Starting phenix.real_space_refine
on Fri Aug 22 22:33:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd9_17607/08_2025/8pd9_17607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd9_17607/08_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_17607/08_2025/8pd9_17607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd9_17607/08_2025/8pd9_17607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd9_17607/08_2025/8pd9_17607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd9_17607/08_2025/8pd9_17607.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.14, per 1000 atoms: 0.26
  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: 0.87
  Conformation dependent library (CDL) restraints added in 332.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.61

  Time building geometry restraints manager: 1.09 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:             2.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.840
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.890
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG A1053 
 TYR   0.069   0.002   TYR A1009 
 PHE   0.018   0.002   PHE A1032 
 TRP   0.042   0.003   TRP A 962 
 HIS   0.002   0.000   HIS A 928 

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

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 0.321 
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: 0.6344 (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: 0.1113
  time to fit residues: 44.6996
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  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7786

-------------------------------------------------------------------------------
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
A1120 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.129386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111095 restraints weight = 12941.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.114371 restraints weight = 5927.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116478 restraints weight = 3452.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.117782 restraints weight = 2345.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.118527 restraints weight = 1798.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8267  Z= 0.188
  Angle     :  0.588   8.822  11218  Z= 0.310
  Chirality :  0.041   0.160   1348
  Planarity :  0.004   0.038   1378
  Dihedral  :  8.249 142.268   1104
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.32 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.27), residues: 1012
  helix:  1.93 (0.19), residues: 711
  sheet: -0.85 (0.64), residues: 61
  loop :  0.63 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 990 
 TYR   0.016   0.001   TYR A 984 
 PHE   0.030   0.002   PHE A 739 
 TRP   0.018   0.002   TRP A 962 
 HIS   0.003   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8267)
  covalent geometry    : angle       0.58833 (11218)
  hydrogen bonds       : bond        0.05379 (  577)
  hydrogen bonds       : angle       4.52491 ( 1701)

*********************** 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
  280 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 261
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8319 (mm) cc_final: 0.7893 (mt)
REVERT: A  134 ASP cc_start: 0.7551 (m-30) cc_final: 0.7180 (p0)
REVERT: A  149 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6965 (tm-30)
REVERT: A  155 ASP cc_start: 0.6468 (t0) cc_final: 0.6112 (t0)
REVERT: A  160 MET cc_start: 0.6892 (mmt) cc_final: 0.6549 (mmt)
REVERT: A  174 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7153 (tp)
REVERT: A  209 ASP cc_start: 0.7427 (t0) cc_final: 0.7006 (t0)
REVERT: A  273 VAL cc_start: 0.8595 (t) cc_final: 0.8365 (m)
REVERT: A  443 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6915 (tm-30)
REVERT: A  475 GLN cc_start: 0.7910 (tp40) cc_final: 0.7663 (tp-100)
REVERT: A  500 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7325 (tpp80)
REVERT: A  579 MET cc_start: 0.6343 (tmm) cc_final: 0.5572 (tmm)
REVERT: A  583 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7528 (ttp80)
REVERT: A  588 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7520 (ttpp)
REVERT: A  591 LYS cc_start: 0.8230 (mtpp) cc_final: 0.8012 (mtpt)
REVERT: A  598 PHE cc_start: 0.8674 (t80) cc_final: 0.8462 (t80)
REVERT: A  609 ARG cc_start: 0.6909 (tpp80) cc_final: 0.6553 (tpp80)
REVERT: A  628 VAL cc_start: 0.8362 (p) cc_final: 0.7247 (m)
REVERT: A  705 MET cc_start: 0.5654 (mmt) cc_final: 0.4279 (mmm)
REVERT: A  810 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5984 (mpp)
REVERT: A  812 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7982 (ttp80)
REVERT: A  828 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7774 (mmtp)
REVERT: A  856 ARG cc_start: 0.6911 (ptp90) cc_final: 0.5578 (ptp90)
REVERT: A  863 ILE cc_start: 0.7409 (mm) cc_final: 0.7017 (mm)
REVERT: A  872 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6191 (mm-30)
REVERT: A  880 LYS cc_start: 0.8334 (tttt) cc_final: 0.7965 (ttpp)
REVERT: A  910 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8044 (ttm170)
REVERT: A  915 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6843 (mt-10)
REVERT: A  938 MET cc_start: 0.7793 (tpp) cc_final: 0.7293 (ttm)
REVERT: A  946 SER cc_start: 0.8064 (p) cc_final: 0.7759 (t)
REVERT: A 1058 THR cc_start: 0.8210 (m) cc_final: 0.7809 (p)
REVERT: A 1059 CYS cc_start: 0.7292 (m) cc_final: 0.6933 (m)
REVERT: A 1085 SER cc_start: 0.8440 (t) cc_final: 0.8068 (p)
REVERT: A 1096 ILE cc_start: 0.8853 (mm) cc_final: 0.8518 (mt)
REVERT: A 1098 ILE cc_start: 0.8723 (tp) cc_final: 0.8514 (tt)
REVERT: A 1105 GLU cc_start: 0.7635 (tt0) cc_final: 0.7411 (pp20)
REVERT: A 1189 VAL cc_start: 0.7805 (m) cc_final: 0.7506 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 268
  average time/residue: 0.1154
  time to fit residues: 39.8374
Evaluate side-chains
  259 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 248
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  640 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1127 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108541 restraints weight = 13107.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111752 restraints weight = 5973.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113774 restraints weight = 3458.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115069 restraints weight = 2360.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115867 restraints weight = 1804.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8267  Z= 0.191
  Angle     :  0.580   8.780  11218  Z= 0.307
  Chirality :  0.041   0.206   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.302 143.608   1104
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 16.02 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 1012
  helix:  1.78 (0.19), residues: 711
  sheet: -0.68 (0.68), residues: 61
  loop :  0.36 (0.44), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 856 
 TYR   0.011   0.001   TYR A1066 
 PHE   0.024   0.002   PHE A 739 
 TRP   0.013   0.002   TRP A 962 
 HIS   0.005   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8267)
  covalent geometry    : angle       0.57973 (11218)
  hydrogen bonds       : bond        0.05103 (  577)
  hydrogen bonds       : angle       4.35955 ( 1701)

