Starting phenix.real_space_refine
on Wed Mar  4 18:59:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w5s_21546/03_2026/6w5s_21546.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6691 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      75      5.16       5
     C    6276      2.51       5
     N    1534      2.21       5
     O    1814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9700
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9360
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1194, 9338
          Classifications: {'peptide': 1194}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 1194, 9338
          Classifications: {'peptide': 1194}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 9558
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 206
          Unusual residues: {'CLR': 1, 'NAG': 9, 'POV': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 579 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 579 " occ=0.50
    residue:
      pdb=" N  AARG A1032 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A1032 " occ=0.50
  Time building chain proxies: 3.78, per 1000 atoms: 0.39
  Number of scatterers: 9700
  At special positions: 0
  Unit cell: (101.374, 88.006, 157.074, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      75     16.00
     P       1     15.00
     O    1814      8.00
     N    1534      7.00
     C    6276      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  63 " - pdb=" SG  CYS A 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 238 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 243 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 247 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 468 " - pdb=" SG  CYS A 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 533 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 914 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 956 " - pdb=" SG  CYS A1011 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 957 " - pdb=" SG  CYS A 979 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 976 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " NAG C   2 " - " MAN C   3 "
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1401 " - " ASN A 452 "
      " NAG A1402 " - " ASN A 459 "
      " NAG A1405 " - " ASN A 524 "
      " NAG A1409 " - " ASN A 598 "
      " NAG A1410 " - " ASN A 916 "
      " NAG A1414 " - " ASN A 961 "
      " NAG A1415 " - " ASN A 968 "
      " NAG A1416 " - " ASN A1064 "
      " NAG A1419 " - " ASN A 158 "
      " NAG B   1 " - " ASN A 478 "
      " NAG C   1 " - " ASN A 557 "
      " NAG D   1 " - " ASN A 931 "
      " NAG E   1 " - " ASN A 222 "
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 811.0 milliseconds
  

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2242

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 7 sheets defined
      58.9% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 63
      removed outlier: 3.693A  pdb=" N   CYS A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 67
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.900A  pdb=" N   THR A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 95
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 3.897A  pdb=" N   ASN A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLU A 110 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 119
    Processing helix  chain 'A' and resid 149 through 161
      removed outlier: 3.675A  pdb=" N   ALA A 155 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 185 through 195
      removed outlier: 3.735A  pdb=" N   TRP A 189 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ILE A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 199
    Processing helix  chain 'A' and resid 268 through 291
      removed outlier: 3.539A  pdb=" N   TRP A 273 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA A 289 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 349
      removed outlier: 3.785A  pdb=" N   CYS A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ARG A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 366
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 376 through 382
    Processing helix  chain 'A' and resid 386 through 399
    Processing helix  chain 'A' and resid 436 through 453
      removed outlier: 3.711A  pdb=" N   ILE A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.574A  pdb=" N   TYR A 487 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 3.661A  pdb=" N   ARG A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 546
      removed outlier: 3.615A  pdb=" N   VAL A 546 " --> pdb=" O   PHE A 542 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 542 through 546'
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 574 through 593
      removed outlier: 3.671A  pdb=" N   GLU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 617
      removed outlier: 3.694A  pdb=" N   ASP A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 639
      removed outlier: 3.642A  pdb=" N   ILE A 626 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 639 " --> pdb=" O   ILE A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 679
    Processing helix  chain 'A' and resid 685 through 711
      Proline residue:  A 691  - end of helix
    Processing helix  chain 'A' and resid 719 through 750
      Proline residue:  A 733  - end of helix
    Processing helix  chain 'A' and resid 754 through 792
      removed outlier: 3.636A  pdb=" N   THR A 759 " --> pdb=" O   PRO A 755 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL A 780 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 824
      removed outlier: 3.525A  pdb=" N   ASN A 823 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 830
      removed outlier: 3.895A  pdb=" N   LEU A 828 " --> pdb=" O   SER A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 852
    Processing helix  chain 'A' and resid 853 through 856
    Processing helix  chain 'A' and resid 870 through 883
      removed outlier: 4.213A  pdb=" N   ASP A 874 " --> pdb=" O   SER A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 907
    Processing helix  chain 'A' and resid 918 through 930
    Processing helix  chain 'A' and resid 942 through 951
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 4.302A  pdb=" N   GLN A 988 " --> pdb=" O   PRO A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 4.318A  pdb=" N   MET A 996 " --> pdb=" O   GLY A 992 " (cutoff:3.500A)
      Proline residue:  A1000  - end of helix
    Processing helix  chain 'A' and resid 1028 through 1031
    Processing helix  chain 'A' and resid 1047 through 1070
      removed outlier: 3.698A  pdb=" N   GLY A1070 " --> pdb=" O   THR A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1090 through 1092
      No H-bonds generated for 'chain 'A' and resid 1090 through 1092'
    Processing helix  chain 'A' and resid 1093 through 1117
    Processing helix  chain 'A' and resid 1120 through 1146
    Processing helix  chain 'A' and resid 1152 through 1177
      removed outlier: 4.147A  pdb=" N   GLY A1162 " --> pdb=" O   VAL A1158 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A1163 " --> pdb=" O   MET A1159 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A1165 " --> pdb=" O   CYS A1161 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A1166 " --> pdb=" O   GLY A1162 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   HIS A1170 " --> pdb=" O   GLU A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1202
      removed outlier: 4.018A  pdb=" N   SER A1197 " --> pdb=" O   HIS A1193 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A1202 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1202 through 1214
    Processing helix  chain 'A' and resid 1218 through 1225
    Processing helix  chain 'A' and resid 1225 through 1252
      Proline residue:  A1245  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.524A  pdb=" N   CYS A  42 " --> pdb=" O   TYR A  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 125
      removed outlier: 6.247A  pdb=" N   LEU A 121 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   TYR A 147 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   VAL A 123 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   GLN A 145 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   LEU A 144 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   VAL A 208 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR A 146 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129
    Processing sheet with id=AA4, first strand: chain 'A' and resid 547 through 548
    Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025
      removed outlier: 5.889A  pdb=" N   ASN A1024 " --> pdb=" O   GLY A1034 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 959

    483 hydrogen bonds defined for protein.
