Starting phenix.real_space_refine
on Wed Sep 17 16:34:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6k_50227/09_2025/9f6k_50227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6k_50227/09_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_50227/09_2025/9f6k_50227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6k_50227/09_2025/9f6k_50227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6k_50227/09_2025/9f6k_50227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6k_50227/09_2025/9f6k_50227.cif"
  }
  resolution = 4.2
  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=   0.005 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.42, per 1000 atoms: 0.25
  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: 1.02
  Conformation dependent library (CDL) restraints added in 380.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 1.30
  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: 2.32

  Time building geometry restraints manager: 1.31 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:             1.090
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.550
-------------------------------------------------------------------------------
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   0.041   9922  Z= 0.140
  Angle     :  0.909  44.015  13528  Z= 0.404
  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 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: -1.36 (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
 ARG   0.022   0.003   ARG A 375 
 TYR   0.027   0.005   TYR A 683 
 PHE   0.032   0.004   PHE A 905 
 TRP   0.021   0.007   TRP A 410 
 HIS   0.007   0.002   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9918)
  covalent geometry    : angle       0.65605 (13516)
  hydrogen bonds       : bond        0.16315 (  453)
  hydrogen bonds       : angle       7.35140 ( 1254)
  metal coordination   : bond        0.02927 (    4)
  metal coordination   : angle      21.14376 (   12)

*********************** 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  : 0.402 
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: 0.1310
  time to fit residues: 33.2997
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  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 379 HIS
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 GLN
A 592 GLN
A 911 GLN
A1049 GLN
A1100 GLN
A1142 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.104357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.081969 restraints weight = 25044.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.084290 restraints weight = 14193.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.085814 restraints weight = 9769.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.086825 restraints weight = 7656.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087341 restraints weight = 6523.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9922  Z= 0.250
  Angle     :  0.852  33.769  13528  Z= 0.397
  Chirality :  0.047   0.163   1456
  Planarity :  0.005   0.046   1655
  Dihedral  : 15.719 151.196   1509
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.23 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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: -0.39 (0.24), residues: 1114
  helix:  0.25 (0.23), residues: 465
  sheet: -0.08 (0.36), residues: 164
  loop : -0.71 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 680 
 TYR   0.023   0.002   TYR A 152 
 PHE   0.028   0.002   PHE A 104 
 TRP   0.015   0.002   TRP A 669 
 HIS   0.009   0.002   HIS A 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 9918)
  covalent geometry    : angle       0.71443 (13516)
  hydrogen bonds       : bond        0.06242 (  453)
  hydrogen bonds       : angle       5.52936 ( 1254)
  metal coordination   : bond        0.02043 (    4)
  metal coordination   : angle      15.61986 (   12)

*********************** 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
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8507 (tpp) cc_final: 0.8270 (tpp)
REVERT: A   66 MET cc_start: 0.9003 (ptt) cc_final: 0.8777 (ptm)
REVERT: A  177 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7526 (m-40)
REVERT: A  221 MET cc_start: 0.8913 (pmm) cc_final: 0.8597 (pmm)
REVERT: A  328 TYR cc_start: 0.7596 (m-80) cc_final: 0.6859 (m-80)
REVERT: A  491 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: A  569 PHE cc_start: 0.8936 (t80) cc_final: 0.8286 (t80)
REVERT: A  618 GLU cc_start: 0.8325 (tt0) cc_final: 0.8124 (tt0)
REVERT: A  627 VAL cc_start: 0.8321 (t) cc_final: 0.8056 (t)
REVERT: A  630 MET cc_start: 0.7940 (ttp) cc_final: 0.7573 (ttp)
REVERT: A  637 THR cc_start: 0.8442 (m) cc_final: 0.7966 (p)
REVERT: A 1024 MET cc_start: 0.7572 (ttm) cc_final: 0.7298 (mtm)
REVERT: A 1055 SER cc_start: 0.9003 (t) cc_final: 0.8649 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1191
  time to fit residues: 18.1368
Evaluate side-chains
  81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0060
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 385 GLN
A 401 GLN
A 735 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.092314 restraints weight = 25824.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.094060 restraints weight = 14391.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.095218 restraints weight = 10171.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.095464 restraints weight = 8090.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.095884 restraints weight = 8004.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9922  Z= 0.121
  Angle     :  0.595  14.647  13528  Z= 0.308
  Chirality :  0.042   0.162   1456
  Planarity :  0.005   0.044   1655
  Dihedral  : 15.019 148.080   1509
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.42 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.44 (0.25), residues: 1114
  helix:  1.12 (0.25), residues: 455
  sheet:  0.29 (0.36), residues: 176
  loop : -0.42 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 742 
 TYR   0.011   0.001   TYR A 328 
 PHE   0.020   0.001   PHE A 815 
 TRP   0.017   0.002   TRP A 347 
 HIS   0.005   0.001   HIS A 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9918)
  covalent geometry    : angle       0.56276 (13516)
  hydrogen bonds       : bond        0.04356 (  453)
  hydrogen bonds       : angle       4.86374 ( 1254)
  metal coordination   : bond        0.00379 (    4)
  metal coordination   : angle       6.47623 (   12)