*********************** 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
  280 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 247
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8375 (mm) cc_final: 0.7942 (mt)
REVERT: A  134 ASP cc_start: 0.7516 (m-30) cc_final: 0.7161 (p0)
REVERT: A  149 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6814 (tm-30)
REVERT: A  155 ASP cc_start: 0.6364 (t0) cc_final: 0.5907 (t0)
REVERT: A  157 HIS cc_start: 0.6521 (m-70) cc_final: 0.5829 (m90)
REVERT: A  160 MET cc_start: 0.6863 (mmt) cc_final: 0.6627 (mmt)
REVERT: A  174 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7261 (tp)
REVERT: A  199 MET cc_start: 0.7833 (mmm) cc_final: 0.7479 (mmm)
REVERT: A  205 MET cc_start: 0.7857 (tpp) cc_final: 0.7066 (mmm)
REVERT: A  209 ASP cc_start: 0.7403 (t0) cc_final: 0.6978 (t70)
REVERT: A  216 LEU cc_start: 0.8797 (mt) cc_final: 0.8431 (mp)
REVERT: A  233 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6500 (tt0)
REVERT: A  273 VAL cc_start: 0.8555 (t) cc_final: 0.8351 (m)
REVERT: A  367 MET cc_start: 0.7244 (mtp) cc_final: 0.6874 (mtm)
REVERT: A  383 MET cc_start: 0.8042 (mmm) cc_final: 0.7502 (tpp)
REVERT: A  443 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: A  475 GLN cc_start: 0.7842 (tp40) cc_final: 0.7426 (tp-100)
REVERT: A  490 LYS cc_start: 0.8296 (mtpp) cc_final: 0.8037 (mtmt)
REVERT: A  500 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7319 (tpp80)
REVERT: A  588 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7545 (ttpp)
REVERT: A  609 ARG cc_start: 0.6979 (tpp80) cc_final: 0.6710 (tpp80)
REVERT: A  705 MET cc_start: 0.5713 (mmt) cc_final: 0.4513 (mmm)
REVERT: A  810 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6053 (mpp)
REVERT: A  823 LEU cc_start: 0.8236 (mt) cc_final: 0.7980 (mt)
REVERT: A  828 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7756 (mmtm)
REVERT: A  835 LEU cc_start: 0.8704 (tp) cc_final: 0.8413 (tt)
REVERT: A  863 ILE cc_start: 0.7454 (mm) cc_final: 0.7133 (mm)
REVERT: A  867 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7733 (mp)
REVERT: A  872 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6287 (mm-30)
REVERT: A  880 LYS cc_start: 0.8408 (tttt) cc_final: 0.7947 (ttpt)
REVERT: A  887 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7500 (mtp85)
REVERT: A  938 MET cc_start: 0.7784 (tpp) cc_final: 0.7332 (ttm)
REVERT: A  946 SER cc_start: 0.8110 (p) cc_final: 0.7772 (t)
REVERT: A  986 GLU cc_start: 0.7011 (tt0) cc_final: 0.6402 (tt0)
REVERT: A 1033 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6485 (tp30)
REVERT: A 1035 TYR cc_start: 0.8023 (m-80) cc_final: 0.7789 (m-10)
REVERT: A 1058 THR cc_start: 0.8217 (m) cc_final: 0.7870 (p)
REVERT: A 1059 CYS cc_start: 0.7317 (m) cc_final: 0.7050 (m)
REVERT: A 1085 SER cc_start: 0.8389 (t) cc_final: 0.8084 (p)
REVERT: A 1098 ILE cc_start: 0.8777 (tp) cc_final: 0.8537 (tp)
REVERT: A 1118 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8209 (mttp)
REVERT: A 1145 VAL cc_start: 0.8546 (t) cc_final: 0.8213 (p)
REVERT: A 1189 VAL cc_start: 0.7783 (m) cc_final: 0.7561 (m)
  outliers start: 33
  outliers final: 22
  residues processed: 259
  average time/residue: 0.1075
  time to fit residues: 36.6018
Evaluate side-chains
  265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 239
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  640 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  900 GLN
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1129 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.3616 r_free = 0.3616 target = 0.128901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110971 restraints weight = 13377.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.114280 restraints weight = 6022.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.116372 restraints weight = 3454.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.117684 restraints weight = 2330.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.118516 restraints weight = 1768.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8267  Z= 0.146
  Angle     :  0.553   8.769  11218  Z= 0.288
  Chirality :  0.040   0.173   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.267 144.379   1104
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.59 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 1012
  helix:  1.86 (0.19), residues: 715
  sheet: -0.48 (0.73), residues: 54
  loop : -0.01 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 976 
 TYR   0.017   0.001   TYR A 984 
 PHE   0.016   0.001   PHE A 598 
 TRP   0.009   0.001   TRP A 962 
 HIS   0.005   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8267)
  covalent geometry    : angle       0.55289 (11218)
  hydrogen bonds       : bond        0.04571 (  577)
  hydrogen bonds       : angle       4.21462 ( 1701)

