Starting phenix.real_space_refine
on Wed Mar  4 17:57:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w5t_21547/03_2026/6w5t_21547.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      71      5.16       5
     C    6156      2.51       5
     N    1496      2.21       5
     O    1782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9505
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1175, 9189
          Classifications: {'peptide': 1175}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 182
          Unusual residues: {'CLR': 2, 'NAG': 9}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
  Time building chain proxies: 2.25, per 1000 atoms: 0.24
  Number of scatterers: 9505
  At special positions: 0
  Unit cell: (103.602, 91.348, 152.618, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      71     16.00
     O    1782      8.00
     N    1496      7.00
     C    6156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A  42 " distance=1.51
    Simple disulfide: pdb=" SG  CYS A  63 " - pdb=" SG  CYS A 109 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 238 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 160 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 184 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 243 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 247 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 468 " - pdb=" SG  CYS A 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 533 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 914 " distance=2.97
    Simple disulfide: pdb=" SG  CYS A 956 " - pdb=" SG  CYS A1011 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 957 " - pdb=" SG  CYS A 979 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 976 " distance=2.03

  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
  Links applied
    ALPHA1-3
      " NAG C   2 " - " MAN C   3 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1401 " - " ASN A 452 "
      " NAG A1402 " - " ASN A 459 "
      " NAG A1405 " - " ASN A 524 "
      " NAG A1409 " - " ASN A 598 "
      " NAG A1410 " - " ASN A 916 "
      " NAG A1414 " - " ASN A 961 "
      " NAG A1415 " - " ASN A 968 "
      " NAG A1416 " - " ASN A1064 "
      " NAG A1419 " - " ASN A 158 "
      " NAG B   1 " - " ASN A 478 "
      " NAG C   1 " - " ASN A 557 "
      " NAG D   1 " - " ASN A 931 "
      " NAG E   1 " - " ASN A 222 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 439.2 milliseconds
  

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      59.1% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 63
      removed outlier: 3.599A  pdb=" N   CYS A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 67
    Processing helix  chain 'A' and resid 76 through 87
    Processing helix  chain 'A' and resid 87 through 95
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 3.608A  pdb=" N   ASN A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU A 110 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 119
    Processing helix  chain 'A' and resid 149 through 161
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 185 through 195
      removed outlier: 4.043A  pdb=" N   ILE A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 199
    Processing helix  chain 'A' and resid 268 through 291
      removed outlier: 3.991A  pdb=" N   ALA A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA A 289 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 295
    Processing helix  chain 'A' and resid 330 through 349
      removed outlier: 4.150A  pdb=" N   CYS A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LEU A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ARG A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 366
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 376 through 382
    Processing helix  chain 'A' and resid 386 through 399
    Processing helix  chain 'A' and resid 436 through 453
      removed outlier: 3.520A  pdb=" N   ASN A 452 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ILE A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.534A  pdb=" N   TYR A 487 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 3.510A  pdb=" N   ARG A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 574 through 594
      removed outlier: 3.652A  pdb=" N   GLU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 617
    Processing helix  chain 'A' and resid 620 through 639
      removed outlier: 4.106A  pdb=" N   ILE A 626 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 679
    Processing helix  chain 'A' and resid 685 through 711
      Proline residue:  A 691  - end of helix
    Processing helix  chain 'A' and resid 720 through 750
      Proline residue:  A 733  - end of helix
    Processing helix  chain 'A' and resid 754 through 789
    Processing helix  chain 'A' and resid 816 through 824
      removed outlier: 3.634A  pdb=" N   PHE A 820 " --> pdb=" O   CYS A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 830
    Processing helix  chain 'A' and resid 833 through 852
      removed outlier: 3.747A  pdb=" N   ILE A 837 " --> pdb=" O   TRP A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 856
    Processing helix  chain 'A' and resid 870 through 883
      removed outlier: 4.029A  pdb=" N   ASP A 874 " --> pdb=" O   SER A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 907
    Processing helix  chain 'A' and resid 918 through 930
    Processing helix  chain 'A' and resid 941 through 951
      removed outlier: 3.983A  pdb=" N   ASP A 945 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 4.073A  pdb=" N   GLN A 988 " --> pdb=" O   PRO A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 4.400A  pdb=" N   MET A 996 " --> pdb=" O   GLY A 992 " (cutoff:3.500A)
      Proline residue:  A1000  - end of helix
    Processing helix  chain 'A' and resid 1047 through 1070
      removed outlier: 3.720A  pdb=" N   GLY A1070 " --> pdb=" O   THR A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1090 through 1092
      No H-bonds generated for 'chain 'A' and resid 1090 through 1092'
    Processing helix  chain 'A' and resid 1093 through 1117
