Starting phenix.real_space_refine
on Wed Sep 17 20:43:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f2y_50166/09_2025/9f2y_50166.cif"
  }
  resolution = 4.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    7070      2.51       5
     N    1792      2.21       5
     O    2094      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10994
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 833
          Classifications: {'peptide': 97}
          Link IDs: {'TRANS': 96}
    Chain: "B"
      Number of atoms: 10094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1239, 10094
          Classifications: {'peptide': 1239}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 1201}
          Chain breaks: 6
    Chain: "C"
      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: "A"
      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
  Time building chain proxies: 2.52, per 1000 atoms: 0.23
  Number of scatterers: 10994
  At special positions: 0
  Unit cell: (115.7, 123.5, 125.45, 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      38     16.00
     O    2094      8.00
     N    1792      7.00
     C    7070      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 454 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A 491 "
      " NAG A 702 " - " ASN A 441 "
      " NAG C   1 " - " ASN A 516 "
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 536.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2548

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 17 sheets defined
      31.0% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 505 through 507
      No H-bonds generated for 'chain 'A' and resid 505 through 507'
    Processing helix  chain 'B' and resid 80 through 101
      removed outlier: 3.776A  pdb=" N   THR B 101 " --> pdb=" O   ARG B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
    Processing helix  chain 'B' and resid 174 through 178
      removed outlier: 3.589A  pdb=" N   ASN B 178 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 233
      removed outlier: 3.535A  pdb=" N   THR B 220 " --> pdb=" O   ASP B 216 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR B 233 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 267
    Processing helix  chain 'B' and resid 269 through 274
      removed outlier: 3.818A  pdb=" N   ILE B 274 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 300
      removed outlier: 3.577A  pdb=" N   GLU B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 321
    Processing helix  chain 'B' and resid 334 through 347
    Processing helix  chain 'B' and resid 350 through 359
    Processing helix  chain 'B' and resid 398 through 405
      removed outlier: 3.607A  pdb=" N   PHE B 401 " --> pdb=" O   ALA B 398 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   GLY B 403 " --> pdb=" O   ASN B 400 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN B 404 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 462
      No H-bonds generated for 'chain 'B' and resid 460 through 462'
    Processing helix  chain 'B' and resid 467 through 471
      removed outlier: 3.610A  pdb=" N   ASN B 470 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 506
    Processing helix  chain 'B' and resid 549 through 556
      removed outlier: 3.611A  pdb=" N   TYR B 553 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 578
      removed outlier: 3.826A  pdb=" N   LEU B 577 " --> pdb=" O   ASN B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 595
    Processing helix  chain 'B' and resid 599 through 601
      No H-bonds generated for 'chain 'B' and resid 599 through 601'
    Processing helix  chain 'B' and resid 602 through 619
    Processing helix  chain 'B' and resid 636 through 642
    Processing helix  chain 'B' and resid 648 through 660
    Processing helix  chain 'B' and resid 689 through 721
    Processing helix  chain 'B' and resid 721 through 753
      removed outlier: 3.523A  pdb=" N   ILE B 725 " --> pdb=" O   VAL B 721 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN B 753 " --> pdb=" O   TYR B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 762
    Processing helix  chain 'B' and resid 766 through 800
      removed outlier: 3.660A  pdb=" N   ASN B 783 " --> pdb=" O   LYS B 779 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET B 800 " --> pdb=" O   LEU B 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 800 through 825
      removed outlier: 3.811A  pdb=" N   GLY B 804 " --> pdb=" O   MET B 800 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B 807 " --> pdb=" O   TYR B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 835 through 845
    Processing helix  chain 'B' and resid 859 through 876
      removed outlier: 4.219A  pdb=" N   THR B 876 " --> pdb=" O   ASN B 872 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
    Processing helix  chain 'B' and resid 1080 through 1092
      removed outlier: 3.566A  pdb=" N   LEU B1087 " --> pdb=" O   GLU B1083 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431
      removed outlier: 6.406A  pdb=" N   LYS A 428 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   GLN A 450 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   PHE A 430 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 444 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 465 " --> pdb=" O   MET A 444 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL A 467 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A 448 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 469 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN A 450 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431
      removed outlier: 6.406A  pdb=" N   LYS A 428 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   GLN A 450 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   PHE A 430 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 444 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 465 " --> pdb=" O   MET A 444 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL A 467 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A 448 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 469 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN A 450 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
      removed outlier: 8.685A  pdb=" N   TYR A 488 " --> pdb=" O   LYS A 465 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   VAL A 467 " --> pdb=" O   TYR A 488 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   LYS A 490 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   PHE A 469 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   PHE A 489 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436