*********************** 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  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8366 (mm) cc_final: 0.7935 (mt)
REVERT: A  134 ASP cc_start: 0.7448 (m-30) cc_final: 0.7112 (p0)
REVERT: A  149 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6817 (tm-30)
REVERT: A  155 ASP cc_start: 0.6250 (t0) cc_final: 0.5883 (t0)
REVERT: A  160 MET cc_start: 0.6886 (mmt) cc_final: 0.6663 (mmt)
REVERT: A  199 MET cc_start: 0.7749 (mmm) cc_final: 0.7448 (mmm)
REVERT: A  205 MET cc_start: 0.7759 (tpp) cc_final: 0.7136 (mmm)
REVERT: A  216 LEU cc_start: 0.8791 (mt) cc_final: 0.8470 (mp)
REVERT: A  233 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6450 (tt0)
REVERT: A  367 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6778 (mtm)
REVERT: A  383 MET cc_start: 0.7930 (mmm) cc_final: 0.7531 (tpp)
REVERT: A  443 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: A  475 GLN cc_start: 0.7745 (tp40) cc_final: 0.7471 (tp40)
REVERT: A  490 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8054 (mtmt)
REVERT: A  500 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7247 (tpp80)
REVERT: A  534 ASP cc_start: 0.7519 (t0) cc_final: 0.7143 (t0)
REVERT: A  579 MET cc_start: 0.5967 (tmm) cc_final: 0.5566 (tmm)
REVERT: A  583 ARG cc_start: 0.7723 (tmm-80) cc_final: 0.7330 (ttp80)
REVERT: A  588 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7507 (ttpp)
REVERT: A  595 TRP cc_start: 0.7765 (m100) cc_final: 0.7473 (m100)
REVERT: A  599 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7224 (mt-10)
REVERT: A  609 ARG cc_start: 0.7010 (tpp80) cc_final: 0.6696 (tpp80)
REVERT: A  630 ASP cc_start: 0.7465 (m-30) cc_final: 0.7088 (m-30)
REVERT: A  648 LEU cc_start: 0.8449 (mp) cc_final: 0.8219 (mp)
REVERT: A  705 MET cc_start: 0.5609 (mmt) cc_final: 0.4479 (mmm)
REVERT: A  810 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5945 (mpp)
REVERT: A  815 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8089 (ttpp)
REVERT: A  823 LEU cc_start: 0.8210 (mt) cc_final: 0.7973 (mt)
REVERT: A  828 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7739 (mmtm)
REVERT: A  832 GLN cc_start: 0.8277 (tp40) cc_final: 0.8054 (tp40)
REVERT: A  835 LEU cc_start: 0.8696 (tp) cc_final: 0.8431 (tt)
REVERT: A  863 ILE cc_start: 0.7298 (mm) cc_final: 0.6923 (mm)
REVERT: A  864 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7628 (tp)
REVERT: A  872 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6355 (mm-30)
REVERT: A  878 VAL cc_start: 0.8473 (p) cc_final: 0.8261 (t)
REVERT: A  880 LYS cc_start: 0.8402 (tttt) cc_final: 0.7974 (ttpt)
REVERT: A  887 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7479 (mtp85)
REVERT: A  938 MET cc_start: 0.7804 (tpp) cc_final: 0.7371 (ttm)
REVERT: A  946 SER cc_start: 0.8142 (p) cc_final: 0.7759 (t)
REVERT: A  986 GLU cc_start: 0.7011 (tt0) cc_final: 0.6201 (tt0)
REVERT: A 1033 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6505 (tp30)
REVERT: A 1058 THR cc_start: 0.8211 (m) cc_final: 0.7882 (p)
REVERT: A 1059 CYS cc_start: 0.7288 (m) cc_final: 0.7014 (m)
REVERT: A 1085 SER cc_start: 0.8368 (t) cc_final: 0.8058 (p)
REVERT: A 1098 ILE cc_start: 0.8756 (tp) cc_final: 0.8518 (tp)
REVERT: A 1118 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7923 (mtpp)
REVERT: A 1145 VAL cc_start: 0.8566 (t) cc_final: 0.8228 (p)
REVERT: A 1189 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7562 (m)
  outliers start: 34
  outliers final: 20
  residues processed: 261
  average time/residue: 0.1078
  time to fit residues: 36.9370
Evaluate side-chains
  266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  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  373 THR
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  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1118 LYS
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 45 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0060
   chunk 97 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.5796

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110027 restraints weight = 13190.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.113341 restraints weight = 6016.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.115449 restraints weight = 3464.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116740 restraints weight = 2340.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117484 restraints weight = 1785.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3268

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= 0.153
  Angle     :  0.551   8.774  11218  Z= 0.288
  Chirality :  0.039   0.156   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.245 144.573   1104
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 16.59 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.27), residues: 1012
  helix:  1.80 (0.19), residues: 718
  sheet: -0.49 (0.74), residues: 53
  loop : -0.11 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 812 
 TYR   0.009   0.001   TYR A1035 
 PHE   0.021   0.001   PHE A 598 
 TRP   0.009   0.001   TRP A 962 
 HIS   0.009   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8267)
  covalent geometry    : angle       0.55075 (11218)
  hydrogen bonds       : bond        0.04493 (  577)
  hydrogen bonds       : angle       4.16837 ( 1701)

