Starting phenix.real_space_refine
on Thu Jan 16 17:49:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.120
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      26      5.49       5
     S      53      5.16       5
     C    6066      2.51       5
     N    1647      2.21       5
     O    1841      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9637
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1118, 9098
          Classifications: {'peptide': 1118}
          Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "T"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4834  SG  CYS A 651      39.686  19.306  54.662  1.00106.69           S
  ATOM   4850  SG  CYS A 654      38.377  17.719  49.063  1.00110.12           S
  ATOM   4916  SG  CYS A 663      44.195  16.679  51.105  1.00102.11           S
  ATOM   5640  SG  CYS A 747      42.848  22.430  50.219  1.00 96.95           S

  Time building chain proxies: 5.61, per 1000 atoms: 0.58
  Number of scatterers: 9637
  At special positions: 0
  Unit cell: (106.58, 110.96, 110.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      53     16.00
     P      26     15.00
     O    1841      8.00
     N    1647      7.00
     C    6066      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1301 "
        pdb="FE3  SF4 A1301 " - pdb=" SG  CYS A 663 "
        pdb="FE4  SF4 A1301 " - pdb=" SG  CYS A 747 "
        pdb="FE2  SF4 A1301 " - pdb=" SG  CYS A 654 "
        pdb="FE1  SF4 A1301 " - pdb=" SG  CYS A 651 "
      Number of angles added : 12


  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      49.4% alpha, 14.5% beta
      11 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 3.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 48
    Processing helix  chain 'A' and resid 112 through 124
    Processing helix  chain 'A' and resid 143 through 147
      removed outlier: 3.501A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 181
      Proline residue:  A 172  - end of helix
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 227 through 237
      removed outlier: 3.651A  pdb=" N   LEU A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER A 233 " --> pdb=" O   HIS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 367 through 375
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 407 through 415
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 4.134A  pdb=" N   CYS A 445 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ARG A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 445 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 460
      removed outlier: 3.623A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.683A  pdb=" N   VAL A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 4.039A  pdb=" N   PHE A 477 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   PHE A 479 " --> pdb=" O   HIS A 475 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA A 480 " --> pdb=" O   PRO A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 495
      removed outlier: 3.532A  pdb=" N   LEU A 493 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.584A  pdb=" N   LEU A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   CYS A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   VAL A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLN A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 572
    Processing helix  chain 'A' and resid 573 through 586
      removed outlier: 3.682A  pdb=" N   GLU A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 593
    Processing helix  chain 'A' and resid 595 through 613
      removed outlier: 3.581A  pdb=" N   VAL A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS A 600 " --> pdb=" O   PHE A 596 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 639
      removed outlier: 3.644A  pdb=" N   ARG A 639 " --> pdb=" O   ILE A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
    Processing helix  chain 'A' and resid 679 through 691
    Processing helix  chain 'A' and resid 711 through 731
      removed outlier: 4.335A  pdb=" N   LYS A 717 " --> pdb=" O   GLU A 713 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS A 729 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 786
    Processing helix  chain 'A' and resid 787 through 819
      removed outlier: 4.166A  pdb=" N   TYR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLY A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   VAL A 819 " --> pdb=" O   PHE A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 854
      removed outlier: 4.044A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 835 " --> pdb=" O   MET A 831 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLN A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 853 " --> pdb=" O   LEU A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 906