      removed outlier: 5.773A  pdb=" N   VAL A 435 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU A 454 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 439 through 440
      removed outlier: 6.280A  pdb=" N   PHE A 459 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 499 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 495
    Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 148
      removed outlier: 4.133A  pdb=" N   TYR B  21 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA B  20 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA B  35 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LYS B  34 " --> pdb=" O   PRO B  46 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL B  44 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY B 155 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLU B  47 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 127
    Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 214
      removed outlier: 4.524A  pdb=" N   VAL B 373 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325
    Processing sheet with id=AB1, first strand: chain 'B' and resid 455 through 458
    Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 481
    Processing sheet with id=AB3, first strand: chain 'B' and resid 567 through 569
      removed outlier: 6.240A  pdb=" N   ALA B 567 " --> pdb=" O   VAL B 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.579A  pdb=" N   LEU B 881 " --> pdb=" O   PHE B1072 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE B1072 " --> pdb=" O   LEU B 881 " (cutoff:3.500A)
      removed outlier: 9.642A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 11.230A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.579A  pdb=" N   LEU B 881 " --> pdb=" O   PHE B1072 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE B1072 " --> pdb=" O   LEU B 881 " (cutoff:3.500A)
      removed outlier: 9.642A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 11.230A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE B1069 " --> pdb=" O   ARG B 948 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ARG B 948 " --> pdb=" O   ILE B1069 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   TYR B1071 " --> pdb=" O   TRP B 946 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TRP B 946 " --> pdb=" O   TYR B1071 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 897 through 900
      removed outlier: 3.766A  pdb=" N   LYS B 897 " --> pdb=" O   ILE B 927 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ASN B1052 " --> pdb=" O   MET B 968 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   MET B 968 " --> pdb=" O   ASN B1052 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ILE B 964 " --> pdb=" O   LYS B1056 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   ASP B1058 " --> pdb=" O   TYR B 962 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   TYR B 962 " --> pdb=" O   ASP B1058 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   THR B 963 " --> pdb=" O   LEU B 978 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   LEU B 978 " --> pdb=" O   THR B 963 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP B 974 " --> pdb=" O   CYS B 967 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1122 through 1126
      removed outlier: 6.539A  pdb=" N   MET B1134 " --> pdb=" O   LEU B1261 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B1261 " --> pdb=" O   MET B1134 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ALA B1259 " --> pdb=" O   LEU B1136 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER B1264 " --> pdb=" O   PHE B1249 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL B1220 " --> pdb=" O   GLN B1240 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 1122 through 1126
      removed outlier: 6.539A  pdb=" N   MET B1134 " --> pdb=" O   LEU B1261 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B1261 " --> pdb=" O   MET B1134 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ALA B1259 " --> pdb=" O   LEU B1136 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER B1264 " --> pdb=" O   PHE B1249 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL B1220 " --> pdb=" O   GLN B1240 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR B1181 " --> pdb=" O   LYS B1163 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LYS B1163 " --> pdb=" O   TYR B1181 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1260 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: 2.42

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3450
        1.34 -     1.46: 1862
        1.46 -     1.57: 5855
        1.57 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 11231
  Sorted by residual:
  bond pdb=" C   GLU B  47 "
       pdb=" N   ARG B  48 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.31e-02 5.83e+03 1.14e+01
  bond pdb=" N   VAL B 857 "
       pdb=" CA  VAL B 857 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.11e-02 8.12e+03 1.03e+01
  bond pdb=" N   ILE B 874 "
       pdb=" CA  ILE B 874 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.035 1.25e-02 6.40e+03 7.62e+00
  bond pdb=" N   ILE B 878 "
       pdb=" CA  ILE B 878 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.08e+00
  bond pdb=" N   ILE B 870 "
       pdb=" CA  ILE B 870 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 1.14e-02 7.69e+03 6.89e+00
  ... (remaining 11226 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 14797
        2.04 -     4.08: 348
        4.08 -     6.11: 41
        6.11 -     8.15: 9
        8.15 -    10.19: 2
  Bond angle restraints: 15197
  Sorted by residual:
  angle pdb=" N   ILE B1084 "
        pdb=" CA  ILE B1084 "
        pdb=" C   ILE B1084 "
      ideal   model   delta    sigma   weight residual
     111.58  106.29    5.29 1.06e+00 8.90e-01 2.49e+01
  angle pdb=" CA  ASP B1086 "
        pdb=" CB  ASP B1086 "
        pdb=" CG  ASP B1086 "
      ideal   model   delta    sigma   weight residual
     112.60  117.02   -4.42 1.00e+00 1.00e+00 1.95e+01
  angle pdb=" N   LEU B1087 "
        pdb=" CA  LEU B1087 "
        pdb=" C   LEU B1087 "
      ideal   model   delta    sigma   weight residual
     111.28  107.15    4.13 1.09e+00 8.42e-01 1.43e+01
  angle pdb=" N   GLU B 617 "
        pdb=" CA  GLU B 617 "
        pdb=" CB  GLU B 617 "