    Processing helix  chain 'A' and resid 1120 through 1146
      removed outlier: 3.537A  pdb=" N   ALA A1124 " --> pdb=" O   GLU A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1177
      removed outlier: 4.007A  pdb=" N   GLY A1162 " --> pdb=" O   VAL A1158 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   VAL A1165 " --> pdb=" O   CYS A1161 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU A1166 " --> pdb=" O   GLY A1162 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE A1167 " --> pdb=" O   ILE A1163 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   HIS A1170 " --> pdb=" O   GLU A1166 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ILE A1171 " --> pdb=" O   PHE A1167 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR A1172 " --> pdb=" O   CYS A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1202
      removed outlier: 4.301A  pdb=" N   SER A1197 " --> pdb=" O   HIS A1193 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER A1200 " --> pdb=" O   SER A1196 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A1202 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1202 through 1214
    Processing helix  chain 'A' and resid 1219 through 1242
      removed outlier: 4.526A  pdb=" N   PHE A1226 " --> pdb=" O   GLN A1222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1242 through 1252
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 127
      removed outlier: 3.915A  pdb=" N   ASN A 122 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN A 145 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   GLU A 143 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   THR A 126 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL A 141 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   THR A 206 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 144 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL A 208 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   TYR A 146 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 547 through 548
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 420
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1039 through 1043
    Processing sheet with id=AA5, first strand: chain 'A' and resid 958 through 960
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025
      removed outlier: 5.328A  pdb=" N   ASN A1024 " --> pdb=" O   GLY A1034 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1392 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.37

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2947
        1.35 -     1.48: 2625
        1.48 -     1.61: 4081
        1.61 -     1.74: 1
        1.74 -     1.87: 99
  Bond restraints: 9753
  Sorted by residual:
  bond pdb=" CA  CYS A 909 "
       pdb=" C   CYS A 909 "
    ideal  model  delta    sigma   weight residual
    1.524  1.579 -0.055 1.27e-02 6.20e+03 1.90e+01
  bond pdb=" N   CYS A 909 "
       pdb=" CA  CYS A 909 "
    ideal  model  delta    sigma   weight residual
    1.459  1.505 -0.046 1.19e-02 7.06e+03 1.47e+01
  bond pdb=" CA  TYR A 269 "
       pdb=" C   TYR A 269 "
    ideal  model  delta    sigma   weight residual
    1.522  1.473  0.049 1.39e-02 5.18e+03 1.23e+01
  bond pdb=" C1  NAG A1405 "
       pdb=" O5  NAG A1405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.26e+00
  bond pdb=" C1  NAG A1410 "
       pdb=" O5  NAG A1410 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.65e+00
  ... (remaining 9748 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.48: 13253
        5.48 -    10.95: 38
       10.95 -    16.43: 4
       16.43 -    21.90: 0
       21.90 -    27.38: 1
  Bond angle restraints: 13296
  Sorted by residual:
  angle pdb=" N   CYS A 909 "
        pdb=" CA  CYS A 909 "
        pdb=" C   CYS A 909 "
      ideal   model   delta    sigma   weight residual
     111.07  138.45  -27.38 1.07e+00 8.73e-01 6.55e+02
  angle pdb=" N   ASN A 823 "
        pdb=" CA  ASN A 823 "
        pdb=" C   ASN A 823 "
      ideal   model   delta    sigma   weight residual
     111.14  121.36  -10.22 1.08e+00 8.57e-01 8.95e+01
  angle pdb=" N   SER A 602 "
        pdb=" CA  SER A 602 "
        pdb=" C   SER A 602 "
      ideal   model   delta    sigma   weight residual
     108.41   97.30   11.11 1.63e+00 3.76e-01 4.64e+01
  angle pdb=" CA  CYS A 909 "
        pdb=" C   CYS A 909 "
        pdb=" N   GLY A 910 "
      ideal   model   delta    sigma   weight residual
     117.07  124.47   -7.40 1.14e+00 7.69e-01 4.21e+01
  angle pdb=" C   GLY A 910 "
        pdb=" N   GLY A 911 "
        pdb=" CA  GLY A 911 "
      ideal   model   delta    sigma   weight residual
     122.42  129.43   -7.01 1.13e+00 7.83e-01 3.85e+01
  ... (remaining 13291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.95: 5696
       27.95 -    55.90: 304
       55.90 -    83.85: 53
       83.85 -   111.80: 33
      111.80 -   139.76: 13
  Dihedral angle restraints: 6099
    sinusoidal: 2677
      harmonic: 3422
  Sorted by residual:
  dihedral pdb=" CB  CYS A 240 "
           pdb=" SG  CYS A 240 "
           pdb=" SG  CYS A 247 "
           pdb=" CB  CYS A 247 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.20  -86.20     1      1.00e+01 1.00e-02 8.96e+01
  dihedral pdb=" CA  ASN A  70 "
           pdb=" C   ASN A  70 "
           pdb=" N   VAL A  71 "
           pdb=" CA  VAL A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.91  -42.09     0      5.00e+00 4.00e-02 7.08e+01
  dihedral pdb=" CA  GLY A  69 "
           pdb=" C   GLY A  69 "
           pdb=" N   ASN A  70 "
           pdb=" CA  ASN A  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.81   38.19     0      5.00e+00 4.00e-02 5.83e+01
  ... (remaining 6096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.948: 1555
       0.948 -    1.896: 0
       1.896 -    2.844: 0
       2.844 -    3.792: 0
       3.792 -    4.740: 2
  Chirality restraints: 1557
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.34   -4.74 2.00e-02 2.50e+03 5.62e+04
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.33   -4.73 2.00e-02 2.50e+03 5.59e+04
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-02 2.50e+03 4.38e+02