    1387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3004
        1.34 -     1.46: 2507
        1.46 -     1.59: 4330
        1.59 -     1.71: 2
        1.71 -     1.84: 105
  Bond restraints: 9948
  Sorted by residual:
  bond pdb=" C31 POV A1421 "
       pdb=" O31 POV A1421 "
    ideal  model  delta    sigma   weight residual
    1.327  1.452 -0.125 2.00e-02 2.50e+03 3.88e+01
  bond pdb=" C21 POV A1421 "
       pdb=" O21 POV A1421 "
    ideal  model  delta    sigma   weight residual
    1.330  1.453 -0.123 2.00e-02 2.50e+03 3.78e+01
  bond pdb=" C1  NAG A1410 "
       pdb=" O5  NAG A1410 "
    ideal  model  delta    sigma   weight residual
    1.406  1.471 -0.065 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" C1  NAG A1405 "
       pdb=" O5  NAG A1405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.465 -0.059 2.00e-02 2.50e+03 8.70e+00
  bond pdb=" O12 POV A1421 "
       pdb=" P   POV A1421 "
    ideal  model  delta    sigma   weight residual
    1.657  1.608  0.049 2.00e-02 2.50e+03 6.03e+00
  ... (remaining 9943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.95: 13508
        4.95 -     9.90: 34
        9.90 -    14.84: 0
       14.84 -    19.79: 0
       19.79 -    24.74: 1
  Bond angle restraints: 13543
  Sorted by residual:
  angle pdb=" N   ASN A  70 "
        pdb=" CA  ASN A  70 "
        pdb=" C   ASN A  70 "
      ideal   model   delta    sigma   weight residual
     110.80   86.06   24.74 2.13e+00 2.20e-01 1.35e+02
  angle pdb=" N   LYS A 142 "
        pdb=" CA  LYS A 142 "
        pdb=" C   LYS A 142 "
      ideal   model   delta    sigma   weight residual
     111.14  118.85   -7.71 1.08e+00 8.57e-01 5.10e+01
  angle pdb=" N   LYS A 822 "
        pdb=" CA  LYS A 822 "
        pdb=" C   LYS A 822 "
      ideal   model   delta    sigma   weight residual
     111.36  118.57   -7.21 1.09e+00 8.42e-01 4.38e+01
  angle pdb=" C   ASN A  70 "
        pdb=" N   VAL A  71 "
        pdb=" CA  VAL A  71 "
      ideal   model   delta    sigma   weight residual
     120.56  113.02    7.54 1.26e+00 6.30e-01 3.58e+01
  angle pdb=" N   SER A 863 "
        pdb=" CA  SER A 863 "
        pdb=" C   SER A 863 "
      ideal   model   delta    sigma   weight residual
     113.97  107.18    6.79 1.28e+00 6.10e-01 2.81e+01
  ... (remaining 13538 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 5981
       35.93 -    71.86: 166
       71.86 -   107.80: 24
      107.80 -   143.73: 21
      143.73 -   179.66: 2
  Dihedral angle restraints: 6194
    sinusoidal: 2706
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" CD BARG A 579 "
           pdb=" NE BARG A 579 "
           pdb=" CZ BARG A 579 "
           pdb=" NH1BARG A 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00 -179.66  179.66     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" CB  CYS A 240 "
           pdb=" SG  CYS A 240 "
           pdb=" SG  CYS A 247 "
           pdb=" CB  CYS A 247 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    1.75  -87.75     1      1.00e+01 1.00e-02 9.22e+01
  dihedral pdb=" CB  CYS A 909 "
           pdb=" SG  CYS A 909 "
           pdb=" SG  CYS A 914 "
           pdb=" CB  CYS A 914 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -14.78  -71.22     1      1.00e+01 1.00e-02 6.51e+01
  ... (remaining 6191 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.939: 1575
       0.939 -    1.877: 0
       1.877 -    2.816: 0
       2.816 -    3.755: 0
       3.755 -    4.694: 1
  Chirality restraints: 1576
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.29   -4.69 2.00e-02 2.50e+03 5.51e+04
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-02 2.50e+03 4.10e+02
  chirality pdb=" C1  MAN C   3 "
            pdb=" O3  NAG C   2 "
            pdb=" C2  MAN C   3 "
            pdb=" O5  MAN C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.18    0.22 2.00e-02 2.50e+03 1.22e+02
  ... (remaining 1573 not shown)

  Planarity restraints: 1711
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "   -0.351 2.00e-02 2.50e+03   3.03e-01 1.15e+03
        pdb=" C7  NAG E   2 "    0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "   -0.084 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "    0.537 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.184 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.339 2.00e-02 2.50e+03   2.92e-01 1.07e+03
        pdb=" C7  NAG D   2 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.044 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.511 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.207 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "    0.264 2.00e-02 2.50e+03   2.19e-01 6.01e+02
        pdb=" C7  NAG B   2 "   -0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "    0.181 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "   -0.365 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1708 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 74
        2.54 -     3.13: 8226
        3.13 -     3.72: 14433
        3.72 -     4.31: 21333
        4.31 -     4.90: 35516
  Nonbonded interactions: 79582
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 164 "
            pdb=" NE2 GLN A 241 "
     model   vdw
     1.946 3.120