      removed outlier: 4.308A  pdb=" N   LYS A 902 " --> pdb=" O   ASN A 898 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU A 903 " --> pdb=" O   ILE A 899 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A 904 " --> pdb=" O   MET A 900 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A 906 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 993
      removed outlier: 3.673A  pdb=" N   LYS A 983 " --> pdb=" O   LEU A 979 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE A 990 " --> pdb=" O   GLN A 986 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLU A 991 " --> pdb=" O   SER A 987 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA A 992 " --> pdb=" O   SER A 988 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   PHE A 993 " --> pdb=" O   VAL A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1020
      removed outlier: 3.926A  pdb=" N   LYS A1008 " --> pdb=" O   GLY A1004 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   TYR A1012 " --> pdb=" O   LYS A1008 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   TRP A1013 " --> pdb=" O   VAL A1009 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU A1014 " --> pdb=" O   ALA A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1033
      removed outlier: 4.077A  pdb=" N   LEU A1029 " --> pdb=" O   PRO A1025 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   PHE A1030 " --> pdb=" O   ASP A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1047
    Processing helix  chain 'A' and resid 1051 through 1062
      removed outlier: 3.722A  pdb=" N   ALA A1061 " --> pdb=" O   ALA A1057 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLU A1062 " --> pdb=" O   LYS A1058 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1071
    Processing helix  chain 'A' and resid 1088 through 1092
      removed outlier: 3.572A  pdb=" N   ARG A1092 " --> pdb=" O   PRO A1088 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1088 through 1092'
    Processing helix  chain 'A' and resid 1096 through 1101
      removed outlier: 4.242A  pdb=" N   GLN A1100 " --> pdb=" O   LEU A1096 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A1101 " --> pdb=" O   ALA A1097 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1096 through 1101'
    Processing helix  chain 'A' and resid 1102 through 1114
      removed outlier: 3.848A  pdb=" N   LEU A1114 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1128
    Processing helix  chain 'A' and resid 1129 through 1145
      removed outlier: 4.188A  pdb=" N   TYR A1133 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE A1134 " --> pdb=" O   TRP A1130 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LYS A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1152
    Processing helix  chain 'A' and resid 1164 through 1175
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 99
      removed outlier: 3.510A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU A  63 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 136
      removed outlier: 3.525A  pdb=" N   LYS A 130 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334
      removed outlier: 6.332A  pdb=" N   LEU A 272 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   MET A 359 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391
    Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 539
      removed outlier: 3.945A  pdb=" N   SER A 536 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 674 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR A 538 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546
      removed outlier: 3.861A  pdb=" N   GLU A 545 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 859 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU A 858 " --> pdb=" O   TRP A 865 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553
      removed outlier: 3.678A  pdb=" N   ALA A 939 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 561
    Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 695
    Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879
    Processing sheet with id=AB2, first strand: chain 'A' and resid 907 through 913
      removed outlier: 6.263A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   GLU A 926 " --> pdb=" O   ASP A 908 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU A 912 " --> pdb=" O   VAL A 922 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080

    426 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 4.14

  Time building geometry restraints manager: 2.57 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.43: 4235
