A  599 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7300 (mt-10)
REVERT: A  648 LEU cc_start: 0.8348 (mp) cc_final: 0.8145 (mp)
REVERT: A  705 MET cc_start: 0.5289 (mmt) cc_final: 0.3730 (mmm)
REVERT: A  810 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5877 (mpp)
REVERT: A  815 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8098 (ttpp)
REVERT: A  823 LEU cc_start: 0.8288 (mt) cc_final: 0.8064 (mt)
REVERT: A  835 LEU cc_start: 0.8675 (tp) cc_final: 0.8404 (tt)
REVERT: A  863 ILE cc_start: 0.7369 (mm) cc_final: 0.6893 (mm)
REVERT: A  867 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7597 (mp)
REVERT: A  872 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6403 (mm-30)
REVERT: A  880 LYS cc_start: 0.8429 (tttt) cc_final: 0.8029 (ttpt)
REVERT: A  938 MET cc_start: 0.7823 (tpp) cc_final: 0.7385 (ttm)
REVERT: A  946 SER cc_start: 0.8060 (p) cc_final: 0.7704 (t)
REVERT: A  986 GLU cc_start: 0.7053 (tt0) cc_final: 0.6176 (tt0)
REVERT: A  993 ASP cc_start: 0.7937 (m-30) cc_final: 0.7461 (m-30)
REVERT: A 1058 THR cc_start: 0.8201 (m) cc_final: 0.7878 (p)
REVERT: A 1059 CYS cc_start: 0.7293 (m) cc_final: 0.7010 (m)
REVERT: A 1085 SER cc_start: 0.8418 (t) cc_final: 0.8076 (p)
REVERT: A 1086 LEU cc_start: 0.8725 (tt) cc_final: 0.8453 (tp)
REVERT: A 1098 ILE cc_start: 0.8779 (tp) cc_final: 0.8513 (tp)
REVERT: A 1145 VAL cc_start: 0.8596 (t) cc_final: 0.8255 (p)
REVERT: A 1189 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7530 (m)
  outliers start: 34
  outliers final: 24
  residues processed: 259
  average time/residue: 0.2396
  time to fit residues: 82.6486
Evaluate side-chains
  269 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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  269 LEU
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  867 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 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:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   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 157 HIS
A 877 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110939 restraints weight = 12982.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.114261 restraints weight = 5953.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.116340 restraints weight = 3422.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3331

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= 0.142
  Angle     :  0.545   8.735  11218  Z= 0.284
  Chirality :  0.039   0.135   1348
  Planarity :  0.004   0.041   1378
  Dihedral  :  8.241 144.760   1104
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 17.84 %
    Favored  : 77.95 %
  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:  1.92 (0.27), residues: 1012
  helix:  1.89 (0.19), residues: 716
  sheet: -0.47 (0.74), residues: 54
  loop : -0.05 (0.42), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 635 
 HIS   0.009   0.001   HIS A 132 
 PHE   0.022   0.001   PHE A 598 
 TYR   0.014   0.001   TYR A 984 
 ARG   0.007   0.000   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  577)
  hydrogen bonds       : angle       4.12714 ( 1701)
  covalent geometry    : bond        0.00309 ( 8267)
  covalent geometry    : angle       0.54499 (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
  281 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 244
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8348 (mm) cc_final: 0.7905 (mt)
REVERT: A  134 ASP cc_start: 0.7543 (m-30) cc_final: 0.7140 (p0)
REVERT: A  149 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6837 (tm-30)
REVERT: A  158 THR cc_start: 0.7984 (p) cc_final: 0.7775 (m)
REVERT: A  160 MET cc_start: 0.6969 (mmt) cc_final: 0.6690 (mmt)
REVERT: A  199 MET cc_start: 0.7788 (mmm) cc_final: 0.7506 (mmm)
REVERT: A  205 MET cc_start: 0.7715 (tpp) cc_final: 0.7117 (mmm)
REVERT: A  216 LEU cc_start: 0.8725 (mt) cc_final: 0.8435 (mp)
REVERT: A  233 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6415 (tt0)
REVERT: A  373 THR cc_start: 0.7528 (m) cc_final: 0.7319 (m)