  nonbonded pdb=" O   PHE A 821 "
            pdb=" OG  SER A 826 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" O   GLN A 119 "
            pdb=" SD  MET A 217 "
     model   vdw
     2.032 3.400
  nonbonded pdb=" NH2 ARG A  78 "
            pdb=" OE1 GLN A  81 "
     model   vdw
     2.055 3.120
  nonbonded pdb=" O   CYS A 909 "
            pdb=" OG  SER A 918 "
     model   vdw
     2.066 3.040
  ... (remaining 79577 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.540
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
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   0.223   9982  Z= 0.280
  Angle     :  0.918  31.637  13630  Z= 0.488
  Chirality :  0.129   4.694   1576
  Planarity :  0.013   0.303   1698
  Dihedral  : 18.493 179.661   3907
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 31.03
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.58 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  3.67 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.22), residues: 1194
  helix: -1.31 (0.19), residues: 626
  sheet: -1.98 (0.56), residues: 88
  loop : -3.30 (0.24), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 372 
 TYR   0.013   0.001   TYR A 570 
 PHE   0.012   0.001   PHE A1079 
 TRP   0.018   0.002   TRP A 949 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 9948)
  covalent geometry    : angle       0.82899 (13543)
  SS BOND              : bond        0.00364 (   15)
  SS BOND              : angle       2.88284 (   30)
  hydrogen bonds       : bond        0.16287 (  483)
  hydrogen bonds       : angle       6.75309 ( 1387)
  link_ALPHA1-3        : bond        0.00402 (    1)
  link_ALPHA1-3        : angle       2.48497 (    3)
  link_ALPHA1-4        : bond        0.00030 (    1)
  link_ALPHA1-4        : angle       1.35425 (    3)
  link_BETA1-4         : bond        0.00662 (    4)
  link_BETA1-4         : angle       4.05345 (   12)
  link_NAG-ASN         : bond        0.06199 (   13)
  link_NAG-ASN         : angle       6.59698 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  156 MET cc_start: 0.8738 (ttt) cc_final: 0.8538 (ttm)
REVERT: A  233 GLU cc_start: 0.7428 (mp0) cc_final: 0.6874 (pm20)
REVERT: A  260 TRP cc_start: 0.6129 (m-10) cc_final: 0.5482 (m-90)
REVERT: A  586 GLU cc_start: 0.6921 (tp30) cc_final: 0.6641 (tp30)
REVERT: A  822 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8388 (tttp)
REVERT: A 1158 VAL cc_start: 0.9175 (t) cc_final: 0.8971 (t)
  outliers start: 27
  outliers final: 10
  residues processed: 173
  average time/residue: 0.5266
  time to fit residues: 97.7412
Evaluate side-chains
  118 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  862 GLN
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1161 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.0970
   chunk 49 optimal weight:    0.0670
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.3454

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  88 GLN
A  92 GLN
A 103 ASN
A 122 ASN
A 136 GLN
** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 GLN
A 397 GLN
A 553 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 707 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN
A 884 HIS
A 906 ASN
** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1016 HIS
A1046 GLN
A1137 ASN
A1193 HIS
A1239 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.163687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.123273 restraints weight = 26942.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 5.96
r_work: 0.2890 rms_B_bonded: 5.17 restraints_weight: 2.0000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9982  Z= 0.149
  Angle     :  0.846  13.337  13630  Z= 0.389
  Chirality :  0.048   0.296   1576
  Planarity :  0.005   0.042   1698
  Dihedral  : 17.243 178.119   1821
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.64 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 11.58 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.23), residues: 1194
  helix: -0.06 (0.20), residues: 637
  sheet: -1.60 (0.54), residues: 88
  loop : -2.48 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 989 
 TYR   0.023   0.002   TYR A 570 
 PHE   0.013   0.001   PHE A1038 
 TRP   0.021   0.002   TRP A 273 
 HIS   0.010   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9948)
  covalent geometry    : angle       0.81224 (13543)
  SS BOND              : bond        0.00341 (   15)
  SS BOND              : angle       2.02734 (   30)
  hydrogen bonds       : bond        0.05071 (  483)
  hydrogen bonds       : angle       5.15674 ( 1387)
  link_ALPHA1-3        : bond        0.01178 (    1)
  link_ALPHA1-3        : angle       2.26582 (    3)
  link_ALPHA1-4        : bond        0.01549 (    1)
  link_ALPHA1-4        : angle       6.53657 (    3)
  link_BETA1-4         : bond        0.00228 (    4)
  link_BETA1-4         : angle       4.59511 (   12)
  link_NAG-ASN         : bond        0.00632 (   13)
  link_NAG-ASN         : angle       2.72397 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8356 (ttt) cc_final: 0.8135 (ttm)
REVERT: A  192 TYR cc_start: 0.7311 (t80) cc_final: 0.6886 (t80)
REVERT: A  260 TRP cc_start: 0.6106 (m-10) cc_final: 0.5167 (m-90)
REVERT: A  265 LEU cc_start: 0.7396 (mp) cc_final: 0.7180 (mm)