        1.43 -     1.64: 5593
        1.64 -     1.85: 78
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 9918
  Sorted by residual:
  bond pdb=" CA  LYS A 355 "
       pdb=" CB  LYS A 355 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 8.90e-03 1.26e+04 1.42e+00
  bond pdb=" C   LYS A 355 "
       pdb=" O   LYS A 355 "
    ideal  model  delta    sigma   weight residual
    1.233  1.238 -0.005 4.80e-03 4.34e+04 9.91e-01
  bond pdb=" C4'  DC P  25 "
       pdb=" O4'  DC P  25 "
    ideal  model  delta    sigma   weight residual
    1.450  1.430  0.020 2.00e-02 2.50e+03 9.60e-01
  bond pdb=" C1'  DC T  12 "
       pdb=" N1   DC T  12 "
    ideal  model  delta    sigma   weight residual
    1.490  1.517 -0.027 3.00e-02 1.11e+03 8.11e-01
  bond pdb=" C2'  DG P  20 "
       pdb=" C1'  DG P  20 "
    ideal  model  delta    sigma   weight residual
    1.525  1.508  0.017 2.00e-02 2.50e+03 7.46e-01
  ... (remaining 9913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 12133
        0.99 -     1.98: 1101
        1.98 -     2.97: 216
        2.97 -     3.97: 56
        3.97 -     4.96: 10
  Bond angle restraints: 13516
  Sorted by residual:
  angle pdb=" N   TYR A 473 "
        pdb=" CA  TYR A 473 "
        pdb=" C   TYR A 473 "
      ideal   model   delta    sigma   weight residual
     112.04  116.90   -4.86 1.44e+00 4.82e-01 1.14e+01
  angle pdb=" C4'  DA P  21 "
        pdb=" C3'  DA P  21 "
        pdb=" O3'  DA P  21 "
      ideal   model   delta    sigma   weight residual
     110.00  105.33    4.67 1.50e+00 4.44e-01 9.71e+00
  angle pdb=" O3'  DA P  21 "
        pdb=" C3'  DA P  21 "
        pdb=" C2'  DA P  21 "
      ideal   model   delta    sigma   weight residual
     111.50  115.86   -4.36 1.50e+00 4.44e-01 8.46e+00
  angle pdb=" N   ASN A 217 "
        pdb=" CA  ASN A 217 "
        pdb=" C   ASN A 217 "
      ideal   model   delta    sigma   weight residual
     111.82  114.94   -3.12 1.16e+00 7.43e-01 7.24e+00
  angle pdb=" O3'  DA P  29 "
        pdb=" C3'  DA P  29 "
        pdb=" C2'  DA P  29 "
      ideal   model   delta    sigma   weight residual
     111.50  115.40   -3.90 1.50e+00 4.44e-01 6.75e+00
  ... (remaining 13511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.46: 5697
       31.46 -    62.93: 241
       62.93 -    94.39: 21
       94.39 -   125.86: 0
      125.86 -   157.32: 1
  Dihedral angle restraints: 5960
    sinusoidal: 2661
      harmonic: 3299
  Sorted by residual:
  dihedral pdb=" CA  PHE A 367 "
           pdb=" C   PHE A 367 "
           pdb=" N   ASP A 368 "
           pdb=" CA  ASP A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  GLU A 329 "
           pdb=" C   GLU A 329 "
           pdb=" N   GLY A 330 "
           pdb=" CA  GLY A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.21  -26.79     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  LEU A1114 "
           pdb=" C   LEU A1114 "
           pdb=" N   LYS A1115 "
           pdb=" CA  LYS A1115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.37  -26.63     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 5957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1199
       0.051 -    0.101: 211
       0.101 -    0.152: 43
       0.152 -    0.202: 2
       0.202 -    0.253: 1
  Chirality restraints: 1456
  Sorted by residual:
  chirality pdb=" C3'  DA P  29 "
            pdb=" C4'  DA P  29 "
            pdb=" O3'  DA P  29 "
            pdb=" C2'  DA P  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.41   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  PHE A 905 "
            pdb=" N   PHE A 905 "
            pdb=" C   PHE A 905 "
            pdb=" CB  PHE A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.39e-01
  chirality pdb=" CA  PRO A1103 "
            pdb=" N   PRO A1103 "
            pdb=" C   PRO A1103 "
            pdb=" CB  PRO A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 1453 not shown)

  Planarity restraints: 1655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 847 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   ARG A 847 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ARG A 847 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A 848 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 843 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.27e+00
        pdb=" C   ILE A 843 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ILE A 843 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   THR A 844 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 838 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   THR A 838 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   THR A 838 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY A 839 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1652 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2743