REVERT: A  383 MET cc_start: 0.7922 (mmm) cc_final: 0.7569 (tpp)
REVERT: A  443 GLU cc_start: 0.7501 (tp30) cc_final: 0.7203 (tp30)
REVERT: A  500 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7259 (tpp80)
REVERT: A  534 ASP cc_start: 0.7443 (t0) cc_final: 0.7032 (t0)
REVERT: A  579 MET cc_start: 0.5987 (tmm) cc_final: 0.5659 (tmm)
REVERT: A  583 ARG cc_start: 0.7708 (tmm-80) cc_final: 0.7458 (ttp-170)
REVERT: A  585 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6863 (ttp-110)
REVERT: A  588 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7562 (ttpp)
REVERT: A  629 ASP cc_start: 0.8230 (t70) cc_final: 0.7992 (t0)
REVERT: A  705 MET cc_start: 0.5425 (mmt) cc_final: 0.3886 (mmm)
REVERT: A  810 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5824 (mpp)
REVERT: A  823 LEU cc_start: 0.8266 (mt) cc_final: 0.8043 (mt)
REVERT: A  835 LEU cc_start: 0.8630 (tp) cc_final: 0.8391 (tt)
REVERT: A  863 ILE cc_start: 0.7278 (mm) cc_final: 0.6601 (mm)
REVERT: A  867 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7650 (mm)
REVERT: A  872 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6284 (mm-30)
REVERT: A  880 LYS cc_start: 0.8358 (tttt) cc_final: 0.7934 (ttpt)
REVERT: A  938 MET cc_start: 0.7803 (tpp) cc_final: 0.7382 (ttm)
REVERT: A  946 SER cc_start: 0.8107 (p) cc_final: 0.7715 (t)
REVERT: A  986 GLU cc_start: 0.7100 (tt0) cc_final: 0.6283 (tt0)
REVERT: A  990 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6645 (mtm-85)
REVERT: A  994 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A 1035 TYR cc_start: 0.7989 (m-80) cc_final: 0.7728 (m-10)
REVERT: A 1058 THR cc_start: 0.8198 (m) cc_final: 0.7920 (p)
REVERT: A 1059 CYS cc_start: 0.7262 (m) cc_final: 0.7010 (m)
REVERT: A 1082 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6909 (tt)
REVERT: A 1085 SER cc_start: 0.8380 (t) cc_final: 0.8107 (p)
REVERT: A 1098 ILE cc_start: 0.8769 (tp) cc_final: 0.8527 (tp)
REVERT: A 1105 GLU cc_start: 0.7144 (pp20) cc_final: 0.6829 (pp20)
REVERT: A 1145 VAL cc_start: 0.8554 (t) cc_final: 0.8225 (p)
REVERT: A 1189 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7567 (m)
  outliers start: 37
  outliers final: 26
  residues processed: 255
  average time/residue: 0.2359
  time to fit residues: 79.1707
Evaluate side-chains
  266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  296 ASP
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  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 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 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:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 56 optimal weight:    0.0970
   chunk 54 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 90 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 157 HIS
A 877 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.130006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111956 restraints weight = 13086.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115288 restraints weight = 5938.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.117402 restraints weight = 3419.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3481

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= 0.125
  Angle     :  0.550   8.719  11218  Z= 0.285
  Chirality :  0.038   0.133   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.236 145.426   1104
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.86 %
    Favored  : 77.27 %
  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:  2.02 (0.19), residues: 707
  sheet: -0.41 (0.75), residues: 52
  loop : -0.01 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 635 
 HIS   0.006   0.001   HIS A 132 
 PHE   0.017   0.001   PHE A 598 
 TYR   0.013   0.001   TYR A 984 
 ARG   0.007   0.000   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  577)
  hydrogen bonds       : angle       4.06820 ( 1701)
  covalent geometry    : bond        0.00267 ( 8267)
  covalent geometry    : angle       0.55028 (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
  276 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 242