*********************** 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
  121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ASP cc_start: 0.8324 (t0) cc_final: 0.7817 (t70)
REVERT: A  328 TYR cc_start: 0.7292 (m-80) cc_final: 0.7035 (m-80)
REVERT: A  562 MET cc_start: 0.8120 (mmt) cc_final: 0.7776 (mmt)
REVERT: A  569 PHE cc_start: 0.8824 (t80) cc_final: 0.8216 (t80)
REVERT: A  630 MET cc_start: 0.7816 (ttp) cc_final: 0.7594 (ttp)
REVERT: A  637 THR cc_start: 0.8579 (m) cc_final: 0.8365 (p)
REVERT: A 1024 MET cc_start: 0.7483 (ttm) cc_final: 0.7175 (mtm)
REVERT: A 1153 GLN cc_start: 0.8432 (mp10) cc_final: 0.8118 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0985
  time to fit residues: 17.3137
Evaluate side-chains
  76 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 83 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0040
   chunk 23 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    2.1596

-------------------------------------------------------------------------------
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**
A1152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.107673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.087724 restraints weight = 26344.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.089563 restraints weight = 14864.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.091048 restraints weight = 10204.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.090965 restraints weight = 7940.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.091433 restraints weight = 7921.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9922  Z= 0.201
  Angle     :  0.674  17.399  13528  Z= 0.343
  Chirality :  0.045   0.286   1456
  Planarity :  0.005   0.049   1655
  Dihedral  : 15.034 147.392   1509
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.30 (0.25), residues: 1114
  helix:  1.05 (0.25), residues: 454
  sheet:  0.21 (0.38), residues: 164
  loop : -0.53 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 247 
 TYR   0.017   0.002   TYR A 152 
 PHE   0.026   0.002   PHE A 104 
 TRP   0.013   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9918)
  covalent geometry    : angle       0.62579 (13516)
  hydrogen bonds       : bond        0.05332 (  453)
  hydrogen bonds       : angle       4.94269 ( 1254)
  metal coordination   : bond        0.01678 (    4)
  metal coordination   : angle       8.42340 (   12)

*********************** 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
  95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 VAL cc_start: 0.9279 (t) cc_final: 0.8864 (p)
REVERT: A  221 MET cc_start: 0.8838 (pmm) cc_final: 0.8486 (pmm)
REVERT: A  488 GLU cc_start: 0.8258 (pm20) cc_final: 0.7972 (pm20)
REVERT: A  491 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8301 (mt-10)
REVERT: A  562 MET cc_start: 0.8196 (mmt) cc_final: 0.7791 (mmt)
REVERT: A  569 PHE cc_start: 0.8950 (t80) cc_final: 0.8309 (t80)
REVERT: A 1024 MET cc_start: 0.7693 (ttm) cc_final: 0.7115 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1131
  time to fit residues: 15.1141
Evaluate side-chains
  74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0570
   chunk 112 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.1704

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

Flipped N/Q/H residues before XYZ refinement:
A 451 GLN
** 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 = 0.3615 r_free = 0.3615 target = 0.110136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090245 restraints weight = 26009.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091967 restraints weight = 14857.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.093231 restraints weight = 10450.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.093268 restraints weight = 8217.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.093802 restraints weight = 8158.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9922  Z= 0.132
  Angle     :  0.584  13.203  13528  Z= 0.300
  Chirality :  0.042   0.207   1456
  Planarity :  0.004   0.049   1655
  Dihedral  : 14.898 145.171   1509
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.22 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.45 (0.25), residues: 1114
  helix:  1.20 (0.25), residues: 459
  sheet:  0.38 (0.36), residues: 174
  loop : -0.55 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  34 
 TYR   0.017   0.001   TYR A 473 
 PHE   0.012   0.001   PHE A 104 
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9918)
  covalent geometry    : angle       0.55397 (13516)
  hydrogen bonds       : bond        0.04430 (  453)
  hydrogen bonds       : angle       4.71661 ( 1254)
  metal coordination   : bond        0.00652 (    4)
  metal coordination   : angle       6.21997 (   12)