        2.82 -     3.34: 9460
        3.34 -     3.86: 14779
        3.86 -     4.38: 16470
        4.38 -     4.90: 27822
  Nonbonded interactions: 71274
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 549 "
            pdb=" O   LEU A 942 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OD2 ASP A 287 "
            pdb=" OG1 THR A 290 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OH  TYR A 105 "
            pdb=" NH2 ARG A 154 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" OE2 GLU A 991 "
            pdb=" NZ  LYS A 995 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" OE1 GLU A 674 "
            pdb=" OG1 THR A 737 "
     model   vdw
     2.355 3.040
  ... (remaining 71269 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     28.320
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9918  Z= 0.174
  Angle     :  0.656   4.957  13516  Z= 0.400
  Chirality :  0.042   0.253   1456
  Planarity :  0.009   0.107   1655
  Dihedral  : 16.571 157.322   3824
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.85 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.22), residues: 1114
  helix: -1.03 (0.20), residues: 440
  sheet:  0.14 (0.36), residues: 158
  loop : -0.98 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.007   TRP A 410 
 HIS   0.007   0.002   HIS A  67 
 PHE   0.032   0.004   PHE A 905 
 TYR   0.027   0.005   TYR A 683 
 ARG   0.022   0.003   ARG A 375 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8045 (tpp) cc_final: 0.7768 (tpp)
REVERT: A   83 ASP cc_start: 0.8006 (t0) cc_final: 0.7509 (t0)
REVERT: A  266 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7354 (mtm180)
REVERT: A  401 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8412 (pp30)
REVERT: A  431 LYS cc_start: 0.9316 (mmpt) cc_final: 0.8701 (mmpt)
REVERT: A  447 MET cc_start: 0.7769 (ttp) cc_final: 0.7529 (ttt)
REVERT: A  491 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7676 (mm-30)
REVERT: A  569 PHE cc_start: 0.8828 (t80) cc_final: 0.8209 (t80)
REVERT: A  627 VAL cc_start: 0.8356 (t) cc_final: 0.7759 (p)
REVERT: A  630 MET cc_start: 0.8364 (ttp) cc_final: 0.7819 (ttp)
REVERT: A  637 THR cc_start: 0.8021 (m) cc_final: 0.7615 (p)
REVERT: A  667 MET cc_start: 0.8202 (mtp) cc_final: 0.7974 (mtt)
REVERT: A  827 TYR cc_start: 0.9045 (t80) cc_final: 0.8685 (t80)
REVERT: A  829 MET cc_start: 0.8765 (mmm) cc_final: 0.8486 (mmm)
REVERT: A  860 ASP cc_start: 0.7745 (t0) cc_final: 0.7341 (t70)
REVERT: A  940 MET cc_start: 0.8815 (ttt) cc_final: 0.8505 (ttm)
REVERT: A 1024 MET cc_start: 0.7902 (ttm) cc_final: 0.7549 (mmm)
REVERT: A 1050 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7020 (ptmt)
REVERT: A 1151 LEU cc_start: 0.9090 (mt) cc_final: 0.8749 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2907
  time to fit residues: 75.4324
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0020
   overall best weight:    1.3770

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A 177 ASN
A 239 HIS
A 342 HIS
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 GLN
A 592 GLN
A 735 HIS
A1049 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.112134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.091383 restraints weight = 24929.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.094654 restraints weight = 13441.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.095210 restraints weight = 8302.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9918  Z= 0.230
  Angle     :  0.635   6.117  13516  Z= 0.350
  Chirality :  0.044   0.161   1456
  Planarity :  0.005   0.046   1655
  Dihedral  : 15.574 150.143   1509
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.52 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.24), residues: 1114
  helix:  0.65 (0.24), residues: 456
  sheet:  0.19 (0.36), residues: 174
  loop : -0.38 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 671 
 HIS   0.006   0.001   HIS A 342 
 PHE   0.020   0.002   PHE A1122 
 TYR   0.019   0.002   TYR A 683 
 ARG   0.006   0.001   ARG A 955 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7598 (m-40)
REVERT: A  221 MET cc_start: 0.8910 (pmm) cc_final: 0.8701 (pmm)
REVERT: A  247 ARG cc_start: 0.8356 (tpt170) cc_final: 0.8120 (tpt170)
REVERT: A  328 TYR cc_start: 0.7327 (m-80) cc_final: 0.6625 (m-80)
REVERT: A  491 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7984 (mm-30)
REVERT: A  569 PHE cc_start: 0.8792 (t80) cc_final: 0.8194 (t80)
REVERT: A  637 THR cc_start: 0.8280 (m) cc_final: 0.7834 (p)