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  108 ILE cc_start: 0.8324 (mm) cc_final: 0.7863 (mt)
REVERT: A  149 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6861 (tm-30)
REVERT: A  160 MET cc_start: 0.6937 (mmt) cc_final: 0.6663 (mmt)
REVERT: A  164 SER cc_start: 0.8421 (m) cc_final: 0.8159 (p)
REVERT: A  168 ILE cc_start: 0.8284 (tt) cc_final: 0.7640 (pt)
REVERT: A  199 MET cc_start: 0.7769 (mmm) cc_final: 0.7499 (mmm)
REVERT: A  205 MET cc_start: 0.7669 (tpp) cc_final: 0.7109 (mmp)
REVERT: A  216 LEU cc_start: 0.8693 (mt) cc_final: 0.8455 (mp)
REVERT: A  219 ASP cc_start: 0.7321 (t0) cc_final: 0.6964 (t0)
REVERT: A  233 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6479 (tt0)
REVERT: A  383 MET cc_start: 0.7867 (mmm) cc_final: 0.7544 (tpp)
REVERT: A  424 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: A  500 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7250 (tpp80)
REVERT: A  534 ASP cc_start: 0.7448 (t0) cc_final: 0.7036 (t0)
REVERT: A  579 MET cc_start: 0.5909 (tmm) cc_final: 0.5615 (tmm)
REVERT: A  583 ARG cc_start: 0.7710 (tmm-80) cc_final: 0.7318 (ttp80)
REVERT: A  588 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7515 (ttpp)
REVERT: A  621 GLU cc_start: 0.7188 (tp30) cc_final: 0.6964 (tp30)
REVERT: A  644 LEU cc_start: 0.8126 (mt) cc_final: 0.7596 (mm)
REVERT: A  648 LEU cc_start: 0.8374 (mp) cc_final: 0.8171 (mp)
REVERT: A  705 MET cc_start: 0.5353 (mmt) cc_final: 0.3854 (mmm)
REVERT: A  810 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5638 (mpp)
REVERT: A  811 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.6001 (mm)
REVERT: A  815 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8096 (ttpp)
REVERT: A  823 LEU cc_start: 0.8253 (mt) cc_final: 0.8023 (mt)
REVERT: A  828 LYS cc_start: 0.8118 (tppt) cc_final: 0.7710 (mmtm)
REVERT: A  835 LEU cc_start: 0.8595 (tp) cc_final: 0.8390 (tt)
REVERT: A  863 ILE cc_start: 0.7200 (mm) cc_final: 0.6328 (mm)
REVERT: A  867 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7555 (mm)
REVERT: A  872 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6289 (mm-30)
REVERT: A  880 LYS cc_start: 0.8333 (tttt) cc_final: 0.7881 (ttpt)
REVERT: A  938 MET cc_start: 0.7807 (tpp) cc_final: 0.7394 (ttm)
REVERT: A  946 SER cc_start: 0.8149 (p) cc_final: 0.7720 (t)
REVERT: A  986 GLU cc_start: 0.7105 (tt0) cc_final: 0.6289 (tt0)
REVERT: A  994 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7516 (tm-30)
REVERT: A 1035 TYR cc_start: 0.7942 (m-80) cc_final: 0.7429 (m-10)
REVERT: A 1058 THR cc_start: 0.8191 (m) cc_final: 0.7905 (p)
REVERT: A 1059 CYS cc_start: 0.7196 (m) cc_final: 0.6932 (m)
REVERT: A 1082 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6939 (tt)
REVERT: A 1085 SER cc_start: 0.8344 (t) cc_final: 0.8067 (p)
REVERT: A 1098 ILE cc_start: 0.8729 (tp) cc_final: 0.8482 (tp)
REVERT: A 1105 GLU cc_start: 0.7111 (pp20) cc_final: 0.6808 (pp20)
REVERT: A 1145 VAL cc_start: 0.8546 (t) cc_final: 0.8281 (p)
REVERT: A 1189 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7615 (m)
  outliers start: 34
  outliers final: 22
  residues processed: 255
  average time/residue: 0.2631
  time to fit residues: 89.4834
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  : 0.878 
-------------------------------------------------------------------------------
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  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  580 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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 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 1189 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 26 optimal weight:    0.1980
   chunk 6 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.129493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111565 restraints weight = 13102.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.114870 restraints weight = 5924.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.116974 restraints weight = 3404.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8267  Z= 0.152