      ideal   model   delta    sigma   weight residual
     110.16  115.65   -5.49 1.48e+00 4.57e-01 1.38e+01
  angle pdb=" N   GLN B 790 "
        pdb=" CA  GLN B 790 "
        pdb=" CB  GLN B 790 "
      ideal   model   delta    sigma   weight residual
     110.22  115.90   -5.68 1.54e+00 4.22e-01 1.36e+01
  ... (remaining 15192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.15: 6274
       22.15 -    44.30: 411
       44.30 -    66.44: 58
       66.44 -    88.59: 17
       88.59 -   110.74: 4
  Dihedral angle restraints: 6764
    sinusoidal: 2811
      harmonic: 3953
  Sorted by residual:
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  177.97  110.74     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" CA  GLN B 991 "
           pdb=" C   GLN B 991 "
           pdb=" N   GLU B 992 "
           pdb=" CA  GLU B 992 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -61.25  108.87     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 6761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.013: 1687
       1.013 -    2.026: 0
       2.026 -    3.039: 0
       3.039 -    4.052: 0
       4.052 -    5.065: 1
  Chirality restraints: 1688
  Sorted by residual:
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 441 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.66   -5.06 2.00e-01 2.50e+01 6.41e+02
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 516 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.96   -0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" CB  ILE B  22 "
            pdb=" CA  ILE B  22 "
            pdb=" CG1 ILE B  22 "
            pdb=" CG2 ILE B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.48e+00
  ... (remaining 1685 not shown)

  Planarity restraints: 1944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 701 "   -0.183 2.00e-02 2.50e+03   1.52e-01 2.87e+02
        pdb=" C7  NAG A 701 "    0.048 2.00e-02 2.50e+03
        pdb=" C8  NAG A 701 "   -0.133 2.00e-02 2.50e+03
        pdb=" N2  NAG A 701 "    0.247 2.00e-02 2.50e+03
        pdb=" O7  NAG A 701 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 441 "   -0.040 2.00e-02 2.50e+03   9.57e-02 1.15e+02
        pdb=" CG  ASN A 441 "   -0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 441 "    0.097 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 441 "   -0.146 2.00e-02 2.50e+03
        pdb=" C1  NAG A 702 "    0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.099 2.00e-02 2.50e+03   8.26e-02 8.53e+01
        pdb=" C7  NAG A 702 "    0.029 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.075 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.133 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1941 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 219
        2.67 -     3.23: 11283
        3.23 -     3.78: 17188
        3.78 -     4.34: 22869
        4.34 -     4.90: 36668
  Nonbonded interactions: 88227
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 755 "
            pdb=" OE1 GLU B 758 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" OD1 ASN B 971 "
            pdb=" NE2 GLN B 988 "
     model   vdw
     2.139 3.120
  nonbonded pdb=" O   THR B 691 "
            pdb=" OG1 THR B 694 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O   ARG B1140 "
            pdb=" OG  SER B1153 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASN B 248 "
            pdb=" OH  TYR B 543 "
     model   vdw
     2.216 3.040
  ... (remaining 88222 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.280
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.278  11237  Z= 0.259
  Angle     :  0.765  21.655  15214  Z= 0.428
  Chirality :  0.134   5.065   1688
  Planarity :  0.007   0.199   1941
  Dihedral  : 14.947 110.737   4213
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.45 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.62 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.22), residues: 1320
  helix:  1.22 (0.27), residues: 369
  sheet:  0.23 (0.43), residues: 140
  loop : -1.33 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1192 
 TYR   0.021   0.002   TYR B 822 
 PHE   0.014   0.001   PHE B 652 
 TRP   0.020   0.002   TRP B 974 
 HIS   0.005   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (11231)
  covalent geometry    : angle       0.71996 (15197)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       0.18551 (    2)
  hydrogen bonds       : bond        0.14633 (  432)
  hydrogen bonds       : angle       6.51497 ( 1260)
  link_BETA1-4         : bond        0.00836 (    2)
  link_BETA1-4         : angle       1.84552 (    6)
  link_NAG-ASN         : bond        0.17308 (    3)
  link_NAG-ASN         : angle      10.57647 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 296
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8006 (mmtm)
REVERT: A  448 ILE cc_start: 0.8950 (pt) cc_final: 0.8608 (mm)
REVERT: A  470 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8610 (mp0)
REVERT: A  500 TYR cc_start: 0.9050 (t80) cc_final: 0.8261 (t80)
REVERT: A  501 ASN cc_start: 0.8612 (t0) cc_final: 0.8252 (t0)
REVERT: A  511 ASN cc_start: 0.8063 (m-40) cc_final: 0.7802 (t0)
REVERT: A  515 ILE cc_start: 0.9255 (mm) cc_final: 0.8975 (mm)
REVERT: B   78 LEU cc_start: 0.8873 (tt) cc_final: 0.8494 (mt)
REVERT: B   83 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7990 (mt-10)
REVERT: B   96 GLU cc_start: 0.8096 (pp20) cc_final: 0.7622 (tp30)
REVERT: B  106 MET cc_start: 0.8987 (mtm) cc_final: 0.8743 (mtm)
REVERT: B  162 GLN cc_start: 0.8299 (tt0) cc_final: 0.7809 (tm-30)
REVERT: B  212 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8666 (mtmm)
REVERT: B  345 LEU cc_start: 0.8959 (mt) cc_final: 0.8700 (mt)
REVERT: B  355 VAL cc_start: 0.8952 (t) cc_final: 0.8290 (t)
REVERT: B  370 ASP cc_start: 0.8923 (m-30) cc_final: 0.8604 (m-30)
REVERT: B  392 LEU cc_start: 0.8343 (tp) cc_final: 0.8095 (mt)
REVERT: B  499 ILE cc_start: 0.9173 (mp) cc_final: 0.8491 (mt)
REVERT: B  502 TYR cc_start: 0.8794 (m-10) cc_final: 0.8593 (m-80)
REVERT: B  602 MET cc_start: 0.6453 (tpt) cc_final: 0.5825 (tpp)
REVERT: B  651 ASP cc_start: 0.7327 (t0) cc_final: 0.6952 (t0)
REVERT: B  714 VAL cc_start: 0.9615 (t) cc_final: 0.9390 (p)
REVERT: B  741 GLU cc_start: 0.8438 (tp30) cc_final: 0.8138 (tp30)
REVERT: B 1004 MET cc_start: 0.8445 (mpp) cc_final: 0.7999 (mpp)
REVERT: B 1035 LEU cc_start: 0.8691 (tp) cc_final: 0.8368 (tp)
REVERT: B 1044 LEU cc_start: 0.8370 (mm) cc_final: 0.7602 (tp)
REVERT: B 1135 TYR cc_start: 0.7834 (p90) cc_final: 0.7587 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 297