*********************** 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
  89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 MET cc_start: 0.8791 (pmm) cc_final: 0.8536 (pmm)
REVERT: A  247 ARG cc_start: 0.8473 (tpt170) cc_final: 0.7829 (tpp-160)
REVERT: A  299 MET cc_start: 0.8145 (tpt) cc_final: 0.7858 (tpp)
REVERT: A  520 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: A  562 MET cc_start: 0.8153 (mmt) cc_final: 0.7772 (mmt)
REVERT: A  569 PHE cc_start: 0.8950 (t80) cc_final: 0.8373 (t80)
REVERT: A 1024 MET cc_start: 0.7554 (ttm) cc_final: 0.6978 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1089
  time to fit residues: 13.6047
Evaluate side-chains
  70 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 451 GLN
** 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 = 0.3609 r_free = 0.3609 target = 0.110015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.088430 restraints weight = 25160.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.091294 restraints weight = 13551.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091972 restraints weight = 8672.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.092269 restraints weight = 7408.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.092524 restraints weight = 6974.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9922  Z= 0.152
  Angle     :  0.586  12.702  13528  Z= 0.303
  Chirality :  0.041   0.205   1456
  Planarity :  0.004   0.049   1655
  Dihedral  : 14.933 143.843   1509
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.50 (0.25), residues: 1114
  helix:  1.29 (0.25), residues: 456
  sheet:  0.29 (0.36), residues: 178
  loop : -0.51 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 266 
 TYR   0.012   0.001   TYR A 726 
 PHE   0.019   0.001   PHE A 104 
 TRP   0.021   0.002   TRP A  62 
 HIS   0.003   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9918)
  covalent geometry    : angle       0.55894 (13516)
  hydrogen bonds       : bond        0.04490 (  453)
  hydrogen bonds       : angle       4.68691 ( 1254)
  metal coordination   : bond        0.00908 (    4)
  metal coordination   : angle       5.98777 (   12)

*********************** 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
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 MET cc_start: 0.8845 (pmm) cc_final: 0.8537 (pmm)
REVERT: A  247 ARG cc_start: 0.8126 (tpt170) cc_final: 0.7602 (tpp-160)
REVERT: A  266 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7977 (mtm180)
REVERT: A  299 MET cc_start: 0.8176 (tpt) cc_final: 0.7845 (tpp)
REVERT: A  562 MET cc_start: 0.8220 (mmt) cc_final: 0.7773 (mmt)
REVERT: A  569 PHE cc_start: 0.8939 (t80) cc_final: 0.8306 (t80)
REVERT: A 1024 MET cc_start: 0.7658 (ttm) cc_final: 0.7157 (mtm)
REVERT: A 1153 GLN cc_start: 0.8538 (mp-120) cc_final: 0.8308 (mp-120)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0981
  time to fit residues: 12.5740
Evaluate side-chains
  71 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0370
   chunk 73 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0770
   chunk 50 optimal weight:    0.0060
   chunk 48 optimal weight:    6.9990
   chunk 90 optimal weight:    0.1980
   overall best weight:    0.2232

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3659 r_free = 0.3659 target = 0.113176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.093333 restraints weight = 25660.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.095335 restraints weight = 14124.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.096519 restraints weight = 9617.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.096699 restraints weight = 7691.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097154 restraints weight = 7654.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9922  Z= 0.107
  Angle     :  0.537   7.947  13528  Z= 0.278
  Chirality :  0.040   0.218   1456
  Planarity :  0.004   0.048   1655
  Dihedral  : 14.777 140.029   1509
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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 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:  0.79 (0.25), residues: 1114
  helix:  1.62 (0.25), residues: 451
  sheet:  0.47 (0.36), residues: 184
  loop : -0.46 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 266 
 TYR   0.013   0.001   TYR A 298 
 PHE   0.023   0.001   PHE A 815 
 TRP   0.013   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 9918)
  covalent geometry    : angle       0.52853 (13516)
  hydrogen bonds       : bond        0.03425 (  453)
  hydrogen bonds       : angle       4.41598 ( 1254)
  metal coordination   : bond        0.00325 (    4)
  metal coordination   : angle       3.18435 (   12)