  Angle     :  0.568   8.726  11218  Z= 0.296
  Chirality :  0.040   0.142   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.229 145.370   1104
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.89 %
    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:  1.95 (0.27), residues: 1012
  helix:  1.92 (0.19), residues: 705
  sheet: -0.54 (0.74), residues: 54
  loop :  0.04 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 595 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.017   0.001   PHE A 598 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.007   0.001   ARG A 990 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  577)
  hydrogen bonds       : angle       4.09847 ( 1701)
  covalent geometry    : bond        0.00343 ( 8267)
  covalent geometry    : angle       0.56814 (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
  270 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 238
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7091 (mptt) cc_final: 0.6883 (mppt)
REVERT: A  108 ILE cc_start: 0.8322 (mm) cc_final: 0.7879 (mt)
REVERT: A  149 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6754 (tm-30)
REVERT: A  160 MET cc_start: 0.7008 (mmt) cc_final: 0.6687 (mmt)
REVERT: A  199 MET cc_start: 0.7756 (mmm) cc_final: 0.7505 (mmm)
REVERT: A  205 MET cc_start: 0.7582 (tpp) cc_final: 0.7326 (mmm)
REVERT: A  216 LEU cc_start: 0.8680 (mt) cc_final: 0.8450 (mp)
REVERT: A  219 ASP cc_start: 0.7299 (t0) cc_final: 0.6927 (t0)
REVERT: A  233 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6436 (tt0)
REVERT: A  373 THR cc_start: 0.7518 (m) cc_final: 0.7311 (m)
REVERT: A  383 MET cc_start: 0.7947 (mmm) cc_final: 0.7613 (tpp)
REVERT: A  424 ILE cc_start: 0.8314 (tp) cc_final: 0.7962 (tp)
REVERT: A  443 GLU cc_start: 0.7531 (tp30) cc_final: 0.7217 (tp30)
REVERT: A  500 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7220 (tpp80)
REVERT: A  534 ASP cc_start: 0.7465 (t0) cc_final: 0.7119 (t0)
REVERT: A  579 MET cc_start: 0.5992 (tmm) cc_final: 0.5683 (tmm)
REVERT: A  583 ARG cc_start: 0.7733 (tmm-80) cc_final: 0.7328 (ttp80)
REVERT: A  588 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7554 (ttpp)
REVERT: A  621 GLU cc_start: 0.7242 (tp30) cc_final: 0.6952 (tp30)
REVERT: A  633 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7938 (mtmm)
REVERT: A  648 LEU cc_start: 0.8388 (mp) cc_final: 0.8182 (mp)
REVERT: A  705 MET cc_start: 0.5278 (mmt) cc_final: 0.4322 (mmt)
REVERT: A  810 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5849 (mpp)
REVERT: A  811 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6081 (mm)
REVERT: A  823 LEU cc_start: 0.8278 (mt) cc_final: 0.8066 (mt)
REVERT: A  828 LYS cc_start: 0.8113 (tppt) cc_final: 0.7712 (mmtm)
REVERT: A  856 ARG cc_start: 0.6970 (ptt180) cc_final: 0.6527 (ptt180)
REVERT: A  863 ILE cc_start: 0.7256 (mm) cc_final: 0.6395 (mm)
REVERT: A  867 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (mm)
REVERT: A  872 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6265 (mm-30)
REVERT: A  878 VAL cc_start: 0.8435 (p) cc_final: 0.8177 (t)
REVERT: A  880 LYS cc_start: 0.8324 (tttt) cc_final: 0.7893 (ttpt)
REVERT: A  938 MET cc_start: 0.7806 (tpp) cc_final: 0.7396 (ttm)
REVERT: A  946 SER cc_start: 0.8150 (p) cc_final: 0.7745 (t)
REVERT: A  966 ASP cc_start: 0.7001 (t0) cc_final: 0.6771 (t70)
REVERT: A  986 GLU cc_start: 0.7125 (tt0) cc_final: 0.6311 (tt0)
REVERT: A 1035 TYR cc_start: 0.7941 (m-80) cc_final: 0.7728 (m-10)
REVERT: A 1058 THR cc_start: 0.8207 (m) cc_final: 0.7883 (p)
REVERT: A 1059 CYS cc_start: 0.7229 (m) cc_final: 0.6960 (m)
REVERT: A 1082 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7005 (tt)
REVERT: A 1085 SER cc_start: 0.8387 (t) cc_final: 0.8111 (p)
REVERT: A 1098 ILE cc_start: 0.8764 (tp) cc_final: 0.8496 (tp)
REVERT: A 1105 GLU cc_start: 0.7072 (pp20) cc_final: 0.6754 (pp20)
REVERT: A 1109 PHE cc_start: 0.6693 (m-10) cc_final: 0.6283 (m-80)
REVERT: A 1189 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7599 (m)
  outliers start: 32