  average time/residue: 0.1155
  time to fit residues: 47.9386
Evaluate side-chains
  178 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0870
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 ASN
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 353 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN
B 470 ASN
B 501 GLN
B 557 GLN
B 697 ASN
B 753 GLN
B 778 ASN
B 940 ASN
B1032 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.108354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.091855 restraints weight = 43524.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.093724 restraints weight = 29152.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.095384 restraints weight = 21423.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.095560 restraints weight = 16704.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.096025 restraints weight = 15934.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11237  Z= 0.157
  Angle     :  0.690  21.905  15214  Z= 0.353
  Chirality :  0.054   1.081   1688
  Planarity :  0.004   0.053   1941
  Dihedral  :  7.415  66.919   1549
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  4.84 %
    Favored  : 94.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.22), residues: 1320
  helix:  1.35 (0.27), residues: 374
  sheet: -0.43 (0.37), residues: 178
  loop : -1.18 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 393 
 TYR   0.015   0.002   TYR B 543 
 PHE   0.021   0.002   PHE A 430 
 TRP   0.024   0.002   TRP B 717 
 HIS   0.004   0.001   HIS B1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11231)
  covalent geometry    : angle       0.65396 (15197)
  SS BOND              : bond        0.00380 (    1)
  SS BOND              : angle       0.48186 (    2)
  hydrogen bonds       : bond        0.04693 (  432)
  hydrogen bonds       : angle       5.25943 ( 1260)
  link_BETA1-4         : bond        0.00607 (    2)
  link_BETA1-4         : angle       3.28888 (    6)
  link_NAG-ASN         : bond        0.00338 (    3)
  link_NAG-ASN         : angle       8.68986 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 216
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 TYR cc_start: 0.8993 (t80) cc_final: 0.8431 (t80)
REVERT: B  212 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8702 (mtmm)
REVERT: B  351 GLU cc_start: 0.6964 (pp20) cc_final: 0.6446 (pp20)
REVERT: B  362 ASN cc_start: 0.8267 (p0) cc_final: 0.8065 (p0)
REVERT: B  383 ASN cc_start: 0.7406 (m110) cc_final: 0.7094 (t0)
REVERT: B  602 MET cc_start: 0.6188 (tpt) cc_final: 0.5576 (mmm)
REVERT: B  697 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5624 (m-40)
REVERT: B  714 VAL cc_start: 0.9517 (t) cc_final: 0.9281 (p)
REVERT: B  725 ILE cc_start: 0.9416 (mm) cc_final: 0.9143 (tp)
REVERT: B  750 GLN cc_start: 0.8590 (mm110) cc_final: 0.8374 (mm-40)
REVERT: B 1004 MET cc_start: 0.8754 (mpp) cc_final: 0.8551 (mpp)
REVERT: B 1011 ILE cc_start: 0.8909 (tt) cc_final: 0.8565 (pt)
  outliers start: 5
  outliers final: 1
  residues processed: 219
  average time/residue: 0.0979
  time to fit residues: 31.6599
Evaluate side-chains
  150 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 124 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0670
   chunk 126 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    2.0122

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

Flipped N/Q/H residues before XYZ refinement:
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 238 ASN
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.104930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088071 restraints weight = 44350.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.089875 restraints weight = 29523.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.091807 restraints weight = 22346.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.091867 restraints weight = 18094.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.092068 restraints weight = 16428.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11237  Z= 0.226
  Angle     :  0.707  18.919  15214  Z= 0.372
  Chirality :  0.055   1.102   1688
  Planarity :  0.005   0.057   1941
  Dihedral  :  6.655  57.376   1549
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  4.75 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.22), residues: 1320
  helix:  1.20 (0.26), residues: 371
  sheet: -0.47 (0.35), residues: 195
  loop : -1.31 (0.20), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1034 
 TYR   0.038   0.002   TYR B 710 
 PHE   0.037   0.002   PHE B 603 
 TRP   0.017   0.002   TRP B1282 
 HIS   0.006   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (11231)
  covalent geometry    : angle       0.67976 (15197)
  SS BOND              : bond        0.00968 (    1)
  SS BOND              : angle       0.97975 (    2)
  hydrogen bonds       : bond        0.04716 (  432)
  hydrogen bonds       : angle       5.33200 ( 1260)
  link_BETA1-4         : bond        0.00885 (    2)
  link_BETA1-4         : angle       3.01459 (    6)
  link_NAG-ASN         : bond        0.00357 (    3)
  link_NAG-ASN         : angle       7.58728 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 198
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 TYR cc_start: 0.8881 (t80) cc_final: 0.8316 (t80)
REVERT: B  212 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8693 (mtmm)
REVERT: B  292 ASP cc_start: 0.8711 (t0) cc_final: 0.8401 (t0)
REVERT: B  602 MET cc_start: 0.6060 (tpt) cc_final: 0.5583 (mmm)
REVERT: B  707 ASP cc_start: 0.9178 (m-30) cc_final: 0.8944 (m-30)
REVERT: B  732 MET cc_start: 0.8768 (mmt) cc_final: 0.8533 (mmm)
REVERT: B  775 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8623 (mm-30)
REVERT: B  795 TYR cc_start: 0.7593 (t80) cc_final: 0.7185 (t80)
REVERT: B  862 LEU cc_start: 0.8834 (tp) cc_final: 0.8566 (tt)
REVERT: B 1011 ILE cc_start: 0.9106 (tt) cc_final: 0.8780 (pt)
REVERT: B 1044 LEU cc_start: 0.8240 (mm) cc_final: 0.7526 (tp)
REVERT: B 1135 TYR cc_start: 0.7508 (p90) cc_final: 0.6688 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 200
  average time/residue: 0.1044
  time to fit residues: 29.8768
Evaluate side-chains
  134 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 129 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  86 ASN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 HIS
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 412 ASN
B 418 ASN
** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 739 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.098677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.081838 restraints weight = 44605.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.082761 restraints weight = 30876.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.084162 restraints weight = 25105.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.084731 restraints weight = 20076.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.085253 restraints weight = 18345.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077  11237  Z= 0.364
  Angle     :  0.871  20.432  15214  Z= 0.461
  Chirality :  0.058   1.036   1688
  Planarity :  0.005   0.069   1941
  Dihedral  :  6.933  54.147   1549
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.05 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.21), residues: 1320
  helix:  0.37 (0.25), residues: 368
  sheet: -0.93 (0.34), residues: 212
  loop : -1.64 (0.20), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B1065 
 TYR   0.030   0.003   TYR B 312 
 PHE   0.029   0.003   PHE B 652 
 TRP   0.026   0.003   TRP B  43 
 HIS   0.006   0.002   HIS A 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00792 (11231)
  covalent geometry    : angle       0.84763 (15197)
  SS BOND              : bond        0.00460 (    1)
  SS BOND              : angle       0.72643 (    2)
  hydrogen bonds       : bond        0.05525 (  432)
  hydrogen bonds       : angle       5.69802 ( 1260)
  link_BETA1-4         : bond        0.00653 (    2)
  link_BETA1-4         : angle       3.01062 (    6)
  link_NAG-ASN         : bond        0.00410 (    3)
  link_NAG-ASN         : angle       7.93258 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 179
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 VAL cc_start: 0.8809 (m) cc_final: 0.8139 (m)
REVERT: A  500 TYR cc_start: 0.8927 (t80) cc_final: 0.8068 (t80)
REVERT: A  513 ARG cc_start: 0.7972 (mpp-170) cc_final: 0.7644 (mpp-170)
REVERT: B  184 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8181 (mm110)
REVERT: B  263 LEU cc_start: 0.9591 (mt) cc_final: 0.9353 (mt)
REVERT: B  292 ASP cc_start: 0.8814 (t0) cc_final: 0.8479 (t0)
REVERT: B  331 PHE cc_start: 0.7591 (m-10) cc_final: 0.7349 (m-80)
REVERT: B  388 ASP cc_start: 0.8333 (t0) cc_final: 0.7786 (t0)
REVERT: B  602 MET cc_start: 0.6388 (tpt) cc_final: 0.5895 (tpp)
REVERT: B  763 ASN cc_start: 0.8281 (p0) cc_final: 0.8033 (p0)
REVERT: B  821 LYS cc_start: 0.6672 (mptt) cc_final: 0.6128 (mmmm)
REVERT: B 1004 MET cc_start: 0.9431 (mmt) cc_final: 0.8991 (mmt)
REVERT: B 1011 ILE cc_start: 0.9288 (tt) cc_final: 0.8938 (pt)
REVERT: B 1044 LEU cc_start: 0.8399 (mm) cc_final: 0.7751 (tp)
REVERT: B 1113 MET cc_start: 0.8374 (tpt) cc_final: 0.7239 (tpp)
REVERT: B 1193 LEU cc_start: 0.7644 (mm) cc_final: 0.7357 (mm)
  outliers start: 6
  outliers final: 3
  residues processed: 185
  average time/residue: 0.1008
  time to fit residues: 27.5216
Evaluate side-chains
  132 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   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 449 HIS
A 507 HIS
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 353 ASN
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN
B 739 GLN
** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.101908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.085609 restraints weight = 42646.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.086744 restraints weight = 30119.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.088584 restraints weight = 23863.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.088825 restraints weight = 18509.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.089674 restraints weight = 17015.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11237  Z= 0.138
  Angle     :  0.660  17.774  15214  Z= 0.348
  Chirality :  0.052   0.911   1688
  Planarity :  0.004   0.062   1941
  Dihedral  :  6.189  59.979   1549
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.95 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.22), residues: 1320
  helix:  1.11 (0.26), residues: 367
  sheet: -0.59 (0.38), residues: 168
  loop : -1.38 (0.20), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.022   0.002   TYR B 754 
 PHE   0.015   0.001   PHE B 537 
 TRP   0.020   0.002   TRP B 974 
 HIS   0.005   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11231)
  covalent geometry    : angle       0.63683 (15197)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.88234 (    2)
  hydrogen bonds       : bond        0.04255 (  432)
  hydrogen bonds       : angle       5.25574 ( 1260)
  link_BETA1-4         : bond        0.00153 (    2)
  link_BETA1-4         : angle       2.31532 (    6)
  link_NAG-ASN         : bond        0.00362 (    3)
  link_NAG-ASN         : angle       6.92858 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 VAL cc_start: 0.8669 (m) cc_final: 0.7804 (m)
REVERT: A  500 TYR cc_start: 0.8772 (t80) cc_final: 0.8539 (t80)
REVERT: A  515 ILE cc_start: 0.9389 (mp) cc_final: 0.8412 (mp)
REVERT: B  292 ASP cc_start: 0.8623 (t0) cc_final: 0.8299 (t0)
REVERT: B  313 MET cc_start: 0.6120 (mmp) cc_final: 0.5711 (mmp)
REVERT: B  351 GLU cc_start: 0.7095 (pp20) cc_final: 0.6423 (pp20)
REVERT: B  362 ASN cc_start: 0.8655 (p0) cc_final: 0.7944 (p0)
REVERT: B  388 ASP cc_start: 0.8154 (t0) cc_final: 0.7674 (t0)
REVERT: B  602 MET cc_start: 0.6256 (tpt) cc_final: 0.5845 (tpp)
REVERT: B  732 MET cc_start: 0.8602 (mmt) cc_final: 0.8344 (mmm)
REVERT: B  763 ASN cc_start: 0.8054 (p0) cc_final: 0.7731 (p0)
REVERT: B  781 MET cc_start: 0.8886 (mmm) cc_final: 0.8660 (mmm)
REVERT: B  821 LYS cc_start: 0.6503 (mptt) cc_final: 0.6025 (mmmm)
REVERT: B  985 TRP cc_start: 0.8896 (t-100) cc_final: 0.8671 (t60)
REVERT: B 1004 MET cc_start: 0.9346 (mmt) cc_final: 0.9054 (mmt)
REVERT: B 1011 ILE cc_start: 0.9209 (tt) cc_final: 0.8934 (pt)
REVERT: B 1044 LEU cc_start: 0.8212 (mm) cc_final: 0.7582 (tp)
REVERT: B 1114 LEU cc_start: 0.9496 (tp) cc_final: 0.9069 (tp)
REVERT: B 1193 LEU cc_start: 0.7763 (mm) cc_final: 0.7477 (mm)
REVERT: B 1283 GLU cc_start: 0.8319 (tp30) cc_final: 0.7931 (tp30)
  outliers start: 1
  outliers final: 1
  residues processed: 195
  average time/residue: 0.1012
  time to fit residues: 28.9481
Evaluate side-chains
  144 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    0.0170
   chunk 18 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 128 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    2.5224