*********************** 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
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 MET cc_start: 0.8689 (pmm) cc_final: 0.8457 (pmm)
REVERT: A  266 ARG cc_start: 0.8231 (mtm110) cc_final: 0.7937 (mtm180)
REVERT: A  275 ASP cc_start: 0.8321 (t0) cc_final: 0.7846 (t70)
REVERT: A  285 PHE cc_start: 0.6750 (t80) cc_final: 0.6464 (m-10)
REVERT: A  562 MET cc_start: 0.8067 (mmt) cc_final: 0.7705 (mmt)
REVERT: A  569 PHE cc_start: 0.8903 (t80) cc_final: 0.8337 (t80)
REVERT: A  797 MET cc_start: 0.8990 (mmm) cc_final: 0.8746 (mpp)
REVERT: A  930 PHE cc_start: 0.7957 (m-80) cc_final: 0.7579 (m-80)
REVERT: A 1024 MET cc_start: 0.7582 (ttm) cc_final: 0.7082 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1115
  time to fit residues: 16.5611
Evaluate side-chains
  77 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.2998

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
** 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 = 0.3615 r_free = 0.3615 target = 0.110324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090150 restraints weight = 26026.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.092185 restraints weight = 14172.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.093867 restraints weight = 9566.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.093734 restraints weight = 7435.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.094079 restraints weight = 7380.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9922  Z= 0.137
  Angle     :  0.563   8.857  13528  Z= 0.293
  Chirality :  0.042   0.316   1456
  Planarity :  0.004   0.047   1655
  Dihedral  : 14.816 140.959   1509
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.75 (0.26), residues: 1114
  helix:  1.57 (0.26), residues: 456
  sheet:  0.42 (0.36), residues: 178
  loop : -0.47 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 266 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.019   0.001   PHE A 104 
 TRP   0.023   0.002   TRP A  62 
 HIS   0.003   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9918)
  covalent geometry    : angle       0.55009 (13516)
  hydrogen bonds       : bond        0.03986 (  453)
  hydrogen bonds       : angle       4.46346 ( 1254)
  metal coordination   : bond        0.00768 (    4)
  metal coordination   : angle       4.00245 (   12)

*********************** 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
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8002 (mtp180)
REVERT: A  221 MET cc_start: 0.8774 (pmm) cc_final: 0.8477 (pmm)
REVERT: A  247 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7808 (tpp-160)
REVERT: A  266 ARG cc_start: 0.8347 (mtm110) cc_final: 0.8008 (mtm180)
REVERT: A  275 ASP cc_start: 0.8399 (t0) cc_final: 0.7796 (t70)
REVERT: A  285 PHE cc_start: 0.6814 (t80) cc_final: 0.6451 (m-10)
REVERT: A  299 MET cc_start: 0.7335 (tpt) cc_final: 0.6949 (tpt)
REVERT: A  562 MET cc_start: 0.8181 (mmt) cc_final: 0.7791 (mmt)
REVERT: A  627 VAL cc_start: 0.8421 (p) cc_final: 0.8150 (p)
REVERT: A  797 MET cc_start: 0.9032 (mmm) cc_final: 0.8826 (mpp)
REVERT: A  930 PHE cc_start: 0.7829 (m-80) cc_final: 0.7481 (m-80)
REVERT: A 1024 MET cc_start: 0.7565 (ttm) cc_final: 0.7034 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1109
  time to fit residues: 13.6907
Evaluate side-chains
  74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 109 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   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  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
** 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 = 0.3619 r_free = 0.3619 target = 0.110613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.090552 restraints weight = 26016.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.092419 restraints weight = 14772.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.094000 restraints weight = 10186.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.093938 restraints weight = 7765.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.094176 restraints weight = 7707.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9922  Z= 0.121
  Angle     :  0.555   8.129  13528  Z= 0.286
  Chirality :  0.041   0.215   1456
  Planarity :  0.004   0.048   1655
  Dihedral  : 14.762 139.678   1509
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.74 (0.26), residues: 1114
  helix:  1.56 (0.25), residues: 458
  sheet:  0.36 (0.35), residues: 194
  loop : -0.49 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 721 
 TYR   0.011   0.001   TYR A 434 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.017   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9918)
  covalent geometry    : angle       0.54270 (13516)
  hydrogen bonds       : bond        0.03787 (  453)
  hydrogen bonds       : angle       4.43025 ( 1254)
  metal coordination   : bond        0.00529 (    4)
  metal coordination   : angle       3.87263 (   12)