  outliers final: 21
  residues processed: 249
  average time/residue: 0.2294
  time to fit residues: 75.4269
Evaluate side-chains
  258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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  378 VAL
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  628 VAL
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  811 LEU
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  956 LEU
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 1189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   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 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 = 0.3628 r_free = 0.3628 target = 0.129791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111839 restraints weight = 13178.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115134 restraints weight = 5961.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.117223 restraints weight = 3407.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8267  Z= 0.148
  Angle     :  0.579   8.677  11218  Z= 0.298
  Chirality :  0.040   0.148   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.250 145.870   1104
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.57 %
    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:  1.92 (0.27), residues: 1012
  helix:  1.91 (0.19), residues: 706
  sheet: -0.56 (0.74), residues: 54
  loop : -0.03 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 595 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.026   0.001   PHE A 268 
 TYR   0.008   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  577)
  hydrogen bonds       : angle       4.08475 ( 1701)
  covalent geometry    : bond        0.00333 ( 8267)
  covalent geometry    : angle       0.57924 (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
  265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 235
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7093 (mptt) cc_final: 0.6876 (mppt)
REVERT: A  108 ILE cc_start: 0.8315 (mm) cc_final: 0.7862 (mt)
REVERT: A  149 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: A  160 MET cc_start: 0.7015 (mmt) cc_final: 0.6703 (mmt)
REVERT: A  168 ILE cc_start: 0.8255 (tt) cc_final: 0.7683 (pt)
REVERT: A  174 LEU cc_start: 0.7546 (tp) cc_final: 0.7256 (tp)
REVERT: A  199 MET cc_start: 0.7709 (mmm) cc_final: 0.7486 (mmm)
REVERT: A  216 LEU cc_start: 0.8674 (mt) cc_final: 0.8467 (mp)
REVERT: A  219 ASP cc_start: 0.7282 (t0) cc_final: 0.6964 (t0)
REVERT: A  233 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6457 (tt0)
REVERT: A  284 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7676 (mmtm)
REVERT: A  383 MET cc_start: 0.7981 (mmm) cc_final: 0.7679 (tpp)
REVERT: A  424 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7968 (tp)
REVERT: A  443 GLU cc_start: 0.7540 (tp30) cc_final: 0.7271 (tp30)
REVERT: A  500 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7217 (tpp80)
REVERT: A  534 ASP cc_start: 0.7471 (t0) cc_final: 0.7120 (t0)
REVERT: A  573 ARG cc_start: 0.7061 (tpp80) cc_final: 0.6825 (tpp80)
REVERT: A  579 MET cc_start: 0.5929 (tmm) cc_final: 0.5589 (tmm)
REVERT: A  583 ARG cc_start: 0.7714 (tmm-80) cc_final: 0.7348 (ttp80)
REVERT: A  585 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.6706 (ttp-110)
REVERT: A  588 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7553 (ttpp)
REVERT: A  648 LEU cc_start: 0.8409 (mp) cc_final: 0.8198 (mp)
REVERT: A  705 MET cc_start: 0.5175 (mmt) cc_final: 0.4180 (mmt)
REVERT: A  810 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5719 (mpp)
REVERT: A  811 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6144 (mm)
REVERT: A  828 LYS cc_start: 0.8105 (tppt) cc_final: 0.7717 (mmtm)
REVERT: A  835 LEU cc_start: 0.8594 (tt) cc_final: 0.8387 (tp)
REVERT: A  856 ARG cc_start: 0.6957 (ptt180) cc_final: 0.6313 (ptt180)
REVERT: A  863 ILE cc_start: 0.7220 (mm) cc_final: 0.6306 (mm)
REVERT: A  867 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7538 (mm)
REVERT: A  872 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6254 (mm-30)