*********************** 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
  282 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 245
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8353 (mm) cc_final: 0.7870 (mt)
REVERT: A  149 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6820 (tm-30)
REVERT: A  155 ASP cc_start: 0.6316 (t0) cc_final: 0.5883 (t0)
REVERT: A  160 MET cc_start: 0.6952 (mmt) cc_final: 0.6700 (mmt)
REVERT: A  199 MET cc_start: 0.7747 (mmm) cc_final: 0.7512 (mmm)
REVERT: A  205 MET cc_start: 0.7655 (tpp) cc_final: 0.7097 (mmm)
REVERT: A  216 LEU cc_start: 0.8787 (mt) cc_final: 0.8454 (mp)
REVERT: A  233 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6445 (tt0)
REVERT: A  367 MET cc_start: 0.7182 (mtp) cc_final: 0.6965 (mtm)
REVERT: A  383 MET cc_start: 0.7895 (mmm) cc_final: 0.7529 (tpp)
REVERT: A  443 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6868 (tm-30)
REVERT: A  475 GLN cc_start: 0.7743 (tp40) cc_final: 0.7484 (tp40)
REVERT: A  500 ARG cc_start: 0.7591 (tpp80) cc_final: 0.7200 (tpp80)
REVERT: A  534 ASP cc_start: 0.7453 (t0) cc_final: 0.7086 (t0)
REVERT: A  579 MET cc_start: 0.5917 (tmm) cc_final: 0.5599 (tmm)
REVERT: A  583 ARG cc_start: 0.7726 (tmm-80) cc_final: 0.7388 (ttp80)
REVERT: A  588 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7465 (ttpp)
REVERT: A  595 TRP cc_start: 0.7775 (m100) cc_final: 0.7448 (m100)
REVERT: A  599 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: A  609 ARG cc_start: 0.7004 (tpp80) cc_final: 0.6779 (tpp80)
REVERT: A  630 ASP cc_start: 0.7476 (m-30) cc_final: 0.7211 (m-30)
REVERT: A  705 MET cc_start: 0.5631 (mmt) cc_final: 0.5078 (mmt)
REVERT: A  810 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5975 (mpp)
REVERT: A  823 LEU cc_start: 0.8220 (mt) cc_final: 0.8002 (mt)
REVERT: A  828 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7617 (mmtp)
REVERT: A  832 GLN cc_start: 0.8277 (tp40) cc_final: 0.8033 (tp40)
REVERT: A  835 LEU cc_start: 0.8641 (tp) cc_final: 0.8394 (tt)
REVERT: A  863 ILE cc_start: 0.7264 (mm) cc_final: 0.6928 (mm)
REVERT: A  864 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7613 (tp)
REVERT: A  872 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6331 (mm-30)
REVERT: A  880 LYS cc_start: 0.8407 (tttt) cc_final: 0.7954 (ttpt)
REVERT: A  887 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7479 (mtp85)
REVERT: A  938 MET cc_start: 0.7818 (tpp) cc_final: 0.7376 (ttm)
REVERT: A  946 SER cc_start: 0.8167 (p) cc_final: 0.7737 (t)
REVERT: A  986 GLU cc_start: 0.7096 (tt0) cc_final: 0.6262 (tt0)
REVERT: A  994 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A 1033 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6590 (tp30)
REVERT: A 1035 TYR cc_start: 0.7990 (m-10) cc_final: 0.7766 (m-10)
REVERT: A 1058 THR cc_start: 0.8214 (m) cc_final: 0.7879 (p)
REVERT: A 1059 CYS cc_start: 0.7275 (m) cc_final: 0.7024 (m)
REVERT: A 1082 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6958 (tt)
REVERT: A 1085 SER cc_start: 0.8351 (t) cc_final: 0.8085 (p)
REVERT: A 1098 ILE cc_start: 0.8779 (tp) cc_final: 0.8544 (tp)
REVERT: A 1105 GLU cc_start: 0.7067 (pp20) cc_final: 0.6765 (pp20)
REVERT: A 1145 VAL cc_start: 0.8557 (t) cc_final: 0.8229 (p)
REVERT: A 1189 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7626 (m)
  outliers start: 37
  outliers final: 25
  residues processed: 261
  average time/residue: 0.1031
  time to fit residues: 35.7924
Evaluate side-chains
  269 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 240
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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  132 HIS
Chi-restraints excluded: chain A residue  154 MET
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  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 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  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 78 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.109792 restraints weight = 13106.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.113110 restraints weight = 6058.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.115200 restraints weight = 3472.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.116374 restraints weight = 2342.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.117283 restraints weight = 1816.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8267  Z= 0.200
  Angle     :  0.580   8.757  11218  Z= 0.304
  Chirality :  0.041   0.168   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.281 144.709   1104
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 17.73 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.27), residues: 1012
  helix:  1.69 (0.19), residues: 715
  sheet: -0.68 (0.73), residues: 54
  loop : -0.24 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 812 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.017   0.002   PHE A 972 
 TRP   0.011   0.001   TRP A 635 
 HIS   0.008   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8267)
  covalent geometry    : angle       0.58022 (11218)
  hydrogen bonds       : bond        0.04830 (  577)
  hydrogen bonds       : angle       4.26257 ( 1701)