REVERT: A  288 PHE cc_start: 0.7195 (m-10) cc_final: 0.5745 (OUTLIER)
REVERT: A  466 ASP cc_start: 0.8324 (t0) cc_final: 0.7781 (m-30)
REVERT: A  498 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8444 (ptmt)
REVERT: A  506 TYR cc_start: 0.8154 (m-80) cc_final: 0.7952 (m-80)
REVERT: A  586 GLU cc_start: 0.7971 (tp30) cc_final: 0.7312 (tp30)
REVERT: A  862 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7792 (pt0)
  outliers start: 25
  outliers final: 9
  residues processed: 128
  average time/residue: 0.4779
  time to fit residues: 66.3085
Evaluate side-chains
  102 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  862 GLN
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1114 MET
Chi-restraints excluded: chain A residue 1161 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  92 GLN
A 117 GLN
A 145 GLN
** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 553 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.160848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120102 restraints weight = 26224.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 5.80
r_work: 0.2819 rms_B_bonded: 5.09 restraints_weight: 2.0000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9982  Z= 0.169
  Angle     :  0.821  14.575  13630  Z= 0.377
  Chirality :  0.048   0.289   1576
  Planarity :  0.005   0.046   1698
  Dihedral  : 16.106 176.122   1803
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.40 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.61 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.24), residues: 1194
  helix:  0.50 (0.20), residues: 638
  sheet: -1.17 (0.57), residues: 88
  loop : -2.04 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 372 
 TYR   0.018   0.002   TYR A1037 
 PHE   0.018   0.002   PHE A 345 
 TRP   0.017   0.002   TRP A 273 
 HIS   0.007   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9948)
  covalent geometry    : angle       0.79176 (13543)
  SS BOND              : bond        0.00332 (   15)
  SS BOND              : angle       1.99159 (   30)
  hydrogen bonds       : bond        0.05301 (  483)
  hydrogen bonds       : angle       5.00129 ( 1387)
  link_ALPHA1-3        : bond        0.00951 (    1)
  link_ALPHA1-3        : angle       2.15646 (    3)
  link_ALPHA1-4        : bond        0.00021 (    1)
  link_ALPHA1-4        : angle       6.51073 (    3)
  link_BETA1-4         : bond        0.00893 (    4)
  link_BETA1-4         : angle       3.82394 (   12)
  link_NAG-ASN         : bond        0.00514 (   13)
  link_NAG-ASN         : angle       2.59283 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6474 (tt0)
REVERT: A  192 TYR cc_start: 0.7377 (t80) cc_final: 0.6909 (t80)
REVERT: A  241 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7016 (tm-30)
REVERT: A  260 TRP cc_start: 0.6168 (m-10) cc_final: 0.5213 (m-90)
REVERT: A  466 ASP cc_start: 0.8361 (t0) cc_final: 0.7779 (m-30)
REVERT: A  586 GLU cc_start: 0.8049 (tp30) cc_final: 0.7357 (tp30)
REVERT: A  666 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8631 (p)
REVERT: A  987 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8286 (mptt)
REVERT: A 1111 LEU cc_start: 0.8598 (tm) cc_final: 0.7921 (mt)
REVERT: A 1179 MET cc_start: 0.7927 (mmm) cc_final: 0.7564 (mpp)
  outliers start: 27
  outliers final: 9
  residues processed: 119
  average time/residue: 0.4709
  time to fit residues: 60.8142
Evaluate side-chains
  106 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 114 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 116 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0370
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.162960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121083 restraints weight = 22659.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 5.40
r_work: 0.2887 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9982  Z= 0.140
  Angle     :  0.791  13.460  13630  Z= 0.361
  Chirality :  0.046   0.280   1576
  Planarity :  0.004   0.046   1698
  Dihedral  : 14.905 177.107   1799
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.06 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.35 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.25), residues: 1194
  helix:  0.81 (0.21), residues: 638
  sheet: -0.50 (0.61), residues: 78
  loop : -1.79 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 372 
 TYR   0.016   0.001   TYR A1037 
 PHE   0.014   0.001   PHE A 345 
 TRP   0.015   0.001   TRP A 273 
 HIS   0.007   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9948)
  covalent geometry    : angle       0.75627 (13543)
  SS BOND              : bond        0.00329 (   15)
  SS BOND              : angle       1.83666 (   30)
  hydrogen bonds       : bond        0.04853 (  483)
  hydrogen bonds       : angle       4.90815 ( 1387)
  link_ALPHA1-3        : bond        0.00793 (    1)
  link_ALPHA1-3        : angle       1.94911 (    3)
  link_ALPHA1-4        : bond        0.00128 (    1)
  link_ALPHA1-4        : angle       6.86522 (    3)
  link_BETA1-4         : bond        0.00548 (    4)
  link_BETA1-4         : angle       4.45879 (   12)
  link_NAG-ASN         : bond        0.00466 (   13)