  ... (remaining 1554 not shown)

  Planarity restraints: 1677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "   -0.345 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG E   2 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "   -0.071 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "    0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.190 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.343 2.00e-02 2.50e+03   2.96e-01 1.09e+03
        pdb=" C7  NAG C   2 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.048 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.518 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.206 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.344 2.00e-02 2.50e+03   2.92e-01 1.07e+03
        pdb=" C7  NAG E   1 "   -0.088 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.179 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.512 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.077 2.00e-02 2.50e+03
  ... (remaining 1674 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 175
        2.62 -     3.19: 9588
        3.19 -     3.76: 14483
        3.76 -     4.33: 20142
        4.33 -     4.90: 32725
  Nonbonded interactions: 77113
  Sorted by model distance:
  nonbonded pdb=" O3  NAG B   2 "
            pdb=" O7  NAG B   2 "
     model   vdw
     2.054 3.040
  nonbonded pdb=" OH  TYR A 487 "
            pdb=" O   VAL A 541 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" N   GLU A  30 "
            pdb=" OE1 GLU A  30 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OD1 ASN A 459 "
            pdb=" N2  NAG A1402 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" N   GLN A 716 "
            pdb=" OE1 GLN A 716 "
     model   vdw
     2.206 3.120
  ... (remaining 77108 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'C' and resid 1 through 2)
  selection = (chain 'D' and resid 1 through 2)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.540
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
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      :  0.013   0.943   9787  Z= 0.654
  Angle     :  1.449  62.516  13383  Z= 0.811
  Chirality :  0.182   4.740   1557
  Planarity :  0.015   0.298   1664
  Dihedral  : 19.767 139.756   3854
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 48.42
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  7.97 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  :  8.95 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -2.80 (0.22), residues: 1167
  helix: -0.92 (0.20), residues: 591
  sheet: -2.19 (0.58), residues: 87
  loop : -2.97 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 518 
 TYR   0.018   0.002   TYR A1225 
 PHE   0.031   0.002   PHE A 747 
 TRP   0.035   0.003   TRP A  27 
 HIS   0.004   0.001   HIS A1239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 ( 9753)
  covalent geometry    : angle       1.14424 (13296)
  SS BOND              : bond        0.27857 (   15)
  SS BOND              : angle      15.44478 (   30)
  hydrogen bonds       : bond        0.14475 (  482)
  hydrogen bonds       : angle       6.57977 ( 1392)
  link_ALPHA1-3        : bond        0.00318 (    1)
  link_ALPHA1-3        : angle       1.51178 (    3)
  link_BETA1-4         : bond        0.04112 (    5)
  link_BETA1-4         : angle      13.35003 (   15)
  link_NAG-ASN         : bond        0.00493 (   13)
  link_NAG-ASN         : angle       4.70561 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 246
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 PRO cc_start: 0.7137 (Cg_exo) cc_final: 0.6527 (Cg_endo)
REVERT: A   83 LEU cc_start: 0.8865 (tt) cc_final: 0.8662 (tt)
REVERT: A   93 PHE cc_start: 0.7739 (m-80) cc_final: 0.7238 (m-80)
REVERT: A  192 TYR cc_start: 0.8081 (t80) cc_final: 0.7659 (t80)
REVERT: A  272 MET cc_start: 0.8537 (mmp) cc_final: 0.8332 (mmm)
REVERT: A  376 ASN cc_start: 0.8793 (t0) cc_final: 0.8496 (p0)
REVERT: A  406 GLU cc_start: 0.8602 (mp0) cc_final: 0.8357 (mp0)
REVERT: A  498 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7105 (mttt)
REVERT: A  550 TYR cc_start: 0.8108 (p90) cc_final: 0.7790 (p90)
REVERT: A  612 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (mm-30)
REVERT: A  714 ARG cc_start: 0.6922 (pmt170) cc_final: 0.6604 (ptp90)
REVERT: A  726 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (ttp-110)
REVERT: A  825 TYR cc_start: 0.8789 (t80) cc_final: 0.8034 (t80)
REVERT: A 1053 ASP cc_start: 0.7015 (t0) cc_final: 0.6808 (t0)
REVERT: A 1089 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: A 1110 PHE cc_start: 0.8557 (t80) cc_final: 0.8330 (t80)
REVERT: A 1137 ASN cc_start: 0.9151 (m110) cc_final: 0.8803 (m110)
REVERT: A 1235 LEU cc_start: 0.8425 (tt) cc_final: 0.7987 (mt)
  outliers start: 57
  outliers final: 23
  residues processed: 286
  average time/residue: 0.0922
  time to fit residues: 36.6958
Evaluate side-chains
  197 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  516 CYS
Chi-restraints excluded: chain A residue  612 GLU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  726 ARG
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  824 SER
Chi-restraints excluded: chain A residue  849 SER
Chi-restraints excluded: chain A residue  909 CYS
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1032 ARG
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1123 SER
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1220 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 119 GLN
A 136 GLN
** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
A 823 ASN
A1024 ASN
A1137 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.143148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111837 restraints weight = 16207.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112938 restraints weight = 8997.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113913 restraints weight = 7377.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.114265 restraints weight = 5563.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114634 restraints weight = 5048.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9787  Z= 0.183