*********************** 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
  288 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 246
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8320 (mm) cc_final: 0.7877 (mt)
REVERT: A  134 ASP cc_start: 0.7268 (p0) cc_final: 0.7064 (p0)
REVERT: A  149 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6794 (tm-30)
REVERT: A  155 ASP cc_start: 0.6457 (t0) cc_final: 0.6005 (t0)
REVERT: A  160 MET cc_start: 0.6953 (mmt) cc_final: 0.6711 (mmt)
REVERT: A  164 SER cc_start: 0.8445 (m) cc_final: 0.8201 (p)
REVERT: A  205 MET cc_start: 0.7601 (tpp) cc_final: 0.7100 (mmm)
REVERT: A  216 LEU cc_start: 0.8737 (mt) cc_final: 0.8452 (mp)
REVERT: A  233 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6478 (tt0)
REVERT: A  367 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6732 (mtm)
REVERT: A  383 MET cc_start: 0.7945 (mmm) cc_final: 0.7594 (tpp)
REVERT: A  424 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7947 (tp)
REVERT: A  443 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6863 (tm-30)
REVERT: A  475 GLN cc_start: 0.7780 (tp40) cc_final: 0.7575 (tp40)
REVERT: A  500 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7236 (tpp80)
REVERT: A  534 ASP cc_start: 0.7479 (t0) cc_final: 0.7109 (t0)
REVERT: A  579 MET cc_start: 0.5925 (tmm) cc_final: 0.5607 (tmm)
REVERT: A  588 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7533 (ttpp)
REVERT: A  609 ARG cc_start: 0.7030 (tpp80) cc_final: 0.6828 (tpp80)
REVERT: A  630 ASP cc_start: 0.7474 (m-30) cc_final: 0.7229 (m-30)
REVERT: A  705 MET cc_start: 0.5570 (mmt) cc_final: 0.3873 (mmm)
REVERT: A  810 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.5900 (mpp)
REVERT: A  823 LEU cc_start: 0.8248 (mt) cc_final: 0.8033 (mt)
REVERT: A  828 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7604 (mmtp)
REVERT: A  835 LEU cc_start: 0.8625 (tp) cc_final: 0.8377 (tt)
REVERT: A  863 ILE cc_start: 0.7294 (mm) cc_final: 0.6944 (mm)
REVERT: A  864 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (tp)
REVERT: A  872 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6345 (mm-30)
REVERT: A  880 LYS cc_start: 0.8395 (tttt) cc_final: 0.7950 (ttpt)
REVERT: A  887 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7504 (mtp85)
REVERT: A  938 MET cc_start: 0.7773 (tpp) cc_final: 0.7386 (ttm)
REVERT: A  946 SER cc_start: 0.8193 (p) cc_final: 0.7748 (t)
REVERT: A  960 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7874 (p)
REVERT: A  986 GLU cc_start: 0.7110 (tt0) cc_final: 0.6296 (tt0)
REVERT: A 1033 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6636 (tp30)
REVERT: A 1035 TYR cc_start: 0.8032 (m-10) cc_final: 0.7780 (m-10)
REVERT: A 1058 THR cc_start: 0.8269 (m) cc_final: 0.7873 (p)
REVERT: A 1059 CYS cc_start: 0.7343 (m) cc_final: 0.7075 (m)
REVERT: A 1085 SER cc_start: 0.8375 (t) cc_final: 0.8083 (p)
REVERT: A 1098 ILE cc_start: 0.8814 (tp) cc_final: 0.8550 (tp)
REVERT: A 1105 GLU cc_start: 0.7103 (pp20) cc_final: 0.6793 (pp20)
REVERT: A 1145 VAL cc_start: 0.8540 (t) cc_final: 0.8236 (p)
REVERT: A 1189 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7598 (m)
  outliers start: 42
  outliers final: 27
  residues processed: 264
  average time/residue: 0.0914
  time to fit residues: 32.4148
Evaluate side-chains
  274 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 241
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  367 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  424 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 ILE
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  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 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 50 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 97 optimal weight:    0.2980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110754 restraints weight = 13150.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.113994 restraints weight = 5997.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116143 restraints weight = 3472.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.117478 restraints weight = 2352.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118264 restraints weight = 1791.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8267  Z= 0.163
  Angle     :  0.588   8.683  11218  Z= 0.306
  Chirality :  0.040   0.150   1348
  Planarity :  0.004   0.044   1378
  Dihedral  :  8.310 145.662   1104
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 19.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.27), residues: 1012
  helix:  1.78 (0.20), residues: 712
  sheet: -0.63 (0.73), residues: 54
  loop : -0.32 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 812 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.023   0.002   PHE A1109 
 TRP   0.017   0.001   TRP A 595 
 HIS   0.003   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8267)
  covalent geometry    : angle       0.58782 (11218)
  hydrogen bonds       : bond        0.04531 (  577)
  hydrogen bonds       : angle       4.21998 ( 1701)

*********************** 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
  279 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 239
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7245 (mppt) cc_final: 0.7029 (mppt)
REVERT: A  108 ILE cc_start: 0.8279 (mm) cc_final: 0.7842 (mt)
REVERT: A  149 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6743 (tm-30)
REVERT: A  155 ASP cc_start: 0.6408 (t0) cc_final: 0.5964 (t0)
REVERT: A  160 MET cc_start: 0.6956 (mmt) cc_final: 0.6690 (mmt)
REVERT: A  164 SER cc_start: 0.8435 (m) cc_final: 0.8228 (p)
REVERT: A  174 LEU cc_start: 0.7564 (tp) cc_final: 0.7327 (tp)
REVERT: A  199 MET cc_start: 0.7502 (mmm) cc_final: 0.7157 (tpp)
REVERT: A  216 LEU cc_start: 0.8731 (mt) cc_final: 0.8497 (mp)
REVERT: A  219 ASP cc_start: 0.7262 (t0) cc_final: 0.6976 (t0)
REVERT: A  233 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6456 (tt0)
REVERT: A  383 MET cc_start: 0.7939 (mmm) cc_final: 0.7620 (tpp)
REVERT: A  424 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7948 (tp)
REVERT: A  443 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6859 (tm-30)
REVERT: A  500 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7216 (tpp80)
REVERT: A  534 ASP cc_start: 0.7469 (t0) cc_final: 0.7105 (t0)
REVERT: A  579 MET cc_start: 0.5900 (tmm) cc_final: 0.5605 (tmm)
REVERT: A  585 ARG cc_start: 0.6956 (ttp-110) cc_final: 0.6723 (ttm170)
REVERT: A  588 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7484 (ttpp)
REVERT: A  609 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6823 (tpp80)
REVERT: A  613 GLN cc_start: 0.7001 (mt0) cc_final: 0.6618 (mt0)
REVERT: A  630 ASP cc_start: 0.7501 (m-30) cc_final: 0.7168 (m-30)
REVERT: A  633 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7943 (mtmm)
REVERT: A  644 LEU cc_start: 0.8149 (mt) cc_final: 0.7896 (mm)
REVERT: A  705 MET cc_start: 0.5504 (mmt) cc_final: 0.3824 (mmm)
REVERT: A  810 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5868 (mpp)
REVERT: A  828 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7579 (mmtp)
REVERT: A  835 LEU cc_start: 0.8599 (tp) cc_final: 0.8328 (tt)
REVERT: A  863 ILE cc_start: 0.7200 (mm) cc_final: 0.6866 (mm)
REVERT: A  864 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7590 (tp)
REVERT: A  872 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6361 (mm-30)
REVERT: A  877 GLN cc_start: 0.7428 (tt0) cc_final: 0.7223 (tt0)
REVERT: A  880 LYS cc_start: 0.8391 (tttt) cc_final: 0.7944 (ttpt)
REVERT: A  887 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7492 (mtp85)
REVERT: A  938 MET cc_start: 0.7777 (tpp) cc_final: 0.7403 (ttm)
REVERT: A  946 SER cc_start: 0.8183 (p) cc_final: 0.7738 (t)
REVERT: A  960 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7818 (p)
REVERT: A  986 GLU cc_start: 0.7094 (tt0) cc_final: 0.6273 (tt0)
REVERT: A 1033 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6579 (tp30)
REVERT: A 1035 TYR cc_start: 0.8009 (m-10) cc_final: 0.7691 (m-10)
REVERT: A 1058 THR cc_start: 0.8245 (m) cc_final: 0.7864 (p)
REVERT: A 1059 CYS cc_start: 0.7311 (m) cc_final: 0.7040 (m)
REVERT: A 1085 SER cc_start: 0.8336 (t) cc_final: 0.8039 (p)
REVERT: A 1098 ILE cc_start: 0.8772 (tp) cc_final: 0.8502 (tp)
REVERT: A 1105 GLU cc_start: 0.7067 (pp20) cc_final: 0.6742 (pp20)
REVERT: A 1109 PHE cc_start: 0.6841 (m-80) cc_final: 0.6394 (m-80)
REVERT: A 1145 VAL cc_start: 0.8533 (t) cc_final: 0.8256 (p)
REVERT: A 1189 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7634 (m)
  outliers start: 40
  outliers final: 27
  residues processed: 256
  average time/residue: 0.0924
  time to fit residues: 31.7190
Evaluate side-chains
  271 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 ILE
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  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 614 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110564 restraints weight = 13080.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113828 restraints weight = 6076.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115898 restraints weight = 3536.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.117201 restraints weight = 2410.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118040 restraints weight = 1837.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8267  Z= 0.167
  Angle     :  0.591   8.654  11218  Z= 0.310
  Chirality :  0.040   0.161   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.327 146.132   1104
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.77 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.27), residues: 1012
  helix:  1.77 (0.20), residues: 713
  sheet: -0.60 (0.73), residues: 54
  loop : -0.37 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 812 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.020   0.002   PHE A1109 
 TRP   0.034   0.002   TRP A 595 
 HIS   0.003   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8267)
  covalent geometry    : angle       0.59095 (11218)
  hydrogen bonds       : bond        0.04529 (  577)
  hydrogen bonds       : angle       4.21144 ( 1701)