  link_NAG-ASN         : angle       2.68589 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 TYR cc_start: 0.7437 (t80) cc_final: 0.6981 (t80)
REVERT: A  241 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6320 (tm-30)
REVERT: A  260 TRP cc_start: 0.5980 (m-10) cc_final: 0.5087 (m-90)
REVERT: A  466 ASP cc_start: 0.8246 (t0) cc_final: 0.7643 (m-30)
REVERT: A  578 GLN cc_start: 0.8383 (mm110) cc_final: 0.8040 (mt0)
REVERT: A  586 GLU cc_start: 0.7950 (tp30) cc_final: 0.7288 (tp30)
REVERT: A  666 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8779 (p)
REVERT: A 1158 VAL cc_start: 0.9037 (t) cc_final: 0.8811 (m)
REVERT: A 1179 MET cc_start: 0.7850 (mmm) cc_final: 0.7489 (mpp)
REVERT: A 1234 LEU cc_start: 0.8151 (tt) cc_final: 0.7869 (tp)
  outliers start: 24
  outliers final: 10
  residues processed: 115
  average time/residue: 0.5010
  time to fit residues: 62.2496
Evaluate side-chains
  103 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1043 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 19 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A  92 GLN
A 145 GLN
A 200 GLN
A 530 HIS
A 553 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.162933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123597 restraints weight = 30762.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 6.09
r_work: 0.2828 rms_B_bonded: 5.60 restraints_weight: 2.0000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9982  Z= 0.136
  Angle     :  0.741  11.434  13630  Z= 0.344
  Chirality :  0.045   0.279   1576
  Planarity :  0.004   0.048   1698
  Dihedral  : 13.624 176.643   1796
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.23 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.25 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.25), residues: 1194
  helix:  1.07 (0.21), residues: 639
  sheet: -0.18 (0.62), residues: 78
  loop : -1.56 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 161 
 TYR   0.017   0.001   TYR A 571 
 PHE   0.014   0.001   PHE A 209 
 TRP   0.014   0.001   TRP A 949 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9948)
  covalent geometry    : angle       0.71038 (13543)
  SS BOND              : bond        0.00223 (   15)
  SS BOND              : angle       1.73070 (   30)
  hydrogen bonds       : bond        0.04698 (  483)
  hydrogen bonds       : angle       4.81776 ( 1387)
  link_ALPHA1-3        : bond        0.00562 (    1)
  link_ALPHA1-3        : angle       1.81226 (    3)
  link_ALPHA1-4        : bond        0.00543 (    1)
  link_ALPHA1-4        : angle       6.28566 (    3)
  link_BETA1-4         : bond        0.00565 (    4)
  link_BETA1-4         : angle       4.09204 (   12)
  link_NAG-ASN         : bond        0.00393 (   13)
  link_NAG-ASN         : angle       2.47325 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 TYR cc_start: 0.7455 (t80) cc_final: 0.7004 (t80)
REVERT: A  241 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6362 (tm-30)
REVERT: A  260 TRP cc_start: 0.5806 (m-10) cc_final: 0.4929 (m-90)
REVERT: A  466 ASP cc_start: 0.8308 (t0) cc_final: 0.7636 (m-30)
REVERT: A  578 GLN cc_start: 0.8446 (mm110) cc_final: 0.8102 (mt0)
REVERT: A  586 GLU cc_start: 0.8086 (tp30) cc_final: 0.7410 (tp30)
REVERT: A  666 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8793 (p)
REVERT: A  748 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8085 (mt)
REVERT: A  869 ASP cc_start: 0.6473 (p0) cc_final: 0.6203 (t0)
REVERT: A  987 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8316 (mptt)
REVERT: A 1158 VAL cc_start: 0.9004 (t) cc_final: 0.8717 (m)
REVERT: A 1179 MET cc_start: 0.7907 (mmm) cc_final: 0.7466 (mpp)
REVERT: A 1234 LEU cc_start: 0.8247 (tt) cc_final: 0.8011 (tp)
  outliers start: 29
  outliers final: 15
  residues processed: 121
  average time/residue: 0.4552
  time to fit residues: 59.8682
Evaluate side-chains
  116 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  651 ASP
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1105 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0980
   chunk 45 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN
A 823 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.164533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123559 restraints weight = 28279.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 6.22
r_work: 0.2844 rms_B_bonded: 5.37 restraints_weight: 2.0000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9982  Z= 0.131
  Angle     :  0.727  10.397  13630  Z= 0.338
  Chirality :  0.045   0.276   1576
  Planarity :  0.004   0.048   1698
  Dihedral  : 13.084 177.079   1796
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.06 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.70 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.25), residues: 1194
  helix:  1.21 (0.21), residues: 637
  sheet: -0.12 (0.62), residues: 78
  loop : -1.43 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.017   0.001   TYR A 571 
 PHE   0.021   0.001   PHE A 360 
 TRP   0.014   0.001   TRP A 949 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9948)
  covalent geometry    : angle       0.69564 (13543)
  SS BOND              : bond        0.00317 (   15)
  SS BOND              : angle       1.95584 (   30)