  Angle     :  0.939  18.281  13383  Z= 0.439
  Chirality :  0.053   0.282   1557
  Planarity :  0.005   0.046   1664
  Dihedral  : 15.735 107.460   1844
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.91 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.22 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -1.38 (0.24), residues: 1167
  helix:  0.17 (0.21), residues: 611
  sheet: -2.44 (0.52), residues: 90
  loop : -2.03 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 372 
 TYR   0.028   0.002   TYR A 293 
 PHE   0.020   0.002   PHE A 101 
 TRP   0.031   0.002   TRP A  27 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9753)
  covalent geometry    : angle       0.88822 (13296)
  SS BOND              : bond        0.00469 (   15)
  SS BOND              : angle       2.41776 (   30)
  hydrogen bonds       : bond        0.05449 (  482)
  hydrogen bonds       : angle       5.28204 ( 1392)
  link_ALPHA1-3        : bond        0.00957 (    1)
  link_ALPHA1-3        : angle       2.26021 (    3)
  link_BETA1-4         : bond        0.01944 (    5)
  link_BETA1-4         : angle       6.44960 (   15)
  link_NAG-ASN         : bond        0.00697 (   13)
  link_NAG-ASN         : angle       3.57013 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 209
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   78 ARG cc_start: 0.8679 (tpt-90) cc_final: 0.8428 (tpp-160)
REVERT: A   93 PHE cc_start: 0.7650 (m-80) cc_final: 0.7366 (m-80)
REVERT: A  127 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4529 (pm20)
REVERT: A  192 TYR cc_start: 0.8085 (t80) cc_final: 0.7775 (t80)
REVERT: A  220 MET cc_start: 0.6245 (ppp) cc_final: 0.6027 (ppp)
REVERT: A  277 MET cc_start: 0.7728 (mmt) cc_final: 0.7257 (mmm)
REVERT: A  288 PHE cc_start: 0.6329 (m-10) cc_final: 0.6037 (m-10)
REVERT: A  376 ASN cc_start: 0.8446 (t0) cc_final: 0.8146 (p0)
REVERT: A  550 TYR cc_start: 0.7991 (p90) cc_final: 0.7744 (p90)
REVERT: A  740 PHE cc_start: 0.8195 (t80) cc_final: 0.7907 (t80)
REVERT: A  751 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7219 (pt)
REVERT: A  825 TYR cc_start: 0.8691 (t80) cc_final: 0.7955 (t80)
REVERT: A 1005 ASP cc_start: 0.8937 (t0) cc_final: 0.8614 (t0)
REVERT: A 1089 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7152 (tm-30)
REVERT: A 1110 PHE cc_start: 0.8546 (t80) cc_final: 0.8286 (t80)
REVERT: A 1127 MET cc_start: 0.8405 (ttp) cc_final: 0.8080 (tpp)
  outliers start: 35
  outliers final: 23
  residues processed: 227
  average time/residue: 0.0720
  time to fit residues: 24.2713
Evaluate side-chains
  185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1106 LEU
Chi-restraints excluded: chain A residue 1123 SER
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.138768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108415 restraints weight = 16759.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.106617 restraints weight = 10482.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108064 restraints weight = 10123.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108643 restraints weight = 6937.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108965 restraints weight = 6493.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9787  Z= 0.191
  Angle     :  0.854  12.401  13383  Z= 0.402
  Chirality :  0.050   0.239   1557
  Planarity :  0.005   0.038   1664
  Dihedral  : 13.567 106.293   1805
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.51 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.47 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.92 (0.24), residues: 1167
  helix:  0.49 (0.21), residues: 609
  sheet: -1.94 (0.54), residues: 84
  loop : -1.79 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 336 
 TYR   0.013   0.002   TYR A 899 
 PHE   0.034   0.002   PHE A 503 
 TRP   0.020   0.002   TRP A  27 
 HIS   0.004   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 9753)
  covalent geometry    : angle       0.82333 (13296)
  SS BOND              : bond        0.00629 (   15)
  SS BOND              : angle       2.15188 (   30)
  hydrogen bonds       : bond        0.05278 (  482)
  hydrogen bonds       : angle       5.16969 ( 1392)
  link_ALPHA1-3        : bond        0.01062 (    1)
  link_ALPHA1-3        : angle       2.26819 (    3)
  link_BETA1-4         : bond        0.01363 (    5)
  link_BETA1-4         : angle       3.11693 (   15)
  link_NAG-ASN         : bond        0.00575 (   13)
  link_NAG-ASN         : angle       3.35609 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 183
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.5647 (tt0) cc_final: 0.4681 (tm-30)
REVERT: A   78 ARG cc_start: 0.8706 (tpt-90) cc_final: 0.8404 (tpp-160)
REVERT: A   93 PHE cc_start: 0.7848 (m-80) cc_final: 0.7522 (m-80)
REVERT: A  127 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4666 (pm20)
REVERT: A  192 TYR cc_start: 0.8269 (t80) cc_final: 0.8023 (t80)
REVERT: A  376 ASN cc_start: 0.8559 (t0) cc_final: 0.8231 (p0)
REVERT: A  550 TYR cc_start: 0.8200 (p90) cc_final: 0.7763 (p90)
REVERT: A  714 ARG cc_start: 0.7449 (ptp90) cc_final: 0.6879 (ptm-80)
REVERT: A  751 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7340 (pt)
REVERT: A  825 TYR cc_start: 0.8815 (t80) cc_final: 0.8091 (t80)
REVERT: A  912 MET cc_start: 0.6955 (mmp) cc_final: 0.6583 (mmt)
REVERT: A 1110 PHE cc_start: 0.8487 (t80) cc_final: 0.8263 (t80)
  outliers start: 41
  outliers final: 25
  residues processed: 204
  average time/residue: 0.0672
  time to fit residues: 20.9284
Evaluate side-chains
  188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1106 LEU
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 102 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 82 optimal weight:    0.3980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 GLN
A1137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.144979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114440 restraints weight = 16934.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114548 restraints weight = 9408.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.115668 restraints weight = 7876.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115964 restraints weight = 6086.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.116473 restraints weight = 5445.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9787  Z= 0.145