REVERT: A 1024 MET cc_start: 0.7563 (ttm) cc_final: 0.7290 (mtm)
REVERT: A 1028 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8919 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2390
  time to fit residues: 41.1032
Evaluate side-chains
  80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 73 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 109 optimal weight:    0.0970
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.113835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093724 restraints weight = 24596.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.095996 restraints weight = 13494.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.097910 restraints weight = 8851.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9918  Z= 0.158
  Angle     :  0.552   7.465  13516  Z= 0.300
  Chirality :  0.041   0.157   1456
  Planarity :  0.004   0.042   1655
  Dihedral  : 15.024 148.442   1509
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1114
  helix:  1.16 (0.25), residues: 452
  sheet:  0.30 (0.36), residues: 174
  loop : -0.20 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1130 
 HIS   0.001   0.001   HIS A 229 
 PHE   0.019   0.001   PHE A 815 
 TYR   0.009   0.001   TYR A 328 
 ARG   0.004   0.000   ARG A 821 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ASP cc_start: 0.8334 (t0) cc_final: 0.7834 (t70)
REVERT: A  569 PHE cc_start: 0.8792 (t80) cc_final: 0.8180 (t80)
REVERT: A 1024 MET cc_start: 0.7404 (ttm) cc_final: 0.7145 (mtm)
REVERT: A 1153 GLN cc_start: 0.8428 (mp10) cc_final: 0.8137 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2319
  time to fit residues: 37.4969
Evaluate side-chains
  84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 385 GLN
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.112121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091939 restraints weight = 24672.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.094198 restraints weight = 13549.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.095956 restraints weight = 8911.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9918  Z= 0.182
  Angle     :  0.543   7.179  13516  Z= 0.295
  Chirality :  0.042   0.275   1456
  Planarity :  0.004   0.044   1655
  Dihedral  : 14.879 147.462   1509
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.25), residues: 1114
  helix:  1.38 (0.25), residues: 451
  sheet:  0.38 (0.36), residues: 174
  loop : -0.22 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1130 
 HIS   0.002   0.001   HIS A 580 
 PHE   0.016   0.001   PHE A 104 
 TYR   0.011   0.001   TYR A 726 
 ARG   0.003   0.000   ARG A 742 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ASP cc_start: 0.8339 (t0) cc_final: 0.7808 (t70)
REVERT: A  295 MET cc_start: 0.8492 (ptp) cc_final: 0.8289 (ptp)
REVERT: A  569 PHE cc_start: 0.8845 (t80) cc_final: 0.8236 (t80)
REVERT: A 1024 MET cc_start: 0.7413 (ttm) cc_final: 0.7071 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2307
  time to fit residues: 32.9621
Evaluate side-chains
  79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 111 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
A 451 GLN
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.113349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093931 restraints weight = 25361.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.095976 restraints weight = 14055.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.097243 restraints weight = 9370.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9918  Z= 0.155
  Angle     :  0.531   8.429  13516  Z= 0.284
  Chirality :  0.041   0.227   1456
  Planarity :  0.004   0.045   1655
  Dihedral  : 14.820 146.878   1509
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.52 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1114
  helix:  1.52 (0.25), residues: 451
  sheet:  0.47 (0.36), residues: 174
  loop : -0.18 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 347 
 HIS   0.002   0.001   HIS A 404 
 PHE   0.012   0.001   PHE A 104 
 TYR   0.014   0.001   TYR A 473 
 ARG   0.009   0.000   ARG A 266 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7843 (mtm180)
REVERT: A  275 ASP cc_start: 0.8347 (t0) cc_final: 0.7810 (t70)
REVERT: A  487 MET cc_start: 0.7763 (mtt) cc_final: 0.7559 (mtm)
REVERT: A  520 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: A  569 PHE cc_start: 0.8814 (t80) cc_final: 0.8220 (t80)
REVERT: A  797 MET cc_start: 0.8997 (mmm) cc_final: 0.8701 (mpp)
REVERT: A 1024 MET cc_start: 0.7454 (ttm) cc_final: 0.7194 (mtm)
REVERT: A 1153 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8151 (mp-120)
  outliers start: 2
  outliers final: 1
  residues processed: 114