  hydrogen bonds       : bond        0.04583 (  483)
  hydrogen bonds       : angle       4.79438 ( 1387)
  link_ALPHA1-3        : bond        0.00499 (    1)
  link_ALPHA1-3        : angle       1.73499 (    3)
  link_ALPHA1-4        : bond        0.01297 (    1)
  link_ALPHA1-4        : angle       6.53240 (    3)
  link_BETA1-4         : bond        0.00510 (    4)
  link_BETA1-4         : angle       3.58670 (   12)
  link_NAG-ASN         : bond        0.00386 (   13)
  link_NAG-ASN         : angle       2.51438 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 TYR cc_start: 0.7423 (t80) cc_final: 0.6992 (t80)
REVERT: A  241 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6393 (tm-30)
REVERT: A  466 ASP cc_start: 0.8331 (t0) cc_final: 0.7697 (m-30)
REVERT: A  506 TYR cc_start: 0.8013 (m-80) cc_final: 0.7686 (m-80)
REVERT: A  578 GLN cc_start: 0.8416 (mm110) cc_final: 0.8071 (mt0)
REVERT: A  586 GLU cc_start: 0.8053 (tp30) cc_final: 0.7386 (tp30)
REVERT: A  666 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8794 (p)
REVERT: A  748 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (mt)
REVERT: A  869 ASP cc_start: 0.6491 (p0) cc_final: 0.6222 (t0)
REVERT: A  987 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8246 (mptt)
REVERT: A 1114 MET cc_start: 0.8361 (ttp) cc_final: 0.8120 (tmm)
REVERT: A 1179 MET cc_start: 0.7884 (mmm) cc_final: 0.7467 (mpp)
REVERT: A 1234 LEU cc_start: 0.8215 (tt) cc_final: 0.8004 (tp)
  outliers start: 19
  outliers final: 13
  residues processed: 111
  average time/residue: 0.4458
  time to fit residues: 53.7945
Evaluate side-chains
  112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1142 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    0.4980
   chunk 105 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0170
   chunk 70 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0370
   chunk 85 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 793 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.167311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126238 restraints weight = 27242.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 6.04
r_work: 0.2918 rms_B_bonded: 5.33 restraints_weight: 2.0000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9982  Z= 0.117
  Angle     :  0.697  10.650  13630  Z= 0.324
  Chirality :  0.044   0.265   1576
  Planarity :  0.004   0.049   1698
  Dihedral  : 11.710 177.432   1796
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.98 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.31 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.25), residues: 1194
  helix:  1.46 (0.21), residues: 633
  sheet: -0.10 (0.62), residues: 80
  loop : -1.42 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 161 
 TYR   0.016   0.001   TYR A 571 
 PHE   0.027   0.001   PHE A 345 
 TRP   0.013   0.001   TRP A 273 
 HIS   0.007   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9948)
  covalent geometry    : angle       0.66989 (13543)
  SS BOND              : bond        0.00205 (   15)
  SS BOND              : angle       1.68930 (   30)
  hydrogen bonds       : bond        0.04119 (  483)
  hydrogen bonds       : angle       4.69209 ( 1387)
  link_ALPHA1-3        : bond        0.00490 (    1)
  link_ALPHA1-3        : angle       1.55010 (    3)
  link_ALPHA1-4        : bond        0.02237 (    1)
  link_ALPHA1-4        : angle       6.10981 (    3)
  link_BETA1-4         : bond        0.00558 (    4)
  link_BETA1-4         : angle       3.18725 (   12)
  link_NAG-ASN         : bond        0.00387 (   13)
  link_NAG-ASN         : angle       2.38986 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 TYR cc_start: 0.7435 (t80) cc_final: 0.7027 (t80)
REVERT: A  241 GLN cc_start: 0.6945 (tm-30) cc_final: 0.6423 (tm-30)
REVERT: A  466 ASP cc_start: 0.8251 (t0) cc_final: 0.7630 (m-30)
REVERT: A  498 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8020 (ptmt)
REVERT: A  506 TYR cc_start: 0.8029 (m-80) cc_final: 0.7638 (m-80)
REVERT: A  578 GLN cc_start: 0.8330 (mm110) cc_final: 0.8041 (mt0)
REVERT: A  586 GLU cc_start: 0.8063 (tp30) cc_final: 0.7426 (tp30)
REVERT: A  666 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8752 (p)
REVERT: A  869 ASP cc_start: 0.6464 (p0) cc_final: 0.6182 (t0)
REVERT: A  987 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8139 (mptt)
REVERT: A 1158 VAL cc_start: 0.8884 (t) cc_final: 0.8597 (m)
REVERT: A 1179 MET cc_start: 0.7933 (mmm) cc_final: 0.7474 (mpp)
  outliers start: 24
  outliers final: 13
  residues processed: 116
  average time/residue: 0.4620
  time to fit residues: 58.1433
Evaluate side-chains
  114 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1105 SER
Chi-restraints excluded: chain A residue 1142 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0470
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 793 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.165815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.124695 restraints weight = 25977.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 5.74
r_work: 0.2933 rms_B_bonded: 5.26 restraints_weight: 2.0000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9982  Z= 0.131
  Angle     :  0.712  11.199  13630  Z= 0.334