REVERT: A  878 VAL cc_start: 0.8470 (p) cc_final: 0.8191 (t)
REVERT: A  880 LYS cc_start: 0.8330 (tttt) cc_final: 0.7926 (ttpt)
REVERT: A  938 MET cc_start: 0.7778 (tpp) cc_final: 0.7375 (ttm)
REVERT: A  946 SER cc_start: 0.8164 (p) cc_final: 0.7752 (t)
REVERT: A  986 GLU cc_start: 0.7141 (tt0) cc_final: 0.6323 (tt0)
REVERT: A 1058 THR cc_start: 0.8196 (m) cc_final: 0.7870 (p)
REVERT: A 1059 CYS cc_start: 0.7209 (m) cc_final: 0.6948 (m)
REVERT: A 1082 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7011 (tt)
REVERT: A 1085 SER cc_start: 0.8396 (t) cc_final: 0.8114 (p)
REVERT: A 1098 ILE cc_start: 0.8743 (tp) cc_final: 0.8488 (tp)
REVERT: A 1105 GLU cc_start: 0.7043 (pp20) cc_final: 0.6717 (pp20)
REVERT: A 1109 PHE cc_start: 0.6623 (m-10) cc_final: 0.6117 (m-80)
REVERT: A 1189 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7547 (m)
  outliers start: 30
  outliers final: 21
  residues processed: 246
  average time/residue: 0.2246
  time to fit residues: 72.8455
Evaluate side-chains
  258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 231
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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  424 ILE
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  729 GLU
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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  956 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 70 optimal weight:    0.2980
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.111388 restraints weight = 13232.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114694 restraints weight = 6022.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.116802 restraints weight = 3462.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8267  Z= 0.161
  Angle     :  0.590   8.636  11218  Z= 0.305
  Chirality :  0.040   0.155   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.273 146.102   1104
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.80 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.27), residues: 1012
  helix:  1.88 (0.20), residues: 705
  sheet: -0.59 (0.74), residues: 54
  loop : -0.09 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 595 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.017   0.001   PHE A 598 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  577)
  hydrogen bonds       : angle       4.10609 ( 1701)
  covalent geometry    : bond        0.00362 ( 8267)
  covalent geometry    : angle       0.58997 (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
  267 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 235
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7091 (mptt) cc_final: 0.6867 (mppt)
REVERT: A  108 ILE cc_start: 0.8316 (mm) cc_final: 0.7870 (mt)
REVERT: A  149 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6739 (tm-30)
REVERT: A  160 MET cc_start: 0.7051 (mmt) cc_final: 0.6736 (mmt)
REVERT: A  168 ILE cc_start: 0.8263 (tt) cc_final: 0.7683 (pt)
REVERT: A  174 LEU cc_start: 0.7501 (tp) cc_final: 0.7239 (tp)
REVERT: A  199 MET cc_start: 0.7721 (mmm) cc_final: 0.7499 (mmm)
REVERT: A  219 ASP cc_start: 0.7271 (t0) cc_final: 0.6964 (t0)
REVERT: A  233 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6477 (tt0)
REVERT: A  284 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7675 (mmtm)
REVERT: A  383 MET cc_start: 0.7994 (mmm) cc_final: 0.7678 (tpp)
REVERT: A  424 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7967 (tp)
REVERT: A  443 GLU cc_start: 0.7478 (tp30) cc_final: 0.7217 (tp30)
REVERT: A  500 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7218 (tpp80)
REVERT: A  534 ASP cc_start: 0.7468 (t0) cc_final: 0.7125 (t0)
REVERT: A  579 MET cc_start: 0.5958 (tmm) cc_final: 0.5642 (tmm)
REVERT: A  583 ARG cc_start: 0.7727 (tmm-80) cc_final: 0.7525 (ttp-170)
REVERT: A  585 ARG cc_start: 0.6946 (ttp-110) cc_final: 0.6693 (ttp-110)
REVERT: A  588 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7427 (ttpp)
REVERT: A  591 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8068 (mtpt)