  average time/residue: 0.2352
  time to fit residues: 37.4032
Evaluate side-chains
  82 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 110 optimal weight:    0.0970
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0470
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 735 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.115177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.093751 restraints weight = 24604.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.096305 restraints weight = 13498.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.098741 restraints weight = 8630.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9918  Z= 0.161
  Angle     :  0.536   8.474  13516  Z= 0.286
  Chirality :  0.040   0.205   1456
  Planarity :  0.004   0.047   1655
  Dihedral  : 14.802 146.038   1509
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.25), residues: 1114
  helix:  1.51 (0.25), residues: 451
  sheet:  0.50 (0.36), residues: 176
  loop : -0.17 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  62 
 HIS   0.004   0.001   HIS A 144 
 PHE   0.015   0.001   PHE A 905 
 TYR   0.024   0.001   TYR A 105 
 ARG   0.007   0.000   ARG A 721 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 ARG cc_start: 0.8426 (tpt170) cc_final: 0.8067 (tpt170)
REVERT: A  275 ASP cc_start: 0.8294 (t0) cc_final: 0.7806 (t70)
REVERT: A  295 MET cc_start: 0.8194 (ptp) cc_final: 0.7993 (ptp)
REVERT: A  562 MET cc_start: 0.7584 (mmt) cc_final: 0.7070 (mmt)
REVERT: A  569 PHE cc_start: 0.8819 (t80) cc_final: 0.8285 (t80)
REVERT: A  797 MET cc_start: 0.8921 (mmm) cc_final: 0.8711 (mpp)
REVERT: A 1024 MET cc_start: 0.7431 (ttm) cc_final: 0.7136 (mtm)
REVERT: A 1153 GLN cc_start: 0.8434 (mp-120) cc_final: 0.8207 (mp-120)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2110
  time to fit residues: 32.9308
Evaluate side-chains
  80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.113313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091974 restraints weight = 24841.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.094565 restraints weight = 13513.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.096204 restraints weight = 8535.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9918  Z= 0.181
  Angle     :  0.534   9.009  13516  Z= 0.283
  Chirality :  0.040   0.213   1456
  Planarity :  0.004   0.046   1655
  Dihedral  : 14.783 145.442   1509
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.25), residues: 1114
  helix:  1.55 (0.26), residues: 451
  sheet:  0.55 (0.36), residues: 176
  loop : -0.24 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 404 
 PHE   0.016   0.001   PHE A 104 
 TYR   0.010   0.001   TYR A 328 
 ARG   0.005   0.000   ARG A 721 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A  247 ARG cc_start: 0.8367 (tpt170) cc_final: 0.8166 (tpt170)
REVERT: A  275 ASP cc_start: 0.8333 (t0) cc_final: 0.7780 (t70)
REVERT: A  295 MET cc_start: 0.8098 (ptp) cc_final: 0.7802 (ptp)
REVERT: A  440 ASP cc_start: 0.8156 (t0) cc_final: 0.7930 (t0)
REVERT: A  569 PHE cc_start: 0.8847 (t80) cc_final: 0.8290 (t80)
REVERT: A  571 LEU cc_start: 0.9027 (pp) cc_final: 0.8711 (tp)
REVERT: A  797 MET cc_start: 0.9117 (mmm) cc_final: 0.8913 (mpp)
REVERT: A 1024 MET cc_start: 0.7544 (ttm) cc_final: 0.7196 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1893
  time to fit residues: 28.1277
Evaluate side-chains
  78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 54 optimal weight:    0.2980
   chunk 48 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0060
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 40 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093882 restraints weight = 26055.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.095857 restraints weight = 14562.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.097116 restraints weight = 9974.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9918  Z= 0.143
  Angle     :  0.523   8.742  13516  Z= 0.275
  Chirality :  0.040   0.227   1456
  Planarity :  0.004   0.046   1655
  Dihedral  : 14.715 144.129   1509
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1114
  helix:  1.62 (0.26), residues: 448
  sheet:  0.71 (0.36), residues: 176
  loop : -0.25 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 144 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.004   0.000   ARG A 721 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8084 (mtp180)
REVERT: A  275 ASP cc_start: 0.8458 (t0) cc_final: 0.7946 (t70)
REVERT: A  294 MET cc_start: 0.8793 (tpp) cc_final: 0.8580 (tpt)
REVERT: A  569 PHE cc_start: 0.8829 (t80) cc_final: 0.8265 (t80)
REVERT: A  797 MET cc_start: 0.9074 (mmm) cc_final: 0.8855 (mpp)