  Chirality :  0.045   0.272   1576
  Planarity :  0.004   0.050   1698
  Dihedral  : 11.411 176.786   1796
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.31 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.80 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.25), residues: 1194
  helix:  1.53 (0.21), residues: 633
  sheet: -0.08 (0.57), residues: 92
  loop : -1.46 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 161 
 TYR   0.015   0.001   TYR A 571 
 PHE   0.016   0.001   PHE A  93 
 TRP   0.012   0.001   TRP A 949 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9948)
  covalent geometry    : angle       0.68238 (13543)
  SS BOND              : bond        0.00236 (   15)
  SS BOND              : angle       1.80618 (   30)
  hydrogen bonds       : bond        0.04396 (  483)
  hydrogen bonds       : angle       4.73506 ( 1387)
  link_ALPHA1-3        : bond        0.00438 (    1)
  link_ALPHA1-3        : angle       1.50977 (    3)
  link_ALPHA1-4        : bond        0.01983 (    1)
  link_ALPHA1-4        : angle       6.32118 (    3)
  link_BETA1-4         : bond        0.00531 (    4)
  link_BETA1-4         : angle       3.06950 (   12)
  link_NAG-ASN         : bond        0.00363 (   13)
  link_NAG-ASN         : angle       2.61088 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6924 (tp40)
REVERT: A  192 TYR cc_start: 0.7450 (t80) cc_final: 0.7049 (t80)
REVERT: A  241 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6552 (tm-30)
REVERT: A  466 ASP cc_start: 0.8311 (t0) cc_final: 0.7682 (m-30)
REVERT: A  498 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8027 (ptmt)
REVERT: A  506 TYR cc_start: 0.8051 (m-80) cc_final: 0.7682 (m-80)
REVERT: A  578 GLN cc_start: 0.8395 (mm110) cc_final: 0.8083 (mt0)
REVERT: A  586 GLU cc_start: 0.8081 (tp30) cc_final: 0.7447 (tp30)
REVERT: A  666 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8779 (p)
REVERT: A  857 ASP cc_start: 0.8331 (m-30) cc_final: 0.8011 (t70)
REVERT: A  869 ASP cc_start: 0.6472 (p0) cc_final: 0.6214 (t0)
REVERT: A  987 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8198 (mptt)
REVERT: A 1179 MET cc_start: 0.7905 (mmm) cc_final: 0.7486 (mpp)
  outliers start: 19
  outliers final: 14
  residues processed: 111
  average time/residue: 0.4705
  time to fit residues: 56.6212
Evaluate side-chains
  116 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1105 SER
Chi-restraints excluded: chain A residue 1142 MET
Chi-restraints excluded: chain A residue 1234 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.160922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119129 restraints weight = 25460.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 5.72
r_work: 0.2858 rms_B_bonded: 5.06 restraints_weight: 2.0000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9982  Z= 0.132
  Angle     :  0.706   9.640  13630  Z= 0.331
  Chirality :  0.044   0.278   1576
  Planarity :  0.004   0.050   1698
  Dihedral  : 10.914 176.982   1796
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.57 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.51 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.25), residues: 1194
  helix:  1.57 (0.21), residues: 634
  sheet: -0.05 (0.57), residues: 92
  loop : -1.44 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.015   0.001   TYR A 571 
 PHE   0.021   0.001   PHE A 360 
 TRP   0.013   0.001   TRP A 949 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9948)
  covalent geometry    : angle       0.67569 (13543)
  SS BOND              : bond        0.00227 (   15)
  SS BOND              : angle       1.82743 (   30)
  hydrogen bonds       : bond        0.04527 (  483)
  hydrogen bonds       : angle       4.72777 ( 1387)
  link_ALPHA1-3        : bond        0.00475 (    1)
  link_ALPHA1-3        : angle       1.54478 (    3)
  link_ALPHA1-4        : bond        0.01923 (    1)
  link_ALPHA1-4        : angle       6.02814 (    3)
  link_BETA1-4         : bond        0.00476 (    4)
  link_BETA1-4         : angle       2.78017 (   12)
  link_NAG-ASN         : bond        0.00397 (   13)
  link_NAG-ASN         : angle       2.74227 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 TYR cc_start: 0.7428 (t80) cc_final: 0.7030 (t80)
REVERT: A  241 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6477 (tm-30)
REVERT: A  466 ASP cc_start: 0.8345 (t0) cc_final: 0.7723 (m-30)
REVERT: A  498 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7969 (ptmt)
REVERT: A  506 TYR cc_start: 0.8005 (m-80) cc_final: 0.7671 (m-80)
REVERT: A  586 GLU cc_start: 0.8085 (tp30) cc_final: 0.7427 (tp30)
REVERT: A  666 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8759 (p)
REVERT: A  857 ASP cc_start: 0.8278 (m-30) cc_final: 0.7948 (t70)
REVERT: A  869 ASP cc_start: 0.6458 (p0) cc_final: 0.6181 (t0)
REVERT: A  987 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8247 (mptt)
REVERT: A 1158 VAL cc_start: 0.8897 (t) cc_final: 0.8629 (m)
REVERT: A 1179 MET cc_start: 0.7881 (mmm) cc_final: 0.7435 (mpp)
  outliers start: 22
  outliers final: 16
  residues processed: 112
  average time/residue: 0.4985
  time to fit residues: 60.2327
Evaluate side-chains
  112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1105 SER