*********************** 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
  272 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 237
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8303 (mm) cc_final: 0.7870 (mt)
REVERT: A  149 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6728 (tm-30)
REVERT: A  155 ASP cc_start: 0.6368 (t0) cc_final: 0.5959 (t0)
REVERT: A  160 MET cc_start: 0.6948 (mmt) cc_final: 0.6674 (mmt)
REVERT: A  164 SER cc_start: 0.8458 (m) cc_final: 0.8241 (p)
REVERT: A  168 ILE cc_start: 0.8385 (tt) cc_final: 0.7712 (pt)
REVERT: A  199 MET cc_start: 0.7475 (mmm) cc_final: 0.7228 (tpp)
REVERT: A  209 ASP cc_start: 0.7407 (t0) cc_final: 0.7021 (t0)
REVERT: A  219 ASP cc_start: 0.7242 (t0) cc_final: 0.6958 (t0)
REVERT: A  233 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6522 (tt0)
REVERT: A  373 THR cc_start: 0.7672 (m) cc_final: 0.7445 (m)
REVERT: A  383 MET cc_start: 0.7952 (mmm) cc_final: 0.7582 (tpp)
REVERT: A  424 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: A  443 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6849 (tm-30)
REVERT: A  500 ARG cc_start: 0.7566 (tpp80) cc_final: 0.7203 (tpp80)
REVERT: A  534 ASP cc_start: 0.7463 (t0) cc_final: 0.7116 (t0)
REVERT: A  573 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6917 (mmm-85)
REVERT: A  579 MET cc_start: 0.5795 (tmm) cc_final: 0.5534 (tmm)
REVERT: A  585 ARG cc_start: 0.6900 (ttp-110) cc_final: 0.6679 (ttm110)
REVERT: A  588 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7441 (ttpp)
REVERT: A  609 ARG cc_start: 0.7034 (tpp80) cc_final: 0.6754 (tpp80)
REVERT: A  630 ASP cc_start: 0.7493 (m-30) cc_final: 0.7166 (m-30)
REVERT: A  633 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7937 (mtmm)
REVERT: A  644 LEU cc_start: 0.8065 (mt) cc_final: 0.7737 (mm)
REVERT: A  705 MET cc_start: 0.5594 (mmt) cc_final: 0.3946 (mmm)
REVERT: A  810 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.5911 (mpp)
REVERT: A  828 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7576 (mmtp)
REVERT: A  835 LEU cc_start: 0.8594 (tp) cc_final: 0.8317 (tt)
REVERT: A  856 ARG cc_start: 0.6691 (tmm-80) cc_final: 0.6247 (ptt-90)
REVERT: A  863 ILE cc_start: 0.7203 (mm) cc_final: 0.6862 (mm)
REVERT: A  872 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6376 (mm-30)
REVERT: A  877 GLN cc_start: 0.7422 (tt0) cc_final: 0.7218 (tt0)
REVERT: A  880 LYS cc_start: 0.8404 (tttt) cc_final: 0.7938 (ttpt)
REVERT: A  887 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7483 (mtp85)
REVERT: A  938 MET cc_start: 0.7769 (tpp) cc_final: 0.7389 (ttm)
REVERT: A  946 SER cc_start: 0.8137 (p) cc_final: 0.7732 (t)
REVERT: A  960 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7786 (p)
REVERT: A  986 GLU cc_start: 0.7088 (tt0) cc_final: 0.6266 (tt0)
REVERT: A 1035 TYR cc_start: 0.7999 (m-10) cc_final: 0.7640 (m-10)
REVERT: A 1058 THR cc_start: 0.8224 (m) cc_final: 0.7830 (p)
REVERT: A 1059 CYS cc_start: 0.7292 (m) cc_final: 0.7031 (m)
REVERT: A 1085 SER cc_start: 0.8301 (t) cc_final: 0.8024 (p)
REVERT: A 1098 ILE cc_start: 0.8777 (tp) cc_final: 0.8497 (tp)
REVERT: A 1105 GLU cc_start: 0.7023 (pp20) cc_final: 0.6763 (pp20)
REVERT: A 1145 VAL cc_start: 0.8530 (t) cc_final: 0.8239 (p)
REVERT: A 1189 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7618 (m)
  outliers start: 35
  outliers final: 26
  residues processed: 254
  average time/residue: 0.0880
  time to fit residues: 30.1654
Evaluate side-chains
  264 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 234
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 ILE
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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  960 VAL
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 27 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 614 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110382 restraints weight = 13173.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113608 restraints weight = 6066.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115640 restraints weight = 3511.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116908 restraints weight = 2383.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117691 restraints weight = 1821.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8267  Z= 0.169
  Angle     :  0.605   8.618  11218  Z= 0.315
  Chirality :  0.040   0.156   1348
  Planarity :  0.004   0.045   1378
  Dihedral  :  8.331 146.623   1104
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.80 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.27), residues: 1012
  helix:  1.76 (0.20), residues: 713
  sheet: -0.53 (0.74), residues: 54
  loop : -0.42 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 812 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.019   0.001   PHE A1109 
 TRP   0.033   0.002   TRP A 595 
 HIS   0.003   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8267)
  covalent geometry    : angle       0.60457 (11218)
  hydrogen bonds       : bond        0.04519 (  577)
  hydrogen bonds       : angle       4.21430 ( 1701)