*********************** 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
  85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7999 (mtp180)
REVERT: A  247 ARG cc_start: 0.8226 (tpt170) cc_final: 0.7879 (tpp-160)
REVERT: A  275 ASP cc_start: 0.8404 (t0) cc_final: 0.7766 (t70)
REVERT: A  285 PHE cc_start: 0.6954 (t80) cc_final: 0.6545 (m-10)
REVERT: A  299 MET cc_start: 0.7314 (tpt) cc_final: 0.6962 (tpt)
REVERT: A  491 GLU cc_start: 0.8772 (mm-30) cc_final: 0.7998 (mt-10)
REVERT: A  562 MET cc_start: 0.8151 (mmt) cc_final: 0.7773 (mmt)
REVERT: A  627 VAL cc_start: 0.8417 (p) cc_final: 0.8127 (p)
REVERT: A  930 PHE cc_start: 0.7799 (m-80) cc_final: 0.7430 (m-80)
REVERT: A 1024 MET cc_start: 0.7539 (ttm) cc_final: 0.6997 (mtm)
REVERT: A 1080 ILE cc_start: 0.6245 (mt) cc_final: 0.6003 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1071
  time to fit residues: 13.1000
Evaluate side-chains
  74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
** 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 = 0.3618 r_free = 0.3618 target = 0.110473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.090579 restraints weight = 25907.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.092606 restraints weight = 14096.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.093977 restraints weight = 9502.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.093986 restraints weight = 7443.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.094481 restraints weight = 7467.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9922  Z= 0.126
  Angle     :  0.563   8.296  13528  Z= 0.290
  Chirality :  0.041   0.213   1456
  Planarity :  0.004   0.048   1655
  Dihedral  : 14.762 138.731   1509
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.67 (0.26), residues: 1114
  helix:  1.55 (0.25), residues: 457
  sheet:  0.33 (0.35), residues: 194
  loop : -0.57 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 721 
 TYR   0.016   0.001   TYR A1018 
 PHE   0.018   0.001   PHE A 104 
 TRP   0.015   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9918)
  covalent geometry    : angle       0.54990 (13516)
  hydrogen bonds       : bond        0.03893 (  453)
  hydrogen bonds       : angle       4.43330 ( 1254)
  metal coordination   : bond        0.00640 (    4)
  metal coordination   : angle       4.03756 (   12)

********************** 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
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8098 (mtp180)
REVERT: A  247 ARG cc_start: 0.8209 (tpt170) cc_final: 0.7865 (tpp-160)
REVERT: A  275 ASP cc_start: 0.8432 (t0) cc_final: 0.7756 (t70)
REVERT: A  285 PHE cc_start: 0.6970 (t80) cc_final: 0.6553 (m-10)
REVERT: A  299 MET cc_start: 0.7328 (tpt) cc_final: 0.6978 (tpt)
REVERT: A  491 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8020 (mt-10)
REVERT: A  562 MET cc_start: 0.8147 (mmt) cc_final: 0.7772 (mmt)
REVERT: A  797 MET cc_start: 0.9115 (mmm) cc_final: 0.8792 (mpp)
REVERT: A 1024 MET cc_start: 0.7690 (ttm) cc_final: 0.7065 (mtp)
REVERT: A 1080 ILE cc_start: 0.6323 (mt) cc_final: 0.6080 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1043
  time to fit residues: 13.0496
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  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0470
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0010
   chunk 7 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
A 451 GLN
A 522 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 = 0.113195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.093660 restraints weight = 25791.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.095576 restraints weight = 14293.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.096998 restraints weight = 9793.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.097000 restraints weight = 7583.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.097519 restraints weight = 7659.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9922  Z= 0.106
  Angle     :  0.558   8.506  13528  Z= 0.284
  Chirality :  0.040   0.214   1456
  Planarity :  0.004   0.048   1655
  Dihedral  : 14.681 136.462   1509
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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 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:  0.78 (0.25), residues: 1114
  helix:  1.58 (0.26), residues: 451
  sheet:  0.64 (0.36), residues: 182
  loop : -0.53 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 266 
 TYR   0.017   0.001   TYR A 362 
 PHE   0.011   0.001   PHE A 104 
 TRP   0.014   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9918)
  covalent geometry    : angle       0.55050 (13516)
  hydrogen bonds       : bond        0.03425 (  453)
  hydrogen bonds       : angle       4.31249 ( 1254)
  metal coordination   : bond        0.00211 (    4)
  metal coordination   : angle       3.15232 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1463.97 seconds
wall clock time: 26 minutes 18.21 seconds (1578.21 seconds total)