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 507 HIS
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 GLN
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN
B 693 GLN
** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.097811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.081779 restraints weight = 42492.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.082526 restraints weight = 31649.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.083886 restraints weight = 25477.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.084322 restraints weight = 19847.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084944 restraints weight = 19006.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  11237  Z= 0.254
  Angle     :  0.731  18.025  15214  Z= 0.386
  Chirality :  0.053   0.889   1688
  Planarity :  0.005   0.068   1941
  Dihedral  :  6.311  57.042   1549
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.70 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.21), residues: 1320
  helix:  0.84 (0.26), residues: 368
  sheet: -0.67 (0.37), residues: 171
  loop : -1.52 (0.20), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B1065 
 TYR   0.023   0.002   TYR B  87 
 PHE   0.021   0.002   PHE B 652 
 TRP   0.018   0.002   TRP B 118 
 HIS   0.005   0.002   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (11231)
  covalent geometry    : angle       0.71027 (15197)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       0.44908 (    2)
  hydrogen bonds       : bond        0.04774 (  432)
  hydrogen bonds       : angle       5.43076 ( 1260)
  link_BETA1-4         : bond        0.00284 (    2)
  link_BETA1-4         : angle       2.25454 (    6)
  link_NAG-ASN         : bond        0.00217 (    3)
  link_NAG-ASN         : angle       6.96581 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.7717 (m-30) cc_final: 0.6861 (t0)
REVERT: A  482 VAL cc_start: 0.8792 (m) cc_final: 0.7959 (m)
REVERT: A  495 GLU cc_start: 0.8804 (tp30) cc_final: 0.8582 (tp30)
REVERT: A  500 TYR cc_start: 0.8737 (t80) cc_final: 0.7955 (t80)
REVERT: A  515 ILE cc_start: 0.9175 (mp) cc_final: 0.8905 (mp)
REVERT: A  521 GLU cc_start: 0.7076 (pp20) cc_final: 0.6867 (tm-30)
REVERT: B  184 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8111 (mm110)
REVERT: B  292 ASP cc_start: 0.8691 (t0) cc_final: 0.8415 (t0)
REVERT: B  313 MET cc_start: 0.5978 (mmp) cc_final: 0.5757 (mmp)
REVERT: B  388 ASP cc_start: 0.8307 (t0) cc_final: 0.7757 (t0)
REVERT: B  418 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7556 (p0)
REVERT: B  420 THR cc_start: 0.9202 (p) cc_final: 0.8847 (p)
REVERT: B  602 MET cc_start: 0.6432 (tpt) cc_final: 0.6005 (tpp)
REVERT: B  732 MET cc_start: 0.8455 (mmt) cc_final: 0.8223 (tpp)
REVERT: B  763 ASN cc_start: 0.8171 (p0) cc_final: 0.7895 (p0)
REVERT: B  821 LYS cc_start: 0.6723 (mptt) cc_final: 0.6238 (mmmm)
REVERT: B 1004 MET cc_start: 0.9294 (mmt) cc_final: 0.8984 (mmt)
REVERT: B 1011 ILE cc_start: 0.9294 (tt) cc_final: 0.8958 (pt)
REVERT: B 1044 LEU cc_start: 0.8309 (mm) cc_final: 0.7701 (tp)
REVERT: B 1114 LEU cc_start: 0.9358 (tp) cc_final: 0.9155 (tp)
REVERT: B 1193 LEU cc_start: 0.7688 (mm) cc_final: 0.7326 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1008
  time to fit residues: 26.2872
Evaluate side-chains
  129 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 GLN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.100399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.083800 restraints weight = 42209.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.085287 restraints weight = 29819.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.086549 restraints weight = 23629.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086732 restraints weight = 19788.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.087143 restraints weight = 18544.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11237  Z= 0.147
  Angle     :  0.648  16.672  15214  Z= 0.342
  Chirality :  0.050   0.752   1688
  Planarity :  0.004   0.066   1941
  Dihedral  :  5.949  56.541   1549
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.21 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.22), residues: 1320
  helix:  1.00 (0.26), residues: 369
  sheet: -0.47 (0.38), residues: 166
  loop : -1.40 (0.20), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 231 
 TYR   0.034   0.002   TYR B 754 
 PHE   0.014   0.001   PHE B 537 
 TRP   0.016   0.002   TRP B1282 
 HIS   0.005   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11231)
  covalent geometry    : angle       0.62809 (15197)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.55392 (    2)
  hydrogen bonds       : bond        0.04180 (  432)
  hydrogen bonds       : angle       5.24817 ( 1260)
  link_BETA1-4         : bond        0.00347 (    2)
  link_BETA1-4         : angle       1.77160 (    6)
  link_NAG-ASN         : bond        0.00404 (    3)
  link_NAG-ASN         : angle       6.45172 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.7725 (m-30) cc_final: 0.6824 (t0)
REVERT: A  482 VAL cc_start: 0.8709 (m) cc_final: 0.8004 (m)
REVERT: A  492 CYS cc_start: 0.7795 (m) cc_final: 0.6990 (m)
REVERT: A  495 GLU cc_start: 0.8794 (tp30) cc_final: 0.8594 (tp30)
REVERT: A  500 TYR cc_start: 0.8750 (t80) cc_final: 0.8074 (t80)
REVERT: A  515 ILE cc_start: 0.9189 (mp) cc_final: 0.8976 (mp)
REVERT: B  292 ASP cc_start: 0.8786 (t0) cc_final: 0.8424 (t0)
REVERT: B  351 GLU cc_start: 0.7128 (pp20) cc_final: 0.6467 (pp20)
REVERT: B  388 ASP cc_start: 0.8187 (t0) cc_final: 0.7648 (t0)
REVERT: B  418 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7509 (p0)
REVERT: B  420 THR cc_start: 0.9102 (p) cc_final: 0.8760 (p)
REVERT: B  602 MET cc_start: 0.6408 (tpt) cc_final: 0.6057 (tpp)
REVERT: B  603 PHE cc_start: 0.8426 (m-80) cc_final: 0.8210 (m-80)
REVERT: B  665 LEU cc_start: 0.9191 (mm) cc_final: 0.8899 (mt)
REVERT: B  732 MET cc_start: 0.8481 (mmt) cc_final: 0.8276 (tpp)
REVERT: B  763 ASN cc_start: 0.8196 (p0) cc_final: 0.7901 (p0)
REVERT: B  781 MET cc_start: 0.8917 (mmm) cc_final: 0.8696 (mmm)
REVERT: B  821 LYS cc_start: 0.6538 (mptt) cc_final: 0.6080 (mmmm)
REVERT: B 1004 MET cc_start: 0.9286 (mmt) cc_final: 0.8998 (mmt)
REVERT: B 1011 ILE cc_start: 0.9241 (tt) cc_final: 0.8960 (pt)
REVERT: B 1044 LEU cc_start: 0.8231 (mm) cc_final: 0.7602 (tp)
REVERT: B 1113 MET cc_start: 0.7634 (tpp) cc_final: 0.7167 (tpp)
REVERT: B 1193 LEU cc_start: 0.7681 (mm) cc_final: 0.7445 (mm)