  Angle     :  0.814  12.574  13383  Z= 0.380
  Chirality :  0.046   0.235   1557
  Planarity :  0.004   0.039   1664
  Dihedral  : 11.875 109.435   1804
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.00 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.26 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.63 (0.24), residues: 1167
  helix:  0.71 (0.21), residues: 610
  sheet: -1.89 (0.48), residues: 95
  loop : -1.61 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 372 
 TYR   0.015   0.001   TYR A  44 
 PHE   0.028   0.002   PHE A 503 
 TRP   0.026   0.001   TRP A1143 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9753)
  covalent geometry    : angle       0.77702 (13296)
  SS BOND              : bond        0.00434 (   15)
  SS BOND              : angle       2.94046 (   30)
  hydrogen bonds       : bond        0.04598 (  482)
  hydrogen bonds       : angle       5.08745 ( 1392)
  link_ALPHA1-3        : bond        0.01168 (    1)
  link_ALPHA1-3        : angle       1.77189 (    3)
  link_BETA1-4         : bond        0.01425 (    5)
  link_BETA1-4         : angle       2.96048 (   15)
  link_NAG-ASN         : bond        0.00634 (   13)
  link_NAG-ASN         : angle       3.38275 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 177
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   43 GLU cc_start: 0.5147 (tt0) cc_final: 0.4507 (tm-30)
REVERT: A   78 ARG cc_start: 0.8725 (tpt-90) cc_final: 0.8395 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8579 (t80) cc_final: 0.8008 (m-80)
REVERT: A  127 GLU cc_start: 0.5158 (OUTLIER) cc_final: 0.4536 (pm20)
REVERT: A  156 MET cc_start: 0.8413 (tmm) cc_final: 0.8082 (ppp)
REVERT: A  277 MET cc_start: 0.7453 (mmt) cc_final: 0.7239 (mmm)
REVERT: A  550 TYR cc_start: 0.7976 (p90) cc_final: 0.7568 (p90)
REVERT: A  714 ARG cc_start: 0.7331 (ptp90) cc_final: 0.6904 (ptm-80)
REVERT: A  751 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (pt)
REVERT: A  825 TYR cc_start: 0.8730 (t80) cc_final: 0.8037 (t80)
REVERT: A  912 MET cc_start: 0.6864 (mmp) cc_final: 0.6543 (mmt)
REVERT: A  958 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7106 (mtm180)
REVERT: A 1235 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8214 (mt)
  outliers start: 46
  outliers final: 28
  residues processed: 200
  average time/residue: 0.0738
  time to fit residues: 22.0946
Evaluate side-chains
  188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1123 SER
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0980
   overall best weight:    0.6062

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.145153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.114925 restraints weight = 16849.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115570 restraints weight = 9211.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116778 restraints weight = 7888.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.116882 restraints weight = 5660.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117203 restraints weight = 5563.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9787  Z= 0.139
  Angle     :  0.790  12.412  13383  Z= 0.371
  Chirality :  0.046   0.233   1557
  Planarity :  0.004   0.040   1664
  Dihedral  : 11.218 107.731   1802
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.51 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.44 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.49 (0.24), residues: 1167
  helix:  0.83 (0.21), residues: 613
  sheet: -1.91 (0.47), residues: 101
  loop : -1.52 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 372 
 TYR   0.014   0.001   TYR A  44 
 PHE   0.045   0.002   PHE A  93 
 TRP   0.024   0.001   TRP A1143 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9753)
  covalent geometry    : angle       0.75628 (13296)
  SS BOND              : bond        0.00335 (   15)
  SS BOND              : angle       2.19953 (   30)
  hydrogen bonds       : bond        0.04467 (  482)
  hydrogen bonds       : angle       5.07692 ( 1392)
  link_ALPHA1-3        : bond        0.01042 (    1)
  link_ALPHA1-3        : angle       1.81460 (    3)
  link_BETA1-4         : bond        0.01510 (    5)
  link_BETA1-4         : angle       2.74874 (   15)
  link_NAG-ASN         : bond        0.00671 (   13)
  link_NAG-ASN         : angle       3.54242 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 172
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.4942 (tt0) cc_final: 0.4476 (tm-30)
REVERT: A   78 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.8411 (tpp-160)
REVERT: A   92 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7865 (pp30)
REVERT: A   93 PHE cc_start: 0.7604 (m-80) cc_final: 0.7012 (m-80)
REVERT: A  111 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: A  277 MET cc_start: 0.7520 (mmt) cc_final: 0.7309 (mmm)
REVERT: A  506 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7384 (t80)
REVERT: A  550 TYR cc_start: 0.7980 (p90) cc_final: 0.7464 (p90)
REVERT: A  751 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7190 (pt)
REVERT: A  825 TYR cc_start: 0.8764 (t80) cc_final: 0.8045 (t80)
REVERT: A  912 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6471 (mmt)
REVERT: A  958 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7114 (mtm180)
REVERT: A  991 GLN cc_start: 0.8651 (pp30) cc_final: 0.8439 (pp30)
REVERT: A 1013 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6314 (mmmt)
REVERT: A 1142 MET cc_start: 0.8950 (mtp) cc_final: 0.8662 (mtp)
REVERT: A 1202 ILE cc_start: 0.8178 (mp) cc_final: 0.7967 (mt)
REVERT: A 1235 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8248 (mt)
  outliers start: 45
  outliers final: 32
  residues processed: 197
  average time/residue: 0.0744
  time to fit residues: 21.9991
Evaluate side-chains