REVERT: A  621 GLU cc_start: 0.7302 (tp30) cc_final: 0.7095 (tp30)
REVERT: A  648 LEU cc_start: 0.8410 (mp) cc_final: 0.8177 (mp)
REVERT: A  705 MET cc_start: 0.5202 (mmt) cc_final: 0.4229 (mmt)
REVERT: A  729 GLU cc_start: 0.3660 (OUTLIER) cc_final: 0.2325 (mt-10)
REVERT: A  810 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5817 (mpp)
REVERT: A  828 LYS cc_start: 0.8113 (tppt) cc_final: 0.7724 (mmtm)
REVERT: A  863 ILE cc_start: 0.7222 (mm) cc_final: 0.6367 (mm)
REVERT: A  867 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7593 (mm)
REVERT: A  872 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6241 (mm-30)
REVERT: A  878 VAL cc_start: 0.8457 (p) cc_final: 0.8196 (t)
REVERT: A  880 LYS cc_start: 0.8361 (tttt) cc_final: 0.7974 (ttpt)
REVERT: A  938 MET cc_start: 0.7788 (tpp) cc_final: 0.7384 (ttm)
REVERT: A  946 SER cc_start: 0.8149 (p) cc_final: 0.7738 (t)
REVERT: A  966 ASP cc_start: 0.6887 (t0) cc_final: 0.6664 (t70)
REVERT: A 1058 THR cc_start: 0.8229 (m) cc_final: 0.7880 (p)
REVERT: A 1059 CYS cc_start: 0.7236 (m) cc_final: 0.6965 (m)
REVERT: A 1082 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7128 (tt)
REVERT: A 1085 SER cc_start: 0.8383 (t) cc_final: 0.8110 (p)
REVERT: A 1098 ILE cc_start: 0.8751 (tp) cc_final: 0.8478 (tp)
REVERT: A 1105 GLU cc_start: 0.7026 (pp20) cc_final: 0.6704 (pp20)
  outliers start: 32
  outliers final: 24
  residues processed: 245
  average time/residue: 0.2187
  time to fit residues: 70.7041
Evaluate side-chains
  262 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 233
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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  296 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  628 VAL
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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue 1005 LEU
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 1145 VAL
Chi-restraints excluded: chain A residue 1147 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.0270
   chunk 0 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.129957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111866 restraints weight = 13066.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115079 restraints weight = 5889.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.117082 restraints weight = 3376.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8267  Z= 0.163
  Angle     :  0.621  11.649  11218  Z= 0.320
  Chirality :  0.041   0.281   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.293 146.305   1104
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.93 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.27), residues: 1012
  helix:  1.78 (0.20), residues: 711
  sheet: -0.52 (0.75), residues: 54
  loop :  0.00 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 595 
 HIS   0.006   0.001   HIS A 157 
 PHE   0.016   0.001   PHE A 598 
 TYR   0.018   0.001   TYR A 267 
 ARG   0.006   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  577)
  hydrogen bonds       : angle       4.12693 ( 1701)
  covalent geometry    : bond        0.00366 ( 8267)
  covalent geometry    : angle       0.62089 (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
  270 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 241
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7083 (mptt) cc_final: 0.6857 (mppt)
REVERT: A  108 ILE cc_start: 0.8331 (mm) cc_final: 0.7890 (mt)
REVERT: A  149 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6746 (tm-30)
REVERT: A  157 HIS cc_start: 0.6410 (m-70) cc_final: 0.5573 (m90)
REVERT: A  164 SER cc_start: 0.8390 (m) cc_final: 0.8189 (p)
REVERT: A  168 ILE cc_start: 0.8281 (tt) cc_final: 0.7660 (pt)
REVERT: A  174 LEU cc_start: 0.7541 (tp) cc_final: 0.7317 (tp)
REVERT: A  199 MET cc_start: 0.7703 (mmm) cc_final: 0.7489 (mmm)
REVERT: A  219 ASP cc_start: 0.7243 (t0) cc_final: 0.6952 (t0)
REVERT: A  233 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6463 (tt0)
REVERT: A  284 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7664 (mmtm)