REVERT: B 1282 TRP cc_start: 0.8068 (m100) cc_final: 0.7773 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0912
  time to fit residues: 24.4939
Evaluate side-chains
  136 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0980
   chunk 119 optimal weight:    0.9990
   chunk 121 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  39 HIS
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.101597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.085046 restraints weight = 42670.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.086291 restraints weight = 30702.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.087812 restraints weight = 24044.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087897 restraints weight = 19548.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.088256 restraints weight = 19127.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.5633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11237  Z= 0.123
  Angle     :  0.637  15.515  15214  Z= 0.333
  Chirality :  0.049   0.651   1688
  Planarity :  0.004   0.067   1941
  Dihedral  :  5.638  53.043   1549
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.07 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.22), residues: 1320
  helix:  1.15 (0.26), residues: 370
  sheet: -0.46 (0.38), residues: 168
  loop : -1.32 (0.20), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 231 
 TYR   0.025   0.001   TYR B 754 
 PHE   0.014   0.001   PHE B 537 
 TRP   0.015   0.002   TRP B 706 
 HIS   0.004   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11231)
  covalent geometry    : angle       0.61973 (15197)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.39206 (    2)
  hydrogen bonds       : bond        0.03936 (  432)
  hydrogen bonds       : angle       5.08543 ( 1260)
  link_BETA1-4         : bond        0.00335 (    2)
  link_BETA1-4         : angle       1.66960 (    6)
  link_NAG-ASN         : bond        0.00606 (    3)
  link_NAG-ASN         : angle       5.99114 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.7661 (m-30) cc_final: 0.6900 (t0)
REVERT: A  482 VAL cc_start: 0.8726 (m) cc_final: 0.8072 (m)
REVERT: A  495 GLU cc_start: 0.8745 (tp30) cc_final: 0.8531 (tp30)
REVERT: A  515 ILE cc_start: 0.9147 (mp) cc_final: 0.8935 (mp)
REVERT: B  152 VAL cc_start: 0.8118 (t) cc_final: 0.7707 (m)
REVERT: B  292 ASP cc_start: 0.8739 (t0) cc_final: 0.8449 (t0)
REVERT: B  351 GLU cc_start: 0.7051 (pp20) cc_final: 0.6424 (pp20)
REVERT: B  362 ASN cc_start: 0.8689 (p0) cc_final: 0.8461 (p0)
REVERT: B  388 ASP cc_start: 0.8132 (t0) cc_final: 0.7654 (t0)
REVERT: B  418 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7437 (p0)
REVERT: B  420 THR cc_start: 0.9064 (p) cc_final: 0.8784 (p)
REVERT: B  602 MET cc_start: 0.6490 (tpt) cc_final: 0.6099 (tpp)
REVERT: B  603 PHE cc_start: 0.8335 (m-80) cc_final: 0.8101 (m-80)
REVERT: B  665 LEU cc_start: 0.9191 (mm) cc_final: 0.8872 (mt)
REVERT: B  763 ASN cc_start: 0.8155 (p0) cc_final: 0.7751 (p0)
REVERT: B  781 MET cc_start: 0.8856 (mmm) cc_final: 0.8611 (mmm)
REVERT: B  821 LYS cc_start: 0.6482 (mptt) cc_final: 0.6074 (mmmm)
REVERT: B  853 LEU cc_start: 0.9597 (mt) cc_final: 0.9355 (mt)
REVERT: B  866 PHE cc_start: 0.8931 (t80) cc_final: 0.8677 (t80)
REVERT: B 1004 MET cc_start: 0.9222 (mmt) cc_final: 0.8899 (mmt)
REVERT: B 1011 ILE cc_start: 0.9250 (tt) cc_final: 0.8963 (pt)
REVERT: B 1044 LEU cc_start: 0.8187 (mm) cc_final: 0.7574 (tp)
REVERT: B 1193 LEU cc_start: 0.7725 (mm) cc_final: 0.7455 (mm)
REVERT: B 1283 GLU cc_start: 0.8367 (tp30) cc_final: 0.7948 (tm-30)
REVERT: B 1284 PHE cc_start: 0.8488 (m-80) cc_final: 0.8102 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0923
  time to fit residues: 26.9365
Evaluate side-chains
  142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 122 optimal weight:    0.6980
   chunk 23 optimal weight:    0.3980
   chunk 105 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0030
   chunk 0 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN
B 765 ASN
B1025 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.102113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.085926 restraints weight = 41039.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.087008 restraints weight = 30125.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.088930 restraints weight = 23648.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.089133 restraints weight = 18504.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.089630 restraints weight = 16792.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.5704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11237  Z= 0.119
  Angle     :  0.624  14.997  15214  Z= 0.327
  Chirality :  0.048   0.602   1688
  Planarity :  0.004   0.068   1941
  Dihedral  :  5.465  53.203   1549
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.82 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.22), residues: 1320
  helix:  1.22 (0.27), residues: 371
  sheet: -0.45 (0.38), residues: 168
  loop : -1.23 (0.21), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 231 
 TYR   0.024   0.001   TYR B 754 
 PHE   0.021   0.001   PHE B 652 
 TRP   0.014   0.001   TRP B 974 
 HIS   0.004   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11231)
  covalent geometry    : angle       0.60728 (15197)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.40457 (    2)
  hydrogen bonds       : bond        0.03804 (  432)
  hydrogen bonds       : angle       5.05883 ( 1260)
  link_BETA1-4         : bond        0.00266 (    2)
  link_BETA1-4         : angle       1.56391 (    6)
  link_NAG-ASN         : bond        0.00676 (    3)
  link_NAG-ASN         : angle       5.74499 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.7554 (m-30) cc_final: 0.6913 (t0)
REVERT: A  482 VAL cc_start: 0.8451 (m) cc_final: 0.7724 (m)
REVERT: A  495 GLU cc_start: 0.8707 (tp30) cc_final: 0.8276 (tp30)
REVERT: A  515 ILE cc_start: 0.9151 (mp) cc_final: 0.8835 (mp)
REVERT: B  152 VAL cc_start: 0.8033 (t) cc_final: 0.7641 (m)
REVERT: B  292 ASP cc_start: 0.8714 (t0) cc_final: 0.8446 (t0)
REVERT: B  351 GLU cc_start: 0.7069 (pp20) cc_final: 0.6462 (pp20)
REVERT: B  362 ASN cc_start: 0.8466 (p0) cc_final: 0.7996 (p0)
REVERT: B  388 ASP cc_start: 0.8065 (t0) cc_final: 0.7621 (t0)
REVERT: B  418 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7391 (p0)
REVERT: B  420 THR cc_start: 0.9000 (p) cc_final: 0.8716 (p)
REVERT: B  602 MET cc_start: 0.6392 (tpt) cc_final: 0.6063 (tpp)