  196 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  506 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  912 MET
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 109 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 ASN ** 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 = 0.3902 r_free = 0.3902 target = 0.144676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.114338 restraints weight = 16779.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114493 restraints weight = 9438.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.115509 restraints weight = 7978.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.117798 restraints weight = 6162.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117609 restraints weight = 5291.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9787  Z= 0.142
  Angle     :  0.781  12.201  13383  Z= 0.367
  Chirality :  0.045   0.231   1557
  Planarity :  0.004   0.043   1664
  Dihedral  : 10.483 101.142   1799
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.43 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.32 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.33 (0.25), residues: 1167
  helix:  0.94 (0.21), residues: 613
  sheet: -1.80 (0.46), residues: 116
  loop : -1.38 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 372 
 TYR   0.022   0.001   TYR A 420 
 PHE   0.029   0.002   PHE A  93 
 TRP   0.018   0.001   TRP A1143 
 HIS   0.005   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9753)
  covalent geometry    : angle       0.75220 (13296)
  SS BOND              : bond        0.00339 (   15)
  SS BOND              : angle       1.92069 (   30)
  hydrogen bonds       : bond        0.04542 (  482)
  hydrogen bonds       : angle       5.04374 ( 1392)
  link_ALPHA1-3        : bond        0.00953 (    1)
  link_ALPHA1-3        : angle       1.72333 (    3)
  link_BETA1-4         : bond        0.01463 (    5)
  link_BETA1-4         : angle       2.60981 (   15)
  link_NAG-ASN         : bond        0.00579 (   13)
  link_NAG-ASN         : angle       3.30741 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 166
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.5230 (tt0) cc_final: 0.4574 (tm-30)
REVERT: A   78 ARG cc_start: 0.8688 (tpt-90) cc_final: 0.8345 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8531 (t80) cc_final: 0.7975 (m-80)
REVERT: A  277 MET cc_start: 0.7604 (mmt) cc_final: 0.7399 (mmm)
REVERT: A  506 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: A  550 TYR cc_start: 0.7998 (p90) cc_final: 0.7442 (p90)
REVERT: A  578 GLN cc_start: 0.8631 (mp10) cc_final: 0.8288 (mp10)
REVERT: A  751 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7268 (pt)
REVERT: A  825 TYR cc_start: 0.8768 (t80) cc_final: 0.8044 (t80)
REVERT: A  912 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.6224 (mmt)
REVERT: A  958 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7208 (mtm180)
REVERT: A 1013 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6353 (mmmt)
REVERT: A 1142 MET cc_start: 0.8938 (mtp) cc_final: 0.8652 (mtp)
REVERT: A 1235 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8222 (mt)
  outliers start: 44
  outliers final: 31
  residues processed: 196
  average time/residue: 0.0747
  time to fit residues: 21.8122
Evaluate side-chains
  186 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  506 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  912 MET
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 112 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 18 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0040
   chunk 102 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   overall best weight:    0.9194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.143809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.113100 restraints weight = 16845.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.112523 restraints weight = 10069.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113624 restraints weight = 8192.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114169 restraints weight = 6463.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.114387 restraints weight = 5977.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9787  Z= 0.145
  Angle     :  0.781  12.087  13383  Z= 0.367
  Chirality :  0.045   0.238   1557
  Planarity :  0.004   0.042   1664
  Dihedral  :  9.909  90.541   1799
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.22 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.25 (0.25), residues: 1167
  helix:  0.95 (0.21), residues: 615
  sheet: -1.55 (0.48), residues: 116
  loop : -1.35 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1183 
 TYR   0.018   0.001   TYR A  44 
 PHE   0.032   0.002   PHE A 152 
 TRP   0.017   0.001   TRP A  27 
 HIS   0.003   0.001   HIS A 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9753)
  covalent geometry    : angle       0.75238 (13296)
  SS BOND              : bond        0.00400 (   15)
  SS BOND              : angle       1.75085 (   30)
  hydrogen bonds       : bond        0.04470 (  482)
  hydrogen bonds       : angle       5.03375 ( 1392)
  link_ALPHA1-3        : bond        0.00897 (    1)
  link_ALPHA1-3        : angle       1.68756 (    3)
  link_BETA1-4         : bond        0.01380 (    5)
  link_BETA1-4         : angle       2.72768 (   15)
  link_NAG-ASN         : bond        0.00560 (   13)
  link_NAG-ASN         : angle       3.33157 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.5395 (tt0) cc_final: 0.4640 (tm-30)
REVERT: A   78 ARG cc_start: 0.8662 (tpt-90) cc_final: 0.8346 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8622 (t80) cc_final: 0.8016 (m-80)
REVERT: A  293 TYR cc_start: 0.7511 (t80) cc_final: 0.7209 (t80)
REVERT: A  407 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8355 (mp10)
REVERT: A  506 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7339 (t80)
REVERT: A  550 TYR cc_start: 0.8039 (p90) cc_final: 0.7451 (p90)
REVERT: A  631 MET cc_start: 0.6788 (mmm) cc_final: 0.6576 (tpp)
REVERT: A  770 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7842 (tt)