REVERT: A  373 THR cc_start: 0.7522 (m) cc_final: 0.7313 (m)
REVERT: A  383 MET cc_start: 0.7992 (mmm) cc_final: 0.7636 (tpp)
REVERT: A  424 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7972 (tp)
REVERT: A  443 GLU cc_start: 0.7480 (tp30) cc_final: 0.7170 (tp30)
REVERT: A  500 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7199 (tpp80)
REVERT: A  534 ASP cc_start: 0.7472 (t0) cc_final: 0.7124 (t0)
REVERT: A  579 MET cc_start: 0.5946 (tmm) cc_final: 0.5610 (tmm)
REVERT: A  588 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7446 (ttpp)
REVERT: A  591 LYS cc_start: 0.8305 (mtpt) cc_final: 0.8055 (mtpt)
REVERT: A  621 GLU cc_start: 0.7308 (tp30) cc_final: 0.7107 (tp30)
REVERT: A  633 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7882 (mtmm)
REVERT: A  705 MET cc_start: 0.5189 (mmt) cc_final: 0.4211 (mmt)
REVERT: A  729 GLU cc_start: 0.3548 (OUTLIER) cc_final: 0.2239 (mt-10)
REVERT: A  810 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5871 (mpp)
REVERT: A  828 LYS cc_start: 0.8117 (tppt) cc_final: 0.7730 (mmtm)
REVERT: A  835 LEU cc_start: 0.8577 (tp) cc_final: 0.8348 (tt)
REVERT: A  863 ILE cc_start: 0.7247 (mm) cc_final: 0.6373 (mm)
REVERT: A  867 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7538 (mm)
REVERT: A  872 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6237 (mm-30)
REVERT: A  878 VAL cc_start: 0.8465 (p) cc_final: 0.8213 (t)
REVERT: A  880 LYS cc_start: 0.8368 (tttt) cc_final: 0.7915 (ttpp)
REVERT: A  938 MET cc_start: 0.7766 (tpp) cc_final: 0.7349 (ttm)
REVERT: A  946 SER cc_start: 0.8150 (p) cc_final: 0.7732 (t)
REVERT: A  966 ASP cc_start: 0.6839 (t0) cc_final: 0.6634 (t70)
REVERT: A 1050 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8317 (mmmt)
REVERT: A 1058 THR cc_start: 0.8239 (m) cc_final: 0.7869 (p)
REVERT: A 1059 CYS cc_start: 0.7259 (m) cc_final: 0.6973 (m)
REVERT: A 1085 SER cc_start: 0.8348 (t) cc_final: 0.8083 (p)
REVERT: A 1098 ILE cc_start: 0.8717 (tp) cc_final: 0.8448 (tp)
REVERT: A 1105 GLU cc_start: 0.7031 (pp20) cc_final: 0.6705 (pp20)
REVERT: A 1189 VAL cc_start: 0.7804 (m) cc_final: 0.7431 (p)
REVERT: A 1190 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7201 (mmm-85)
REVERT: A 1191 ASN cc_start: 0.7731 (m-40) cc_final: 0.7481 (m110)
  outliers start: 29
  outliers final: 24
  residues processed: 250
  average time/residue: 0.2252
  time to fit residues: 74.1176
Evaluate side-chains
  266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 238
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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  296 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  628 VAL
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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  877 GLN
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1147 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.130432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.112350 restraints weight = 13206.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.115577 restraints weight = 5934.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117581 restraints weight = 3398.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8267  Z= 0.164
  Angle     :  0.625   8.974  11218  Z= 0.324
  Chirality :  0.041   0.250   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.312 146.671   1104
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.93 %
    Favored  : 74.55 %
  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:  1.74 (0.20), residues: 712
  sheet: -0.46 (0.76), residues: 54
  loop : -0.03 (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 A1120 
 PHE   0.015   0.001   PHE A 598 
 TYR   0.016   0.001   TYR A 267 
 ARG   0.006   0.001   ARG A 812 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  577)
  hydrogen bonds       : angle       4.14045 ( 1701)
  covalent geometry    : bond        0.00370 ( 8267)
  covalent geometry    : angle       0.62491 (11218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4511.06 seconds
wall clock time: 81 minutes 17.76 seconds (4877.76 seconds total)