REVERT: B  603 PHE cc_start: 0.8340 (m-80) cc_final: 0.8113 (m-80)
REVERT: B  665 LEU cc_start: 0.9176 (mm) cc_final: 0.8856 (mt)
REVERT: B  732 MET cc_start: 0.8441 (mmt) cc_final: 0.8119 (mmm)
REVERT: B  763 ASN cc_start: 0.8107 (p0) cc_final: 0.7624 (p0)
REVERT: B  781 MET cc_start: 0.8841 (mmm) cc_final: 0.8630 (mmm)
REVERT: B  821 LYS cc_start: 0.6412 (mptt) cc_final: 0.5985 (mmmm)
REVERT: B  827 ARG cc_start: 0.4817 (ptt90) cc_final: 0.4408 (mtm-85)
REVERT: B 1004 MET cc_start: 0.9211 (mmt) cc_final: 0.8878 (mmt)
REVERT: B 1011 ILE cc_start: 0.9270 (tt) cc_final: 0.8975 (pt)
REVERT: B 1113 MET cc_start: 0.7727 (tpp) cc_final: 0.7449 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1012
  time to fit residues: 28.0310
Evaluate side-chains
  136 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 58 optimal weight:    0.0770
   chunk 80 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN
B1003 GLN
** B1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.085648 restraints weight = 44400.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.087740 restraints weight = 29743.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.089890 restraints weight = 21152.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.090018 restraints weight = 16743.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.090927 restraints weight = 15284.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.5928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11237  Z= 0.149
  Angle     :  0.630  14.963  15214  Z= 0.333
  Chirality :  0.048   0.603   1688
  Planarity :  0.004   0.070   1941
  Dihedral  :  5.498  52.233   1549
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.41 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.22), residues: 1320
  helix:  1.16 (0.27), residues: 374
  sheet: -0.42 (0.38), residues: 169
  loop : -1.28 (0.21), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 231 
 TYR   0.025   0.002   TYR B 754 
 PHE   0.019   0.001   PHE B 652 
 TRP   0.011   0.001   TRP B 606 
 HIS   0.004   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11231)
  covalent geometry    : angle       0.61461 (15197)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.33306 (    2)
  hydrogen bonds       : bond        0.03938 (  432)
  hydrogen bonds       : angle       5.12010 ( 1260)
  link_BETA1-4         : bond        0.00329 (    2)
  link_BETA1-4         : angle       1.60912 (    6)
  link_NAG-ASN         : bond        0.00435 (    3)
  link_NAG-ASN         : angle       5.69252 (    9)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 HIS cc_start: 0.8122 (t70) cc_final: 0.7852 (t-90)
REVERT: A  482 VAL cc_start: 0.8604 (m) cc_final: 0.7924 (m)
REVERT: A  492 CYS cc_start: 0.7774 (m) cc_final: 0.7070 (m)
REVERT: A  495 GLU cc_start: 0.8775 (tp30) cc_final: 0.8497 (tp30)
REVERT: A  515 ILE cc_start: 0.9167 (mp) cc_final: 0.8919 (mp)
REVERT: B  152 VAL cc_start: 0.8184 (t) cc_final: 0.7758 (m)
REVERT: B  219 VAL cc_start: 0.9663 (t) cc_final: 0.9403 (p)
REVERT: B  235 ILE cc_start: 0.9320 (pt) cc_final: 0.9022 (tt)
REVERT: B  292 ASP cc_start: 0.8790 (t0) cc_final: 0.8506 (t0)
REVERT: B  351 GLU cc_start: 0.7222 (pp20) cc_final: 0.6598 (pp20)
REVERT: B  388 ASP cc_start: 0.8106 (t0) cc_final: 0.7632 (t0)
REVERT: B  418 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7428 (p0)
REVERT: B  420 THR cc_start: 0.8993 (p) cc_final: 0.8674 (p)
REVERT: B  602 MET cc_start: 0.6491 (tpt) cc_final: 0.6145 (tpp)
REVERT: B  603 PHE cc_start: 0.8398 (m-80) cc_final: 0.8110 (m-80)
REVERT: B  665 LEU cc_start: 0.9215 (mm) cc_final: 0.8896 (mt)
REVERT: B  732 MET cc_start: 0.8448 (mmt) cc_final: 0.8039 (mmm)
REVERT: B  763 ASN cc_start: 0.8271 (p0) cc_final: 0.7838 (p0)
REVERT: B  781 MET cc_start: 0.8887 (mmm) cc_final: 0.8677 (mmm)
REVERT: B  821 LYS cc_start: 0.6551 (mptt) cc_final: 0.6086 (mmmm)
REVERT: B  827 ARG cc_start: 0.4903 (ptt90) cc_final: 0.4454 (mtm-85)
REVERT: B  853 LEU cc_start: 0.9570 (mt) cc_final: 0.9349 (mt)
REVERT: B  866 PHE cc_start: 0.8945 (t80) cc_final: 0.8710 (t80)
REVERT: B 1004 MET cc_start: 0.8991 (mmt) cc_final: 0.8647 (mmp)
REVERT: B 1011 ILE cc_start: 0.9310 (tt) cc_final: 0.8991 (pt)
REVERT: B 1113 MET cc_start: 0.7882 (tpp) cc_final: 0.7549 (tpp)
REVERT: B 1193 LEU cc_start: 0.7613 (mm) cc_final: 0.7407 (mm)
REVERT: B 1283 GLU cc_start: 0.8316 (tp30) cc_final: 0.7790 (tm-30)
REVERT: B 1284 PHE cc_start: 0.8572 (m-80) cc_final: 0.8300 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1000
  time to fit residues: 27.5486
Evaluate side-chains
  140 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 26 optimal weight:    5.9990
   chunk 108 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 94 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 418 ASN
** B1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.102275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.084263 restraints weight = 43571.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.086523 restraints weight = 31551.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088055 restraints weight = 21996.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.088567 restraints weight = 17656.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.089194 restraints weight = 16213.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11237  Z= 0.139
  Angle     :  0.620  14.566  15214  Z= 0.328
  Chirality :  0.047   0.580   1688
  Planarity :  0.004   0.070   1941
  Dihedral  :  5.445  52.325   1549
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.49 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.22), residues: 1320
  helix:  1.23 (0.27), residues: 372
  sheet: -0.31 (0.39), residues: 169
  loop : -1.24 (0.21), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 231 
 TYR   0.025   0.002   TYR B 754 
 PHE   0.018   0.001   PHE B 652 
 TRP   0.016   0.002   TRP B 717 
 HIS   0.004   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11231)
  covalent geometry    : angle       0.60496 (15197)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.39110 (    2)
  hydrogen bonds       : bond        0.03904 (  432)
  hydrogen bonds       : angle       5.06090 ( 1260)
  link_BETA1-4         : bond        0.00370 (    2)
  link_BETA1-4         : angle       1.48383 (    6)
  link_NAG-ASN         : bond        0.00509 (    3)
  link_NAG-ASN         : angle       5.52152 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2279.36 seconds
wall clock time: 40 minutes 25.75 seconds (2425.75 seconds total)