REVERT: A  825 TYR cc_start: 0.8768 (t80) cc_final: 0.8062 (t80)
REVERT: A  991 GLN cc_start: 0.8710 (pp30) cc_final: 0.8509 (pp30)
REVERT: A 1013 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6383 (mmmt)
REVERT: A 1142 MET cc_start: 0.8958 (mtp) cc_final: 0.8635 (mtp)
REVERT: A 1235 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8226 (mt)
  outliers start: 45
  outliers final: 29
  residues processed: 197
  average time/residue: 0.0707
  time to fit residues: 21.0682
Evaluate side-chains
  188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  506 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue 1013 LYS
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 897 HIS
A1170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.141943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.111195 restraints weight = 16839.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110802 restraints weight = 10108.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111700 restraints weight = 8782.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112356 restraints weight = 6243.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.112618 restraints weight = 5506.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9787  Z= 0.174
  Angle     :  0.831  12.898  13383  Z= 0.398
  Chirality :  0.046   0.235   1557
  Planarity :  0.004   0.044   1664
  Dihedral  :  9.738  83.455   1799
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 23.30 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -0.21 (0.25), residues: 1167
  helix:  0.95 (0.21), residues: 614
  sheet: -1.30 (0.51), residues: 102
  loop : -1.35 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.017   0.001   TYR A  44 
 PHE   0.044   0.002   PHE A 503 
 TRP   0.029   0.002   TRP A1143 
 HIS   0.002   0.001   HIS A 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9753)
  covalent geometry    : angle       0.79643 (13296)
  SS BOND              : bond        0.00408 (   15)
  SS BOND              : angle       2.74893 (   30)
  hydrogen bonds       : bond        0.04781 (  482)
  hydrogen bonds       : angle       5.06656 ( 1392)
  link_ALPHA1-3        : bond        0.00887 (    1)
  link_ALPHA1-3        : angle       1.74487 (    3)
  link_BETA1-4         : bond        0.01344 (    5)
  link_BETA1-4         : angle       2.96997 (   15)
  link_NAG-ASN         : bond        0.00551 (   13)
  link_NAG-ASN         : angle       3.39662 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 161
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.5605 (tt0) cc_final: 0.4810 (tm-30)
REVERT: A   78 ARG cc_start: 0.8709 (tpt-90) cc_final: 0.8397 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8493 (t80) cc_final: 0.8003 (m-80)
REVERT: A  293 TYR cc_start: 0.7541 (t80) cc_final: 0.7229 (t80)
REVERT: A  407 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8382 (mp10)
REVERT: A  506 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7442 (t80)
REVERT: A  528 LEU cc_start: 0.7575 (mt) cc_final: 0.7197 (mm)
REVERT: A  550 TYR cc_start: 0.8101 (p90) cc_final: 0.7498 (p90)
REVERT: A  770 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7833 (tt)
REVERT: A  825 TYR cc_start: 0.8798 (t80) cc_final: 0.8046 (t80)
REVERT: A  958 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7192 (mtm180)
REVERT: A  991 GLN cc_start: 0.8761 (pp30) cc_final: 0.8541 (pp30)
REVERT: A 1235 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8288 (mt)
  outliers start: 45
  outliers final: 34
  residues processed: 187
  average time/residue: 0.0759
  time to fit residues: 21.2327
Evaluate side-chains
  190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  506 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1194 MET
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 100 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 897 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.143795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.113355 restraints weight = 16793.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112937 restraints weight = 10065.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113921 restraints weight = 8529.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114673 restraints weight = 5946.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.114870 restraints weight = 5269.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9787  Z= 0.145
  Angle     :  0.805  12.052  13383  Z= 0.385
  Chirality :  0.046   0.247   1557
  Planarity :  0.004   0.042   1664
  Dihedral  :  9.112  81.539   1795
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 23.89 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -0.15 (0.25), residues: 1167
  helix:  0.97 (0.21), residues: 615
  sheet: -1.22 (0.51), residues: 101
  loop : -1.30 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 372 
 TYR   0.027   0.001   TYR A 420 
 PHE   0.039   0.002   PHE A 503 
 TRP   0.027   0.002   TRP A  27 
 HIS   0.003   0.001   HIS A 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9753)
  covalent geometry    : angle       0.77322 (13296)
  SS BOND              : bond        0.00464 (   15)
  SS BOND              : angle       2.21350 (   30)
  hydrogen bonds       : bond        0.04506 (  482)
  hydrogen bonds       : angle       5.01910 ( 1392)
  link_ALPHA1-3        : bond        0.00925 (    1)
  link_ALPHA1-3        : angle       1.61412 (    3)
  link_BETA1-4         : bond        0.01011 (    5)
  link_BETA1-4         : angle       3.23005 (   15)
  link_NAG-ASN         : bond        0.00575 (   13)
  link_NAG-ASN         : angle       3.25437 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.5408 (tt0) cc_final: 0.4798 (tm-30)
REVERT: A   78 ARG cc_start: 0.8705 (tpt-90) cc_final: 0.8363 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8490 (t80) cc_final: 0.8080 (m-80)
REVERT: A  293 TYR cc_start: 0.7550 (t80) cc_final: 0.7236 (t80)
REVERT: A  407 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8307 (mp10)
REVERT: A  506 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7450 (t80)
REVERT: A  550 TYR cc_start: 0.8055 (p90) cc_final: 0.7432 (p90)