*********************** 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: 30
    poor density    : 237
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7260 (mppt) cc_final: 0.6981 (mppt)
REVERT: A  108 ILE cc_start: 0.8309 (mm) cc_final: 0.7875 (mt)
REVERT: A  149 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6742 (tm-30)
REVERT: A  155 ASP cc_start: 0.6307 (t0) cc_final: 0.5888 (t70)
REVERT: A  160 MET cc_start: 0.6923 (mmt) cc_final: 0.6649 (mmt)
REVERT: A  199 MET cc_start: 0.7451 (mmm) cc_final: 0.7237 (tpp)
REVERT: A  209 ASP cc_start: 0.7455 (t0) cc_final: 0.7070 (t0)
REVERT: A  219 ASP cc_start: 0.7184 (t0) cc_final: 0.6900 (t0)
REVERT: A  233 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6458 (tt0)
REVERT: A  373 THR cc_start: 0.7649 (m) cc_final: 0.7422 (m)
REVERT: A  383 MET cc_start: 0.8008 (mmm) cc_final: 0.7679 (tpp)
REVERT: A  424 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7987 (tp)
REVERT: A  443 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6837 (tm-30)
REVERT: A  500 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7163 (tpp80)
REVERT: A  534 ASP cc_start: 0.7456 (t0) cc_final: 0.7113 (t0)
REVERT: A  573 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6882 (tpp80)
REVERT: A  579 MET cc_start: 0.5749 (tmm) cc_final: 0.5506 (tmm)
REVERT: A  588 LYS cc_start: 0.8014 (ttpp) cc_final: 0.7421 (ttpp)
REVERT: A  609 ARG cc_start: 0.7023 (tpp80) cc_final: 0.6774 (tpp80)
REVERT: A  630 ASP cc_start: 0.7467 (m-30) cc_final: 0.7154 (m-30)
REVERT: A  633 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7936 (mtmm)
REVERT: A  705 MET cc_start: 0.5523 (mmt) cc_final: 0.3881 (mmm)
REVERT: A  810 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.5944 (mpp)
REVERT: A  828 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7588 (mmtp)
REVERT: A  835 LEU cc_start: 0.8590 (tp) cc_final: 0.8318 (tt)
REVERT: A  863 ILE cc_start: 0.7197 (mm) cc_final: 0.6854 (mm)
REVERT: A  864 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7653 (tp)
REVERT: A  872 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6354 (mm-30)
REVERT: A  880 LYS cc_start: 0.8403 (tttt) cc_final: 0.7954 (ttpt)
REVERT: A  887 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7485 (mtp85)
REVERT: A  938 MET cc_start: 0.7746 (tpp) cc_final: 0.7359 (ttm)
REVERT: A  946 SER cc_start: 0.8131 (p) cc_final: 0.7726 (t)
REVERT: A  960 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7768 (p)
REVERT: A  970 ILE cc_start: 0.8965 (tt) cc_final: 0.8746 (tp)
REVERT: A  986 GLU cc_start: 0.7075 (tt0) cc_final: 0.6249 (tt0)
REVERT: A 1035 TYR cc_start: 0.7971 (m-10) cc_final: 0.7586 (m-10)
REVERT: A 1058 THR cc_start: 0.8217 (m) cc_final: 0.7869 (p)
REVERT: A 1059 CYS cc_start: 0.7286 (m) cc_final: 0.7038 (m)
REVERT: A 1085 SER cc_start: 0.8293 (t) cc_final: 0.8000 (p)
REVERT: A 1098 ILE cc_start: 0.8744 (tp) cc_final: 0.8468 (tp)
REVERT: A 1105 GLU cc_start: 0.6996 (pp20) cc_final: 0.6736 (pp20)
REVERT: A 1145 VAL cc_start: 0.8507 (t) cc_final: 0.8260 (p)
REVERT: A 1189 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7615 (m)
  outliers start: 30
  outliers final: 24
  residues processed: 251
  average time/residue: 0.0961
  time to fit residues: 32.2220
Evaluate side-chains
  264 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 ILE
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  850 VAL
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  960 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 17 optimal weight:    0.2980
   chunk 87 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.128711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110852 restraints weight = 13078.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.114058 restraints weight = 6019.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.116071 restraints weight = 3478.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117343 restraints weight = 2361.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118053 restraints weight = 1800.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8267  Z= 0.174
  Angle     :  0.618   8.581  11218  Z= 0.324
  Chirality :  0.041   0.257   1348
  Planarity :  0.005   0.079   1378
  Dihedral  :  8.359 146.928   1104
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.82 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.27), residues: 1012
  helix:  1.72 (0.20), residues: 713
  sheet: -0.52 (0.74), residues: 54
  loop : -0.47 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 856 
 TYR   0.017   0.001   TYR A 267 
 PHE   0.019   0.001   PHE A 598 
 TRP   0.031   0.002   TRP A 595 
 HIS   0.003   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8267)
  covalent geometry    : angle       0.61820 (11218)
  hydrogen bonds       : bond        0.04570 (  577)
  hydrogen bonds       : angle       4.22328 ( 1701)