Chi-restraints excluded: chain A residue 1142 MET
Chi-restraints excluded: chain A residue 1234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 118 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.161048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.119690 restraints weight = 27170.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 6.03
r_work: 0.2847 rms_B_bonded: 5.15 restraints_weight: 2.0000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9982  Z= 0.132
  Angle     :  0.707   9.633  13630  Z= 0.333
  Chirality :  0.044   0.280   1576
  Planarity :  0.004   0.050   1698
  Dihedral  : 10.756 176.930   1796
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.57 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.08 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.25), residues: 1194
  helix:  1.61 (0.21), residues: 634
  sheet: -0.04 (0.57), residues: 92
  loop : -1.42 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.016   0.001   TYR A 571 
 PHE   0.022   0.001   PHE A 360 
 TRP   0.017   0.001   TRP A 273 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9948)
  covalent geometry    : angle       0.67820 (13543)
  SS BOND              : bond        0.00220 (   15)
  SS BOND              : angle       1.79342 (   30)
  hydrogen bonds       : bond        0.04510 (  483)
  hydrogen bonds       : angle       4.74133 ( 1387)
  link_ALPHA1-3        : bond        0.00471 (    1)
  link_ALPHA1-3        : angle       1.54260 (    3)
  link_ALPHA1-4        : bond        0.01927 (    1)
  link_ALPHA1-4        : angle       5.95795 (    3)
  link_BETA1-4         : bond        0.00486 (    4)
  link_BETA1-4         : angle       2.79534 (   12)
  link_NAG-ASN         : bond        0.00395 (   13)
  link_NAG-ASN         : angle       2.71330 (   39)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7146 (tp40)
REVERT: A  192 TYR cc_start: 0.7443 (t80) cc_final: 0.7050 (t80)
REVERT: A  241 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6484 (tm-30)
REVERT: A  466 ASP cc_start: 0.8354 (t0) cc_final: 0.7730 (m-30)
REVERT: A  498 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7979 (ptmt)
REVERT: A  506 TYR cc_start: 0.8012 (m-80) cc_final: 0.7683 (m-80)
REVERT: A  586 GLU cc_start: 0.8098 (tp30) cc_final: 0.7444 (tp30)
REVERT: A  666 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8770 (p)
REVERT: A  857 ASP cc_start: 0.8323 (m-30) cc_final: 0.7984 (t70)
REVERT: A  869 ASP cc_start: 0.6476 (p0) cc_final: 0.6163 (t0)
REVERT: A  987 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8234 (mptt)
  outliers start: 19
  outliers final: 15
  residues processed: 108
  average time/residue: 0.4678
  time to fit residues: 55.1082
Evaluate side-chains
  111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  987 LYS
Chi-restraints excluded: chain A residue 1043 THR
Chi-restraints excluded: chain A residue 1069 MET
Chi-restraints excluded: chain A residue 1105 SER
Chi-restraints excluded: chain A residue 1142 MET
Chi-restraints excluded: chain A residue 1234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 86 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0470
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0470
   chunk 15 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0870
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.3754

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

Flipped N/Q/H residues before XYZ refinement:
A 554 ASN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.163107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.122036 restraints weight = 26358.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 5.79
r_work: 0.2872 rms_B_bonded: 5.22 restraints_weight: 2.0000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9982  Z= 0.120
  Angle     :  0.690   9.605  13630  Z= 0.324
  Chirality :  0.044   0.275   1576
  Planarity :  0.004   0.050   1698
  Dihedral  : 10.484 177.502   1796
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.48 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.57 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1194
  helix:  1.70 (0.21), residues: 633
  sheet:  0.00 (0.57), residues: 92
  loop : -1.39 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.015   0.001   TYR A 571 
 PHE   0.028   0.001   PHE A  93 
 TRP   0.021   0.001   TRP A 273 
 HIS   0.006   0.001   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9948)
  covalent geometry    : angle       0.66253 (13543)
  SS BOND              : bond        0.00210 (   15)
  SS BOND              : angle       1.64987 (   30)
  hydrogen bonds       : bond        0.04286 (  483)
  hydrogen bonds       : angle       4.71474 ( 1387)
  link_ALPHA1-3        : bond        0.00429 (    1)
  link_ALPHA1-3        : angle       1.48264 (    3)
  link_ALPHA1-4        : bond        0.01794 (    1)
  link_ALPHA1-4        : angle       5.92442 (    3)
  link_BETA1-4         : bond        0.00505 (    4)
  link_BETA1-4         : angle       2.77693 (   12)
  link_NAG-ASN         : bond        0.00376 (   13)
  link_NAG-ASN         : angle       2.59297 (   39)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3212.04 seconds
wall clock time: 55 minutes 18.79 seconds (3318.79 seconds total)