REVERT: A  770 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7873 (tt)
REVERT: A  819 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6854 (tpt-90)
REVERT: A  825 TYR cc_start: 0.8780 (t80) cc_final: 0.8101 (t80)
REVERT: A  958 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7139 (mtm180)
REVERT: A  991 GLN cc_start: 0.8778 (pp30) cc_final: 0.8557 (pp30)
REVERT: A 1050 ASP cc_start: 0.8149 (m-30) cc_final: 0.7859 (m-30)
REVERT: A 1235 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8300 (mt)
  outliers start: 38
  outliers final: 30
  residues processed: 180
  average time/residue: 0.0746
  time to fit residues: 20.0444
Evaluate side-chains
  187 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  506 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1161 CYS
Chi-restraints excluded: chain A residue 1194 MET
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 109 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 897 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.142741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111366 restraints weight = 16813.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.113434 restraints weight = 9316.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114071 restraints weight = 7218.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114268 restraints weight = 5711.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.114559 restraints weight = 5462.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9787  Z= 0.164
  Angle     :  0.814  11.961  13383  Z= 0.390
  Chirality :  0.046   0.243   1557
  Planarity :  0.004   0.044   1664
  Dihedral  :  9.003  80.265   1795
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.78 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -0.13 (0.25), residues: 1167
  helix:  0.97 (0.21), residues: 615
  sheet: -1.14 (0.51), residues: 102
  loop : -1.27 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 372 
 TYR   0.016   0.001   TYR A 709 
 PHE   0.030   0.002   PHE A 152 
 TRP   0.032   0.002   TRP A  27 
 HIS   0.002   0.001   HIS A 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9753)
  covalent geometry    : angle       0.78393 (13296)
  SS BOND              : bond        0.00384 (   15)
  SS BOND              : angle       2.13820 (   30)
  hydrogen bonds       : bond        0.04630 (  482)
  hydrogen bonds       : angle       5.04272 ( 1392)
  link_ALPHA1-3        : bond        0.00794 (    1)
  link_ALPHA1-3        : angle       1.66673 (    3)
  link_BETA1-4         : bond        0.00988 (    5)
  link_BETA1-4         : angle       3.14097 (   15)
  link_NAG-ASN         : bond        0.00544 (   13)
  link_NAG-ASN         : angle       3.20614 (   39)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.4932 (tt0) cc_final: 0.4589 (tm-30)
REVERT: A   78 ARG cc_start: 0.8691 (tpt-90) cc_final: 0.8428 (tpp-160)
REVERT: A  101 PHE cc_start: 0.8355 (t80) cc_final: 0.7940 (m-80)
REVERT: A  407 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8320 (mp10)
REVERT: A  528 LEU cc_start: 0.7571 (mt) cc_final: 0.7192 (mm)
REVERT: A  550 TYR cc_start: 0.8034 (p90) cc_final: 0.7530 (p90)
REVERT: A  770 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: A  819 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6982 (tpt-90)
REVERT: A  825 TYR cc_start: 0.8786 (t80) cc_final: 0.8061 (t80)
REVERT: A  958 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7260 (mtm180)
REVERT: A  991 GLN cc_start: 0.8796 (pp30) cc_final: 0.8572 (pp30)
REVERT: A 1235 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8344 (mt)
  outliers start: 36
  outliers final: 27
  residues processed: 173
  average time/residue: 0.0740
  time to fit residues: 19.2782
Evaluate side-chains
  181 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  556 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  778 CYS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  819 ARG
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  958 ARG
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1207 PHE
Chi-restraints excluded: chain A residue 1235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A1170 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.143831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113276 restraints weight = 16751.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.112978 restraints weight = 10409.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113888 restraints weight = 8831.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114667 restraints weight = 6067.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114848 restraints weight = 5345.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9787  Z= 0.150
  Angle     :  0.819  11.962  13383  Z= 0.393
  Chirality :  0.046   0.248   1557
  Planarity :  0.004   0.043   1664
  Dihedral  :  8.783  78.281   1794
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.43 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 24.68 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -0.06 (0.25), residues: 1167
  helix:  1.02 (0.21), residues: 610
  sheet: -1.11 (0.51), residues: 101
  loop : -1.20 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 372 
 TYR   0.017   0.001   TYR A  44 
 PHE   0.031   0.002   PHE A 152 
 TRP   0.034   0.002   TRP A  27 
 HIS   0.003   0.001   HIS A 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9753)
  covalent geometry    : angle       0.78848 (13296)
  SS BOND              : bond        0.00473 (   15)
  SS BOND              : angle       2.36237 (   30)
  hydrogen bonds       : bond        0.04523 (  482)
  hydrogen bonds       : angle       5.02162 ( 1392)
  link_ALPHA1-3        : bond        0.00869 (    1)
  link_ALPHA1-3        : angle       1.58033 (    3)
  link_BETA1-4         : bond        0.01107 (    5)
  link_BETA1-4         : angle       3.10887 (   15)
  link_NAG-ASN         : bond        0.00561 (   13)
  link_NAG-ASN         : angle       3.14343 (   39)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1438.30 seconds
wall clock time: 25 minutes 35.26 seconds (1535.26 seconds total)