REVERT: A  980 GLN cc_start: 0.8060 (mp10) cc_final: 0.7634 (tp40)
REVERT: A 1024 MET cc_start: 0.7540 (ttm) cc_final: 0.7206 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2136
  time to fit residues: 32.7858
Evaluate side-chains
  78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 79 optimal weight:    0.0050
   chunk 57 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.4532

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

Flipped N/Q/H residues before XYZ refinement:
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093976 restraints weight = 25681.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.095910 restraints weight = 14332.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097221 restraints weight = 9803.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9918  Z= 0.145
  Angle     :  0.536   8.740  13516  Z= 0.279
  Chirality :  0.040   0.225   1456
  Planarity :  0.004   0.046   1655
  Dihedral  : 14.688 143.939   1509
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1114
  helix:  1.62 (0.26), residues: 449
  sheet:  0.80 (0.36), residues: 182
  loop : -0.26 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  40 
 HIS   0.004   0.000   HIS A 404 
 PHE   0.012   0.001   PHE A 104 
 TYR   0.010   0.001   TYR A 248 
 ARG   0.004   0.000   ARG A 721 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7980 (mtp180)
REVERT: A  275 ASP cc_start: 0.8493 (t0) cc_final: 0.7908 (t70)
REVERT: A  294 MET cc_start: 0.8781 (tpp) cc_final: 0.8553 (tpt)
REVERT: A  569 PHE cc_start: 0.8850 (t80) cc_final: 0.8324 (t80)
REVERT: A  797 MET cc_start: 0.9076 (mmm) cc_final: 0.8869 (mpp)
REVERT: A 1024 MET cc_start: 0.7528 (ttm) cc_final: 0.7215 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.2242
  time to fit residues: 33.3221
Evaluate side-chains
  80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 84 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 144 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.112845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.093067 restraints weight = 26059.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.094895 restraints weight = 14282.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.096107 restraints weight = 9959.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9918  Z= 0.175
  Angle     :  0.554  10.845  13516  Z= 0.288
  Chirality :  0.040   0.238   1456
  Planarity :  0.004   0.060   1655
  Dihedral  : 14.677 144.058   1509
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1114
  helix:  1.60 (0.26), residues: 449
  sheet:  0.79 (0.35), residues: 182
  loop : -0.27 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 404 
 PHE   0.015   0.001   PHE A 104 
 TYR   0.010   0.001   TYR A 298 
 ARG   0.003   0.000   ARG A 721 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8029 (mtp180)
REVERT: A  275 ASP cc_start: 0.8253 (t0) cc_final: 0.7648 (t70)
REVERT: A  294 MET cc_start: 0.8765 (tpp) cc_final: 0.8466 (tpt)
REVERT: A  569 PHE cc_start: 0.8787 (t80) cc_final: 0.8448 (t80)
REVERT: A  627 VAL cc_start: 0.8485 (p) cc_final: 0.8276 (p)
REVERT: A  797 MET cc_start: 0.9095 (mmm) cc_final: 0.8892 (mpp)
REVERT: A  898 ASN cc_start: 0.8762 (m-40) cc_final: 0.8537 (m-40)
REVERT: A  980 GLN cc_start: 0.8072 (mp10) cc_final: 0.7607 (tp40)
REVERT: A 1024 MET cc_start: 0.7519 (ttm) cc_final: 0.7205 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2169
  time to fit residues: 30.7124
Evaluate side-chains
  75 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:    0.0870
   chunk 95 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 85 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8962

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.112339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092538 restraints weight = 25923.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.094167 restraints weight = 14567.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.095361 restraints weight = 10329.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9918  Z= 0.169
  Angle     :  0.541   8.269  13516  Z= 0.284
  Chirality :  0.040   0.219   1456
  Planarity :  0.004   0.047   1655
  Dihedral  : 14.659 143.602   1509
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1114
  helix:  1.62 (0.26), residues: 448
  sheet:  0.76 (0.35), residues: 182
  loop : -0.31 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  40 
 HIS   0.002   0.001   HIS A 404 
 PHE   0.015   0.001   PHE A 104 
 TYR   0.010   0.001   TYR A 298 
 ARG   0.003   0.000   ARG A 721 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2480.88 seconds
wall clock time: 45 minutes 34.61 seconds (2734.61 seconds total)