********************** 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
  269 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 238
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7255 (mppt) cc_final: 0.6963 (mppt)
REVERT: A  108 ILE cc_start: 0.8306 (mm) cc_final: 0.7873 (mt)
REVERT: A  149 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6744 (tm-30)
REVERT: A  155 ASP cc_start: 0.6319 (t0) cc_final: 0.5905 (t70)
REVERT: A  160 MET cc_start: 0.6969 (mmt) cc_final: 0.6704 (mmt)
REVERT: A  162 SER cc_start: 0.8356 (p) cc_final: 0.8074 (t)
REVERT: A  199 MET cc_start: 0.7439 (mmm) cc_final: 0.7221 (tpp)
REVERT: A  219 ASP cc_start: 0.7208 (t0) cc_final: 0.6935 (t0)
REVERT: A  233 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6512 (tt0)
REVERT: A  373 THR cc_start: 0.7610 (m) cc_final: 0.7366 (m)
REVERT: A  383 MET cc_start: 0.8000 (mmm) cc_final: 0.7665 (tpp)
REVERT: A  424 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7983 (tp)
REVERT: A  443 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6841 (tm-30)
REVERT: A  500 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7168 (tpp80)
REVERT: A  534 ASP cc_start: 0.7451 (t0) cc_final: 0.7116 (t0)
REVERT: A  579 MET cc_start: 0.5777 (tmm) cc_final: 0.5500 (tmm)
REVERT: A  588 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7443 (ttpp)
REVERT: A  609 ARG cc_start: 0.7057 (tpp80) cc_final: 0.6794 (tpp80)
REVERT: A  630 ASP cc_start: 0.7469 (m-30) cc_final: 0.7157 (m-30)
REVERT: A  633 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7943 (mtmm)
REVERT: A  705 MET cc_start: 0.5518 (mmt) cc_final: 0.3835 (mmm)
REVERT: A  810 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.5968 (mpp)
REVERT: A  828 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7589 (mmtp)
REVERT: A  835 LEU cc_start: 0.8581 (tp) cc_final: 0.8297 (tt)
REVERT: A  856 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7023 (tmm-80)
REVERT: A  863 ILE cc_start: 0.7195 (mm) cc_final: 0.6847 (mm)
REVERT: A  872 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6283 (mm-30)
REVERT: A  880 LYS cc_start: 0.8401 (tttt) cc_final: 0.7952 (ttpt)
REVERT: A  887 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7473 (mtp85)
REVERT: A  938 MET cc_start: 0.7754 (tpp) cc_final: 0.7366 (ttm)
REVERT: A  946 SER cc_start: 0.8111 (p) cc_final: 0.7725 (t)
REVERT: A  970 ILE cc_start: 0.8987 (tt) cc_final: 0.8677 (tp)
REVERT: A  986 GLU cc_start: 0.7074 (tt0) cc_final: 0.6272 (tt0)
REVERT: A 1035 TYR cc_start: 0.7946 (m-10) cc_final: 0.7600 (m-10)
REVERT: A 1058 THR cc_start: 0.8223 (m) cc_final: 0.7848 (p)
REVERT: A 1059 CYS cc_start: 0.7289 (m) cc_final: 0.7048 (m)
REVERT: A 1085 SER cc_start: 0.8259 (t) cc_final: 0.7985 (p)
REVERT: A 1098 ILE cc_start: 0.8730 (tp) cc_final: 0.8447 (tp)
REVERT: A 1105 GLU cc_start: 0.7015 (pp20) cc_final: 0.6743 (pp20)
REVERT: A 1189 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7608 (m)
REVERT: A 1191 ASN cc_start: 0.7853 (m-40) cc_final: 0.7651 (m110)
  outliers start: 31
  outliers final: 28
  residues processed: 254
  average time/residue: 0.0949
  time to fit residues: 32.2462
Evaluate side-chains
  271 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 240
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  688 ILE
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  850 VAL
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0670
   chunk 10 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0170
   chunk 91 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.129781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111771 restraints weight = 13087.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114997 restraints weight = 6017.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117060 restraints weight = 3485.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.118352 restraints weight = 2365.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.119042 restraints weight = 1801.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8267  Z= 0.143
  Angle     :  0.610   9.320  11218  Z= 0.318
  Chirality :  0.040   0.226   1348
  Planarity :  0.005   0.067   1378
  Dihedral  :  8.365 147.969   1104
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.39 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.27), residues: 1012
  helix:  1.84 (0.20), residues: 713
  sheet: -0.58 (0.75), residues: 54
  loop : -0.40 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 856 
 TYR   0.021   0.001   TYR A 267 
 PHE   0.026   0.001   PHE A 268 
 TRP   0.027   0.001   TRP A 595 
 HIS   0.002   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8267)
  covalent geometry    : angle       0.60963 (11218)
  hydrogen bonds       : bond        0.04200 (  577)
  hydrogen bonds       : angle       4.14285 ( 1701)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1575.44 seconds
wall clock time: 27 minutes 51.43 seconds (1671.43 seconds total)